-
1
-
-
0031793928
-
PSI-BLAST-A tool for making discoveries in sequence databases
-
Altschul, S.F., & Koonin, E.V. (1998). PSI-BLAST-a tool for making discoveries in sequence databases. Trends in Biochemical Sciences, 23, 444-447.
-
(1998)
Trends in Biochemical Sciences
, vol.23
, pp. 444-447
-
-
Altschul, S.F.1
Koonin, E.V.2
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
-
(1997)
Nucleic Acids Research
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
3
-
-
12344283074
-
Determinants of adaptive evolution at the molecular level: The extended complexity hypothesis
-
Aris-Brosou, S. (2005). Determinants of adaptive evolution at the molecular level: The extended complexity hypothesis. Molecular Biology and Evolution, 22, 200-209.
-
(2005)
Molecular Biology and Evolution
, vol.22
, pp. 200-209
-
-
Aris-Brosou, S.1
-
4
-
-
0034127014
-
A second [2Fe-2S] ferredoxin from Sphingomonas sp. strain RW1 can function as an electron donor for the dioxin dioxygenase
-
Armengaud, J., Gaillard, J., & Timmis, K.N. (2000). A second [2Fe-2S] ferredoxin from Sphingomonas sp. strain RW1 can function as an electron donor for the dioxin dioxygenase. Journal of Bacteriology, 182, 2238-2244.
-
(2000)
Journal of Bacteriology
, vol.182
, pp. 2238-2244
-
-
Armengaud, J.1
Gaillard, J.2
Timmis, K.N.3
-
5
-
-
0031859323
-
Genetic analysis of dioxin dioxygenase of Sphingomonas sp. Strain RW1: Catabolic genes dispersed on the genome
-
Armengaud, J., Happe, B., & Timmis, K.N. (1998). Genetic analysis of dioxin dioxygenase of Sphingomonas sp. Strain RW1: Catabolic genes dispersed on the genome. Journal of Bacteriology, 180, 3954-3966.
-
(1998)
Journal of Bacteriology
, vol.180
, pp. 3954-3966
-
-
Armengaud, J.1
Happe, B.2
Timmis, K.N.3
-
6
-
-
2942512907
-
Detection and characterization of conjugative degradative plasmids in xenobiotics degrading Sphingomonas strains
-
Basta, T., Keck, A., Klein, J., & Stolz, A. (2004). Detection and characterization of conjugative degradative plasmids in xenobiotics degrading Sphingomonas strains. Journal of Bacteriology, 186, 3862-3872.
-
(2004)
Journal of Bacteriology
, vol.186
, pp. 3862-3872
-
-
Basta, T.1
Keck, A.2
Klein, J.3
Stolz, A.4
-
7
-
-
0002557598
-
Phthalate dioxygenase reductase and related flavin-iron-sulfur containing electron transferases
-
F. Müller (Ed.) Boca Raton, FL: CRC Press
-
Batie, C.J., Ballou, D.P., & Correll, C.C. (1992). Phthalate dioxygenase reductase and related flavin-iron-sulfur containing electron transferases. In F. Müller (Ed.), Chemistry and biochemistry of flavoenzymes (pp. 543-556). Boca Raton, FL: CRC Press.
-
(1992)
Chemistry and Biochemistry of Flavoenzymes
, pp. 543-556
-
-
Batie, C.J.1
Ballou, D.P.2
Correll, C.C.3
-
8
-
-
0030868605
-
Iron-sulfur clusters: Nature's modular multipurpose structures
-
Beinert, H., Holm, R.H., & Münck, E. (1997). Iron-sulfur clusters: Nature's modular multipurpose structures. Science, 277, 653-659.
-
(1997)
Science
, vol.277
, pp. 653-659
-
-
Beinert, H.1
Holm, R.H.2
Münck, E.3
-
9
-
-
0343485080
-
Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10
-
Bosch, R., García-Valdés, E., & Moore, E.R.B. (2000). Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10. Gene, 245, 65-74.
-
(2000)
Gene
, vol.245
, pp. 65-74
-
-
Bosch, R.1
García-Valdés, E.2
Moore, E.R.B.3
-
10
-
-
0001326286
-
Evidence for a ferredoxin-dependent choline monooxygenase from spinach chloroplast stroma
-
Brouquisse, R., Weigel, P., Rhodes, D., Yocum, C.F., & Hanson, A.D. (1989). Evidence for a ferredoxin-dependent choline monooxygenase from spinach chloroplast stroma. Plant Physiology, 90, 322-329.
-
(1989)
Plant Physiology
, vol.90
, pp. 322-329
-
-
Brouquisse, R.1
Weigel, P.2
Rhodes, D.3
Yocum, C.F.4
Hanson, A.D.5
-
11
-
-
0031463305
-
The chloroplastic protein import machinery contains a Rieske-type iron-sulfur cluster and a mononuclear iron-binding protein
-
Caliebe, A., Grimm, R., Kaiser, G., Beck, J.L., Soll, J., & Heins, L. (1997). The chloroplastic protein import machinery contains a Rieske-type iron-sulfur cluster and a mononuclear iron-binding protein. EMBO Journal, 16, 7342-7350.
-
(1997)
EMBO Journal
, vol.16
, pp. 7342-7350
-
-
Caliebe, A.1
Grimm, R.2
Kaiser, G.3
Beck, J.L.4
Soll, J.5
Heins, L.6
-
12
-
-
0004264770
-
Iron-sulfur proteins
-
R. Cammack & A.G. Sykes (Eds.) San Diego, CA: Academic Press
-
Cammack, R.C. (1992). Iron-Sulfur Proteins. In R. Cammack & A.G. Sykes (Eds.), Advances in inorganic chemistry (pp. 281-322). San Diego, CA: Academic Press.
