GenomeMatcher: A graphical user interface for DNA sequence comparison (2008)
Ohtsubo, Yoshiyuki, Ikeda-Ohtsubo, Wakako, Nagata, Yuji, Tsuda, Masataka
Abstract Background The number of available genome sequences is increasing, and easy-to-use software that enables efficient comparative analysis is needed. Results We developed GenomeMatcher, a...
Shimoda, Yoshikazu, Mitsui, Hisayuki, Kamimatsuse, Hiroko, Minamisawa, Kiwamu, Nishiyama, Eri, Ohtsubo, Yoshiyuki, ...
Rhizobia are nitrogen-fixing soil bacteria that establish endosymbiosis with some leguminous plants. The completion of several rhizobial genome sequences provides opportunities for genome-wide...
Site-Specific Recombination System Encoded by Toluene Catabolic (2002)
Transposon Tn, Hiroyuki Genka, Yuji Nagata, Masataka Tsuda
The 56-kb class II toluene catabolic transposon Tn4651 from Pseudomonas putida plasmid pWW0 is unique in that (i) its efficient resolution requires, in addition to the 0.2-kb resolution (res) site,...
Tsuda, Masataka, Genka, Hiroyuki
It has been reported that the toluene-degrading (xyl) genes from Pseudomonas putida plasmid pWW53 are able to translocate to broad-host-range drug resistance plasmid RP4, and pWW53-4 is one of the...
Gotoh, Naomasa, Tsujimoto, Hideto, Tsuda, Masataka, Okamoto, Kiyomi, Nomura, Atsuko, Wada, Takaomi, ...
Expression of the multidrug efflux system MexC-MexD-OprJ in nfxB mutants of Pseudomonas aeruginosa contributes to resistance to fluoroquinolones and the “fourth-generation” cephems (cefpirome and...
Takeuchi, Hiroaki, Shirai, Mutsunori, Akada, Junko K., Tsuda, Masataka, Nakazawa, Teruko
We identified cell division-related gene cdrA in Helicobacter pylori HPK5. The putative gene product, CdrA, is a 367-amino-acid polypeptide that exhibited a high level of homology to conserved...
Sota, Masahiro, Endo, Masahiro, Nitta, Keiji, Kawasaki, Haruhiko, Tsuda, Masataka
The two haloacetate dehalogenase genes, dehH1 and dehH2, on the 65-kb plasmid pUO1 from Delftia acidovorans strain B were found to be located on transposable elements. The dehH2 gene was carried on...
Site-Specific Recombination System Encoded by Toluene Catabolic Transposon Tn4651
Genka, Hiroyuki, Nagata, Yuji, Tsuda, Masataka
The 56-kb class II toluene catabolic transposon Tn4651 from Pseudomonas putida plasmid pWW0 is unique in that (i) its efficient resolution requires, in addition to the 0.2-kb resolution (res) site,...
Nagata, Yuji, Prokop, Zbyněk, Marvanová, Soňa, Sýkorová, Jana, Monincová, Marta, Tsuda, Masataka, ...
The homology model of protein Rv2579 from Mycobacterium tuberculosis H37Rv was compared with the crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26, and this...
Sota, Masahiro, Kawasaki, Haruhiko, Tsuda, Masataka
The self-transmissible plasmid pUO1 from Delftia acidovorans strain B carries two haloacetate-catabolic transposons, TnHad1 and TnHad2, and the mer genes for resistance to mercury. The complete...
Endo, Ryo, Kamakura, Mayuko, Miyauchi, Keisuke, Fukuda, Masao, Ohtsubo, Yoshiyuki, Tsuda, Masataka, ...
Sphingomonas paucimobilis UT26 utilizes γ-hexachlorocyclohexane (γ-HCH) as a sole source of carbon and energy. In our previous study, we cloned and characterized genes that are involved in the...
High-Temperature-Induced Transposition of Insertion Elements in Burkholderia multivorans ATCC 17616
Ohtsubo, Yoshiyuki, Genka, Hiroyuki, Komatsu, Harunobu, Nagata, Yuji, Tsuda, Masataka
An efficient and quantitative method to analyze the transposition of various insertion sequence (IS) elements in Burkholderia multivorans ATCC 17616 was devised. pGEN500, a plasmid carrying a...
Nagata, Yuji, Prokop, Zbyněk, Sato, Yukari, Jerabek, Petr, Kumar, Ashwani, Ohtsubo, Yoshiyuki, ...
β-Hexachlorocyclohexane (β-HCH) is the most recalcitrant among the α-, β-, γ-, and δ-isomers of HCH and causes serious environmental pollution problems. We demonstrate here that the haloalkane...
