Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| thiosulfate disproportionation I (thiol-dependent) Accession ID: BioCyc:META_PWY-5277 |
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Frederiksen TM, Finster K. Sulfite-oxido-reductase is involved in the oxidation of sulfite in Desulfocapsa sulfoexigens during disproportionation of thiosulfate and elemental sulfur. Biodegradation. 2003 Jun;14(3):189–98. doi: 10.1023/a:1024255830925. PMID: 12889609. |
| all-trans-farnesol biosynthesis Accession ID: BioCyc:META_PWY-6859 |
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Song L. A soluble form of phosphatase in Saccharomyces cerevisiae capable of converting farnesyl diphosphate into E,E-farnesol. Appl Biochem Biotechnol. 2006 Feb;128(2):149–58. doi: 10.1385/abab:128:2:149. PMID: 16484724. |
| 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. |
| (3S)-linalool biosynthesis Accession ID: BioCyc:META_PWY-7141 |
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Tholl D, Kish CM, Orlova I, Sherman D, Gershenzon J, Pichersky E, Dudareva N. Formation of Monoterpenes in Antirrhinum majus and Clarkia breweri Flowers Involves Heterodimeric Geranyl Diphosphate Synthases. Plant Cell. 2004 Mar 18;16(4):977–92. doi: 10.1105/tpc.020156. |
| bisabolene biosynthesis (engineered) Accession ID: BioCyc:META_PWY-7102 |
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Bohlmann J, Crock J, Jetter R, Croteau R. Terpenoid-based defenses in conifers: cDNA cloning, characterization, and functional expression of wound-inducible ( E )-a-bisabolene synthase from grand fir ( Abies grandis ). Proc. Natl. Acad. Sci. U.S.A. 1998 Jun 09;95(12):6756–61. doi: 10.1073/pnas.95.12.6756. |
| superpathway of linalool biosynthesis Accession ID: BioCyc:META_PWY2OL-4 |
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van Schie CCN, Haring MA, Schuurink RC. Tomato linalool synthase is induced in trichomes by jasmonic acid. Plant Molecular Biology. 2007 Apr 12;64(3):251–63. doi: 10.1007/s11103-007-9149-8.; Carrau FM, Medina K, Boido E, Farina L, Gaggero C, Dellacassa E, Versini G, Henschke PA. De novo synthesis of monoterpenes by Saccharomyces cerevisiae wine yeasts. FEMS Microbiol Lett. 2005 Feb 01;243(1):107–15. doi: 10.1016/j.femsle.2004.11.050. PMID: 15668008. |
| N-acetylneuraminate and N-acetylmannosamine degradation II Accession ID: BioCyc:META_PWY-7581 |
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Brigham C, Caughlan R, Gallegos R, Dallas MB, Godoy VG, Malamy MH. Sialic Acid ( N -Acetyl Neuraminic Acid) Utilization by Bacteroides fragilis Requires a Novel N -Acetyl Mannosamine Epimerase. J Bacteriol. 2009 Jun;191(11):3629–38. doi: 10.1128/jb.00811-08. |
| N-acetylneuraminate and N-acetylmannosamine degradation I Accession ID: BioCyc:META_PWY0-1324 |
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Walters DM, Stirewalt VL, Melville SB. Cloning, Sequence, and Transcriptional Regulation of the Operon Encoding a Putative N -Acetylmannosamine-6-Phosphate Epimerase ( nanE ) and Sialic Acid Lyase ( nanA ) in Clostridium perfringens. J Bacteriol. 1999 Aug;181(15):4526–32. doi: 10.1128/jb.181.15.4526-4532.1999.; Plumbridge J, Vimr E. Convergent Pathways for Utilization of the Amino Sugars N -Acetylglucosamine, N -Acetylmannosamine, and N -Acetylneuraminic Acid by Escherichia coli. J Bacteriol. 1999 Jan;181(1):47–54. doi: 10.1128/jb.181.1.47-54.1999. |
| 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. |
| anthranilate degradation II (aerobic) Accession ID: BioCyc:META_PWY-6077 |
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ALTENSCHMIDT U, ECKERSKORN C, FUCHS G. Evidence that enzymes of a novel aerobic 2-amino-benzoate metabolism in denitrifying Pseudomonas are coded on a small plasmid. European Journal of Biochemistry. 1990 Dec;194(2):647–53. doi: 10.1111/j.1432-1033.1990.tb15664.x. |
| Kdo transfer to lipid IVA II Accession ID: BioCyc:META_PWY-7675 |
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White KA, Lin S, Cotter RJ, Raetz CR. A Haemophilus influenzae gene that encodes a membrane bound 3-deoxy-D-manno-octulosonic acid (Kdo) kinase. Possible involvement of kdo phosphorylation in bacterial virulence. J Biol Chem. 1999 Oct 29;274(44):31391–400. doi: 10.1074/jbc.274.44.31391. PMID: 10531340. |
| 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. |
| Kdo8N transfer to lipid IVA Accession ID: BioCyc:META_PWY-7676 |
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Gattis SG, Chung HS, Trent MS, Raetz CRH. The Origin of 8-Amino-3,8-dideoxy-d-manno-octulosonic Acid (Kdo8N) in the Lipopolysaccharide of Shewanella oneidensis. Journal of Biological Chemistry. 2013 Mar;288(13):9216–25. doi: 10.1074/jbc.m113.453324. |