-
(1992)
Advances in Inorganic Chemistry
, pp. 281-322
-
-
Cammack, R.C.1
-
13
-
-
0033303302
-
Studies of hyperfine interactions in [2Fe-2S] proteins by EPR and double resonance spectroscopy
-
Cammack, R., Gay, E., & Shergill, J.K. (1999). Studies of hyperfine interactions in [2Fe-2S] proteins by EPR and double resonance spectroscopy. Coordination Chemistry Reviews, 192, 1003-1022.
-
(1999)
Coordination Chemistry Reviews
, vol.192
, pp. 1003-1022
-
-
Cammack, R.1
Gay, E.2
Shergill, J.K.3
-
15
-
-
0035166840
-
Genetic and molecular organization of the alkylbenzene catabolism operon in the psychrotrophic strain Pseudomonas putida 01G3
-
Chablain, P.A., Zgoda, A.L., Sarde, C.-O., & Truffaut, N. (2001). Genetic and molecular organization of the alkylbenzene catabolism operon in the psychrotrophic strain Pseudomonas putida 01G3. Applied and Environmental Microbiology, 67, 453-458.
-
(2001)
Applied and Environmental Microbiology
, vol.67
, pp. 453-458
-
-
Chablain, P.A.1
Zgoda, A.L.2
Sarde, C.-O.3
Truffaut, N.4
-
16
-
-
79959435267
-
From lipid transport to oxygenation of aromatic compounds: Evolution within the Bet v1-like superfamily
-
Chakraborty, J., & Dutta, T.K. (2011). From lipid transport to oxygenation of aromatic compounds: Evolution within the Bet v1-like superfamily. Journal of Biomolecular Structure and Dynamics, 29, 67-78.
-
(2011)
Journal of Biomolecular Structure and Dynamics
, vol.29
, pp. 67-78
-
-
Chakraborty, J.1
Dutta, T.K.2
-
17
-
-
0345583676
-
Cis-dihydroxylation of olefins by a non-heme iron catalyst: A functional model for Rieske dioxygenases
-
Chen, K., & Que, L. (1999). Cis-dihydroxylation of olefins by a non-heme iron catalyst: A functional model for Rieske dioxygenases. Angewandte Chemie International Edition, 38, 2227-2228.
-
(1999)
Angewandte Chemie International Edition
, vol.38
, pp. 2227-2228
-
-
Chen, K.1
Que, L.2
-
18
-
-
15444381232
-
Mupirocin W, a novel pseudomonic acid produced by targeted mutation of the mupirocin biosynthetic gene cluster
-
Cooper, S.M., Cox, R.J., Crosby, J., Crump, M.P., Hothersall, J., Laosripaiboon, W., ... Thomas, C.M. (2005). Mupirocin W, a novel pseudomonic acid produced by targeted mutation of the mupirocin biosynthetic gene cluster. Chemical Communications, 9, 1179-1181.
-
(2005)
Chemical Communications
, vol.9
, pp. 1179-1181
-
-
Cooper, S.M.1
Cox, R.J.2
Crosby, J.3
Crump, M.P.4
Hothersall, J.5
Laosripaiboon, W.6
Thomas, C.M.7
-
19
-
-
20144366949
-
Crystal structure of the terminal oxygenase component of cumene dioxygenase from Pseudomonas fluorescens IP01
-
Dong, X., Fushinobu, S., Fukuda, E., Terada, T., Nakamura, S., Shimizu, K., ... Wakagi, T. (2005). Crystal structure of the terminal oxygenase component of cumene dioxygenase from Pseudomonas fluorescens IP01. Journal of Bacteriology, 187, 2483-2490.
-
(2005)
Journal of Bacteriology
, vol.187
, pp. 2483-2490
-
-
Dong, X.1
Fushinobu, S.2
Fukuda, E.3
Terada, T.4
Nakamura, S.5
Shimizu, K.6
Wakagi, T.7
-
20
-
-
0036209157
-
Horizontal gene transfer and bacterial diversity
-
Dutta, C., & Pan, A. (2002). Horizontal gene transfer and bacterial diversity. Journal of Biosciences, 27, 27-33.
-
(2002)
Journal of Biosciences
, vol.27
, pp. 27-33
-
-
Dutta, C.1
Pan, A.2
-
21
-
-
0031761306
-
Isopropylbenzene catabolic pathway in Pseudomonas putida RE204: Nucleotide sequence analysis of the ipb operon and neighboring DNA from pRE4
-
Eaton, R.W., Selifonova, O.V., & Gedney, R.M. (1998). Isopropylbenzene catabolic pathway in Pseudomonas putida RE204: Nucleotide sequence analysis of the ipb operon and neighboring DNA from pRE4. Biodegradation, 9, 119-132.
-
(1998)
Biodegradation
, vol.9
, pp. 119-132
-
-
Eaton, R.W.1
Selifonova, O.V.2
Gedney, R.M.3
-
22
-
-
0035190139
-
Characterization and evolution of anthranilate 1,2-dioxygenase from Acinetobacter sp. strain ADP1
-
Eby, D.M., Beharry, Z.M., Coulter, E.D., Kurtz, D.M., & Neidle, E.L. (2001). Characterization and evolution of anthranilate 1,2-dioxygenase from Acinetobacter sp. strain ADP1. Journal of Bacteriology, 183, 109-118.
-
(2001)
Journal of Bacteriology
, vol.183
, pp. 109-118
-
-
Eby, D.M.1
Beharry, Z.M.2
Coulter, E.D.3
Kurtz, D.M.4
Neidle, E.L.5
-
23
-
-
39549098697
-
Persistence drives gene clustering in bacterial genomes
-
Fang, G., Rocha, E.P.C., & Danchin, A. (2008). Persistence drives gene clustering in bacterial genomes. BMC Genomics, 9, 4.
