Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| L-carnitine degradation III Accession ID: BioCyc:META_PWY-3641 |
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Kleber HP. Bacterial carnitine metabolism. FEMS Microbiol Lett. 1997 Feb 01;147(1):1–9. doi: 10.1111/j.1574-6968.1997.tb10212.x. PMID: 9037756. |
| 3-chlorobenzoate degradation I (via chlorocatechol) Accession ID: BioCyc:META_PWY-6088 |
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Harayama S, Rekik M, Bairoch A, Neidle EL, Ornston LN. Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases. J Bacteriol. 1991 Dec;173(23):7540–8. doi: 10.1128/jb.173.23.7540-7548.1991.; Dorn E, Hellwig M, Reineke W, Knackmuss HJ. Isolation and characterization of a 3-chlorobenzoate degrading pseudomonad. Arch Microbiol. 1974;99(1):61–70. doi: 10.1007/bf00696222. PMID: 4852581. |
| methylthiopropanoate degradation I (cleavage) Accession ID: BioCyc:META_PWY-6048 |
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Reisch CR, Stoudemayer MJ, Varaljay VA, Amster IJ, Moran MA, Whitman WB. Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature. 2011 May 12;473(7346):208–11. doi: 10.1038/nature10078. PMID: 21562561. |
| p-cymene degradation Accession ID: BioCyc:META_PWY-5266 |
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Eaton RW. p-Cumate catabolic pathway in Pseudomonas putida Fl: cloning and characterization of DNA carrying the cmt operon. J Bacteriol. 1996 Mar;178(5):1351–62. doi: 10.1128/jb.178.5.1351-1362.1996.; DeFrank JJ, Ribbons DW. p-cymene pathway in Pseudomonas putida: initial reactions. J Bacteriol. 1977 Mar;129(3):1356–64. doi: 10.1128/jb.129.3.1356-1364.1977.; DeFrank JJ, Ribbons DW. p-Cymene pathway in Pseudomonas putida: ring cleavage of 2,3-dihydroxy-p-cumate and subsequent reactions. J Bacteriol. 1977 Mar;129(3):1365–74. doi: 10.1128/jb.129.3.1365-1374.1977. |
| superpathway of nicotinate degradation Accession ID: BioCyc:META_PWY-5062 |
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| L-glutamate degradation V (via hydroxyglutarate) Accession ID: BioCyc:META_P162-PWY |
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Thorpe C, Kim JP. Structure and mechanism of action of the Acyl-CoA dehydrogenases 1. The FASEB Journal. 1995 Jun;9(9):718–25. doi: 10.1096/fasebj.9.9.7601336.; Schweiger G, Dutscho R, Buckel W. Purification of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. An iron-sulfur protein. Eur J Biochem. 1987 Dec 01;169(2):441–8. doi: 10.1111/j.1432-1033.1987.tb13631.x. PMID: 3691501.; Buckel W, Barker HA. Two Pathways of Glutamate Fermentation by Anaerobic Bacteria. J Bacteriol. 1974 Mar;117(3):1248–60. doi: 10.1128/jb.117.3.1248-1260.1974.; Hauge JG, Crane FL, Beinert H. ON THE MECHANISM OF DEHYDROGENATION OF FATTY ACYL DERIVATIVES OF COENZYME A. Journal of Biological Chemistry. 1956 Apr;219(2):727–33. doi: 10.1016/s0021-9258(18)65732-1.; Green DE, Mii S, Mahler HR, Bock RM. STUDIES ON THE FATTY ACID OXIDIZING SYSTEM OF ANIMAL TISSUES. Journal of Biological Chemistry. 1954 Jan;206(1):1–12. doi: 10.1016/s0021-9258(18)71290-8.; MAHLER HR. Studies on the fatty acid oxidizing system of animal tissues. IV. The prosthetic group of butyryl coenzyme A dehydrogenase. J Biol Chem. 1954 Jan;206(1):13–26. PMID: 13130522. |
| 4-amino-3-hydroxybenzoate degradation Accession ID: BioCyc:META_PWY-7006 |
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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.; ORII C, TAKENAKA S, MURAKAMI S, AOKI K. Metabolism of 4-Amino-3-hydroxybenzoic Acid byBordetellasp. Strain 10d: A Different ModifiedMeta-Cleavage Pathway for 2-Aminophenols. Bioscience, Biotechnology, and Biochemistry. 2006 Nov 23;70(11):2653–61. doi: 10.1271/bbb.60264. |
| anaerobic energy metabolism (invertebrates, mitochondrial) Accession ID: BioCyc:META_PWY-7384 |