| 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. |
| Kdo transfer to lipid IVA III (Chlamydia) Accession ID: BioCyc:META_PWY-6467 |
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Holst O, Bock K, Brade L, Brade H. The Structures of Oligosaccharide Bisphosphates Isolated from the Lipopolysaccharide of a Recombinant Escherichia coli Strain Expressing the Gene gseA [3-deoxy-d-manno-Octulopyranosonic Acid (Kdo) Transferase] of Chlamydia psittaci 6BC. Eur J Biochem. 1995 Apr;229(1):194–200. doi: 10.1111/j.1432-1033.1995.tb20455.x. |
| 3-chlorotoluene degradation I Accession ID: BioCyc:META_PWY-6103 |
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Pollmann K, Wray V, Pieper DH. Chloromethylmuconolactones as Critical Metabolites in the Degradation of Chloromethylcatechols: Recalcitrance of 2-Chlorotoluene. J Bacteriol. 2005 Apr;187(7):2332–40. doi: 10.1128/jb.187.7.2332-2340.2005. |
| bisbenzylisoquinoline alkaloid biosynthesis Accession ID: BioCyc:META_PWY-5472 |
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Kraus PF, Kutchan TM. Molecular cloning and heterologous expression of a cDNA encoding berbamunine synthase, a C--O phenol-coupling cytochrome P450 from the higher plant Berberis stolonifera. Proc. Natl. Acad. Sci. U.S.A. 1995 Mar 14;92(6):2071–5. doi: 10.1073/pnas.92.6.2071. |
| chelerythrine biosynthesis Accession ID: BioCyc:META_PWY-7507 |
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Takemura T, Ikezawa N, Iwasa K, Sato F. Molecular cloning and characterization of a cytochrome P450 in sanguinarine biosynthesis from Eschscholzia californica cells. Phytochemistry. 2013 Jul;91():100–8. doi: 10.1016/j.phytochem.2012.02.013. PMID: 22421633.; Hagel JM, Facchini PJ. Benzylisoquinoline alkaloid metabolism: a century of discovery and a brave new world. Plant Cell Physiol. 2013 May;54(5):647–72. doi: 10.1093/pcp/pct020. PMID: 23385146.; Beaudoin GAW, Facchini PJ. Isolation and characterization of a cDNA encoding (S)-cis-N-methylstylopine 14-hydroxylase from opium poppy, a key enzyme in sanguinarine biosynthesis. Biochemical and Biophysical Research Communications. 2013 Feb;431(3):597–603. doi: 10.1016/j.bbrc.2012.12.129.; Díaz Chávez ML, Rolf M, Gesell A, Kutchan TM. Characterization of two methylenedioxy bridge-forming cytochrome P450-dependent enzymes of alkaloid formation in the Mexican prickly poppy Argemone mexicana. Archives of Biochemistry and Biophysics. 2011 Mar;507(1):186–93. doi: 10.1016/j.abb.2010.11.016.; Kosina P, Gregorova J, Gruz J, Vacek J, Kolar M, Vogel M, Roos W, Naumann K, Simanek V, Ulrichova J. Phytochemical and antimicrobial characterization of Macleaya cordata herb. Fitoterapia. 2010 Dec;81(8):1006–12. doi: 10.1016/j.fitote.2010.06.020. PMID: 20600683.; Vogel M, Lawson M, Sippl W, Conrad U, Roos W. Structure and Mechanism of Sanguinarine Reductase, an Enzyme of Alkaloid Detoxification. Journal of Biological Chemistry. 2010 Jun;285(24):18397–406. doi: 10.1074/jbc.m109.088989.; Ziegler J, Facchini PJ. Alkaloid biosynthesis: metabolism and trafficking. Annu Rev Plant Biol. 2008;59():735–69. doi: 10.1146/annurev.arplant.59.032607.092730. PMID: 18251710.; Cho HY, Rhee HS, Yoon SY, Park JM. Differential induction of protein expression and benzophenanthridine alkaloid accumulation in Eschscholtzia californica suspension cultures by methyl jasmonate and yeast extract. J Microbiol Biotechnol. 2008 Feb;18(2):255–62. PMID: 18309269.; Malíková J, Zdarilová A, Hlobilková A, Ulrichová J. The effect of chelerythrine on cell growth, apoptosis, and cell cycle in human normal and cancer cells in comparison with sanguinarine. Cell Biol Toxicol. 2006 Nov;22(6):439–53. doi: 10.1007/s10565-006-0109-x. PMID: 16964588.; Malikova J, Zdarilova A, Hlobilkova A. Effects of sanguinarine and chelerythrine on the cell cycle and apoptosis. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2006 Jul;150(1):5–12. doi: 10.5507/bp.2006.001. PMID: 16936897.; Weiss D, Baumert A, Vogel M, Roos W. Sanguinarine reductase, a key enzyme of benzophenanthridine detoxification. Plant Cell Environ. 2006 Feb;29(2):291–302. doi: 10.1111/j.1365-3040.2005.01421.x. PMID: 17080644.; Arakawa H, Clark WG, Psenak M, Coscia CJ. Purification and characterization of dihydrobenzophenanthridine oxidase from elicited Sanguinaria canadensis cell cultures. Archives of Biochemistry and Biophysics. 1992 Nov;299(1):1–7. doi: 10.1016/0003-9861(92)90236-p.; Schumacher HM, Gundlach H, Fiedler F, Zenk MH. Elicitation of benzophenanthridine alkaloid synthesis in Eschscholtzia cell cultures. Plant Cell Rep. 1987 Dec;6(6):410–3. doi: 10.1007/bf00272770. PMID: 24248920. |
| 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. |