Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| (S)-propane-1,2-diol degradation Accession ID: BioCyc:META_PWY-7013 |
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Cheng S, Liu Y, Crowley CS, Yeates TO, Bobik TA. Bacterial microcompartments: their properties and paradoxes. BioEssays. 2008 Oct 20;30(11-12):1084–95. doi: 10.1002/bies.20830.; Liu Y, Leal NA, Sampson EM, Johnson CLV, Havemann GD, Bobik TA. PduL Is an Evolutionarily Distinct Phosphotransacylase Involved in B 12 -Dependent 1,2-Propanediol Degradation by Salmonella enterica Serovar Typhimurium LT2. J Bacteriol. 2007 Mar;189(5):1589–96. doi: 10.1128/jb.01151-06. |
| 2'-deoxy-α-D-ribose 1-phosphate degradation Accession ID: BioCyc:META_PWY-7180 |
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| detoxification of reactive carbonyls in chloroplasts Accession ID: BioCyc:ARA_PWY-6786 |
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Yamauchi Y, Hasegawa A, Taninaka A, Mizutani M, Sugimoto Y. NADPH-dependent Reductases Involved in the Detoxification of Reactive Carbonyls in Plants. Journal of Biological Chemistry. 2011 Mar;286(9):6999–7009. doi: 10.1074/jbc.m110.202226.; Simpson PJ, Tantitadapitak C, Reed AM, Mather OC, Bunce CM, White SA, Ride JP. Characterization of two novel aldo-keto reductases from Arabidopsis: expression patterns, broad substrate specificity, and an open active-site structure suggest a role in toxicant metabolism following stress. J Mol Biol. 2009 Sep 18;392(2):465–80. doi: 10.1016/j.jmb.2009.07.023. PMID: 19616008. |
| androstenedione degradation Accession ID: BioCyc:THAPS_PWY-6944 |
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| isopropylamine degradation Accession ID: BioCyc:META_PWY-5736 |
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de Azevedo Wa¨sch SI, van der Ploeg JR, Maire T, Lebreton A, Kiener A, Leisinger T. Transformation of Isopropylamine to |
| detoxification of reactive carbonyls in chloroplasts Accession ID: BioCyc:META_PWY-6786 |
|
Yamauchi Y, Hasegawa A, Taninaka A, Mizutani M, Sugimoto Y. NADPH-dependent Reductases Involved in the Detoxification of Reactive Carbonyls in Plants. Journal of Biological Chemistry. 2011 Mar;286(9):6999–7009. doi: 10.1074/jbc.m110.202226.; Simpson PJ, Tantitadapitak C, Reed AM, Mather OC, Bunce CM, White SA, Ride JP. Characterization of two novel aldo-keto reductases from Arabidopsis: expression patterns, broad substrate specificity, and an open active-site structure suggest a role in toxicant metabolism following stress. J Mol Biol. 2009 Sep 18;392(2):465–80. doi: 10.1016/j.jmb.2009.07.023. PMID: 19616008. |
| superpathway of testosterone and androsterone degradation Accession ID: BioCyc:META_PWY-6937 |
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van der Geize R, Grommen AWF, Hessels GI, Jacobs AAC, Dijkhuizen L. The Steroid Catabolic Pathway of the Intracellular Pathogen Rhodococcus equi Is Important for Pathogenesis and a Target for Vaccine Development. PLoS Pathog. 2011 Aug 25;7(8):e1002181. doi: 10.1371/journal.ppat.1002181.; Kreit J, Sampson NS. Cholesterol oxidase: physiological functions. The FEBS Journal. 2009 Nov 16;276(23):6844–56. doi: 10.1111/j.1742-4658.2009.07378.x.; Petrusma M, Dijkhuizen L, van der Geize R. Rhodococcus rhodochrous DSM 43269 3-ketosteroid 9alpha-hydroxylase, a two-component iron-sulfur-containing monooxygenase with subtle steroid substrate specificity. Appl Environ Microbiol. 2009 Aug;75(16):5300–7. PMID: 19561185; PMCID: PMC2725467.; Horinouchi M, Hayashi T, Koshino H, Kurita T, Kudo T. Identification of 9,17-Dioxo-1,2,3,4,10,19-Hexanorandrostan-5-oic Acid, 4-Hydroxy-2-Oxohexanoic Acid, and 2-Hydroxyhexa-2,4-Dienoic Acid and Related Enzymes Involved in Testosterone Degradation in Comamonas testosteroni TA441. Appl Environ Microbiol. 