Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| 4-hydroxybenzoate biosynthesis II (bacteria) Accession ID: BioCyc:ECO_PWY-5755 |
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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. |
| taxiphyllin bioactivation Accession ID: BioCyc:BTHE_PWY-7089 |
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| 4-hydroxybenzoate biosynthesis IV (plants) Accession ID: BioCyc:META_PWY-6431 |
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Sircar D, Mitra A. Evidence for p-hydroxybenzoate formation involving enzymatic phenylpropanoid side-chain cleavage in hairy roots of Daucus carota. J Plant Physiol. 2008 Mar 13;165(4):407–14. doi: 10.1016/j.jplph.2007.05.005. PMID: 17658659.; 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. |
| 4-hydroxymandelate degradation Accession ID: BioCyc:META_4-HYDROXYMANDELATE-DEGRADATION-PWY |
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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.; Hosokawa K, Stanier RY. Crystallization and Properties of p-Hydroxybenzoate Hydroxylase from Pseudomonas putida. Journal of Biological Chemistry. 1966 May;241(10):2453–60. doi: 10.1016/s0021-9258(18)96639-1.; Hegeman GD. Synthesis of the Enzymes of the Mandelate Pathway by Pseudomonas putida I. Synthesis of Enzymes by the Wild Type. J Bacteriol. 1966 Mar;91(3):1140–54. doi: 10.1128/jb.91.3.1140-1154.1966.; Gunter SE. THE ENZYMATIC OXIDATION OF p -HYDROXYMANDELIC ACID TO p -HYDROXYBENZOIC ACID. J Bacteriol. 1953 Sep;66(3):341–6. doi: 10.1128/jb.66.3.341-346.1953. |
| taxiphyllin bioactivation Accession ID: BioCyc:META_PWY-7089 |
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Ahn YO, Saino H, Mizutani M, Shimizu B, Sakata K. Vicianin hydrolase is a novel cyanogenic beta-glycosidase specific to beta-vicianoside (6-O-alpha-L-arabinopyranosyl-beta-D-glucopyranoside) in seeds of Vicia angustifolia. Plant Cell Physiol. 2007 Jul;48(7):938–47. doi: 10.1093/pcp/pcm065. PMID: 17548373.; PETRUCCIOLI M, BRIMER L, CICALINI AR, PULCI V, FEDERICI F. Production and Properties of the Linamarase and Amygdalase Activities ofPenicillium aurantiogriseumP35. Bioscience, Biotechnology, and Biochemistry. 1999 Jan;63(5):805–12. doi: 10.1271/bbb.63.805.; Jones DA. Why are so many food plants cyanogenic? Phytochemistry. 1998 Jan;47(2):155–62. doi: 10.1016/s0031-9422(97)00425-1. PMID: 9431670.; Poulton JE. Cyanogenesis in plants. Plant Physiol. 1990 Oct;94(2):401–5. PMID: 16667728; PMCID: PMC1077245.; Hösel W, Klewitz O. [beta-Glucosidases specific for the cyanogenic glucoside triglochinin from Alocasia macrorrhiza Schott: further characterization of properties (author's transl)]. Hoppe Seylers Z Physiol Chem. 1977 Aug;358(8):959–66. PMID: 411729.; Hösel W, Nahrstedt A. [Glucosidases specific for the cyanogenic glucoside triglochinin. Purification and characterization of beta-glucosidases from Alocasia macrorrhiza Schott]. Hoppe Seylers Z Physiol Chem. 1975 Aug;356(8):1265–75. PMID: 240769. |
| superpathway of aromatic compound degradation via 3-oxoadipate Accession ID: BioCyc:META_PWY-2504 |
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Ca´mara B, Bielecki P, Kaminski F, dos Santos VM, Plumeier I, Nikodem P, Pieper DH. A Gene Cluster Involved in Degradation of Substituted Salicylates viaorthoCleavage inPseudomonassp. Strain MT1 Encodes Enzymes Specifically Adapted for Transformation of 4-Methylcatechol and 3-Methylmuconate. J Bacteriol. 2007 Mar;189(5):1664–74. doi: 10.1128/jb.01192-06.; 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.; 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. |
| L-glutamate degradation IV Accession ID: BioCyc:META_PWY-4321 |
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Clark SM, Di Leo R, Van Cauwenberghe OR, Mullen RT, Shelp BJ. Subcellular localization and expression of multiple tomato gamma-aminobutyrate transaminases that utilize both pyruvate and glyoxylate. J Exp Bot. 2009;60(11):3255–67. PMID: 19470656; PMCID: PMC2718222.; Clark SM, Di Leo R, Dhanoa PK, Van Cauwenberghe OR, Mullen RT, Shelp BJ. Biochemical characterization, mitochondrial localization, expression, and potential functions for an Arabidopsis gamma-aminobutyrate transaminase that utilizes both pyruvate and glyoxylate. J Exp Bot. 2009;60(6):1743–57. PMID: 19264755; PMCID: PMC2671622.; Zhu X, Lapthorn AJ, Ellis EM. Crystal structure of mouse succinic semialdehyde reductase AKR7A5: structural basis for substrate specificity. Biochemistry. 2006 Feb 14;45(6):1562–70. doi: 10.1021/bi051610k. PMID: 16460003.; Palanivelu R, Brass L, Edlund AF, Preuss D. Pollen tube growth and guidance is regulated by POP2, an Arabidopsis gene that controls GABA levels. Cell. 2003 Jul 11;114(1):47–59. doi: 10.1016/s0092-8674(03)00479-3. PMID: 12859897. |
| 4-hydroxymandelate degradation Accession ID: BioCyc:CAULO_4-HYDROXYMANDELATE-DEGRADATION-PWY |
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| superpathway of aromatic compound degradation via 3-oxoadipate Accession ID: BioCyc:SCO_PWY-2504 |
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| 4-hydroxymandelate degradation Accession ID: BioCyc:PCHR_4-HYDROXYMANDELATE-DEGRADATION-PWY |
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| toluene degradation III (aerobic) (via p-cresol) Accession ID: BioCyc:META_PWY-5181 |
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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.; 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.; 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. |
| 4-methylphenol degradation to protocatechuate Accession ID: BioCyc:META_PWY-7700 |
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DAGLEY S, PATEL MD. Oxidation of p-cresol and related compounds by a Pseudomonas. Biochem J. 1957 Jun;66(2):227–33. PMID: 13445676; PMCID: PMC1199997. |
| vanillin biosynthesis I Accession ID: BioCyc:META_PWY-5665 |
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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. |
| superpathway of chorismate metabolism Accession ID: BioCyc:ECO_ALL-CHORISMATE-PWY |
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| superpathway of ubiquinol-8 biosynthesis (prokaryotic) Accession ID: BioCyc:ECO_UBISYN-PWY |
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| dhurrin degradation Accession ID: PlantCyc:AHYPOCHONDRIACUS_PWY-5976 |
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| dhurrin degradation Accession ID: PlantCyc:RUBBERTREE_PWY-5976 |
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| dhurrin degradation Accession ID: PlantCyc:CZOFINGIENSIS_PWY-5976 |
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| dhurrin degradation Accession ID: PlantCyc:DROTUNDATA_PWY-5976 |
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| 4-hydroxybenzoate biosynthesis I (eukaryotes) Accession ID: PlantCyc:ORYZA_PWY-5754 |
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