Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| syringate degradation Accession ID: BioCyc:META_PWY-6339 |
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Kasai D, Masai E, Katayama Y, Fukuda M. Degradation of 3-O-methylgallate in Sphingomonas paucimobilis SYK-6 by pathways involving protocatechuate 4,5-dioxygenase. FEMS Microbiol Lett. 2007 Sep;274(2):323–8. doi: 10.1111/j.1574-6968.2007.00855.x. PMID: 17645527.; Abe T, Masai E, Miyauchi K, Katayama Y, Fukuda M. A Tetrahydrofolate-Dependent O -Demethylase, LigM, Is Crucial for Catabolism of Vanillate and Syringate in Sphingomonas paucimobilis SYK-6. J Bacteriol. 2005 Mar 15;187(6):2030–7. doi: 10.1128/jb.187.6.2030-2037.2005.; Kasai D, Masai E, Miyauchi K, Katayama Y, Fukuda M. Characterization of the 3- O -Methylgallate Dioxygenase Gene and Evidence of Multiple 3- O -Methylgallate Catabolic Pathways in Sphingomonas paucimobilis SYK-6. J Bacteriol. 2004 Aug;186(15):4951–9. doi: 10.1128/jb.186.15.4951-4959.2004.; Nishikawa S, Sonoki T, Kasahara T, Obi T, Kubota S, Kawai S, Morohoshi N, Katayama Y. Cloning and Sequencing of the Sphingomonas ( Pseudomonas ) paucimobilis Gene Essential for the O Demethylation of Vanillate and Syringate. Appl Environ Microbiol. 1998 Mar;64(3):836–42. doi: 10.1128/aem.64.3.836-842.1998.; Kersten PJ, Dagley S, Whittaker JW, Arciero DM, Lipscomb JD. 2-pyrone-4,6-dicarboxylic acid, a catabolite of gallic acids in Pseudomonas species. J Bacteriol. 1982 Dec;152(3):1154–62. doi: 10.1128/jb.152.3.1154-1162.1982. |
| rhodoquinone-9 biosynthesis Accession ID: BioCyc:META_PWY-5889 |
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Parson WW, Rudney H. The Biosynthesis of Ubiquinone and Rhodoquinone from p-Hydroxybenzoate and p-Hydroxybenzaldehyde in Rhodospirillum rubrum. Journal of Biological Chemistry. 1965 Apr;240(4):1855–63. doi: 10.1016/s0021-9258(18)97517-4. |
| L-threonate degradation Accession ID: BioCyc:META_PWY-7874 |
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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. |
| norspermidine biosynthesis Accession ID: BioCyc:META_PWY-6562 |
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Lee J, Sperandio V, Frantz DE, Longgood J, Camilli A, Phillips MA, Michael AJ. An Alternative Polyamine Biosynthetic Pathway Is Widespread in Bacteria and Essential for Biofilm Formation in Vibrio cholerae. Journal of Biological Chemistry. 2009 Apr;284(15):9899–907. doi: 10.1074/jbc.m900110200. |
| achromobactin biosynthesis Accession ID: BioCyc:META_PWY-6574 |
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Berti AD, Thomas MG. Analysis of achromobactin biosynthesis by Pseudomonas syringae pv. syringae B728a. J Bacteriol. 2009 Jul;191(14):4594–604. PMID: 19482931; PMCID: PMC2704727.; Schmelz S, Kadi N, McMahon SA, Song L, Oves-Costales D, Oke M, Liu H, Johnson KA, Carter LG, Botting CH, White MF, Challis GL, Naismith JH. AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis. Nature Chemical Biology. 2009 Feb 01;5(3):174–82. doi: 10.1038/nchembio.145. |
| L-tryptophan degradation VI (via tryptamine) Accession ID: BioCyc:META_PWY-3181 |
- | Büki KG, Vinh DQ, Horváth I. Partial purification and some properties of tryptophan decarboxylase from a Bacillus strain. Acta Microbiol Hung. 1985;32(1):65–73. PMID: 4036551. |
| methanofuran biosynthesis Accession ID: BioCyc:META_PWY-5254 |