2005 Sep;71(9):5275–81. doi: 10.1128/aem.71.9.5275-5281.2005.; Horinouchi M, Hayashi T, Yamamoto T, Kudo T. A New Bacterial Steroid Degradation Gene Cluster in Comamonas testosteroni TA441 Which Consists of Aromatic-Compound Degradation Genes for Seco-Steroids and 3-Ketosteroid Dehydrogenase Genes. Appl Environ Microbiol. 2003 Aug;69(8):4421–30. doi: 10.1128/aem.69.8.4421-4430.2003.; Horinouchi M, Hayashi T, Koshino H, Yamamoto T, Kudo T. Gene Encoding the Hydrolase for the Product of the meta -Cleavage Reaction in Testosterone Degradation by Comamonas testosteroni. Appl Environ Microbiol. 2003 Apr;69(4):2139–52. doi: 10.1128/aem.69.4.2139-2152.2003.; Florin C, Köhler T, Grandguillot M, Plesiat P. Comamonas testosteroni 3-ketosteroid-delta 4(5 alpha)-dehydrogenase: gene and protein characterization. J Bacteriol. 1996 Jun;178(11):3322–30. doi: 10.1128/jb.178.11.3322-3330.1996. |
| superpathway of pyrimidine deoxyribonucleosides degradation Accession ID: BioCyc:ECO_PWY0-1298 |
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| superpathway of testosterone and androsterone degradation Accession ID: BioCyc:MTBCDC1551_PWY-6937 |
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| 4-nitrotoluene degradation II Accession ID: BioCyc:META_PWY-5644 |
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Horinouchi M, Hayashi T, Koshino H, Kurita T, Kudo T. Identification of 9,17-Dioxo-1,2,3,4,10,19-Hexanorandrostan-5-oic Acid, 4-Hydroxy-2-Oxohexanoic Acid, and 2-Hydroxyhexa-2,4-Dienoic Acid and Related Enzymes Involved in Testosterone Degradation in Comamonas testosteroni TA441. Appl Environ Microbiol. 2005 Sep;71(9):5275–81. doi: 10.1128/aem.71.9.5275-5281.2005.; He Z, Spain JC. Reactions Involved in the Lower Pathway for Degradation of 4-Nitrotoluene by Mycobacterium Strain HL 4-NT-1. Appl Environ Microbiol. 2000 Jul;66(7):3010–5. doi: 10.1128/aem.66.7.3010-3015.2000.; Spiess T, Desiere F, Fischer P, Spain JC, Knackmuss H, Lenke H. A New 4-Nitrotoluene Degradation Pathway in a Mycobacterium Strain. Appl Environ Microbiol. 1998 Feb;64(2):446–52. doi: 10.1128/aem.64.2.446-452.1998. |
| alkylnitronates degradation Accession ID: BioCyc:META_PWY-723 |
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Gorlatova N, Tchorzewski M, Kurihara T, Soda K, Esaki N. Purification, Characterization, and Mechanism of a Flavin Mononucleotide-Dependent 2-Nitropropane Dioxygenase from Neurospora crassa. Appl Environ Microbiol. 1998 Mar;64(3):1029–33. doi: 10.1128/aem.64.3.1029-1033.1998.; Colandene JD, Garrett RH. Functional Dissection and Site-directed Mutagenesis of the Structural Gene for NAD(P)H-Nitrite Reductase in Neurospora crassa. Journal of Biological Chemistry. 1996 Sep;271(39):24096–104. doi: 10.1074/jbc.271.39.24096.; Exley GE, Colandene JD, Garrett RH. Molecular cloning, characterization, and nucleotide sequence of nit-6, the structural gene for nitrite reductase in Neurospora crassa. J Bacteriol. 1993 Apr;175(8):2379–92. doi: 10.1128/jb.175.8.2379-2392.1993.; Prodouz KN, Garrett RH. Neurospora crassa NAD(P)H-nitrite reductase. Studies on its composition and structure. Journal of Biological Chemistry. 1981 Sep;256(18):9711–7. doi: 10.1016/s0021-9258(19)68821-6.; Greenbaum P, Prodouz KN, Garrett RH. Preparation and some properties of homogeneous Neurospora crassa assimilatory NADPH-nitrite reductase. Biochimica et Biophysica Acta (BBA) - Enzymology. 1978 Sep;526(1):52–64. doi: 10.1016/0005-2744(78)90289-9.; Kido T, Soda K, Suzuki T, Asada K. A new oxygenase, 2-nitropropane dioxygenase of Hansenula mrakii. Enzymologic and spectrophotometric properties. Journal of Biological Chemistry. 