NCBI BLAST: a better web interface

Johnson, Mark W.; Zaretskaya, Irena; Raytselis, Yan; Merezhuk, Yuri; McGinnis, Scott D.; Madden, Thomas

doi:10.1093/nar/gkn201

Cited by 3,404 publications

(2,701 citation statements)

References 8 publications

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“…We used Specialized BLAST (NCBI) program (Johnson et al, 2008) to align two protein sequences. Algorithm parameters were set to automatic, and the method used was "Compositional matrix adjust."…”

Section: Methodsmentioning

confidence: 99%

“…To further compare the sequence of SLO-1a (NP_001024259) and KCNMA1 (NP_002238), we performed basic local alignment (NCBI BLAST) (Johnson et al, 2008) of translated protein sequences of the channels and their individual regions. The alignment for SLO-1a and KCNMA1 shows 55% identity and 69% similarity between the two sequences (Supplemental Information S3).…”

Section: Structural Comparison Of Slo-1 and Kcnma1mentioning

confidence: 99%

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Selective Toxicity of the Anthelmintic Emodepside Revealed by Heterologous Expression of Human KCNMA1 inCaenorhabditis elegans

Crisford¹,

Murray²,

O’Connor³

et al. 2011

Mol Pharmacol

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Emodepside is a resistance-breaking anthelmintic of a new chemical class, the cyclooctadepsipeptides. A major determinant of its anthelmintic effect is the calcium-activated potassium channel SLO-1. SLO-1 belongs to a family of channels that are highly conserved across the animal phyla and regulate neurosecretion, hormone release, muscle contraction, and neuronal network excitability. To investigate the selective toxicity of emodepside, we performed transgenic experiments in which the nematode SLO-1 channel was swapped for a mammalian ortholog, human KCNMA1. Expression of either the human channel or Caenorhabditis elegans slo-1 from the native slo-1 promoter in a C. elegans slo-1 functional null mutant rescued behavioral deficits that otherwise resulted from loss of slo-1 signaling. However, worms expressing the human channel were 10-to 100-fold less sensitive to emodepside than those expressing the nematode channel. Strains expressing the human KCNMA1 channel were preferentially sensitive to the mammalian channel agonists NS1619 and rottlerin. In the C. elegans pharyngeal nervous system, slo-1 is expressed in neurons, not muscle, and cell-specific rescue experiments have previously shown that emodepside inhibits serotonin-stimulated feeding by interfering with SLO-1 signaling in the nervous system. Here we show that ectopic overexpression of slo-1 in pharyngeal muscle confers sensitivity of the muscle to emodepside, consistent with a direct interaction of emodepside with the channel. Taken together, these data predict an emodepside-selective pharmacophore harbored by SLO-1. This has implications for the development of this drug/ target interface for the treatment of helminth infections.

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Section: Methodsmentioning

confidence: 99%

Section: Structural Comparison Of Slo-1 and Kcnma1mentioning

confidence: 99%

Selective Toxicity of the Anthelmintic Emodepside Revealed by Heterologous Expression of Human KCNMA1 inCaenorhabditis elegans

Crisford¹,

Murray²,

O’Connor³

et al. 2011

Mol Pharmacol

View full text Add to dashboard Cite

show abstract

“…Sequencing was performed using the same PCR primers with ABI Big Dye Terminator chemistry on an ABI 3730 automated sequencer (Applied Biosystems, Inc.) at Tsingke Biological Technology Co., Ltd (Chengdu, China). Sequences were then submitted for BLAST searching (Johnson et al 2008) in the GenBank to verify the data, with the accession numbers KT261771-KT2 61783, KT970676-KT970677 for 16S rRNA, KU15 8386-KU158400 for rpoB, KU158401-KU158413 for khe.…”

Section: Pcr Protocol and Sequence Determinationmentioning

confidence: 99%

Comparative analyses of phenotypic methods and 16S rRNA, khe, rpoB genes sequencing for identification of clinical isolates of Klebsiella pneumoniae