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Graham DE, White RH. Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Nat Prod Rep. 2002 Apr;19(2):133–47. doi: 10.1039/b103714p. PMID: 12013276. |
| octopamine biosynthesis Accession ID: BioCyc:META_PWY-7297 |
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Osborne RL, Zhu H, Iavarone AT, Hess CR, Klinman JP. Inactivation of Met471Cys tyramine ß-monooxygenase results from site-specific cysteic acid formation. Biochemistry. 2012 Sep 25;51(38):7488–95. PMID: 22891760; PMCID: PMC3567250.; Lange AB. Tyramine: from octopamine precursor to neuroactive chemical in insects. Gen Comp Endocrinol. 2009 May 15;162(1):18–26. doi: 10.1016/j.ygcen.2008.05.021. PMID: 18588893. |
| superpathway of (R,R)-butanediol biosynthesis Accession ID: BioCyc:META_P125-PWY |
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| superpathway of polyamine biosynthesis II Accession ID: BioCyc:META_POLYAMINSYN3-PWY |
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Piotrowski M, Janowitz T, Kneifel H. Plant C-N Hydrolases and the Identification of a Plant N-Carbamoylputrescine Amidohydrolase Involved in Polyamine Biosynthesis. Journal of Biological Chemistry. 2003 Jan;278(3):1708–12. doi: 10.1074/jbc.m205699200. |
| superpathway of 2,3-butanediol biosynthesis Accession ID: BioCyc:META_PWY-6396 |
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| taxadiene biosynthesis (engineered) Accession ID: BioCyc:META_PWY-7392 |
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Huang Q, Roessner CA, Croteau R, Scott AI. Engineering Escherichia coli for the synthesis of taxadiene, a key intermediate in the biosynthesis of taxol. Bioorg Med Chem. 2001 Sep;9(9):2237–42. doi: 10.1016/s0968-0896(01)00072-4. PMID: 11553461. |
| brassicicene C biosynthesis Accession ID: BioCyc:META_PWY-7517 |
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Kenmoku H, Tada H, Oogushi M, Esumi T, Takahashi H, Noji M, Sassa T, Toyota M, Asakawa Y. Seed Dormancy Breaking Diterpenoids from the Liverwort Plagiochila sciophila and their Differentiation Inducing Activity in Human Promyelocytic Leukemia HL-60 Cells. Natural Product Communications. 2014 Jul;9(7). doi: 10.1177/1934578x1400900708.; Ono Y, Minami A, Noike M, Higuchi Y, Toyomasu T, Sassa T, Kato N, Dairi T. Dioxygenases, key enzymes to determine the aglycon structures of fusicoccin and brassicicene, diterpene compounds produced by fungi. J Am Chem Soc. 2011 Mar 02;133(8):2548–55. doi: 10.1021/ja107785u. PMID: 21299202.; Hashimoto M, Higuchi Y, Takahashi S, Osada H, Sakaki T, Toyomasu T, Sassa T, Kato N, Dairi T. Functional analyses of cytochrome P450 genes responsible for the early steps of brassicicene C biosynthesis. Bioorganic & Medicinal Chemistry Letters. 2009 Oct;19(19):5640–3. doi: 10.1016/j.bmcl.2009.08.026.; Minami A, Tajima N, Higuchi Y, Toyomasu T, Sassa T, Kato N, Dairi T. Identification and functional analysis of brassicicene C biosynthetic gene cluster in Alternaria brassicicola. Bioorganic & Medicinal Chemistry Letters. 2009 Feb;19(3):870–4. doi: 10.1016/j.bmcl.2008.11.108.; Pedras MS, Chumala PB, Jin W, Islam MS, Hauck DW. The phytopathogenic fungus Alternaria brassicicola: phytotoxin production and phytoalexin elicitation. Phytochemistry. 2009 Feb;70(3):394–402. doi: 10.1016/j.phytochem.2009.01.005. PMID: 19223049. |
| 1-butanol autotrophic biosynthesis (engineered) Accession ID: BioCyc:META_PWY-6886 |
