Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| chrysin biosynthesis Accession ID: BioCyc:META_PWY-5363 |
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Leonard E, Yan Y, Lim KH, Koffas MAG. Investigation of Two Distinct Flavone Synthases for Plant-Specific Flavone Biosynthesis inSaccharomyces cerevisiae. Appl Environ Microbiol. 2005 Dec;71(12):8241–8. doi: 10.1128/aem.71.12.8241-8248.2005.; Miyahisa I, Funa N, Ohnishi Y, Martens S, Moriguchi T, Horinouchi S. Combinatorial biosynthesis of flavones and flavonols in Escherichia coli. Applied Microbiology and Biotechnology. 2005 Aug 18;71(1):53–8. doi: 10.1007/s00253-005-0116-5. |
| polymethylated quercetin glucoside biosynthesis II - quercetagetin series (Chrysosplenium) Accession ID: BioCyc:META_PWY-7151 |
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Anzellotti D, Ibrahim RK. Molecular characterization and functional expression of flavonol 6-hydroxylase. BMC Plant Biol. 2004 Dec 13;4():20. PMID: 15596008; PMCID: PMC544895.; Gauthier A, Gulick PJ, Ibrahim RK. cDNA cloning and characterization of a 3'/5'-O-methyltransferase for partially methylated flavonols from Chrysosplenium americanum. Plant Mol Biol. 1996 Dec;32(6):1163–9. doi: 10.1007/bf00041401. PMID: 9002616.; Latchinian-Sadek L, Ibrahim RK. Flavonol ring B-specific O-glucosyltransferases: Purification, production of polyclonal antibodies, and immunolocalization. Archives of Biochemistry and Biophysics. 1991 Aug;289(1):230–6. doi: 10.1016/0003-9861(91)90466-v.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. I. Partial purification and some properties of S-adenosyl-l-methionine: Flavonol 3-, 6-, 7-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):596–605. doi: 10.1016/0003-9861(85)90205-x.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. II. Substrate interaction and product inhibition studies of flavonol 3-, 6-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):606–18. doi: 10.1016/0003-9861(85)90206-1.; KHOURI H, IBRAHIM RK. Kinetic mechanism of a flavonol-ring-B O-glucosyltransferase from Chrysosplenium americanum. European Journal of Biochemistry. 1984 Aug;142(3):559–64. doi: 10.1111/j.1432-1033.1984.tb08322.x.; Bajaj KL, de Luca V, Khouri H, Ibrahim RK. Purification and Properties of Flavonol-Ring B Glucosyltransferase from Chrysosplenium americanum. Plant Physiol. 1983 Jul 01;72(3):891–6. doi: 10.1104/pp.72.3.891.; Schnitsky S. Own your own telephone system? Dent Manage. 1976 Jun;16(6):15–6, 19, 21. PMID: 1068865. |
| putrescine biosynthesis III Accession ID: BioCyc:META_PWY-46 |
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Gupta R, Hamasaki-Katagiri N, Tabor CW, Tabor H. Effect of spermidine on the in vivo degradation of ornithine decarboxylase in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 2001 Sep 04;98(19):10620–3. doi: 10.1073/pnas.181341298.; Schwartz B, Hittelman A, Daneshvar L, Basu HS, Marton LJ, Feuerstein BG. A new model for disruption of the ornithine decarboxylase gene, SPE1, in Saccharomyces cerevisiae exhibits growth arrest and genetic instability at the MAT locus. Biochem J. 1995 Nov 15;312 ( Pt 1)():83–90. PMID: 7492339; PMCID: PMC1136230.; Balasundaram D, Xie QW, Tabor CW, Tabor H. The presence of an active S-adenosylmethionine decarboxylase gene increases the growth defect observed in Saccharomyces cerevisiae mutants unable to synthesize putrescine, spermidine, and spermine. J Bacteriol. 1994 Oct;176(20):6407–9. doi: 10.1128/jb.176.20.6407-6409.1994.; Morris DR, Jorstad CM. Isolation of Conditionally Putrescine-Deficient Mutants ofEscherichia coli. J Bacteriol. 1970 Mar;101(3):731–7. doi: 10.1128/jb.101.3.731-737.1970. |
