Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| nitrate reduction I (denitrification) Accession ID: BioCyc:META_DENITRIFICATION-PWY |
|
Knowles R. Denitrification. Microbiol Rev. 1982 Mar;46(1):43–70. doi: 10.1128/mr.46.1.43-70.1982.; Delwiche CC, Bryan BA. Denitrification. Annu Rev Microbiol. 1976;30():241–62. doi: 10.1146/annurev.mi.30.100176.001325. PMID: 10827. |
| thiosulfate oxidation II (via tetrathionate) Accession ID: BioCyc:META_PWY-5303 |
|
Dahl C. Cytoplasmic sulfur trafficking in sulfur-oxidizing prokaryotes. IUBMB Life. 2015 Apr;67(4):268–74. doi: 10.1002/iub.1371. PMID: 25913822.; Liu L, Stockdreher Y, Koch T, Sun S, Fan Z, Josten M, Sahl H, Wang Q, Luo Y, Liu S, Dahl C, Jiang C. Thiosulfate Transfer Mediated by DsrE/TusA Homologs from Acidothermophilic Sulfur-oxidizing Archaeon Metallosphaera cuprina. Journal of Biological Chemistry. 2014 Sep;289(39):26949–59. doi: 10.1074/jbc.m114.591669.; Müller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM, Kletzin A. Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Mol Microbiol. 2004 Aug;53(4):1147–60. doi: 10.1111/j.1365-2958.2004.04193.x. PMID: 15306018. |
| glycolate and glyoxylate degradation I Accession ID: BioCyc:META_GLYCOLATEMET-PWY |
- | |
| superpathway of sulfur oxidation (Acidianus ambivalens) Accession ID: BioCyc:META_PWY-5304 |
|
Liu L, Stockdreher Y, Koch T, Sun S, Fan Z, Josten M, Sahl H, Wang Q, Luo Y, Liu S, Dahl C, Jiang C. Thiosulfate Transfer Mediated by DsrE/TusA Homologs from Acidothermophilic Sulfur-oxidizing Archaeon Metallosphaera cuprina. Journal of Biological Chemistry. 2014 Sep;289(39):26949–59. doi: 10.1074/jbc.m114.591669.; Müller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM, Kletzin A. Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Mol Microbiol. 2004 Aug;53(4):1147–60. doi: 10.1111/j.1365-2958.2004.04193.x. PMID: 15306018.; Laska S, Lottspeich F, Kletzin A. Membrane-bound hydrogenase and sulfur reductase of the hyperthermophilic and acidophilic archaeon Acidianus ambivalens. Microbiology (Reading). 2003 Sep;149(Pt 9):2357–71. doi: 10.1099/mic.0.26455-0. PMID: 12949162.; Zimmermann P, Laska S, Kletzin A. Two modes of sulfite oxidation in the extremely thermophilic and acidophilic archaeon Acidianus ambivalens. Archives of Microbiology. 1999 Jul 26;172(2):76–82. doi: 10.1007/s002030050743.; Kletzin A. Coupled enzymatic production of sulfite, thiosulfate, and hydrogen sulfide from sulfur: purification and properties of a sulfur oxygenase reductase from the facultatively anaerobic archaebacterium Desulfurolobus ambivalens. J Bacteriol. 1989 Mar;171(3):1638–43. doi: 10.1128/jb.171.3.1638-1643.1989. |
| superpathway of glycol metabolism and degradation Accession ID: BioCyc:ECO_GLYCOL-GLYOXDEG-PWY |
- | |
| (aminomethyl)phosphonate degradation Accession ID: BioCyc:META_PWY-7805 |
|
Hove-Jensen B, Zechel DL, Jochimsen B. Utilization of glyphosate as phosphate source: biochemistry and genetics of bacterial carbon-phosphorus lyase. Microbiol Mol Biol Rev. 2014 Mar;78(1):176–97. PMID: 24600043; PMCID: PMC3957732.; Kamat SS, Williams HJ, Raushel FM. Intermediates in the transformation of phosphonates to phosphate by bacteria. Nature. 2011 Nov 16;480(7378):570–3. doi: 10.1038/nature10622.; He SM, Wathier M, Podzelinska K, Wong M, McSorley FR, Asfaw A, Hove-Jensen B, Jia Z, Zechel DL. Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway. Biochemistry. 2011 Oct 11;50(40):8603–15. doi: 10.1021/bi2005398. PMID: 21830807.; Hove-Jensen B, McSorley FR, Zechel DL. Physiological role of phnP-specified phosphoribosyl cyclic phosphodiesterase in catabolism of organophosphonic acids by the carbon-phosphorus lyase pathway. J Am Chem Soc. 2011 Mar 16;133(10):3617–24. doi: 10.1021/ja1102713. PMID: 21341651.; Podzelinska K, He S, Wathier M, Yakunin A, Proudfoot M, Hove-Jensen B, Zechel DL, Jia Z. Structure of PhnP, a Phosphodiesterase of the Carbon-Phosphorus Lyase Pathway for Phosphonate Degradation. Journal of Biological Chemistry. 2009 Jun;284(25):17216–26. doi: 10.1074/jbc.m808392200. |
