Wackett LP, Hershberger CD: Biocatalysis and Biodegradation: Microbial Transformation of Organic Compounds. 2001, Washington, DC: ASM Press
Chapter
Google Scholar
van Deursen R, Reymond J-L: Chemical space travel. Chem Med Chem. 2007, 2: 636-640.
Article
CAS
PubMed
Google Scholar
Whitman WB, Coleman DC, Wiebe WJ: Prokaryotes: the unseen majority. Proc Natl Acad Sci, USA. 1998, 95: 6578-6583. 10.1073/pnas.95.12.6578.
Article
PubMed Central
CAS
PubMed
Google Scholar
Isambert H, Stein RR: One the need for widespread horizontal gene transfers under genome size constraint. Biol Direct. 2009, 4: 28-10.1186/1745-6150-4-28.
Article
PubMed Central
PubMed
Google Scholar
Garg RP, Alemany LB, Moran S, Parry RJ: Identification, characterization, and bioconversion of a new intermediate in valanimycin biosynthesis. J Am Chem Soc. 2009, 131: 9608-9609. 10.1021/ja901243p.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gao J, Ellis LB, Wackett LP: The University of Minnesota Pathway Prediction System: multi-level prediction and visualization. Nucleic Acids Res. 2011, 39: W406-411. 10.1093/nar/gkr200.
Article
PubMed Central
CAS
PubMed
Google Scholar
The University of Minnesota Biocatalysis/Biodegradation Database. [http://umbbd.msi.umn.edu/]
UM-BBD Aerobic Metabolic Pathway for Toluene. [http://umbbd.msi.umn.edu/tol/tol_map.html]
UM-BBD Aerobic Metabolic Pathway for Isoniazid. [http://umbbd.msi.umn.edu/inh/inh_map.html]
Kanehisa M, Goto S, Kawashima S, Nakaya A: The KEGG databases at GenomeNet. Nucleic Acids Res. 2002, 30: 42-46. 10.1093/nar/30.1.42.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A: ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003, 31: 3784-3788. 10.1093/nar/gkg563.
Article
PubMed Central
CAS
PubMed
Google Scholar
Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D: BRENDA, the enzyme information system in 2011. Nucleic Acids Res. 2011, 39: D670-6. 10.1093/nar/gkq1089.
Article
PubMed Central
CAS
PubMed
Google Scholar
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW: GenBank. Nucleic Acids Res. 2011, 39: D32-37. 10.1093/nar/gkq1079.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gans J, Wolinsky M, Dunbar J: Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science. 2005, 309: 1387-90. 10.1126/science.1112665.
Article
CAS
PubMed
Google Scholar
UM-BBD Microorganism List. [http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=allmicros]
Sutherland JB, Selby AL, Freeman JP, Fu PP, Miller DW, Cerniglia CE: Identification of xyloside conjugates formed from anthracene by Rhizoctonia solani. Myco Res. 1992, 96: 509-517. 10.1016/S0953-7562(09)81100-3.
Article
CAS
Google Scholar
Zablotowicz RM, Hoagland RE, Locke MA, Hickey WJ: Glutathione-s-transferase activity and metabolism of glutathione conjugates by rhizosphere bacteria. Appl Environ Microbiol. 1995, 61: 1054-60.
PubMed Central
CAS
PubMed
Google Scholar
Stamper DM, Tuovinen OH: Biodegradation of the acetanilide herbicides alachlor, metolachlor, and propachlor. Crit Rev Microbiol. 1998, 24: 1-22. 10.1080/10408419891294163.
Article
CAS
PubMed
Google Scholar
Postle JK, Rheineck BD, Allen PE, Baldock JO, Cook CJ, Zogbaum R, Vandenbrook JP: Chloroacetanilide herbicide metabolites in Wisconsin groundwater: 2001 survey results. Environ Sci Technol. 2004, 38: 5339-43. 10.1021/es040399h.
Article
CAS
PubMed
Google Scholar
Thurman EM, Ferrer I, Parry R: Accurate mass analysis of ethanesulfonic acid degradates of acetochlor and alachlor using high-performance liquid chromatography and time-of-flight mass spectrometry. J Chromatogr A. 2002, 957: 3-9. 10.1016/S0021-9673(01)01470-4.