1976 Nov;251(22):6994–7000. doi: 10.1016/s0021-9258(17)32932-0.; Kido T, Yamamoto T, Soda K. Microbial assimilation of alkyl nitro compounds and formation of nitrite. Arch Microbiol. 1975 Dec 31;106(3):165–9. doi: 10.1007/bf00446519. PMID: 1217935.; Vega J, Garrett R. Siroheme: a prosthetic group of the Neurospora crassa assimilatory nitrite reductase. Journal of Biological Chemistry. 1975 Oct;250(20):7980–9. doi: 10.1016/s0021-9258(19)40804-1.; Lafferty MA, Garrett RH. Purification and Properties of the Neurospora crassa Assimilatory Nitrite Reductase. Journal of Biological Chemistry. 1974 Dec;249(23):7555–67. doi: 10.1016/s0021-9258(19)81274-7.; Prakash O, Sadana JC. Purification, characterization and properties of nitrite reductase of Achromobacter fischeri. Archives of Biochemistry and Biophysics. 1972 Feb;148(2):614–32. doi: 10.1016/0003-9861(72)90181-6.; Pateman JA, Rever BM, Cove DJ. Genetic and biochemical studies of nitrate reduction in Aspergillus nidulans. Biochem J. 1967 Jul;104(1):103–11. PMID: 4382427; PMCID: PMC1270550. |
| androstenedione degradation Accession ID: BioCyc:META_PWY-6944 |
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van der Geize R, Grommen AWF, Hessels GI, Jacobs AAC, Dijkhuizen L. The Steroid Catabolic Pathway of the Intracellular Pathogen Rhodococcus equi Is Important for Pathogenesis and a Target for Vaccine Development. PLoS Pathog. 2011 Aug 25;7(8):e1002181. doi: 10.1371/journal.ppat.1002181.; Kreit J, Sampson NS. Cholesterol oxidase: physiological functions. The FEBS Journal. 2009 Nov 16;276(23):6844–56. doi: 10.1111/j.1742-4658.2009.07378.x.; Petrusma M, Dijkhuizen L, van der Geize R. Rhodococcus rhodochrous DSM 43269 3-ketosteroid 9alpha-hydroxylase, a two-component iron-sulfur-containing monooxygenase with subtle steroid substrate specificity. Appl Environ Microbiol. 2009 Aug;75(16):5300–7. PMID: 19561185; PMCID: PMC2725467.; Horinouchi M, Hayashi T, Koshino H, Kurita T, Kudo T. Identification of 9,17-Dioxo-1,2,3,4,10,19-Hexanorandrostan-5-oic Acid, 4-Hydroxy-2-Oxohexanoic Acid, and 2-Hydroxyhexa-2,4-Dienoic Acid and Related Enzymes Involved in Testosterone Degradation in Comamonas testosteroni TA441. Appl Environ Microbiol. 2005 Sep;71(9):5275–81. doi: 10.1128/aem.71.9.5275-5281.2005.; Horinouchi M, Hayashi T, Yamamoto T, Kudo T. A New Bacterial Steroid Degradation Gene Cluster in Comamonas testosteroni TA441 Which Consists of Aromatic-Compound Degradation Genes for Seco-Steroids and 3-Ketosteroid Dehydrogenase Genes. Appl Environ Microbiol. 2003 Aug;69(8):4421–30. doi: 10.1128/aem.69.8.4421-4430.2003.; Horinouchi M, Hayashi T, Koshino H, Yamamoto T, Kudo T. Gene Encoding the Hydrolase for the Product of the meta -Cleavage Reaction in Testosterone Degradation by Comamonas testosteroni. Appl Environ Microbiol. 2003 Apr;69(4):2139–52. doi: 10.1128/aem.69.4.2139-2152.2003. |
| superpathway of cholesterol degradation II (cholesterol dehydrogenase) Accession ID: BioCyc:MTBH37RV_PWY-6947 |
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| superpathway of cholesterol degradation II (cholesterol dehydrogenase) Accession ID: BioCyc:MTBCDC1551_PWY-6947 |
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| superpathway of cholesterol degradation I (cholesterol oxidase) Accession ID: BioCyc:THAPS_PWY-6928 |
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| androstenedione degradation Accession ID: BioCyc:CLOSSAC_PWY-6944 |
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| superpathway of pyrimidine deoxyribonucleosides degradation Accession ID: BioCyc:META_PWY0-1298 |
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| superpathway of purine deoxyribonucleosides degradation Accession ID: BioCyc:META_PWY0-1297 |