| L-homophenylalanine biosynthesis Accession ID: BioCyc:META_PWY-7275 |
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Koketsu K, Mitsuhashi S, Tabata K. Identification of homophenylalanine biosynthetic genes from the cyanobacterium Nostoc punctiforme PCC73102 and application to its microbial production by Escherichia coli. Appl Environ Microbiol. 2013 Apr;79(7):2201–8. PMID: 23354699; PMCID: PMC3623235. |
| 4-methyl-proline biosynthesis Accession ID: BioCyc:META_PWY-7648 |
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Bills G, Li Y, Chen L, Yue Q, Niu XM, An Z. New insights into the echinocandins and other fungal non-ribosomal peptides and peptaibiotics. Nat Prod Rep. 2014 Oct;31(10):1348–75. doi: 10.1039/c4np00046c. PMID: 25156669.; Jiang W, Cacho RA, Chiou G, Garg NK, Tang Y, Walsh CT. EcdGHK are three tailoring iron oxygenases for amino acid building blocks of the echinocandin scaffold. J Am Chem Soc. 2013 Mar 20;135(11):4457–66. PMID: 23451921; PMCID: PMC3628723.; Emri T, Majoros L, Tóth V, Pócsi I. Echinocandins: production and applications. Applied Microbiology and Biotechnology. 2013 Mar 06;97(8):3267–84. doi: 10.1007/s00253-013-4761-9.; Hibi M, Kawashima T, Sokolov PM, Smirnov SV, Kodera T, Sugiyama M, Shimizu S, Yokozeki K, Ogawa J. l-Leucine 5-hydroxylase of Nostoc punctiforme is a novel type of Fe(II)/a-ketoglutarate-dependent dioxygenase that is useful as a biocatalyst. Applied Microbiology and Biotechnology. 2012 May 16;97(6):2467–72. doi: 10.1007/s00253-012-4136-7.; Zambias RA, Hammond ML, Heck JV, Bartizal K, Trainor C, Abruzzo G, Schmatz DM, Nollstadt KM. Preparation and structure-activity relationships of simplified analogues of the antifungal agent cilofungin: a total synthesis approach. J Med Chem. 1992 Jul 24;35(15):2843–55. doi: 10.1021/jm00093a018. PMID: 1495015. |
| allantoin degradation to glyoxylate III Accession ID: BioCyc:META_PWY-5705 |
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Cusa E, Obradors N, Baldoma` L, Badi´a J, Aguilar J. Genetic Analysis of a Chromosomal Region Containing Genes Required for Assimilation of Allantoin Nitrogen and Linked Glyoxylate Metabolism in Escherichia coli. J Bacteriol. 1999 Dec 15;181(24):7479–84. doi: 10.1128/jb.181.24.7479-7484.1999.; Bongaerts GP, Vogels GD. Uric acid degradation by Bacillus fastidiosus strains. J Bacteriol. 1976 Feb;125(2):689–97. doi: 10.1128/jb.125.2.689-697.1976. |
| 2-nitrobenzoate degradation II Accession ID: BioCyc:META_PWY-5648 |
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Chauhan A, Jain RK. Degradation of o-Nitrobenzoate via Anthranilic Acid (o-Aminobenzoate) by Arthrobacter protophormiae: A Plasmid-Encoded New Pathway. Biochemical and Biophysical Research Communications. 2000 Jan;267(1):236–44. doi: 10.1006/bbrc.1999.1949. |
| L-glutamate degradation VII (to butanoate) Accession ID: BioCyc:META_GLUDEG-II-PWY |
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Buckel W. Unusual enzymes involved in five pathways of glutamate fermentation. Applied Microbiology and Biotechnology. 2001 Oct 01;57(3):263–73. doi: 10.1007/s002530100773.; 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.; 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. |
| sciadonate biosynthesis Accession ID: BioCyc:META_PWY-6598 |
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Sayanova O, Haslam R, Venegas Caleron M, Napier JA. Cloning and Characterization of Unusual Fatty Acid Desaturases from Anemone leveillei: Identification of an Acyl-Coenzyme A C20 ?5-Desaturase Responsible for the Synthesis of Sciadonic Acid. 2007 Mar 23;144(1):455–67. doi: 10.1104/pp.107.098202. |
| chitin degradation to ethanol Accession ID: BioCyc:META_PWY-7118 |