-
(2008)
BMC Genomics
, vol.9
, pp. 4
-
-
Fang, G.1
Rocha, E.P.C.2
Danchin, A.3
-
24
-
-
0029901637
-
Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
-
Felsenstein, J. (1996). Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods in Enzymology, 266, 418-427.
-
(1996)
Methods in Enzymology
, vol.266
, pp. 418-427
-
-
Felsenstein, J.1
-
25
-
-
0036796467
-
CDART: Protein homology by domain architecture
-
Geer, L.Y., Domrachev, M., Lipman, D.J., & Bryant, S.H. (2002). CDART: Protein homology by domain architecture. Genome Research, 12, 1619-1623.
-
(2002)
Genome Research
, vol.12
, pp. 1619-1623
-
-
Geer, L.Y.1
Domrachev, M.2
Lipman, D.J.3
Bryant, S.H.4
-
26
-
-
0034029015
-
Aromatic hydrocarbon dioxygenases in environmental biotechnology
-
Gibson, D.T., & Parales, R.E. (2000). Aromatic hydrocarbon dioxygenases in environmental biotechnology. Current Opinion in Biotechnology, 11, 236-243.
-
(2000)
Current Opinion in Biotechnology
, vol.11
, pp. 236-243
-
-
Gibson, D.T.1
Parales, R.E.2
-
27
-
-
0029012851
-
Desaturation, dioxygenation, and monooxygenation reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain 9816-4
-
Gibson, D.T., Resnick, S.M., Lee, K., Brand, J.M., Torok, D.S., Wackett, L.P., ... Haigler, B.E. (1995). Desaturation, dioxygenation, and monooxygenation reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain 9816-4. Journal of Bacteriology, 177, 2615-2621.
-
(1995)
Journal of Bacteriology
, vol.177
, pp. 2615-2621
-
-
Gibson, D.T.1
Resnick, S.M.2
Lee, K.3
Brand, J.M.4
Torok, D.S.5
Wackett, L.P.6
Haigler, B.E.7
-
28
-
-
0000757667
-
Microbial degradation of aromatic hydrocarbons
-
D.T. Gibson (Ed.) New York, NY: Marcel Dekker
-
Gibson, D.T., & Subramanian, V. (1984). Microbial degradation of aromatic hydrocarbons. In D.T. Gibson (Ed.), Microbial degradation of organic compounds (pp. 181-252). New York, NY: Marcel Dekker.
-
(1984)
Microbial Degradation of Organic Compounds
, pp. 181-252
-
-
Gibson, D.T.1
Subramanian, V.2
-
29
-
-
3442885737
-
A small family of LLS1-related non-heme oxygenases in plants with an origin amongst oxygenic photosynthesizers
-
Gray, J., Wardzala, E., Yang, M., Reinbothe, S., Haller, S., & Pauli, F. (2004). A small family of LLS1-related non-heme oxygenases in plants with an origin amongst oxygenic photosynthesizers. Plant Molecular Biology, 54, 39-54.
-
(2004)
Plant Molecular Biology
, vol.54
, pp. 39-54
-
-
Gray, J.1
Wardzala, E.2
Yang, M.3
Reinbothe, S.4
Haller, S.5
Pauli, F.6
-
31
-
-
0025895757
-
Reactions and significance of cytochrome P-450 enzymes
-
Guengerich, F.P. (1991). Reactions and significance of cytochrome P-450 enzymes. The Journal of Biological Chemistry, 266, 10019-10022.
-
(1991)
The Journal of Biological Chemistry
, vol.266
, pp. 10019-10022
-
-
Guengerich, F.P.1
-
32
-
-
0022573421
-
Genetic analysis of a relaxed substrate specificity aromatic ring dioxygenase, toluate 1,2-dioxygenase, encoded by TOL plasmid pWWO of Pseudomonas putida
-
Harayama, S., Rekik, M., & Timmis, K.N. (1986). Genetic analysis of a relaxed substrate specificity aromatic ring dioxygenase, toluate 1,2-dioxygenase, encoded by TOL plasmid pWWO of Pseudomonas putida. Molecular and General Genetics, 202, 226-234.
-
(1986)
Molecular and General Genetics
, vol.202
, pp. 226-234
-
-
Harayama, S.1
Rekik, M.2
Timmis, K.N.3
-
33
-
-
31144439476
-
Gene cloning and in vivo characterization of a dibenzothiophene dioxygenase from Xanthobacter polyaromaticivorans
-
Hirano, S., Haruki, M., Takano, K., Imanaka, T., Morikawa, M., & Kanaya, S. (2006). Gene cloning and in vivo characterization of a dibenzothiophene dioxygenase from Xanthobacter polyaromaticivorans. Applied Microbiology and Biotechnology, 69, 672-681.
-
(2006)
Applied Microbiology and Biotechnology
, vol.69
, pp. 672-681
-
-
Hirano, S.1
Haruki, M.2
Takano, K.3
Imanaka, T.4
Morikawa, M.5
Kanaya, S.6
-
34
-
-
0028215858
-
Construction of hybrid biphenyl (bph) and toluene (tod) genes for functional analysis of aromatic ring dioxygenases
-
Hirose, J., Suyama, A., Hayashida, S., & Furukawa, K. (1994). Construction of hybrid biphenyl (bph) and toluene (tod) genes for functional analysis of aromatic ring dioxygenases. Gene, 138, 27-33.