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Müller M, Mentel M, van Hellemond JJ, Henze K, Woehle C, Gould SB, Yu R, van der Giezen M, Tielens AGM, Martin WF. Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes. Microbiol Mol Biol Rev. 2012 Jun;76(2):444–95. doi: 10.1128/mmbr.05024-11.; Tielens AG, Rotte C, van Hellemond JJ, Martin W. Mitochondria as we don't know them. Trends Biochem Sci. 2002 Nov;27(11):564–72. doi: 10.1016/s0968-0004(02)02193-x. PMID: 12417132.; Van Hellemond JJ, Klockiewicz M, Gaasenbeek CPH, Roos MH, Tielens AGM. Rhodoquinone and Complex II of the Electron Transport Chain in Anaerobically Functioning Eukaryotes. Journal of Biological Chemistry. 1995 Dec;270(52):31065–70. doi: 10.1074/jbc.270.52.31065.; Grieshaber MK, Hardewig I, Kreutzer U, Pörtner HO. Physiological and metabolic responses to hypoxia in invertebrates. Rev Physiol Biochem Pharmacol. 1994;125():43–147. doi: 10.1007/bfb0030909. PMID: 7984874.; Campbell T, Rubin N, Komuniecki R. Succinate-dependent energy generation in Ascaris suum mitochondria. Molecular and Biochemical Parasitology. 1989 Feb;33(1):1–12. doi: 10.1016/0166-6851(89)90036-4.; Saz HJ, Pietrzak SM. Phosphorylation associated with succinate decarboxylation to propionate in Ascaris mitochondria. Archives of Biochemistry and Biophysics. 1980 Jul;202(2):388–95. doi: 10.1016/0003-9861(80)90442-7. |
| superpathway of aromatic compound degradation via 2-hydroxypentadienoate Accession ID: BioCyc:META_PWY-6954 |
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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.; Harwood CS, Parales RE. The beta-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol. 1996;50():553–90. doi: 10.1146/annurev.micro.50.1.553. PMID: 8905091.; Kukor JJ, Olsen RH. Genetic organization and regulation of a meta cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol, and cresols by Pseudomonas pickettii PKO1. J Bacteriol. 1991 Aug;173(15):4587–94. doi: 10.1128/jb.173.15.4587-4594.1991.; Menn FM, Zylstra GJ, Gibson DT. Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase in Pseudomonas putida F1. Gene. 1991 Jul 31;104(1):91–4. doi: 10.1016/0378-1119(91)90470-v. PMID: 1916282.; Kishore G, Sugumaran M, Vaidyanathan CS. Metabolism of DL-(+/-)-phenylalanine by Aspergillus niger. J Bacteriol. 1976 Oct;128(1):182–91. doi: 10.1128/jb.128.1.182-191.1976.; Wheelis ML, Stanier RY. The genetic control of dissimilatory pathways in Pseudomonas putida. Genetics. 1970 Oct;66(2):245–66. PMID: 5525301; PMCID: PMC1212492. |
| ephedrine biosynthesis Accession ID: BioCyc:META_PWY-5883 |
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| p-cumate degradation to 2-hydroxypentadienoate Accession ID: BioCyc:META_PWY-5163 |
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Eaton RW. p-Cumate catabolic pathway in Pseudomonas putida Fl: cloning and characterization of DNA carrying the cmt operon. J Bacteriol. 1996 Mar;178(5):1351–62. doi: 10.1128/jb.178.5.1351-1362.1996. |
| Amaryllidacea alkaloids biosynthesis Accession ID: BioCyc:META_PWY-7826 |
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Kilgore MB, Holland CK, Jez JM, Kutchan TM. Identification of a Noroxomaritidine Reductase with Amaryllidaceae Alkaloid Biosynthesis Related Activities. Journal of Biological Chemistry. 2016 Aug;291(32):16740–52. doi: 10.1074/jbc.m116.717827.; Kilgore MB, Augustin MM, May GD, Crow JA, Kutchan TM. CYP96T1 of Narcissus sp. aff. pseudonarcissus Catalyzes Formation of the Para-Para' C-C Phenol Couple in the Amaryllidaceae Alkaloids. Front Plant Sci. 2016;7():225. PMID: 26941773; PMCID: PMC4766306.; Kilgore MB, Augustin MM, Starks CM, O’Neil-Johnson M, May GD, Crow JA, Kutchan TM. Cloning and Characterization of a Norbelladine 4'-O-Methyltransferase Involved in the Biosynthesis of the Alzheimer’s Drug Galanthamine in Narcissus sp. aff. pseudonarcissus. PLoS ONE. 2014 Jul 25;9(7):e103223. doi: 10.1371/journal.pone.0103223.; Pak FE, Gropper S, Dai WD, Havkin-Frenkel D, Belanger FC. Characterization of a multifunctional methyltransferase from the orchid Vanilla planifolia. Plant Cell Rep. 2004 Jul;22(12):959–66. doi: 10.1007/s00299-004-0795-x. PMID: 15118832.; Podstolski A, Havkin-Frenkel D, Malinowski J, Blount JW, Kourteva G, Dixon RA. Unusual 4-hydroxybenzaldehyde synthase activity from tissue cultures of the vanilla orchid Vanilla planifolia. Phytochemistry. 