Pathways Knowlegdes
Necessitatibus eius consequatur ex aliquid fuga eum quidem sint consectetur velit
| Pathway | DOIs | Note |
|---|---|---|
| 4-aminobutyrate degradation Accession ID: BioCyc:HUMAN_PWY-6535 |
|
Dover S, Halpern YS. Utilization of ?-Aminobutyric Acid as the Sole Carbon and Nitrogen Source by Escherichia coli K-12 Mutants. J Bacteriol. 1972 Feb;109(2):835–43. doi: 10.1128/jb.109.2.835-843.1972. |
| 4-hydroxybenzoate biosynthesis II (bacteria) Accession ID: BioCyc:META_PWY-5755 |
|
Gallagher DT, Mayhew M, Holden MJ, Howard A, Kim KJ, Vilker VL. The crystal structure of chorismate lyase shows a new fold and a tightly retained product. Proteins. 2001 Aug 15;44(3):304–11. doi: 10.1002/prot.1095. PMID: 11455603. |
| superpathway of aromatic compound degradation via 2-hydroxypentadienoate Accession ID: BioCyc:META_PWY-6954 |
|
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. |
| dhurrin degradation Accession ID: BioCyc:META_PWY-5976 |
|
Cicek M, Esen A. Structure and expression of a dhurrinase (beta-glucosidase) from sorghum. Plant Physiol. 1998 Apr;116(4):1469–78. PMID: 9536065; PMCID: PMC35055. |
| Amaryllidacea alkaloids biosynthesis Accession ID: BioCyc:META_PWY-7826 |
|
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. |
| 4-aminobutanoate degradation I Accession ID: BioCyc:META_PWY-6535 |
|
Dover S, Halpern YS. Utilization of ?-Aminobutyric Acid as the Sole Carbon and Nitrogen Source by Escherichia coli K-12 Mutants. J Bacteriol. 1972 Feb;109(2):835–43. doi: 10.1128/jb.109.2.835-843.1972. |
| superpathway of chorismate metabolism Accession ID: BioCyc:META_ALL-CHORISMATE-PWY |
|
Keating TA, Marshall CG, Walsh CT. Reconstitution and characterization of the Vibrio cholerae vibriobactin synthetase from VibB, VibE, VibF, and VibH. Biochemistry. 2000 Dec 19;39(50):15522–30. doi: 10.1021/bi0016523. PMID: 11112538. |
| superpathway of ubiquinol-8 biosynthesis (prokaryotic) Accession ID: BioCyc:META_UBISYN-PWY |
|
Meganathan R. Ubiquinone biosynthesis in microorganisms. FEMS Microbiol Lett. 2001 Sep 25;203(2):131–9. doi: 10.1111/j.1574-6968.2001.tb10831.x. PMID: 11583838. |
| superpathway of aerobic toluene degradation Accession ID: BioCyc:META_PWY-5183 |
|
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.; Johnson DR, Park J, Kukor JJ, Abriola LM. Effect of carbon starvation on toluene degradation activity by toluene monooxygenase-expressing bacteria. Biodegradation. 2006 Oct;17(5):437–45. doi: 10.1007/s10532-005-9014-x. PMID: 16477358.; Fishman A, Tao Y, Wood TK. Toluene 3-Monooxygenase of Ralstonia pickettii PKO1 Is a para -Hydroxylating Enzyme. J Bacteriol. 2004 May 15;186(10):3117–23. doi: 10.1128/jb.186.10.3117-3123.2004.; Newman LM, Wackett LP. Purification and characterization of toluene 2-monooxygenase from Burkholderia cepacia G4. Biochemistry. 1995 Oct 31;34(43):14066–76. doi: 10.1021/bi00043a012. PMID: 7578004.; Inoue J, Shaw JP, Rekik M, Harayama S. Overlapping substrate specificities of benzaldehyde dehydrogenase (the xylC gene product) and 2-hydroxymuconic semialdehyde dehydrogenase (the xylG gene product) encoded by TOL plasmid pWW0 of Pseudomonas putida. J Bacteriol. 1995 Mar;177(5):1196–201. doi: 10.1128/jb.177.5.1196-1201.1995.; Olsen RH, Kukor JJ, Kaphammer B. A novel toluene-3-monooxygenase pathway cloned from Pseudomonas pickettii PKO1. J Bacteriol. 1994 Jun;176(12):3749–56. doi: 10.1128/jb.176.12.3749-3756.1994.; Shaw JP, Rekik M, Schwager F, Harayama S. Kinetic studies on benzyl alcohol dehydrogenase encoded by TOL plasmid pWWO. A member of the zinc-containing long chain alcohol dehydrogenase family. Journal of Biological Chemistry. 1993 May;268(15):10842–50. doi: 10.1016/s0021-9258(18)82062-2.; Yen KM, Karl MR, Blatt LM, Simon MJ, Winter RB, Fausset PR, Lu HS, Harcourt AA, Chen KK. Cloning and characterization of a Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J Bacteriol. 1991 Sep;173(17):5315–27. doi: 10.1128/jb.173.17.5315-5327.1991.; 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. |