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Lan EI, Liao JC. Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. Metab Eng. 2011 Jul;13(4):353–63. doi: 10.1016/j.ymben.2011.04.004. PMID: 21569861.; Guskov A, Kern J, Gabdulkhakov A, Broser M, Zouni A, Saenger W. Cyanobacterial photosystem II at 2.9-Å resolution and the role of quinones, lipids, channels and chloride. Nature Structural & Molecular Biology. 2009 Feb 15;16(3):334–42. doi: 10.1038/nsmb.1559.; 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.; Knaff DB, Malkin R, Clark Myron J, Stoller M. The role of plastoquinone and ß-carotene in the primary reaction of plant Photosystem II. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1977 Mar;459(3):402–11. doi: 10.1016/0005-2728(77)90041-x. |
| polyacyltrehalose biosynthesis Accession ID: BioCyc:META_PWY-7738 |
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Touchette MH, Holsclaw CM, Previti ML, Solomon VC, Leary JA, Bertozzi CR, Seeliger JC. The rv1184c locus encodes Chp2, an acyltransferase in Mycobacterium tuberculosis polyacyltrehalose lipid biosynthesis. J Bacteriol. 2015 Jan 01;197(1):201–10. PMID: 25331437; PMCID: PMC4288680.; Hatzios SK, Schelle MW, Holsclaw CM, Behrens CR, Botyanszki Z, Lin FL, Carlson BL, Kumar P, Leary JA, Bertozzi CR. PapA3 Is an Acyltransferase Required for Polyacyltrehalose Biosynthesis in Mycobacterium tuberculosis. Journal of Biological Chemistry. 2009 May;284(19):12745–51. doi: 10.1074/jbc.m809088200. |
| aurachin RE biosynthesis Accession ID: BioCyc:META_PWY-7405 |
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Kitagawa W, Ozaki T, Nishioka T, Yasutake Y, Hata M, Nishiyama M, Kuzuyama T, Tamura T. Cloning and heterologous expression of the aurachin RE biosynthesis gene cluster afford a new cytochrome P450 for quinoline N-hydroxylation. Chembiochem. 2013 Jun 17;14(9):1085–93. doi: 10.1002/cbic.201300167. PMID: 23677853. |
| folate transformations II Accession ID: BioCyc:META_PWY-3841 |
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Goyer A, Collakova E, Díaz de la Garza R, Quinlivan EP, Williamson J, Gregory JF, Shachar-Hill Y, Hanson AD. 5-Formyltetrahydrofolate is an inhibitory but well tolerated metabolite in Arabidopsis leaves. J Biol Chem. 2005 Jul 15;280(28):26137–42. doi: 10.1074/jbc.m503106200. PMID: 15888445.; Basset GJC, Ravanel S, Quinlivan EP, White R, Giovannoni JJ, Rébeillé F, Nichols BP, Shinozaki K, Seki M, Gregory JF, Hanson AD. Folate synthesis in plants: the last step of the p-aminobenzoate branch is catalyzed by a plastidial aminodeoxychorismate lyase. The Plant Journal. 2004 Sep 27;40(4):453–61. doi: 10.1111/j.1365-313x.2004.02231.x.; Basset GJC, Quinlivan EP, Ravanel S, Rébeillé F, Nichols BP, Shinozaki K, Seki M, Adams-Phillips LC, Giovannoni JJ, Gregory JF, Hanson AD. Folate synthesis in plants: The p -aminobenzoate branch is initiated by a bifunctional PabA-PabB protein that is targeted to plastids. Proc. Natl. Acad. Sci. U.S.A. 2004 Jan 26;101(6):1496–501. doi: 10.1073/pnas.0308331100.; Jabrin S, Ravanel S, Gambonnet B, Douce R, Rébeillé F. One-carbon metabolism in plants. Regulation of tetrahydrofolate synthesis during germination and seedling development. Plant Physiol. 2003 Mar;131(3):1431–9. PMID: 12644692; PMCID: PMC166902.; Roje S, Janave MT, Ziemak MJ, Hanson AD. Cloning and Characterization of Mitochondrial 5-Formyltetrahydrofolate Cycloligase from Higher Plants. Journal of Biological Chemistry. 