-
(1994)
Gene
, vol.138
, pp. 27-33
-
-
Hirose, J.1
Suyama, A.2
Hayashida, S.3
Furukawa, K.4
-
35
-
-
0001846314
-
Enzymatic dihydroxylation of aromatics in enantioselective synthesis: Expanding asymmetric methodology
-
Hudlicky, T., Gonzalez, D., & Gibson, D.T. (1999). Enzymatic dihydroxylation of aromatics in enantioselective synthesis: Expanding asymmetric methodology. Aldrichimica Acta, 32, 35-62.
-
Aldrichimica Acta
, vol.32
, pp. 35-62
-
-
Hudlicky, T.1
Gonzalez, D.2
Gibson, D.T.3
-
36
-
-
0031733410
-
Involvement of the terminal oxygenase ? subunit in the biphenyl dioxygenase reactivity pattern toward chlorobiphenyls
-
Hurtubise, Y., Barriault, D., & Sylvestre, M. (1998). Involvement of the terminal oxygenase ? subunit in the biphenyl dioxygenase reactivity pattern toward chlorobiphenyls. Journal of Bacteriology, 180, 5828-5835.
-
(1998)
Journal of Bacteriology
, vol.180
, pp. 5828-5835
-
-
Hurtubise, Y.1
Barriault, D.2
Sylvestre, M.3
-
38
-
-
19944426997
-
Divergent structures of carbazole degradative car operons isolated from gram-negative bacteria
-
Inoue, K., Widada, J., Nakai, S., Endoh, T., Urata, M., Ashikawa, Y., ... Nojiri, H. (2004). Divergent structures of carbazole degradative car operons isolated from gram-negative bacteria. Bioscience, Biotechnology, and Biochemistry, 68, 1467-1480.
-
(2004)
Bioscience, Biotechnology, and Biochemistry
, vol.68
, pp. 1467-1480
-
-
Inoue, K.1
Widada, J.2
Nakai, S.3
Endoh, T.4
Urata, M.5
Ashikawa, Y.6
Nojiri, H.7
-
39
-
-
0033058895
-
Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes
-
Itoh, T., Takemoto, K., Mori, H., & Gojobori, T. (1999). Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Molecular Biology and Evolution, 16, 332-346.
-
(1999)
Molecular Biology and Evolution
, vol.16
, pp. 332-346
-
-
Itoh, T.1
Takemoto, K.2
Mori, H.3
Gojobori, T.4
-
40
-
-
34247578182
-
The crystal structure of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1
-
Jakoncic, J., Jouanneau, Y., Meyer, C., & Stojanoff, V. (2007). The crystal structure of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1. FEBS Journal, 274, 2470-2481.
-
(2007)
FEBS Journal
, vol.274
, pp. 2470-2481
-
-
Jakoncic, J.1
Jouanneau, Y.2
Meyer, C.3
Stojanoff, V.4
-
41
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N., & Barabasi, A.L. (2000). The large-scale organization of metabolic networks. Nature, 407, 651-654.
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
42
-
-
0029953163
-
Site-directed mutagenesis of conserved amino acids in the alpha subunit of toluene dioxygenase: Potential mononuclear non-heme iron coordination sites
-
Jiang, H., Parales, R.E., Lynch, N.A., & Gibson, D.T. (1996). Site-directed mutagenesis of conserved amino acids in the alpha subunit of toluene dioxygenase: Potential mononuclear non-heme iron coordination sites. Journal of Bacteriology, 178, 3133-3139.
-
(1996)
Journal of Bacteriology
, vol.178
, pp. 3133-3139
-
-
Jiang, H.1
Parales, R.E.2
Lynch, N.A.3
Gibson, D.T.4
-
43
-
-
0032524127
-
Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2- dioxygenase
-
Kauppi, B., Lee, K., Carredano, E., Parales, R.E., Gibson, D.T., Eklund, H., & Ramaswamy, S. (1998). Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2- dioxygenase. Structure, 6, 571-586.
-
(1998)
Structure
, vol.6
, pp. 571-586
-
-
Kauppi, B.1
Lee, K.2
Carredano, E.3
Parales, R.E.4
Gibson, D.T.5
Eklund, H.6
Ramaswamy, S.7
-
44
-
-
36549009124
-
Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101
-
Kimura, N., Kitagawa, W., Mori, T., Nakashima, N., Tamura, T., & Kamagata, Y. (2006). Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101. Applied Microbiology and Biotechnology, 73, 474-484.
-
(2006)
Applied Microbiology and Biotechnology
, vol.73
, pp. 474-484
-
-
Kimura, N.1
Kitagawa, W.2
Mori, T.3
Nakashima, N.4
Tamura, T.5
Kamagata, Y.6
-
45
-
-
17444397489
-
Web-type evolution of Rhodococcus gene clusters associated with utilization of naphthalene
-
Kulakov, L.A., Chen, S., Allen, C.C.R., & Larkin, M.J. (2005). Web-type evolution of Rhodococcus gene clusters associated with utilization of naphthalene. Applied and Environmental Microbiology, 71, 1754-1764.
-
(2005)
Applied and Environmental Microbiology
, vol.71
, pp. 1754-1764
-
-
Kulakov, L.A.1
Chen, S.2
Allen, C.C.R.3
Larkin, M.J.4
-
46
-
-
43149093388
-
A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases
-
Kweon, O., Kim, S.-J., Baek, S., Chae, J.-C., Adjei, M.D., Baek, D.-H., ... Cerniglia, C.E. (2008). A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases. BMC Biochemistry, 9, 11.