| 4-hydroxymandelate degradation Accession ID: BioCyc:AURANTIMONAS_4-HYDROXYMANDELATE-DEGRADATION-PWY |
- | |
| 4-hydroxymandelate degradation Accession ID: BioCyc:SCO_4-HYDROXYMANDELATE-DEGRADATION-PWY |
- | |
| taxiphyllin bioactivation Accession ID: BioCyc:CLOSSAC_PWY-7089 |
- | |
| proline degradation Accession ID: BioCyc:HUMAN_PROUT-PWY |
|
Srivastava D, Singh RK, Moxley MA, Henzl MT, Becker DF, Tanner JJ. The Three-Dimensional Structural Basis of Type II Hyperprolinemia. Journal of Molecular Biology. 2012 Jul;420(3):176–89. doi: 10.1016/j.jmb.2012.04.010. |
| GABA shunt Accession ID: BioCyc:HUMAN_GLUDEG-I-PWY |
- | |
| resveratrol degradation Accession ID: BioCyc:META_PWY-6667 |
|
Brefort T, Scherzinger D, Limón MC, Estrada AF, Trautmann D, Mengel C, Avalos J, Al-Babili S. Cleavage of resveratrol in fungi: characterization of the enzyme Rco1 from Ustilago maydis. Fungal Genet Biol. 2011 Feb;48(2):132–43. doi: 10.1016/j.fgb.2010.10.009. PMID: 21073977. |
| 4-coumarate degradation (aerobic) Accession ID: BioCyc:META_PWY-8002 |
|
Hirakawa H, Schaefer AL, Greenberg EP, Harwood CS. Anaerobic p -Coumarate Degradation by Rhodopseudomonas palustris and Identification of CouR, a MarR Repressor Protein That Binds p -Coumaroyl Coenzyme A. J Bacteriol. 2012 Apr 15;194(8):1960–7. doi: 10.1128/jb.06817-11.; Carmona M, Zamarro MT, Bla´zquez B, Durante-Rodri´guez G, Jua´rez JF, Valderrama JA, Barraga´n MJL, Garci´a JL, Di´az E. Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View. Microbiol Mol Biol Rev. 2009 Mar;73(1):71–133. doi: 10.1128/mmbr.00021-08. |
| 4-hydroxybenzoate biosynthesis I (eukaryotes) Accession ID: BioCyc:META_PWY-5754 |
|
Payet LA, Leroux M, Willison JC, Kihara A, Pelosi L, Pierrel F. Mechanistic Details of Early Steps in Coenzyme Q Biosynthesis Pathway in Yeast. Cell Chem Biol. 2016 Oct 20;23(10):1241–50. doi: 10.1016/j.chembiol.2016.08.008. PMID: 27693056.; 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.; Meganathan R. Ubiquinone biosynthesis in microorganisms. FEMS Microbiol Lett. 2001 Sep 25;203(2):131–9. doi: 10.1111/j.1574-6968.2001.tb10831.x. PMID: 11583838. |
| GABA shunt Accession ID: BioCyc:META_GLUDEG-I-PWY |
|
Bessman SP, Rossen J, Layne EC. ?-AMINOBUTYRIC ACID-GLUTAMIC ACID TRANSAMINATION IN BRAIN. Journal of Biological Chemistry. 1953 Mar;201(1):385–91. doi: 10.1016/s0021-9258(18)71381-1. |
| L-proline degradation Accession ID: BioCyc:META_PROUT-PWY |
|
Abrahamson JL, Baker LG, Stephenson JT, Wood JM. Proline dehydrogenase from Escherichia coli K12. Properties of the membrane-associated enzyme. Eur J Biochem. 1983 Jul 15;134(1):77–82. doi: 10.1111/j.1432-1033.1983.tb07533.x. PMID: 6305659. |
| L-arginine degradation I (arginase pathway) Accession ID: BioCyc:META_ARGASEDEG-PWY |
|
Cañas RA, Villalobos DP, Díaz-Moreno SM, Cánovas FM, Cantón FR. Molecular and functional analyses support a role of Ornithine-{delta}-aminotransferase in the provision of glutamate for glutamine biosynthesis during pine germination. Plant Physiol. 2008 Sep;148(1):77–88. PMID: 18621980; PMCID: PMC2528089.; Funck D, Stadelhofer B, Koch W. Ornithine-delta-aminotransferase is essential for arginine catabolism but not for proline biosynthesis. BMC Plant Biol. 2008 Apr 17;8():40. PMID: 18419821; PMCID: PMC2377265. |