| methylphosphonate degradation I Accession ID: BioCyc:META_PWY0-1533 |
|
Kamat SS, Williams HJ, Raushel FM. Intermediates in the transformation of phosphonates to phosphate by bacteria. Nature. 2011 Nov 16;480(7378):570–3. doi: 10.1038/nature10622.; He SM, Wathier M, Podzelinska K, Wong M, McSorley FR, Asfaw A, Hove-Jensen B, Jia Z, Zechel DL. Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway. Biochemistry. 2011 Oct 11;50(40):8603–15. doi: 10.1021/bi2005398. PMID: 21830807.; Hove-Jensen B, McSorley FR, Zechel DL. Physiological role of phnP-specified phosphoribosyl cyclic phosphodiesterase in catabolism of organophosphonic acids by the carbon-phosphorus lyase pathway. J Am Chem Soc. 2011 Mar 16;133(10):3617–24. doi: 10.1021/ja1102713. PMID: 21341651.; Podzelinska K, He S, Wathier M, Yakunin A, Proudfoot M, Hove-Jensen B, Zechel DL, Jia Z. Structure of PhnP, a Phosphodiesterase of the Carbon-Phosphorus Lyase Pathway for Phosphonate Degradation. Journal of Biological Chemistry. 2009 Jun;284(25):17216–26. doi: 10.1074/jbc.m808392200.; Makino K, Kim SK, Shinagawa H, Amemura M, Nakata A. Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12. J Bacteriol. 1991 Apr;173(8):2665–72. doi: 10.1128/jb.173.8.2665-2672.1991. |
| glycolate and glyoxylate degradation I Accession ID: BioCyc:ECO_GLYCOLATEMET-PWY |
|
Zelcbuch L, Razo-Mejia M, Herz E, Yahav S, Antonovsky N, Kroytoro H, Milo R, Bar-Even A. An In Vivo Metabolic Approach for Deciphering the Product Specificity of Glycerate Kinase Proves that Both E. coli’s Glycerate Kinases Generate 2-Phosphoglycerate. PLoS ONE. 2015 Mar 30;10(3):e0122957. doi: 10.1371/journal.pone.0122957. |
| methylphosphonate degradation I Accession ID: BioCyc:ECO_PWY0-1533 |
|
Hove-Jensen B, Zechel DL, Jochimsen B. Utilization of glyphosate as phosphate source: biochemistry and genetics of bacterial carbon-phosphorus lyase. Microbiol Mol Biol Rev. 2014 Mar;78(1):176–97. PMID: 24600043; PMCID: PMC3957732.; Kamat SS, Williams HJ, Raushel FM. Intermediates in the transformation of phosphonates to phosphate by bacteria. Nature. 2011 Nov 16;480(7378):570–3. doi: 10.1038/nature10622.; Makino K, Kim SK, Shinagawa H, Amemura M, Nakata A. Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12. J Bacteriol. 1991 Apr;173(8):2665–72. doi: 10.1128/jb.173.8.2665-2672.1991. |
| superpathway of glycol metabolism and degradation Accession ID: BioCyc:META_GLYCOL-GLYOXDEG-PWY |
- | |
| L-tryptophan degradation I (via anthranilate) Accession ID: BioCyc:META_TRPCAT-PWY |
|
Kurnasov O, Jablonski L, Polanuyer B, Dorrestein P, Begley T, Osterman A. Aerobic tryptophan degradation pathway in bacteria: novel kynurenine formamidase. FEMS Microbiol Lett. 2003 Oct 24;227(2):219–27. doi: 10.1016/s0378-1097(03)00684-0. PMID: 14592712.; Bouknight RR, Sadoff HL. Tryptophan catabolism in Bacillus megaterium. J Bacteriol. 1975 Jan;121(1):70–6. doi: 10.1128/jb.121.1.70-76.1975. |
| (aminomethyl)phosphonate degradation Accession ID: BioCyc:ECO_PWY-7805 |
|
Hove-Jensen B, McSorley FR, Zechel DL. Catabolism and Detoxification of 1-Aminoalkylphosphonic Acids: N-Acetylation by the phnO Gene Product. PLoS ONE. 2012 Oct 03;7(10):e46416. doi: 10.1371/journal.pone.0046416. |