Sato, Yukari, Monincová, Marta, Chaloupková, Radka, Prokop, Zbyňek, Ohtsubo, Yoshiyuki, Minamisawa, Kiwamu, ...
Haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, have open...
Functional Analysis of Unique Class II Insertion Sequence IS1071
Sota, Masahiro, Yano, Hirokazu, Nagata, Yuji, Ohtsubo, Yoshiyuki, Genka, Hiroyuki, Anbutsu, Hisashi, ...
Various xenobiotic-degrading genes on many catabolic plasmids are often flanked by two copies of an insertion sequence, IS1071. This 3.2-kb IS element has long (110-bp) terminal inverted repeats...
Komatsu, Harunobu, Imura, Yoshiyuki, Ohori, Akira, Nagata, Yuji, Tsuda, Masataka
The Burkholderia multivorans strain ATCC 17616 carries three circular chromosomes with sizes of 3.4, 2.5, and 0.9 Mb. To determine the distribution and organization of the amino acid biosynthetic...
Shintani, Masaki, Yano, Hirokazu, Habe, Hiroshi, Omori, Toshio, Yamane, Hisakazu, Tsuda, Masataka, ...
Isolated from Pseudomonas resinovorans CA10, pCAR1 is a 199-kb plasmid that carries genes involved in the degradation of carbazole and dioxin. The nucleotide sequence of pCAR1 has been determined...
Sota, Masahiro, Yano, Hirokazu, Ono, Akira, Miyazaki, Ryo, Ishii, Hidenori, Genka, Hiroyuki, ...
The naphthalene-catabolic (nah) genes on the incompatibility group P-9 (IncP-9) self-transmissible plasmid NAH7 from Pseudomonas putida G7 are some of the most extensively characterized genetic...
Tsuda, Masataka, Genka, Hiroyuki
It has been reported that the toluene-degrading (xyl) genes from Pseudomonas putida plasmid pWW53 are able to translocate to broad-host-range drug resistance plasmid RP4, and pWW53-4 is one of the...
Gotoh, Naomasa, Tsujimoto, Hideto, Tsuda, Masataka, Okamoto, Kiyomi, Nomura, Atsuko, Wada, Takaomi, ...
Expression of the multidrug efflux system MexC-MexD-OprJ in nfxB mutants of Pseudomonas aeruginosa contributes to resistance to fluoroquinolones and the “fourth-generation” cephems (cefpirome and...
Takeuchi, Hiroaki, Shirai, Mutsunori, Akada, Junko K., Tsuda, Masataka, Nakazawa, Teruko
We identified cell division-related gene cdrA in Helicobacter pylori HPK5. The putative gene product, CdrA, is a 367-amino-acid polypeptide that exhibited a high level of homology to conserved...
Sota, Masahiro, Endo, Masahiro, Nitta, Keiji, Kawasaki, Haruhiko, Tsuda, Masataka
The two haloacetate dehalogenase genes, dehH1 and dehH2, on the 65-kb plasmid pUO1 from Delftia acidovorans strain B were found to be located on transposable elements. The dehH2 gene was carried on...
Site-Specific Recombination System Encoded by Toluene Catabolic Transposon Tn4651
Genka, Hiroyuki, Nagata, Yuji, Tsuda, Masataka
The 56-kb class II toluene catabolic transposon Tn4651 from Pseudomonas putida plasmid pWW0 is unique in that (i) its efficient resolution requires, in addition to the 0.2-kb resolution (res) site,...
Nagata, Yuji, Prokop, Zbyněk, Marvanová, Soňa, Sýkorová, Jana, Monincová, Marta, Tsuda, Masataka, ...
The homology model of protein Rv2579 from Mycobacterium tuberculosis H37Rv was compared with the crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26, and this...
Komatsu, Harunobu, Imura, Yoshiyuki, Ohori, Akira, Nagata, Yuji, Tsuda, Masataka
The Burkholderia multivorans strain ATCC 17616 carries three circular chromosomes with sizes of 3.4, 2.5, and 0.9 Mb. To determine the distribution and organization of the amino acid biosynthetic...
Sota, Masahiro, Kawasaki, Haruhiko, Tsuda, Masataka
The self-transmissible plasmid pUO1 from Delftia acidovorans strain B carries two haloacetate-catabolic transposons, TnHad1 and TnHad2, and the mer genes for resistance to mercury. The complete...
Endo, Ryo, Kamakura, Mayuko, Miyauchi, Keisuke, Fukuda, Masao, Ohtsubo, Yoshiyuki, Tsuda, Masataka, ...