-
(2008)
BMC Biochemistry
, vol.9
, pp. 11
-
-
Kweon, O.1
Kim, S.-J.2
Baek, S.3
Chae, J.-C.4
Adjei, M.D.5
Baek, D.-H.6
Cerniglia, C.E.7
-
47
-
-
0032819205
-
Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038
-
Larkin, M.J., Christopher, C.R.A., Kulakov, L.A., & Lipscomb, D.A. (1999). Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038. Journal of Bacteriology, 181, 6200-6204.
-
(1999)
Journal of Bacteriology
, vol.181
, pp. 6200-6204
-
-
Larkin, M.J.1
Christopher, C.R.A.2
Kulakov, L.A.3
Lipscomb, D.A.4
-
48
-
-
0029847554
-
Selfish operons: Horizontal transfer may drive the evolution of gene clusters
-
Lawrence, J.G., & Roth, J.R. (1996). Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics, 143, 1843-1860.
-
(1996)
Genetics
, vol.143
, pp. 1843-1860
-
-
Lawrence, J.G.1
Roth, J.R.2
-
49
-
-
0030902353
-
Metabolism of chlorotoluenes by Burkholderia sp. strain PS12 and toluene dioxygenase of Pseudomonas putida F1: Evidence for monooxygenation by toluene and chlorobenzene dioxygenases
-
Lehning, A., Fock, U., Wittich, R., Timmis, K.N., & Pieper, D.H. (1997). Metabolism of chlorotoluenes by Burkholderia sp. strain PS12 and toluene dioxygenase of Pseudomonas putida F1: Evidence for monooxygenation by toluene and chlorobenzene dioxygenases. Applied and Environmental Microbiology, 63, 1974-1979.
-
(1997)
Applied and Environmental Microbiology
, vol.63
, pp. 1974-1979
-
-
Lehning, A.1
Fock, U.2
Wittich, R.3
Timmis, K.N.4
Pieper, D.H.5
-
50
-
-
0442331120
-
The structures of Rieske and Rieske-type proteins
-
Link, T.A. (1999). The structures of Rieske and Rieske-type proteins. Advances in Inorganic Chemistry, 47, 83-157.
-
(1999)
Advances in Inorganic Chemistry
, vol.47
, pp. 83-157
-
-
Link, T.A.1
-
51
-
-
78651393911
-
Role of oxygenases in guiding diverse metabolic pathways in the bacterial degradation of low-molecular weight polycyclic aromatic hydrocarbons: A review
-
Mallick, S., Chakraborty, J., & Dutta, T.K. (2011). Role of oxygenases in guiding diverse metabolic pathways in the bacterial degradation of low-molecular weight polycyclic aromatic hydrocarbons: A review. Critical Reviews in Microbiology, 37, 64-90.
-
(2011)
Critical Reviews in Microbiology
, Issue.37
, pp. 64-90
-
-
Mallick, S.1
Chakraborty, J.2
Dutta, T.K.3
-
52
-
-
0036087630
-
CDD: A database of conserved domain alignments with links to domain threedimensional structure
-
Marchler-Bauer, A., Panchenko, A., Shoemaker, B., Thiessen, P., Geer, L., & Bryant, S. (2002). CDD: A database of conserved domain alignments with links to domain threedimensional structure. Nucleic Acids Research, 30, 281-283.
-
(2002)
Nucleic Acids Research
, vol.30
, pp. 281-283
-
-
Marchler-Bauer, A.1
Panchenko, A.2
Shoemaker, B.3
Thiessen, P.4
Geer, L.5
Bryant, S.6
-
53
-
-
29144454726
-
Isolation and characterization of o-xylene oxygenase genes from Rhodococcus opacus TKN14
-
Maruyama, T., Ishikura, M., Taki, H., Shindo, K., Kasai, H., Haga, M., ... Misawa, N. (2005). Isolation and characterization of o-xylene oxygenase genes from Rhodococcus opacus TKN14. Applied and Environmental Microbiology, 71, 7705-7715.
-
(2005)
Applied and Environmental Microbiology
, vol.71
, pp. 7705-7715
-
-
Maruyama, T.1
Ishikura, M.2
Taki, H.3
Shindo, K.4
Kasai, H.5
Haga, M.6
Misawa, N.7
-
54
-
-
0031060718
-
Structure-function analysis of the bacterial ring-hydroxylating dioxygenases
-
Mason, J.R., & Butler, C.S. (1997). Structure-function analysis of the bacterial ring-hydroxylating dioxygenases. Advances in Microbial Physiology, 38, 47-84.
-
(1997)
Advances in Microbial Physiology
, vol.38
, pp. 47-84
-
-
Mason, J.R.1
Butler, C.S.2
-
55
-
-
54949131361
-
The Genome of Polaromonas sp. strain JS666: Insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology
-
Mattes, T.E., Alexander, A.K., Richardson, P.M., Munk, A.C., Han, C.S., Stothard, P., & Coleman, N.V. (2008). The Genome of Polaromonas sp. strain JS666: Insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology. Applied and Environmental Microbiology, 74, 6405-6416.
-
(2008)
Applied and Environmental Microbiology
, vol.74
, pp. 6405-6416
-
-
Mattes, T.E.1
Alexander, A.K.2
Richardson, P.M.3
Munk, A.C.4
Han, C.S.5
Stothard, P.6
Coleman, N.V.7
-
56
-
-
0035465271
-
Isolation of a choline monooxygenase cDNA clone from Amaranthus tricolor and its expressions under stress conditions
-
Meng, Y.L., Wang, Y.M., Zhang, B., & Nii, N. (2001). Isolation of a choline monooxygenase cDNA clone from Amaranthus tricolor and its expressions under stress conditions. Cell Research, 11, 187-193.
