Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| methylglyoxal degradation I Accession ID: BioCyc:HUMAN_PWY-5386 |
|
Kalapos MP. Methylglyoxal in living organisms: chemistry, biochemistry, toxicology and biological implications. Toxicol Lett. 1999 Nov 22;110(3):145–75. doi: 10.1016/s0378-4274(99)00160-5. PMID: 10597025. |
| glycolysis Accession ID: BioCyc:HUMAN_PWY66-400 |
|
Dang CV. Links between metabolism and cancer. Genes Dev. 2012 May 01;26(9):877–90. PMID: 22549953; PMCID: PMC3347786. |
| 7-(3-amino-3-carboxypropyl)-wyosine biosynthesis Accession ID: BioCyc:HUMAN_PWY-7286 |
- | |
| superpathway of methionine degradation Accession ID: BioCyc:HUMAN_PWY-5328 |
- | |
| glutathione-mediated detoxification I Accession ID: BioCyc:HUMAN_PWY-4061 |
|
Hinchman CA, Ballatori N. Glutathione conjugation and conversion to mercapturic acids can occur as an intrahepatic process. Journal of Toxicology and Environmental Health. 1994 Apr;41(4):387–409. doi: 10.1080/15287399409531852. |
| L-serine degradation Accession ID: BioCyc:HUMAN_SERDEG-PWY |
- | |
| 2-chloroacrylate degradation II Accession ID: BioCyc:META_PWY-7428 |
|
KURIHARA T. A Mechanistic Analysis of Enzymatic Degradation of Organohalogen Compounds. Bioscience, Biotechnology, and Biochemistry. 2011 Feb 23;75(2):189–98. doi: 10.1271/bbb.100746.; Mowafy AM, Kurihara T, Kurata A, Uemura T, Esaki N. 2-haloacrylate hydratase, a new class of flavoenzyme that catalyzes the addition of water to the substrate for dehalogenation. Appl Environ Microbiol. 2010 Sep;76(18):6032–7. PMID: 20656877; PMCID: PMC2937477. |
| L-homophenylalanine biosynthesis Accession ID: BioCyc:META_PWY-7275 |
|
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. |
| L-alanine biosynthesis II Accession ID: BioCyc:META_ALANINE-SYN2-PWY |
|
Wang MD, Buckley L, Berg CM. Cloning of genes that suppress an Escherichia coli K-12 alanine auxotroph when present in multicopy plasmids. J Bacteriol. 1987 Dec;169(12):5610–4. doi: 10.1128/jb.169.12.5610-5614.1987. |
| L-glutamate degradation VII (to butanoate) Accession ID: BioCyc:META_GLUDEG-II-PWY |
|
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. |
| pyruvate fermentation to propanoate I Accession ID: BioCyc:META_P108-PWY |
|
Swick RW, Wood HG. THE ROLE OF TRANSCARBOXYLATION IN PROPIONIC ACID FERMENTATION. Proc Natl Acad Sci U S A. 1960 Jan;46(1):28–41. PMID: 16590594; PMCID: PMC285006. |
| N-acetylneuraminate and N-acetylmannosamine degradation II Accession ID: BioCyc:META_PWY-7581 |
|
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 |
|
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 |
|
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. |
| pyruvate fermentation to acetate and alanine Accession ID: BioCyc:META_PWY-5096 |
|
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. |
| 2-aminoethylphosphonate degradation II Accession ID: BioCyc:META_PWY-6832 |
|
Borisova SA, Christman HD, Metcalf MEM, Zulkepli NA, Zhang JK, van der Donk WA, Metcalf WW. Genetic and Biochemical Characterization of a Pathway for the Degradation of 2-Aminoethylphosphonate in Sinorhizobium meliloti 1021. Journal of Biological Chemistry. 2011 Jun;286(25):22283–90. doi: 10.1074/jbc.m111.237735. |
| pyruvate fermentation to acetate IV Accession ID: BioCyc:META_PWY-5485 |
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| 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. |
| pyruvate fermentation to acetate I Accession ID: BioCyc:META_P142-PWY |
|
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. |
| indole-3-acetate biosynthesis I Accession ID: BioCyc:META_PWYDQC-4 |
|
Zhao Y. Auxin Biosynthesis: A Simple Two-Step Pathway Converts Tryptophan to Indole-3-Acetic Acid in Plants. Molecular Plant. 2012 Mar;5(2):334–8. doi: 10.1093/mp/ssr104.; Won C, Shen X, Mashiguchi K, Zheng Z, Dai X, Cheng Y, Kasahara H, Kamiya Y, Chory J, Zhao Y. Conversion of tryptophan to indole-3-acetic acid by TRYPTOPHAN AMINOTRANSFERASES OF ARABIDOPSIS and YUCCAs in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2011 Oct 24;108(45):18518–23. doi: 10.1073/pnas.1108436108.; Mashiguchi K, Tanaka K, Sakai T, Sugawara S, Kawaide H, Natsume M, Hanada A, Yaeno T, Shirasu K, Yao H, McSteen P, Zhao Y, Hayashi K, Kamiya Y, Kasahara H. The main auxin biosynthesis pathway in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2011 Oct 24;108(45):18512–7. doi: 10.1073/pnas.1108434108.; Tao Y, Ferrer J, Ljung K, Pojer F, Hong F, Long JA, Li L, Moreno JE, Bowman ME, Ivans LJ, Cheng Y, Lim J, Zhao Y, Ballaré CL, Sandberg G, Noel JP, Chory J. Rapid Synthesis of Auxin via a New Tryptophan-Dependent Pathway Is Required for Shade Avoidance in Plants. Cell. 2008 Apr;133(1):164–76. doi: 10.1016/j.cell.2008.01.049. |