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| superpathway of cholesterol degradation II (cholesterol dehydrogenase) Accession ID: BioCyc:META_PWY-6947 |
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Thomas ST, VanderVen BC, Sherman DR, Russell DG, Sampson NS. Pathway profiling in Mycobacterium tuberculosis: elucidation of cholesterol-derived catabolite and enzymes that catalyze its metabolism. J Biol Chem. 2011 Dec 23;286(51):43668–78. PMID: 22045806; PMCID: PMC3243565.; van der Geize R, Grommen AWF, Hessels GI, Jacobs AAC, Dijkhuizen L. The Steroid Catabolic Pathway of the Intracellular Pathogen Rhodococcus equi Is Important for Pathogenesis and a Target for Vaccine Development. PLoS Pathog. 2011 Aug 25;7(8):e1002181. doi: 10.1371/journal.ppat.1002181.; Kreit J, Sampson NS. Cholesterol oxidase: physiological functions. The FEBS Journal. 2009 Nov 16;276(23):6844–56. doi: 10.1111/j.1742-4658.2009.07378.x.; Petrusma M, Dijkhuizen L, van der Geize R. Rhodococcus rhodochrous DSM 43269 3-ketosteroid 9alpha-hydroxylase, a two-component iron-sulfur-containing monooxygenase with subtle steroid substrate specificity. Appl Environ Microbiol. 2009 Aug;75(16):5300–7. PMID: 19561185; PMCID: PMC2725467.; Yang X, Dubnau E, Smith I, Sampson NS. Rv1106c from Mycobacterium tuberculosis Is a 3ß-Hydroxysteroid Dehydrogenase. Biochemistry. 2007 Jul 14;46(31):9058–67. doi: 10.1021/bi700688x.; Horinouchi M, Hayashi T, Koshino H, Kurita T, Kudo T. Identification of 9,17-Dioxo-1,2,3,4,10,19-Hexanorandrostan-5-oic Acid, 4-Hydroxy-2-Oxohexanoic Acid, and 2-Hydroxyhexa-2,4-Dienoic Acid and Related Enzymes Involved in Testosterone Degradation in Comamonas testosteroni TA441. Appl Environ Microbiol. 2005 Sep;71(9):5275–81. doi: 10.1128/aem.71.9.5275-5281.2005. |
| superpathway of cholesterol degradation I (cholesterol oxidase) Accession ID: BioCyc:META_PWY-6928 |
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Thomas ST, VanderVen BC, Sherman DR, Russell DG, Sampson NS. Pathway profiling in Mycobacterium tuberculosis: elucidation of cholesterol-derived catabolite and enzymes that catalyze its metabolism. J Biol Chem. 2011 Dec 23;286(51):43668–78. PMID: 22045806; PMCID: PMC3243565.; van der Geize R, Grommen AWF, Hessels GI, Jacobs AAC, Dijkhuizen L. The Steroid Catabolic Pathway of the Intracellular Pathogen Rhodococcus equi Is Important for Pathogenesis and a Target for Vaccine Development. PLoS Pathog. 2011 Aug 25;7(8):e1002181. doi: 10.1371/journal.ppat.1002181.; Kreit J, Sampson NS. Cholesterol oxidase: physiological functions. The FEBS Journal. 2009 Nov 16;276(23):6844–56. doi: 10.1111/j.1742-4658.2009.07378.x.; Petrusma M, Dijkhuizen L, van der Geize R. Rhodococcus rhodochrous DSM 43269 3-ketosteroid 9alpha-hydroxylase, a two-component iron-sulfur-containing monooxygenase with subtle steroid substrate specificity. Appl Environ Microbiol. 2009 Aug;75(16):5300–7. PMID: 19561185; PMCID: PMC2725467.; Horinouchi M, Hayashi T, Koshino H, Kurita T, Kudo T. Identification of 9,17-Dioxo-1,2,3,4,10,19-Hexanorandrostan-5-oic Acid, 4-Hydroxy-2-Oxohexanoic Acid, and 2-Hydroxyhexa-2,4-Dienoic Acid and Related Enzymes Involved in Testosterone Degradation in Comamonas testosteroni TA441. Appl Environ Microbiol. 2005 Sep;71(9):5275–81. doi: 10.1128/aem.71.9.5275-5281.2005.; Richmond W. Preparation and Properties of a Cholesterol Oxidase from Nocardia sp. and Its Application to the Enzymatic Assay of Total Cholesterol in Serum. 1973 Dec 01;19(12):1350–6. doi: 10.1093/clinchem/19.12.1350.; Stadtman TC, Cherkes A, Anfinsen CB. STUDIES ON THE MICROBIOLOGICAL DEGRADATION OF CHOLESTEROL. Journal of Biological Chemistry. 1954 Feb;206(2):511–23. doi: 10.1016/s0021-9258(19)50819-5. |