2002 Nov;277(45):42748–54. doi: 10.1074/jbc.m205632200.; Hanson AD, Gregory III JF. Synthesis and turnover of folates in plants. Current Opinion in Plant Biology. 2002 Jun;5(3):244–9. doi: 10.1016/s1369-5266(02)00249-2.; Ravanel S, Cherest H, Jabrin S, Grunwald D, Surdin-Kerjan Y, Douce R, Rébeillé F. Tetrahydrofolate biosynthesis in plants: Molecular and functional characterization of dihydrofolate synthetase and three isoforms of folylpolyglutamate synthetase in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 2001 Dec 18;98(26):15360–5. doi: 10.1073/pnas.261585098.; Hanson AD, Roje S. O |
| folate transformations I Accession ID: BioCyc:META_PWY-2201 |
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| heme d1 biosynthesis Accession ID: BioCyc:META_PWY-7554 |
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Bali S, Lawrence AD, Lobo SA, Saraiva LM, Golding BT, Palmer DJ, Howard MJ, Ferguson SJ, Warren MJ. Molecular hijacking of siroheme for the synthesis of heme and d 1 heme. Proc. Natl. Acad. Sci. U.S.A. 2011 Oct 03;108(45):18260–5. doi: 10.1073/pnas.1108228108. |
| aliphatic glucosinolate biosynthesis, side chain elongation cycle Accession ID: BioCyc:META_PWYQT-4450 |
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Textor S, de Kraker JW, Hause B, Gershenzon J, Tokuhisa JG. MAM3 catalyzes the formation of all aliphatic glucosinolate chain lengths in Arabidopsis. Plant Physiol. 2007 May;144(1):60–71. PMID: 17369439; PMCID: PMC1913788.; Heidel AJ, Clauss MJ, Kroymann J, Savolainen O, Mitchell-Olds T. Natural Variation inMAMWithin and Between Populations ofArabidopsis lyrataDetermines Glucosinolate Phenotype. 2006 Jul 01;173(3):1629–36. doi: 10.1534/genetics.106.056986.; Halkier BA, Gershenzon J. Biology and biochemistry of glucosinolates. Annu Rev Plant Biol. 2006;57():303–33. doi: 10.1146/annurev.arplant.57.032905.105228. PMID: 16669764.; D'Auria JC, Gershenzon J. The secondary metabolism of Arabidopsis thaliana: growing like a weed. Curr Opin Plant Biol. 2005 Jun;8(3):308–16. doi: 10.1016/j.pbi.2005.03.012. PMID: 15860428.; Textor S, Bartram S, Kroymann J, Falk KL, Hick A, Pickett JA, Gershenzon J. Biosynthesis of methionine-derived glucosinolates in Arabidopsis thaliana: recombinant expression and characterization of methylthioalkylmalate synthase, the condensing enzyme of the chain-elongation cycle. Planta. 2004 Apr;218(6):1026–35. doi: 10.1007/s00425-003-1184-3. PMID: 14740211.; Wittstock U, Halkier BA. Glucosinolate research in the Arabidopsis era. Trends Plant Sci. 2002 Jun;7(6):263–70. doi: 10.1016/s1360-1385(02)02273-2. PMID: 12049923.; Kroymann J, Textor S, Tokuhisa JG, Falk KL, Bartram S, Gershenzon J, Mitchell-Olds T. A gene controlling variation in Arabidopsis glucosinolate composition is part of the methionine chain elongation pathway. Plant Physiol. 2001 Nov;127(3):1077–88. PMID: 11706188; PMCID: PMC129277.; Kliebenstein DJ, Kroymann J, Brown P, Figuth A, Pedersen D, Gershenzon J, Mitchell-Olds T. Genetic control of natural variation in Arabidopsis glucosinolate accumulation. Plant Physiol. 2001 Jun;126(2):811–25. PMID: 11402209; PMCID: PMC111171.; Fahey JW, Zalcmann AT, Talalay P. The chemical diversity and distribution of glucosinolates and isothiocyanates among plants. Phytochemistry. 2001 Jan;56(1):5–51. doi: 10.1016/s0031-9422(00)00316-2. PMID: 11198818. |