RESUMO
Novosphingobium sp. strain Rr 2-17 is an N-acyl homoserine lactone (AHL)-producing bacterium isolated from the crown gall tumor of a grapevine. To our knowledge, this is the first draft genome announcement of a plant-associated strain from the genus Novosphingobium.
Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Análise de Sequência de DNA , Sphingomonadaceae/genética , Acil-Butirolactonas/metabolismo , Arginina/análogos & derivados , Arginina/metabolismo , Dados de Sequência Molecular , Tumores de Planta/microbiologia , Sphingomonadaceae/isolamento & purificação , Sphingomonadaceae/metabolismo , Vitis/microbiologiaRESUMO
Methylobacterium sp. strain GXF4 is an isolate from grapevine. Here we present the sequence, assembly, and annotation of its genome, which may shed light on its role as a grapevine xylem inhabitant. To our knowledge, this is the first genome announcement of a plant xylem-associated strain of the genus Methylobacterium.
Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Methylobacterium/genética , Análise de Sequência de DNA , Methylobacterium/isolamento & purificação , Dados de Sequência Molecular , Vitis/microbiologia , Xilema/microbiologiaRESUMO
Hydrogenophaga sp. strain PBC is an effective degrader of 4-aminobenzenesulfonate isolated from textile wastewater. Here we present the assembly and annotation of its genome, which may provide further insights into its metabolic potential. This is the first announcement of the draft genome sequence of a strain from the genus Hydrogenophaga.
Assuntos
Comamonadaceae/genética , Comamonadaceae/metabolismo , Genoma Bacteriano , Ácidos Sulfanílicos/metabolismo , Sequência de Bases , Biodegradação Ambiental , Mapeamento Cromossômico , Comamonadaceae/classificação , DNA Bacteriano/genética , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNARESUMO
Ralstonia sp. strain PBA was isolated from textile wastewater in a coculture with Hydrogenophaga sp. strain PBC. Here we present the assembly and annotation of its genome, which may provide further insights into the mechanism of its interaction with strain PBC during 4-aminobenzenesulfonate degradation.
Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Ralstonia/genética , Análise de Sequência de DNA , Biotransformação , Microbiologia Industrial , Dados de Sequência Molecular , Ralstonia/isolamento & purificação , Ralstonia/metabolismo , Ácidos Sulfanílicos/metabolismo , Microbiologia da ÁguaRESUMO
Enterobacter sp. strain SST3 is an endophytic bacterium isolated from Saccharum spp. Here we present its annotated draft genome that may shed light on its role as a bacterial endophyte of sugarcane. To our knowledge, this is the first genome announcement of a sugarcane-associated bacterium from the genus Enterobacter.
Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Enterobacter/genética , Genoma Bacteriano , Análise de Sequência de DNA , Endófitos/genética , Endófitos/isolamento & purificação , Enterobacter/isolamento & purificação , Dados de Sequência Molecular , Caules de Planta/microbiologia , Saccharum/microbiologiaRESUMO
UNLABELLED: birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in parallel by simply booting the birgHPC CD or flash drive from the head node, which immediately positions the rest of the PCs on the network as computing nodes. Thus, a temporary, affordable, scalable and high-performance computing environment can be built by non-computing-based researchers using low-cost commodity hardware. AVAILABILITY: The birgHPC Live CD and relevant user guide are available for free at http://birg1.fbb.utm.my/birghpc.
Assuntos
Biologia Computacional/métodos , Metodologias Computacionais , Simulação de Dinâmica Molecular , Software , Análise por ConglomeradosRESUMO
UNLABELLED: We present the development of a web server, a protein short motif search tool that allows users to simultaneously search for a protein sequence motif and its secondary structure assignments. The web server is able to query very short motifs searches against PDB structural data from the RCSB Protein Databank, with the users defining the type of secondary structures of the amino acids in the sequence motif. The output utilises 3D visualisation ability that highlights the position of the motif in the structure and on the corresponding sequence. Researchers can easily observe the locations and conformation of multiple motifs among the results. Protein short motif search also has an application programming interface (API) for interfacing with other bioinformatics tools. AVAILABILITY: The database is available for free at http://birg3.fbb.utm.my/proteinsms.