Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| aflatrem biosynthesis Accession ID: BioCyc:META_PWY-7540 |
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Liu C, Minami A, Noike M, Toshima H, Oikawa H, Dairi T. Regiospecificities and prenylation mode specificities of the fungal indole diterpene prenyltransferases AtmD and PaxD. Appl Environ Microbiol. 2013 Dec;79(23):7298–304. PMID: 24038699; PMCID: PMC3837767.; Nicholson MJ, Koulman A, Monahan BJ, Pritchard BL, Payne GA, Scott B. Identification of Two Aflatrem Biosynthesis Gene Loci inAspergillus flavusand Metabolic Engineering ofPenicillium paxilliTo Elucidate Their Function. Appl Environ Microbiol. 2009 Dec;75(23):7469–81. doi: 10.1128/aem.02146-08. |
| 2-aminoethylphosphonate biosynthesis Accession ID: BioCyc:META_PWY-6839 |
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Kim J, Dunaway-Mariano D. Phosphoenolpyruvate mutase catalysis of phosphoryl transfer in phosphoenolpyruvate: kinetics and mechanism of phosphorus-carbon bond formation. Biochemistry. 1996 Apr 09;35(14):4628–35. doi: 10.1021/bi952944k. PMID: 8605214.; Bowman ED, McQueney MS, Scholten JD, Dunaway-Mariano D. Purification and characterization of the Tetrahymena pyriformis P-C bond forming enzyme phosphoenolpyruvate phosphomutase. Biochemistry. 1990 Jul 31;29(30):7059–63. doi: 10.1021/bi00482a016. PMID: 2121271.; Barry RJ, Bowman E, McQueney M, Dunaway-Mariano D. Elucidation of the 2-aminoethylphosphonate biosynthetic pathway in Tetrahymena pyriformis. Biochemical and Biophysical Research Communications. 1988 May;153(1):177–82. doi: 10.1016/s0006-291x(88)81205-1.; Horiguchi M. Biosynthesis of 2-aminoethylphosphonic acid in cell-free preparations from tetrahymena. Biochimica et Biophysica Acta (BBA) - General Subjects. 1972 Jan;261(1):102–13. doi: 10.1016/0304-4165(72)90319-4. |
| 3-amino-5-hydroxybenzoate biosynthesis Accession ID: BioCyc:META_PWY-5979 |
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Floss HG, Yu TW. Rifamycin-mode of action, resistance, and biosynthesis. Chem Rev. 2005 Feb;105(2):621–32. doi: 10.1021/cr030112j. PMID: 15700959.; Guo J, Frost JW. Kanosamine biosynthesis: a likely source of the aminoshikimate pathway's nitrogen atom. J Am Chem Soc. 2002 Sep 11;124(36):10642–3. doi: 10.1021/ja026628m. PMID: 12207504.; Arakawa K, Müller R, Mahmud T, Yu TW, Floss HG. Characterization of the early stage aminoshikimate pathway in the formation of 3-amino-5-hydroxybenzoic acid: the RifN protein specifically converts kanosamine into kanosamine 6-phosphate. J Am Chem Soc. 2002 Sep 11;124(36):10644–5. doi: 10.1021/ja0206339. PMID: 12207505.; Guo J, Frost JW. Biosynthesis of 1-deoxy-1-imino-D-erythrose 4-phosphate: a defining metabolite in the aminoshikimate pathway. J Am Chem Soc. 2002 Jan 30;124(4):528–9. doi: 10.1021/ja016963v. PMID: 11804477. |
| 4-deoxy-L-threo-hex-4-enopyranuronate degradation Accession ID: BioCyc:META_PWY-6507 |
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Blot N, Berrier C, Hugouvieux-Cotte-Pattat N, Ghazi A, Condemine G. The Oligogalacturonate-specific Porin KdgM of Erwinia chrysanthemi Belongs to a New Porin Family. Journal of Biological Chemistry. 2002 Mar;277(10):7936–44. doi: 10.1074/jbc.m109193200.; Hugouvieux-Cotte-Pattat N, Condemine G, Nasser W, Reverchon S. Regulation of pectinolysis in Erwinia chrysanthemi. Annu Rev Microbiol. 1996;50():213–57. doi: 10.1146/annurev.micro.50.1.213. PMID: 8905080. |
| phosphatidylinositol biosynthesis II (eukaryotes) Accession ID: BioCyc:META_PWY-7625 |
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Lykidis A, Jackson PD, Rock CO, Jackowski S. The Role of CDP-Diacylglycerol Synthetase and Phosphatidylinositol Synthase Activity Levels in the Regulation of Cellular Phosphatidylinositol Content. Journal of Biological Chemistry. 1997 Dec;272(52):33402–9. doi: 10.1074/jbc.272.52.33402. |
| aflatoxins B2 and G2 biosynthesis Accession ID: BioCyc:META_PWY-5960 |
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Yabe K, Nakajima H. Enzyme reactions and genes in aflatoxin biosynthesis. Applied Microbiology and Biotechnology. 2004 Jun 01;64(6):745–55. doi: 10.1007/s00253-004-1566-x. |
| nitrobenzene degradation I Accession ID: BioCyc:META_PWY-5637 |
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Park H, Lim S, Chang YK, Livingston AG, Kim H. Degradation of Chloronitrobenzenes by a Coculture of Pseudomonas putida and a Rhodococcus sp. Appl Environ Microbiol. 1999 Mar;65(3):1083–91. doi: 10.1128/aem.65.3.1083-1091.1999.; Nishino SF, Spain JC. Degradation of nitrobenzene by a Pseudomonas pseudoalcaligenes. Appl Environ Microbiol. 1993 Aug;59(8):2520–5. doi: 10.1128/aem.59.8.2520-2525.1993. |
| L-glutamate and L-glutamine biosynthesis Accession ID: BioCyc:META_PWY-5505 |