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Boles E, de Jong-Gubbels P, Pronk JT. Identification and Characterization of MAE1 , the Saccharomyces cerevisiae Structural Gene Encoding Mitochondrial Malic Enzyme. J Bacteriol. 1998 Jun;180(11):2875–82. doi: 10.1128/jb.180.11.2875-2882.1998. |
| heme b biosynthesis II (anaerobic) Accession ID: BioCyc:META_HEMESYN2-PWY |
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Troup B, Hungerer C, Jahn D. Cloning and characterization of the Escherichia coli hemN gene encoding the oxygen-independent coproporphyrinogen III oxidase. J Bacteriol. 1995 Jun;177(11):3326–31. doi: 10.1128/jb.177.11.3326-3331.1995. |
| methylaspartate cycle Accession ID: BioCyc:META_PWY-6728 |
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Khomyakova M, Bükmez Ö, Thomas LK, Erb TJ, Berg IA. A methylaspartate cycle in haloarchaea. Science. 2011 Jan 21;331(6015):334–7. doi: 10.1126/science.1196544. PMID: 21252347. |
| superpathway of b heme biosynthesis from glycine Accession ID: BioCyc:META_PWY-5920 |
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Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD. Computational prediction of human metabolic pathways from the complete human genome. Genome Biology. 2004 Dec 22;6(1):r2. doi: 10.1186/gb-2004-6-1-r2.; Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB. Computational Analysis of Plasmodium falciparum Metabolism: Organizing Genomic Information to Facilitate Drug Discovery. Genome Res. 2004 Apr 12;14(5):917–24. doi: 10.1101/gr.2050304.; Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 01;32(Database issue):D311–4. PMID: 14681421; PMCID: PMC308767.; Frankenberg N, Moser J, Jahn D. Bacterial heme biosynthesis and its biotechnological application. Applied Microbiology and Biotechnology. 2003 Dec 01;63(2):115–27. doi: 10.1007/s00253-003-1432-2.; Panek H, O'Brian MR. A whole genome view of prokaryotic haem biosynthesis. Microbiology (Reading). 2002 Aug;148(Pt 8):2273–82. doi: 10.1099/00221287-148-8-2273. PMID: 12177321. |
| 2,3-dihydroxybenzoate degradation Accession ID: BioCyc:META_PWY-7480 |
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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.; Andreoni V, Canonica L, Galli E, Gennari C, Treccani V. 2,3-Dihydroxybenzoate pathway in Pseudomonas putida. 1H n.m.r. study on the ring-cleavage site. Biochem J. 1981 Feb 15;194(2):607–10. PMID: 7306005; PMCID: PMC1162785.; Ribbons DW, Senior PJ. 2,3-Dihydroxybenzoate 3,4-oxygenase from Pseudomonas fluorescens: determination of the site of ring cleavage with a substrate analogue. Biochem J. 1970 Apr;117(2):28P–29P. PMID: 5420036; PMCID: PMC1178909. |
| conversion of succinate to propanoate Accession ID: BioCyc:META_PWY0-43 |
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| pyruvate fermentation to acetate and alanine Accession ID: BioCyc:META_PWY-5096 |
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Sakuraba H, Ohshima T. Novel energy metabolism in anaerobic hyperthermophilic archaea: a modified Embden-Meyerhof pathway. Journal of Bioscience and Bioengineering. 2002 May;93(5):441–8. doi: 10.1016/s1389-1723(02)80090-1.; Ward DE, Kengen SWM, van der Oost J, de Vos WM. Purification and Characterization of the Alanine Aminotransferase from the Hyperthermophilic Archaeon Pyrococcus furiosus and Its Role in Alanine Production. J Bacteriol. 2000 May;182(9):2559–66. doi: 10.1128/jb.182.9.2559-2566.2000.; de Vos WM, Kengen SW, Voorhorst WG, van der Oost J. Sugar utilization and its control in hyperthermophiles. Extremophiles. 1998 Aug;2(3):201–5. doi: 10.1007/s007920050061. PMID: 9783166. |
| spermidine biosynthesis I Accession ID: BioCyc:META_BSUBPOLYAMSYN-PWY |