-
(2001)
Cell Research
, vol.11
, pp. 187-193
-
-
Meng, Y.L.1
Wang, Y.M.2
Zhang, B.3
Nii, N.4
-
57
-
-
0035257614
-
New classification system for oxygenase components involved in ring-hydroxylating oxygenations
-
Nam, J.W., Nojiri, H., Yoshida, T., Habe, H., Yamane, H., & Omori, T. (2001). New classification system for oxygenase components involved in ring-hydroxylating oxygenations. Bioscience, Biotechnology, and Biochemistry, 65, 254-263.
-
(2001)
Bioscience, Biotechnology, and Biochemistry
, vol.65
, pp. 254-263
-
-
Nam, J.W.1
Nojiri, H.2
Yoshida, T.3
Habe, H.4
Yamane, H.5
Omori, T.6
-
58
-
-
0026017943
-
Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases
-
Neidle, E.L., Hartnett, C., Ornston, L.N., Bairoch, A., Rekik, M., & Harayama, S. (1991). Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases. Journal of Bacteriology, 173, 5385-5395.
-
(1991)
Journal of Bacteriology
, vol.173
, pp. 5385-5395
-
-
Neidle, E.L.1
Hartnett, C.2
Ornston, L.N.3
Bairoch, A.4
Rekik, M.5
Harayama, S.6
-
59
-
-
22444433648
-
Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase
-
Nojiri, H., Ashikawa, Y., Noguchi, H., Nam, J.W., Urata, M., Fujimoto, Z., ... Omori, T. (2005). Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase. Journal of Molecular Biology, 351, 355-370.
-
(2005)
Journal of Molecular Biology
, vol.351
, pp. 355-370
-
-
Nojiri, H.1
Ashikawa, Y.2
Noguchi, H.3
Nam, J.W.4
Urata, M.5
Fujimoto, Z.6
Omori, T.7
-
60
-
-
2142659318
-
Divergence of mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity
-
Nojiri, H., Shintani, M., & Omori, T. (2004). Divergence of mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity. Applied Microbiology and Biotechnology, 64, 154-174.
-
(2004)
Applied Microbiology and Biotechnology
, vol.64
, pp. 154-174
-
-
Nojiri, H.1
Shintani, M.2
Omori, T.3
-
61
-
-
0030203863
-
TreeView: An application to display phylogenetic trees on personal computers
-
Page, R.D.M. (1996). TreeView: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences, 12, 357-358.
-
(1996)
Computer Applications in the Biosciences
, vol.12
, pp. 357-358
-
-
Page, R.D.M.1
-
62
-
-
20544472750
-
Iron-sulfur proteins
-
P.D. Boyer (Ed.) 3rd ed. New York, NY: Academic Press
-
Palmer, G. (1975). Iron-sulfur proteins. In P.D. Boyer (Ed.), The enzymes (3rd ed., pp. 1-56). New York, NY: Academic Press.
-
(1975)
The Enzymes
, pp. 1-56
-
-
Palmer, G.1
-
64
-
-
0033797753
-
Regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cisdihydroxylation: Control by phenylalanine 352 in the α-subunit
-
Parales, R.E., Resnick, S.M., Yu, C.-L., Boyd, D.R., Sharma, N.D., & Gibson, D.T. (2000). Regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cisdihydroxylation: Control by phenylalanine 352 in the α-subunit. Journal of Bacteriology, 182, 5495-5504.
-
(2000)
Journal of Bacteriology
, vol.182
, pp. 5495-5504
-
-
Parales, R.E.1
Resnick, S.M.2
Yu, C.-L.3
Boyd, D.R.4
Sharma, N.D.5
Gibson, D.T.6
-
65
-
-
53749102061
-
Microbial biodegradation of polyaromatic hydrocarbons
-
Peng, R.-H., Xiong, A.-S., Xue, Y., Fu, X.-Y., Gao, F., Zhao, W., ... Yao, Q.-H. (2008). Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiology Reviews, 32, 927-955.
-
(2008)
FEMS Microbiology Reviews
, vol.32
, pp. 927-955
-
-
Peng, R.-H.1
Xiong, A.-S.2
Xue, Y.3
Fu, X.-Y.4
Gao, F.5
Zhao, W.6
Yao, Q.-H.7
-
66
-
-
0030513196
-
Diverse reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816
-
Resnick, S.M., Lee, K., & Gibson, D.T. (1996). Diverse reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816. Journal of Industrial Microbiology, 17, 438-457.
-
(1996)
Journal of Industrial Microbiology
, vol.17
, pp. 438-457
-
-
Resnick, S.M.1
Lee, K.2
Gibson, D.T.3
-
67
-
-
0001367075
-
Isolation and properties of an iron-protein from the (reduced coenzyme Q)-cytochrome C reductase complex of the respiratory chain
-
Rieske, J.S., MacLennan, D.H., & Coleman, R. (1964). Isolation and properties of an iron-protein from the (reduced coenzyme Q)-cytochrome C reductase complex of the respiratory chain. Biochemical and Biophysical Research Communications, 15, 338-344.
-
(1964)
Biochemical and Biophysical Research Communications
, vol.15
, pp. 338-344
-
-
Rieske, J.S.1
MacLennan, D.H.2
Coleman, R.3
-
68
-
-
0026654843
-
Oxidation of nitrotoluenes by toluene dioxygenase: Evidence for a monooxygenase reaction
-
Robertson, J.B., Spain, J.C., Haddock, J.D., & Gibson, D.T. (1992). Oxidation of nitrotoluenes by toluene dioxygenase: Evidence for a monooxygenase reaction. Applied and Environmental Microbiology, 58, 2643-2648.