Article
CAS
PubMed
Google Scholar
Wackett LP: Pathways to discovering new microbial metabolism for functional genomics and biotechnology. Adv Micro Physiol. 2007, 61: 219-232.
CAS
Google Scholar
Stanier R: The Microbial World. 1986, New York: Prentice Hall
Google Scholar
UM-BBD Naphthalene 1,2-Dioxygenase Reactions. [http://umbbd.msi.umn.edu/naph/ndo.html]
UM-BBD Toluene 1,2-Dioxygenase Reactions. [http://umbbd.msi.umn.edu/tol/tdo.html]
UM-BBD Anaerobic Metabolic Pathway for Toluene. [http://umbbd.msi.umn.edu/tol2/tol2_map.html]
Beller HR, Spormann AM: Anaerobic activation of toluene and o-xylene by addition to fumarate in denitrifying strain T. J Bacteriol. 1997, 179: 670-6.
PubMed Central
CAS
PubMed
Google Scholar
Boll M, Fuchs G: Benzoyl-coenzyme A reductase (dearomatizing), a key enzyme of anaerobic aromatic metabolism. ATP dependence of the reaction, purification and some properties of the enzyme from Thauera aromatica strain K172. Eur J Biochem. 1995, 234: 921-33. 10.1111/j.1432-1033.1995.921_a.x.
Article
CAS
PubMed
Google Scholar
UM-BBD BTEX Metapathway Map. [http://umbbd.msi.umn.edu/BTEX/BTEX_map.html]
Rosner BM, Schink B: Purification and characterization of acetylene hydratase of Pelobacter acetylenicus, a tungsten iron-sulfur protein. J Bacteriol. 1995, 177: 5767-5772.
PubMed Central
CAS
PubMed
Google Scholar
Rosner BM, Rainey FA, Kroppenstedt RM, Schink B: Acetylene degradation by new isolates of aerobic bacteria and comparison of acetylene hydratase enzymes. FEMS Microbiol Lett. 1997, 148: 175-180. 10.1111/j.1574-6968.1997.tb10285.x.
Article
CAS
PubMed
Google Scholar
Diluccio RC, Kirwan DJ: Effect of dissolved oxygen on nitrogen fixation by A. vinelandii. I. Free cell cultures. Biotechnol Bioeng. 1984, 26: 81-86. 10.1002/bit.260260115.
Article
CAS
PubMed
Google Scholar
Wu ML, Ettwig KF, Jetten MS, Strous M, Keltjens JT, van Niftrik L: A new intra-aerobic metabolism in the nitrite-dependent anaerobic methane-oxidizing bacterium Candidatus 'Methylomirabilis oxyfera'. Biochem Soc Trans. 2011, 39: 243-8. 10.1042/BST0390243.
Article
CAS
PubMed
Google Scholar
Chiang YR, Ismail W, Heintz D, Schaeffer C, Van Dorsselaer A, Fuchs G: Study of anoxic and oxic cholesterol metabolism by Sterolibacterium denitrificans. J Bacteriol. 2008, 190: 905-914. 10.1128/JB.01525-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lee CH, Lewis TA, Paszczynski A, Crawford RL: Identification of an extracellular agent of carbon tetrachloride dehalogentation from Pseudomonas stutzeri strain KC as pyridine-2,6-bis(thiocarboxylate). Biochem Biophys Res Commun. 1999, 261: 562-566. 10.1006/bbrc.1999.1077.
Article
CAS
PubMed
Google Scholar
Middeldorp PJM, Jaspers M, Zehnder AJB, Schraa G: Biotransformation of alpha- hexachlorocyclohexane, beta-hexachlorocyclohexane, gamma-hexachlorocyclohexane, and delta- hexachlorocyclohexane under methanogenic conditions. Environ Sci Technol. 1996, 30: 2345-2349. 10.1021/es950782+.
Article
CAS
Google Scholar
Warner JR, Behlen LS, Copley SD: A trade-off between catalytic power and substrate inhibition in TCHQ dehalogenase. Biochemistry. 2008, 47: 3258-65. 10.1021/bi702431n.
Article
CAS
PubMed
Google Scholar
Li S, Wackett LP: Reductive dehalogenation by cytochrome P450CAM: substrate binding and catalysis. Biochemistry. 1993, 32: 9355-61. 10.1021/bi00087a014.