2002 Nov;61(6):611–20. doi: 10.1016/s0031-9422(02)00285-6. PMID: 12423881.; Wildman WC, Heimer NE. Alkaloid biosynthesis and interconversions. The conversion of caranine to lycorine. J Am Chem Soc. 1967 Sep 27;89(20):5265–9. doi: 10.1021/ja00996a032. PMID: 6065044. |
| purine nucleobases degradation II (anaerobic) Accession ID: BioCyc:META_PWY-5497 |
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Vogels GD, Van der Drift C. Degradation of purines and pyrimidines by microorganisms. Bacteriol Rev. 1976 Jun;40(2):403–68. doi: 10.1128/br.40.2.403-468.1976. |
| acridone alkaloid biosynthesis Accession ID: BioCyc:META_PWY-5958 |
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Rohde B, Hans J, Martens S, Baumert A, Hunziker P, Matern U. Anthranilate N-methyltransferase, a branch-point enzyme of acridone biosynthesis. The Plant Journal. 2007 Nov 06;53(3):541–53. doi: 10.1111/j.1365-313x.2007.03360.x. |
| phosphatidylethanolamine biosynthesis I Accession ID: BioCyc:META_PWY-5669 |
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Nerlich A, von Orlow M, Rontein D, Hanson AD, Dörmann P. Deficiency in Phosphatidylserine Decarboxylase Activity in the psd1 psd2 psd3 Triple Mutant of Arabidopsis Affects Phosphatidylethanolamine Accumulation in Mitochondria. Plant Physiol. 2007 Apr 20;144(2):904–14. doi: 10.1104/pp.107.095414. |
| prunasin and amygdalin biosynthesis Accession ID: BioCyc:META_PWY-7824 |
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Yamaguchi T, Yamamoto K, Asano Y. Identification and characterization of CYP79D16 and CYP71AN24 catalyzing the first and second steps in L-phenylalanine-derived cyanogenic glycoside biosynthesis in the Japanese apricot, Prunus mume Sieb. et Zucc. Plant Mol Biol. 2014 Sep;86(1-2):215–23. doi: 10.1007/s11103-014-0225-6. PMID: 25015725.; Wittstock U, Halkier BA. Cytochrome P450 CYP79A2 from Arabidopsis thaliana L. Catalyzes the Conversion of l-Phenylalanine to Phenylacetaldoxime in the Biosynthesis of Benzylglucosinolate. Journal of Biological Chemistry. 2000 May;275(19):14659–66. doi: 10.1074/jbc.275.19.14659. |
| D-erythronate degradation I Accession ID: BioCyc:META_PWY-7872 |
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Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S, Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crécy-Lagard V, Jacobson MP, Almo SC, Gerlt JA. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4161–9. PMID: 27402745; PMCID: PMC4961189. |
| UDP-sugars interconversion Accession ID: BioCyc:META_PWY-5114 |
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Oka T, Nemoto T, Jigami Y. Functional Analysis of Arabidopsis thaliana RHM2/MUM4, a Multidomain Protein Involved in UDP-D-glucose to UDP-L-rhamnose Conversion. Journal of Biological Chemistry. 2007 Feb;282(8):5389–403. doi: 10.1074/jbc.m610196200. |
| demethylmenaquinol-8 biosynthesis I Accession ID: BioCyc:META_PWY-5852 |
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Holländer R. Correlation of the function of demethylmenaquinone in bacterial electron transport with its redox potential. FEBS Lett. 1976 Dec 15;72(1):98–100. doi: 10.1016/0014-5793(76)80821-6. PMID: 187454.; Whistance GR, Threlfall DR. Effect of anaerobiosis on the concentrations of demethylmenaquinone, menaquinone and ubiquinone in Escherichia freundii, Proteus mirabilis and Aeromonas punctata. Biochem J. 1968 Jul;108(3):505–7. PMID: 4875411; PMCID: PMC1198837. |
| N10-formyl-tetrahydrofolate biosynthesis Accession ID: BioCyc:META_1CMET2-PWY |
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