-
(1992)
Applied and Environmental Microbiology
, vol.58
, pp. 2643-2648
-
-
Robertson, J.B.1
Spain, J.C.2
Haddock, J.D.3
Gibson, D.T.4
-
69
-
-
0029930904
-
Iron-sulfur clusters as biosensors of oxidants and iron
-
Rouault, T.A., & Klausner, R.D. (1996). Iron-sulfur clusters as biosensors of oxidants and iron. Trends in Biochemical Sciences, 21, 174-180.
-
(1996)
Trends in Biochemical Sciences
, vol.21
, pp. 174-180
-
-
Rouault, T.A.1
Klausner, R.D.2
-
70
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
-
(1987)
Molecular Biology and Evolution
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
71
-
-
0035067599
-
A comprehensive phylogenetic analysis of Rieske and Rieske-type iron-sulfur proteins
-
Schmidt, C.L., & Shaw, L. (2001). A comprehensive phylogenetic analysis of Rieske and Rieske-type iron-sulfur proteins. Journal of Bioenergetics and Biomembranes, 33, 9-26.
-
(2001)
Journal of Bioenergetics and Biomembranes
, vol.33
, pp. 9-26
-
-
Schmidt, C.L.1
Shaw, L.2
-
72
-
-
67349163014
-
Characterization of a ring-hydroxylating dioxygenase from phenanthrenedegrading Sphingomonas sp. strain LH128 able to oxidize benz[a]anthracene
-
Schuler, L., Jouanneau, Y., Chadhain, S.M.N., Meyer, C., Pouli, M., Zylstra, G.J., ... Agathos, S.N. (2009). Characterization of a ring-hydroxylating dioxygenase from phenanthrenedegrading Sphingomonas sp. strain LH128 able to oxidize benz[a]anthracene. Applied Microbiology and Biotechnology, 83, 465-475.
-
(2009)
Applied Microbiology and Biotechnology
, vol.83
, pp. 465-475
-
-
Schuler, L.1
Jouanneau, Y.2
Chadhain, S.M.N.3
Meyer, C.4
Pouli, M.5
Zylstra, G.J.6
Agathos, S.N.7
-
73
-
-
65549153949
-
Pathway and evolutionary implications of diphenylamine biodegradation by Burkholderia sp. strain JS667
-
Shin, K.A., & Spain, J.C. (2009). Pathway and evolutionary implications of diphenylamine biodegradation by Burkholderia sp. strain JS667. Applied and Environmental Microbiology, 75, 2694-2704.
-
(2009)
Applied and Environmental Microbiology
, vol.75
, pp. 2694-2704
-
-
Shin, K.A.1
Spain, J.C.2
-
74
-
-
33947380626
-
The Sphingomonas plasmid pCAR3 is involved in complete mineralization of carbazole
-
Shintani, M., Urata, M., Inoue, K., Eto, K., Habe, H., Omori, T., ... Nojiri, H. (2007). The Sphingomonas plasmid pCAR3 is involved in complete mineralization of carbazole. Journal of Bacteriology, 189, 2007-2020.
-
(2007)
Journal of Bacteriology
, vol.189
, pp. 2007-2020
-
-
Shintani, M.1
Urata, M.2
Inoue, K.3
Eto, K.4
Habe, H.5
Omori, T.6
Nojiri, H.7
-
75
-
-
34548493672
-
A large gene cluster in Burkholderia xenovorans encoding abietane diterpenoid catabolism
-
Smith, D.J., Park, J., Tiedje, J.M., & Mohn, W.W. (2007). A large gene cluster in Burkholderia xenovorans encoding abietane diterpenoid catabolism. Journal of Bacteriology, 189, 6195-6204.
-
(2007)
Journal of Bacteriology
, vol.189
, pp. 6195-6204
-
-
Smith, D.J.1
Park, J.2
Tiedje, J.M.3
Mohn, W.W.4
-
76
-
-
33744718828
-
Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase
-
Sota, M., Yano, H., Ono, A., Miyazaki, R., Ishii, H., Genka, H., ... Tsuda, M. (2006). Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. Journal of Bacteriology, 188, 4057-4067.
-
(2006)
Journal of Bacteriology
, vol.188
, pp. 4057-4067
-
-
Sota, M.1
Yano, H.2
Ono, A.3
Miyazaki, R.4
Ishii, H.5
Genka, H.6
Tsuda, M.7
-
78
-
-
58149142969
-
Molecular characteristics of xenobioticdegrading sphingomonads
-
Stolz, A. (2009). Molecular characteristics of xenobioticdegrading sphingomonads. Applied Microbiology and Biotechnology, 81, 793-811.
-
(2009)
Applied Microbiology and Biotechnology
, vol.81
, pp. 793-811
-
-
Stolz, A.1
-
79
-
-
0027284359
-
Isolation and preliminary characterization of the subunits of the terminal component of naphthalene dioxygenase from Pseudomonas putida NCIB 9816-4
-
Suen, W.-C., & Gibson, D.T. (1993). Isolation and preliminary characterization of the subunits of the terminal component of naphthalene dioxygenase from Pseudomonas putida NCIB 9816-4. Journal of Bacteriology, 175, 5877-5881.
-
(1993)
Journal of Bacteriology
, vol.175
, pp. 5877-5881
-
-
Suen, W.-C.1
Gibson, D.T.2
-
80
-
-
0010414313
-
Evolution of gene order conservation in prokaryotes
-
research0020.1-0020.11
-
Tamames, J. (2001). Evolution of gene order conservation in prokaryotes. Genome Biology, 2, research0020.1-0020.11.
-
Genome Biology
, vol.2
-
-
Tamames, J.1
-
81
-
-
34547781750
-
MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0
-
Tamura, K., Dudley, J., Nei, M., & Kumar, S. (2007). MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 1596-1599
-
-
Tamura, K.1
Dudley, J.2
Nei, M.3
Kumar, S.4
-
82
-
-
0031574072
-
The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
-
Thompson, J.D., Gilson, T.J., Plewniak, F., Jeanmougin, F., & Higgins, D.G. (1997). The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 24, 4876-4882.