Article
CAS
PubMed
Google Scholar
Copley SD: Evolution of efficient pathways for degradation of anthropogenic chemicals. Nat Chem Biol. 2009, 5: 559-566. 10.1038/nchembio.197.
Article
PubMed Central
CAS
PubMed
Google Scholar
Seffernick JL, Wackett LP: Rapid evolution of bacterial catabolic enzymes: a case study with atrazine chlorohydrolase. Biochemistry. 2001, 40: 12747-53. 10.1021/bi011293r.
Article
CAS
PubMed
Google Scholar
Aharoni A, Gaidukov L, Khersonsky O, McQ Gould S, Roodveldt C, Tawfik DS: The 'evolvability' of promiscuous protein functions. Nat Genet. 2005, 37: 73-6.
CAS
PubMed
Google Scholar
Krutz LJ, Shaner DL, Weaver MA, Webb RM, Zablotowicz RM, Reddy KN, Huang Y, Thomson SJ: Agronomic and environmental implications of enhanced s-triazine degradation. Pest Manag Sci. 2010, 66: 461-481. 10.1002/ps.1909.
Article
Google Scholar
UM-BBD Atrazine Pathway. [http://umbbd.msi.umn.edu/atr/atr_map.html]
DeSouza ML, Sadowsky MJ, Seffernick J, Martinez B, Wackett LP: The atzABC genes encoding atrazine catabolism are widespread and highly conserved. J Bacteriol. 1998, 180: 1951-1954.
CAS
Google Scholar
Martinez B, Tomkins J, Wackett LP, Wing R, Sadowsky MJ: Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. ADP. J Bacteriol. 2001, 183: 5684-5697. 10.1128/JB.183.19.5684-5697.2001.
Article
PubMed Central
CAS
PubMed
Google Scholar
Raillard S-A, Krebber A, Chen Y, Ness JE, Bermudez E, Trinidad R, Fullem R, Davis C, Welch M, Seffernick J, Wackett LP, Stemmer WPC, Minshull J: Novel enzyme activities and functional plasticity revealed by recombining homologous enzymes. Chem Biol. 2001, 8: 891-898. 10.1016/S1074-5521(01)00061-8.
Article
CAS
PubMed
Google Scholar
Blum LC, Reymond JL: 970 million druglike small molecules for virtual screening in the chemical universe database GDB-13. J Am Chem Soc. 2009, 131: 8732-3. 10.1021/ja902302h.
Article
CAS
PubMed
Google Scholar
UM-BBD Functional Groups. [http://umbbd.msi.umn.edu/search/FuncGrps.html]
UM-BBD Pathway Prediction System. [http://umbbd.msi.umn.edu/predict/]
PathPred. [http://www.genome.jp/tools/pathpred/]
Ellis LB, Gao J, Fenner K, Wackett LP: The University of Minnesota pathway prediction system: predicting metabolic logic. Nucleic Acids Res. 2008, 36: W427-32. 10.1093/nar/gkn315.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kern S, Fenner K, Singer HP, Schwarzenbach RP, Hollender J: Identification of transformation products of organic contaminants in natural waters by computer-aided prediction and high-resolution mass spectrometry. Environ Sci Technol. 2009, 43: 7039-7046. 10.1021/es901979h.
Article
CAS
PubMed
Google Scholar
Helbling DE, Hollender J, Kohler HP, Singer H, Fenner K: High-throughput identification of microbial transformation products of organic micropollutants. Environ Sci Technol. 2010, 44: 6621-6627. 10.1021/es100970m.
Article
CAS
PubMed
Google Scholar
Prasse C, Wagner M, Schulz R, Ternes TA: Biotransformation of the antiviral drugs acyclovir and penciclovir in activated sludge treatment. Environ Sci Technol. 2011, 45: 2761-2679. 10.1021/es103732y.
Article
CAS
PubMed
Google Scholar
Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH: PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res. 2009, 37: W623-33. 10.1093/nar/gkp456.
Article
PubMed Central
CAS
PubMed
Google Scholar
Moriya Y, Shigemizu D, Hattori M, Tokimatsu T, Kotera M, Goto S, Kanehisa M: PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res. 2010, 38: W138-43. 10.1093/nar/gkq318.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M: KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 2010, 38: D355-360. 10.1093/nar/gkp896.
Article
PubMed Central
CAS
PubMed
Google Scholar