Guo

Shifei

et al. 2016

Antonie van Leeuwenhoek

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The present work aimed to evaluate 16S rRNA, khe and rpoB gene sequencing for the identification of Klebsiella pneumoniae in comparison with phenotypic methods. Fifteen clinical isolates were examined, which were initially identified as K. pneumoniae subsp. pneumoniae using the automated VITEK 32 system in two hospitals in Enshi City, China. Their identity was further supported by conventional phenotypic methods on the basis of morphological and biochemical characteristics. Using Bayesian phylogenetic analyses and haplotypes network reconstruction, 13 isolates were identified as K.pneumoniae, whereas the other two isolates (K19, K24) were classified as Shigella sp. and Enterobacter sp., respectively. Of the three genes, 16S rRNA and khe gene could discriminate the clinical isolates at the genus level, whereas rpoB could discriminate Klebsiella at the species and even subspecies level. Overall, the gene tree based on rpoB is more compatible with the currently accepted classification of Klebsiella than those based on 16S rRNA and khe genes, showing that rpoB can be a powerful tool for identification of K. pneumoniae isolates. Above all, our study challenges the utility of khe as a species-specific marker for identification of K. pneumoniae.Electronic supplementary material The online version of this article

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“…The strain DCY84 T sequence obtained was compared with those in public databases by using the EzTaxon-e server (http:// eztaxon-e.ezbiocloud.net/; Kim et al 2012) and NCBI database (http://blast.ncbi.nlm.nih.gov/Blast. cgi; Johnson et al 2008). …”

Section: Molecular Characterizationmentioning

confidence: 99%

Paenibacillus yonginensis sp. nov., a potential plant growth promoting bacterium isolated from humus soil of Yongin forest

Sukweenadhi

Kim

Lee

et al. 2014

Antonie van Leeuwenhoek

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Strain DCY84 T , a Gram-stain positive, rodshaped, aerobic, spore-forming bacterium, motile by means of peritrichous flagella, was isolated from humus soil from Yongin forest in Gyeonggi province, South Korea. Strain DCY84 T shared the highest sequence similarity with Paenibacillus barengoltzii KACC 15270 T (96.86 %), followed by Paenibacillus timonensis KACC 11491 T (96.49 %) and Paenibacillus phoenicis NBRC 106274 T (95.77 %). Strain DCY84 T was found to able to grow best in TSA at temperature 30°C, at pH 8 and at 0.5 % NaCl. MK-7 menaquinone was identified as the isoprenoid quinone. The major polar lipids were identified as phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified aminolipids and an unidentified polar lipid. The peptidoglycan was found to contain the amino acids meso-diaminopimelic acid, alanine and D-glutamic acid. The major fatty acids of strain DCY84 T were identified as branched chain anteiso-C 15:0 , saturated C 16:0 and branched chain anteiso-C 17:0 . The cell wall sugars of strain DCY84 T were found to comprise of ribose, galactose and xylose. The major polyamine was identified as spermidine. The DNA G?C content was determined to be 62.6 mol%. After 6 days of incubation, strain DCY84 T produced 52.96 ± 1.85 and 72.83 ± 2.86 lg/ml L-indole-3-acetic acid, using media without L-tryptophan and supplemented with Ltryptophan, respectively. Strain DCY84 T was also found to be able to solubilize phosphate and produce siderophores. On the basis of the phenotypic characteristics, genotypic analysis and chemotaxonomic characteristics, strain DCY84 T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus yonginensis sp. nov. is proposed. The type strain is DCY84 T (=KCTC 33428 T = JCM 19885 T ).

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NCBI BLAST: a better web interface

Cited by 3,404 publications

References 8 publications

Selective Toxicity of the Anthelmintic Emodepside Revealed by Heterologous Expression of Human KCNMA1 inCaenorhabditis elegans

Selective Toxicity of the Anthelmintic Emodepside Revealed by Heterologous Expression of Human KCNMA1 inCaenorhabditis elegans

Comparative analyses of phenotypic methods and 16S rRNA, khe, rpoB genes sequencing for identification of clinical isolates of Klebsiella pneumoniae

Paenibacillus yonginensis sp. nov., a potential plant growth promoting bacterium isolated from humus soil of Yongin forest

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