WU-Blast2 server at the European Bioinformatics Institute

López, Rodrigo; Silventoinen, Ville; Robinson, Stephen J.; Kibria, Asif; Gish, Warren

doi:10.1093/nar/gkg573

Cited by 120 publications

(96 citation statements)

References 24 publications

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“…The annotation procedure consists of two major steps. First, C. remanei genomic sequences that encode candidate ABC genes by using C. elegans ABC genes as query to search the C. remanei genomic sequences database using WU-BLAST (tblastn) (Lopez et al 2003). Regions that best match the query C. elegans ABC genes were parsed and recorded.…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics and Adaptive Selection of the ATP-Binding-Cassette Gene Family in Caenorhabditis Species

et al. 2007

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ABC transporters constitute one of the largest gene families in all species. They are mostly involved in transport of substrates across membranes. We have previously demonstrated that the Caenorhabditis elegans ABC family shows poor one-to-one gene orthology with other distant model organisms. To address the evolution dynamics of this gene family among closely related species, we carried out a comparative analysis of the ABC family among the three nematode species C. elegans, C. briggsae, and C. remanei. In contrast to the previous observations, the majority of ABC genes in the three species were found in orthologous trios, including many tandemly duplicated ABC genes, indicating that the gene duplication took place before speciation. Species-specific expansions of ABC members are rare and mostly observed in subfamilies A and B. C. briggsae and C. remanei orthologous ABC genes tend to cluster on trees, with those of C. elegans as an outgroup, consistent with their proposed species phylogeny. Comparison of intron/exon structures of the highly conserved ABCE subfamily members also indicates a closer relationship between C. briggsae and C. remanei than between either of these species and C. elegans. A comparison between insect and mammalian species indicates lineage-specific duplications or deletions of ABC genes, while the family size remains relatively constant. Sites undergoing positive selection within subfamily D, which are implicated in very-long-chain fatty acid transport, were identified. The evolution of these sites might be driven by the changes in food source with time.

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Section: Methodsmentioning

confidence: 99%

Comparative Genomics and Adaptive Selection of the ATP-Binding-Cassette Gene Family in Caenorhabditis Species

et al. 2007

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“…Structural and Functional Homologs-In a search for related homologs of B. subtilis imidazolonepropionase using BLAST (32), it is observed that the enzyme exists widely in various organisms. We picked HutI proteins from representative Gram-negative, Gram-positive bacteria, and eukaryotes, respectively and aligned these sequences with ClustalX and ESPript (Fig.…”

Section: ⑀2mentioning

confidence: 99%

A Catalytic Mechanism Revealed by the Crystal Structures of the Imidazolonepropionase from Bacillus subtilis

Bröstromer

et al. 2006

Journal of Biological Chemistry

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Imidazolonepropionase (EC 3.5.2.7) catalyzes the third step in the universal histidine degradation pathway, hydrolyzing the carbon-nitrogen bonds in 4-imidazolone-5-propionic acid to yield N-formimino-L-glutamic acid. Here we report the crystal structures of the Bacillus subtilis imidazolonepropionase and its complex at 2.0-Å resolution with substrate analog imidazole-4-acetic acid sodium (I4AA). The structure of the native enzyme contains two domains, a TIM (triose-phosphate isomerase) barrel domain with two insertions and a small ␤-sandwich domain. The TIM barrel domain is quite similar to the members of the ␣/␤ barrel metallo-dependent hydrolase superfamily, especially to Escherichia coli cytosine deaminase. A metal ion was found in the central cavity of the TIM barrel and was tightly coordinated to residues His-80, His-82, His-249, Asp-324, and a water molecule. X-ray fluorescence scan analysis confirmed that the bound metal ion was a zinc ion. An acetate ion, 6 Å away from the zinc ion, was also found in the potential active site. In the complex structure with I4AA, a substrate analog, I4AA replaced the acetate ion and contacted with Arg-89, Try-102, Tyr-152, His-185, and Glu-252, further defining and confirming the active site. The detailed structural studies allowed us to propose a zinc-activated nucleophilic attack mechanism for the hydrolysis reaction catalyzed by the enzyme.The histidine degradation pathway is highly conserved from prokaryotes to eukaryotes (1, 2). In bacteria, the histidine degradation pathway is operated by the hut (histidine utilization) genes, and the Bacillus subtilis hut operon encodes proteins in the order of HutP, HutH, HutU, HutI, HutG, HutM (3-6).There (Fig. 1A); 4) N-formimino-L-glutamic acid ϩ H 2 O 3 glutamate ϩ HCONH 2 (catalyzed by formiminoglutamase, EC 3.5.3.8).Among the four enzymes, the first three-dimensional structure determined was the 2.1-Å resolution crystal structure of histidase or HutH from Pseudomonas putida by Schulz and co-workers in 1999 (7,8). It was found that there was a polypeptide modification, forming a novel catalytically essential electrophilic group. The second structure was of urocanase or HutU, also from P. putida, and the structure was determined by the same group who solved the histidase in 2004 (9). The third structure solved was the last enzyme in the histidine degradation pathway, formiminoglutamase or HutG from Vibrio cholerae, which was determined by Wu et al. 5 and deposited in the Protein Data Bank under accession number 1XFK. The imidazolonepropionase or HutI is the only enzyme left in this pathway that has no published structural information so far, although some properties of this enzyme have been studied in Salmonella typhimurium (10), Pseudomonas fluorescens ATCC 11299 (11), rat liver (12), and other organisms during 1960s and 1970s. The maximal activity of this enzyme occurred at pH 7.4 with a narrow pH optimum, and its Michaelis constant was calculated to be 7 M (12). It was also mentioned in the literature that 1 mM EDTA could...