-
(1997)
Nucleic Acids Research
, vol.24
, pp. 4876-4882
-
-
Thompson, J.D.1
Gilson, T.J.2
Plewniak, F.3
Jeanmougin, F.4
Higgins, D.G.5
-
83
-
-
57549083624
-
Systemic approaches to biodegradation
-
Trigo, A., Valencia, A., & Cases, I. (2009). Systemic approaches to biodegradation. FEMS Microbiology Reviews, 33, 98-108.
-
(2009)
FEMS Microbiology Reviews
, vol.33
, pp. 98-108
-
-
Trigo, A.1
Valencia, A.2
Cases, I.3
-
84
-
-
0025073507
-
Naphthalene degrading genes on plasmid NAH7 are on a defective transposon
-
Tsuda, M., & Iino, T. (1990). Naphthalene degrading genes on plasmid NAH7 are on a defective transposon. Molecular and General Genetics, 223, 33-39.
-
(1990)
Molecular and General Genetics
, vol.223
, pp. 33-39
-
-
Tsuda, M.1
Iino, T.2
-
85
-
-
58149083269
-
Alteration of the substrate specificity of the angular dioxygenase carbazole 1,9a-dioxygenase
-
Uchimura, H., Horisaki, T., Umeda, T., Noguchi, H., Usami, Y., Li, L., ... Nojiri, H. (2008). Alteration of the substrate specificity of the angular dioxygenase carbazole 1,9a-dioxygenase. Bioscience, Biotechnology, and Biochemistry, 72, 3237-3248.
-
(2008)
Bioscience, Biotechnology, and Biochemistry
, vol.72
, pp. 3237-3248
-
-
Uchimura, H.1
Horisaki, T.2
Umeda, T.3
Noguchi, H.4
Usami, Y.5
Li, L.6
Nojiri, H.7
-
86
-
-
0036188916
-
Rubredoxins involved in alkane oxidation
-
van Beilen, J.B., Neuenschwander, M., Smits, T.H., Roth, C., Balada, S.B., & Witholt, B. (2002). Rubredoxins involved in alkane oxidation. Journal of Bacteriology, 184, 1722-1732.
-
(2002)
Journal of Bacteriology
, vol.184
, pp. 1722-1732
-
-
Van Beilen, J.B.1
Neuenschwander, M.2
Smits, T.H.3
Roth, C.4
Balada, S.B.5
Witholt, B.6
-
87
-
-
0026480282
-
Molecular mechanisms of genetic adaptation to xenobiotics compounds
-
van der Meer, J.R., de Vos, W.M., Harayama, S., & Zehnder, A.J. (1992). Molecular mechanisms of genetic adaptation to xenobiotics compounds. Microbiology Reviews, 56, 677-694.
-
(1992)
Microbiology Reviews
, vol.56
, pp. 677-694
-
-
Van Der Meer, J.R.1
De Vos, W.M.2
Harayama, S.3
Zehnder, A.J.4
-
88
-
-
0029920974
-
The broad substrate chlorobenzene dioxygenase and cis-chlorobenzene dihydrodiol dehydrogenase of Pseudomonas sp. strain P51 are linked evolutionarily to the enzymes for benzene and toluene degradation
-
Werlen, C., Kohler, H.P., & van der Meer, J.R. (1996). The broad substrate chlorobenzene dioxygenase and cis-chlorobenzene dihydrodiol dehydrogenase of Pseudomonas sp. strain P51 are linked evolutionarily to the enzymes for benzene and toluene degradation. The Journal of Biological Chemistry, 271, 4009-4016.
-
(1996)
The Journal of Biological Chemistry
, vol.271
, pp. 4009-4016
-
-
Werlen, C.1
Kohler, H.P.2
Van Der Meer, J.R.3
-
89
-
-
0028672045
-
The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas
-
Williams, P.A., & Sayers, J.R. (1994). The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation, 5, 195-217.
-
(1994)
Biodegradation
, vol.5
, pp. 195-217
-
-
Williams, P.A.1
Sayers, J.R.2
-
90
-
-
0035910409
-
Single turnover chemistry and regulation of O2 activation by the oxygenase component of naphthalene 1,2- dioxygenase
-
Wolfe, M.D., Parales, J.V., Gibson, D.T., & Lipscomb, J.D. (2001). Single turnover chemistry and regulation of O2 activation by the oxygenase component of naphthalene 1,2- dioxygenase. The Journal of Biological Chemistry, 276, 1945-1953.
-
(2001)
The Journal of Biological Chemistry
, vol.276
, pp. 1945-1953
-
-
Wolfe, M.D.1
Parales, J.V.2
Gibson, D.T.3
Lipscomb, J.D.4
-
91
-
-
0036185925
-
Salicylate 5-hydroxylase from Ralstonia sp. strain U2: A monooxygenase with close relationships to and shared electron transport proteins with naphthalene dioxygenase
-
Zhou, N.-Y., Al-Dulayymi, J., Baird, M.S., & Williams, P.A. (2002). Salicylate 5-hydroxylase from Ralstonia sp. strain U2: A monooxygenase with close relationships to and shared electron transport proteins with naphthalene dioxygenase. Journal of Bacteriology, 184, 1547-1555.
-
(2002)
Journal of Bacteriology
, vol.184
, pp. 1547-1555
-
-
Zhou, N.-Y.1
Al-Dulayymi, J.2
Baird, M.S.3
Williams, P.A.4
|