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Li Y, Hess S, Pannell LK, Tabor CW, Tabor H. In vivo mechanism-based inactivation of S -adenosylmethionine decarboxylases from Escherichia coli , Salmonella typhimurium , and Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 2001 Aug 28;98(19):10578–83. doi: 10.1073/pnas.181341198.; Hamasaki-Katagiri N, Tabor CW, Tabor H. Spermidine biosynthesis in Saccharomyces cerevisae: polyamine requirement of a null mutant of the SPE3 gene (spermidine synthase). Gene. 1997 Mar 10;187(1):35–43. doi: 10.1016/s0378-1119(96)00660-9. PMID: 9073064. |
| spermidine biosynthesis II Accession ID: BioCyc:META_PWY-6559 |
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Hanfrey CC, Pearson BM, Hazeldine S, Lee J, Gaskin DJ, Woster PM, Phillips MA, Michael AJ. Alternative Spermidine Biosynthetic Route Is Critical for Growth of Campylobacter jejuni and Is the Dominant Polyamine Pathway in Human Gut Microbiota. Journal of Biological Chemistry. 2011 Dec;286(50):43301–12. doi: 10.1074/jbc.m111.307835.; Deng X, Lee J, Michael AJ, Tomchick DR, Goldsmith EJ, Phillips MA. Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine. J Biol Chem. 2010 Aug 13;285(33):25708–19. PMID: 20534592; PMCID: PMC2919134.; 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. |
| pyruvate fermentation to acetate I Accession ID: BioCyc:META_P142-PWY |
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Boynton ZL, Bennett GN, Rudolph FB. Cloning, sequencing, and expression of genes encoding phosphotransacetylase and acetate kinase from Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol. 1996 Aug;62(8):2758–66. doi: 10.1128/aem.62.8.2758-2766.1996. |
| camalexin biosynthesis Accession ID: BioCyc:META_CAMALEXIN-SYN |
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Glawischnig E. The role of cytochrome P450 enzymes in the biosynthesis of camalexin. Biochem Soc Trans. 2006 Dec;34(Pt 6):1206–8. doi: 10.1042/bst0341206. PMID: 17073786.; Schuhegger R, Nafisi M, Mansourova M, Petersen BL, Olsen CE, Svatos A, Halkier BA, Glawischnig E. CYP71B15 (PAD3) catalyzes the final step in camalexin biosynthesis. Plant Physiol. 2006 Aug;141(4):1248–54. PMID: 16766671; PMCID: PMC1533948.; Glawischnig E, Hansen BG, Olsen CE, Halkier BA. Camalexin is synthesized from indole-3-acetaldoxime, a key branching point between primary and secondary metabolism in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2004 May 17;101(21):8245–50. doi: 10.1073/pnas.0305876101.; Naur P, Hansen CH, Bak S, Hansen BG, Jensen NB, Nielsen HL, Halkier BA. CYP79B1 from Sinapis alba converts tryptophan to indole-3-acetaldoxime. Archives of Biochemistry and Biophysics. 2003 Jan;409(1):235–41. doi: 10.1016/s0003-9861(02)00567-2.; Zhao Y, Hull AK, Gupta NR, Goss KA, Alonso J, Ecker JR, Normanly J, Chory J, Celenza JL. Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes Dev. 2002 Dec 01;16(23):3100–12. PMID: 12464638; PMCID: PMC187496.; Mikkelsen MD, Hansen CH, Wittstock U, Halkier BA. Cytochrome P450 CYP79B2 from Arabidopsis Catalyzes the Conversion of Tryptophan to Indole-3-acetaldoxime, a Precursor of Indole Glucosinolates and Indole-3-acetic Acid. Journal of Biological Chemistry. 2000 Oct;275(43):33712–7. doi: 10.1074/jbc.m001667200.; Hull AK, Vij R, Celenza JL. Arabidopsis cytochrome P450s that catalyze the first step of tryptophan-dependent indole-3-acetic acid biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 2000 Feb 18;97(5):2379–84. doi: 10.1073/pnas.040569997.; Zook M, Hammerschmidt R. Origin of the thiazole ring of camalexin, a phytoalexin from Arabidopsis thaliana. Plant Physiol. 1997 Feb;113(2):463–8. PMID: 9046593; PMCID: PMC158161. |