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“…We compared the performance of genBlastA with two existing programs with similar functionalities-WU-BLAST (Lopez et al 2003) and the program by Cui et al (2007). WU-BLAST is available by an academic license.…”

Section: Test Gene Set Preparation and Test Strategymentioning

confidence: 99%

“…With recent advances in sequencing technologies (Margulies et al 2005;Bentley 2006), the volume of the nucleotide sequences is expanding at an accelerating pace, further enriching genomic sequence resources. To effectively exploit these resources for biological and medical research, many homology-based similarity search and alignment tools have been developed over the past 20 yr. Representative similarity search and alignment tools include BLAST (Altschul et al 1990), FASTA (Pearson and Lipman 1988), sim4 (Florea et al 1998), WU-BLAST (Lopez et al 2003), and BLAT (Kent 2002). These tools have been extremely useful, especially for comparative genomics, in which genomes of both closely and distantly related species are compared in order that knowledge of the genome of one species can be used to understand the genome of other species (Hardison 2003).…”

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confidence: 99%

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genBlastA: Enabling BLAST to identify homologous gene sequences

She¹,

Chu²,

Wang³

et al. 2008

Genome Res.

290

212

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BLAST is an extensively used local similarity search tool for identifying homologous sequences. When a gene sequence (either protein sequence or nucleotide sequence) is used as a query to search for homologous sequences in a genome, the search results, represented as a list of high-scoring pairs (HSPs), are fragments of candidate genes rather than full-length candidate genes. Relevant HSPs (“signals”), which represent candidate genes in the target genome sequences, are buried within a report that contains also hundreds to thousands of random HSPs (“noises”). Consequently, BLAST results are often overwhelming and confusing even to experienced users. For effective use of BLAST, a program is needed for extracting relevant HSPs that represent candidate homologous genes from the entire HSP report. To achieve this goal, we have designed a graph-based algorithm, genBlastA, which automatically filters HSPs into well-defined groups, each representing a candidate gene in the target genome. The novelty of genBlastA is an edge length metric that reflects a set of biologically motivated requirements so that each shortest path corresponds to an HSP group representing a homologous gene. We have demonstrated that this novel algorithm is both efficient and accurate for identifying homologous sequences, and that it outperforms existing approaches with similar functionalities.

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WU-Blast2 server at the European Bioinformatics Institute

Cited by 120 publications

References 24 publications

Comparative Genomics and Adaptive Selection of the ATP-Binding-Cassette Gene Family in Caenorhabditis Species

Comparative Genomics and Adaptive Selection of the ATP-Binding-Cassette Gene Family in Caenorhabditis Species

A Catalytic Mechanism Revealed by the Crystal Structures of the Imidazolonepropionase from Bacillus subtilis

genBlastA: Enabling BLAST to identify homologous gene sequences

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