Sphingomonas paucimobilis UT26 utilizes γ-hexachlorocyclohexane (γ-HCH) as a sole source of carbon and energy. In our previous study, we cloned and characterized genes that are involved in the...
High-Temperature-Induced Transposition of Insertion Elements in Burkholderia multivorans ATCC 17616
Ohtsubo, Yoshiyuki, Genka, Hiroyuki, Komatsu, Harunobu, Nagata, Yuji, Tsuda, Masataka
An efficient and quantitative method to analyze the transposition of various insertion sequence (IS) elements in Burkholderia multivorans ATCC 17616 was devised. pGEN500, a plasmid carrying a...
Nagata, Yuji, Prokop, Zbyněk, Sato, Yukari, Jerabek, Petr, Kumar, Ashwani, Ohtsubo, Yoshiyuki, ...
β-Hexachlorocyclohexane (β-HCH) is the most recalcitrant among the α-, β-, γ-, and δ-isomers of HCH and causes serious environmental pollution problems. We demonstrate here that the haloalkane...
Sato, Yukari, Monincová, Marta, Chaloupková, Radka, Prokop, Zbyňek, Ohtsubo, Yoshiyuki, Minamisawa, Kiwamu, ...
Haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, have open...
Functional Analysis of Unique Class II Insertion Sequence IS1071
Sota, Masahiro, Yano, Hirokazu, Nagata, Yuji, Ohtsubo, Yoshiyuki, Genka, Hiroyuki, Anbutsu, Hisashi, ...
Various xenobiotic-degrading genes on many catabolic plasmids are often flanked by two copies of an insertion sequence, IS1071. This 3.2-kb IS element has long (110-bp) terminal inverted repeats...
Shintani, Masaki, Yano, Hirokazu, Habe, Hiroshi, Omori, Toshio, Yamane, Hisakazu, Tsuda, Masataka, ...
Isolated from Pseudomonas resinovorans CA10, pCAR1 is a 199-kb plasmid that carries genes involved in the degradation of carbazole and dioxin. The nucleotide sequence of pCAR1 has been determined...
Sota, Masahiro, Yano, Hirokazu, Ono, Akira, Miyazaki, Ryo, Ishii, Hidenori, Genka, Hiroyuki, ...
The naphthalene-catabolic (nah) genes on the incompatibility group P-9 (IncP-9) self-transmissible plasmid NAH7 from Pseudomonas putida G7 are some of the most extensively characterized genetic...
Miyazaki, Ryo, Sato, Yukari, Ito, Michihiro, Ohtsubo, Yoshiyuki, Nagata, Yuji, Tsuda, Masataka
The α-proteobacterial strain Sphingobium japonicum UT26 utilizes a highly chlorinated pesticide, γ-hexachlorocyclohexane (γ-HCH), as a sole source of carbon and energy, and haloalkane dehalogenase...
Sota, Masahiro, Tsuda, Masataka, Yano, Hirokazu, Suzuki, Haruo, Forney, Larry J., Top, Eva M.
The overall architecture of IncP-1 plasmids is very conserved in that the accessory genes are typically located in one or two specific regions: between oriV and trfA and between the tra and trb...
Endo, Ryo, Ohtsubo, Yoshiyuki, Tsuda, Masataka, Nagata, Yuji
Sphingobium japonicum UT26 utilizes γ-hexachlorocyclohexane (γ-HCH) as its sole source of carbon and energy. In our previous studies, we cloned and characterized genes encoding enzymes for the...
GenomeMatcher: A graphical user interface for DNA sequence comparison
Ohtsubo, Yoshiyuki, Ikeda-Ohtsubo, Wakako, Nagata, Yuji, Tsuda, Masataka
Sato, Yukari, Natsume, Ryo, Tsuda, Masataka, Damborsky, Jiri, Nagata, Yuji, Senda, Toshiya
A haloalkane dehalogenase, DbjA, was crystallized by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The crystal belongs to the orthorhombic system, space group P21212 and...
Miyazaki, Ryo, Ohtsubo, Yoshiyuki, Nagata, Yuji, Tsuda, Masataka
Pseudomonas putida G7 carries a naphthalene-catabolic and self-transmissible plasmid, NAH7, which belongs to the IncP-9 incompatibility group. Adjacent to the putative origin of conjugative transfer...
Shimoda, Yoshikazu, Mitsui, Hisayuki, Kamimatsuse, Hiroko, Minamisawa, Kiwamu, Nishiyama, Eri, Ohtsubo, Yoshiyuki, ...
Rhizobia are nitrogen-fixing soil bacteria that establish endosymbiosis with some leguminous plants. The completion of several rhizobial genome sequences provides opportunities for genome-wide...