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| L-glutamine biosynthesis III Accession ID: BioCyc:META_PWY-6549 |
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Taylor L, Nunes-Nesi A, Parsley K, Leiss A, Leach G, Coates S, Wingler A, Fernie AR, Hibberd JM. Cytosolic pyruvate,orthophosphate dikinase functions in nitrogen remobilization during leaf senescence and limits individual seed growth and nitrogen content. Plant J. 2010 May 01;62(4):641–52. doi: 10.1111/j.1365-313x.2010.04179.x. PMID: 20202167. |
| 1,3-β-D-glucan biosynthesis Accession ID: BioCyc:META_PWY-6773 |
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Jacobs AK, Lipka V, Burton RA, Panstruga R, Strizhov N, Schulze-Lefert P, Fincher GB. An Arabidopsis Callose Synthase, GSL5, Is Required for Wound and Papillary Callose Formation. Plant Cell. 2003 Nov;15(11):2503–13. PMID: 14555698; PMCID: PMC280557. |
| heme degradation IV Accession ID: BioCyc:META_PWY-7843 |
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Ouellet YH, Ndiaye CT, Gagné SM, Sebilo A, Suits MDL, Jubinville É, Jia Z, Ivancich A, Couture M. An alternative reaction for heme degradation catalyzed by the Escherichia coli O157:H7 ChuS protein: Release of hematinic acid, tripyrrole and Fe(III). Journal of Inorganic Biochemistry. 2016 Jan;154():103–13. doi: 10.1016/j.jinorgbio.2015.11.002. |
| adenosine nucleotides degradation III Accession ID: BioCyc:META_PWY-6617 |
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Leung HB, Schramm VL. Adenylate degradation in Escherichia coli. The role of AMP nucleosidase and properties of the purified enzyme. Journal of Biological Chemistry. 1980 Nov;255(22):10867–74. doi: 10.1016/s0021-9258(19)70387-1. |
| adenosine nucleotides degradation II Accession ID: BioCyc:META_SALVADEHYPOX-PWY |
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Bzowska A, Kulikowska E, Shugar D. Purine nucleoside phosphorylases: properties, functions, and clinical aspects. Pharmacol Ther. 2000 Dec;88(3):349–425. doi: 10.1016/s0163-7258(00)00097-8. PMID: 11337031.; Elshafei AM, Abu-Shady MR, el-Beih FM, Mohamed LA. Mode and extent of degradation of adenosine and guanosine by extracts of Aspergillus terricola. Microbiol Res. 1995 Sep;150(3):291–5. doi: 10.1016/s0944-5013(11)80008-x. PMID: 7551735. |
| 2,6-dinitrotoluene degradation Accession ID: BioCyc:META_PWY-5643 |
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Nishino SF, Paoli GC, Spain JC. Aerobic Degradation of Dinitrotoluenes and Pathway for Bacterial Degradation of 2,6-Dinitrotoluene. Appl Environ Microbiol. 2000 May;66(5):2139–47. doi: 10.1128/aem.66.5.2139-2147.2000. |
| heme degradation II Accession ID: BioCyc:META_PWY-7845 |
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Wegele R, Tasler R, Zeng Y, Rivera M, Frankenberg-Dinkel N. The Heme Oxygenase(s)-Phytochrome System of Pseudomonas aeruginosa. Journal of Biological Chemistry. 2004 Oct;279(44):45791–802. doi: 10.1074/jbc.m408303200. |
| dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis Accession ID: BioCyc:META_PWY-7318 |
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Pföstl A, Zayni S, Hofinger A, Kosma P, Schäffer C, Messner P. Biosynthesis of dTDP-3-acetamido-3,6-dideoxy-a- |
| pseudouridine degradation Accession ID: BioCyc:META_PWY-6019 |
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Preumont A, Snoussi K, Stroobant V, Collet J, Van Schaftingen E. Molecular Identification of Pseudouridine-metabolizing Enzymes. Journal of Biological Chemistry. 2008 Sep;283(37):25238–46. doi: 10.1074/jbc.m804122200. |
| purine nucleotides degradation I (plants) Accession ID: BioCyc:META_PWY-5044 |
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Hesberg C, Hänsch R, Mendel RR, Bittner F. Tandem orientation of duplicated xanthine dehydrogenase genes from Arabidopsis thaliana: differential gene expression and enzyme activities. J Biol Chem. 2004 Apr 02;279(14):13547–54. doi: 10.1074/jbc.m312929200. PMID: 14726515.; Capote-Maínez N, Sánchez F. Characterization of the common bean uricase II and its expression in organs other than nodules. Plant Physiol. 1997 Dec;115(4):1307–17. PMID: 9414545; PMCID: PMC158596. |
| coenzyme B/coenzyme M regeneration III (coenzyme F420-dependent) Accession ID: BioCyc:META_PWY-7866 |
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Yan Z, Wang M, Ferry JG. A Ferredoxin- and F 420 H 2 -Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea. mBio. 2017 Mar 08;8(1). doi: 10.1128/mbio.02285-16. |
| 4-hydroxycoumarin and dicoumarol biosynthesis Accession ID: BioCyc:META_PWY-6418 |
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Liu B, Raeth T, Beuerle T, Beerhues L. A novel 4-hydroxycoumarin biosynthetic pathway. Plant Mol Biol. 2010 Jan;72(1-2):17–25. doi: 10.1007/s11103-009-9548-0. PMID: 19757094. |