PSI protein classifier: A new program automating PSI-BLAST search results

Naumoff, D. G.; Carreras, Marco

doi:10.1134/s0026893309040189

Cited by 14 publications

(2 citation statements)

References 44 publications

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“…Detection of a protein using the respective domain of a known family as a query after the first PSI-BLAST iteration with E-value 610 À7 was the criterion used to classify this protein as the family member [15][16][17].…”

Section: Methods and Algorithmsmentioning

confidence: 99%

Lateral gene transfer between the Bacteroidetes and Acidobacteria: The case of α‐l‐rhamnosidases

Naumoff

Dedysh

2012

FEBS Letters

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a b s t r a c t a-L-Rhamnosidases catalyze the hydrolysis of the terminal a-L-rhamnose residues in various carbohydrates. The catalytic domains in most of these enzymes belong to the families GH78 and GH106 of glycoside hydrolases. In this study, we show that almost all genes encoding the GH78-and GH106-containing proteins from members of the poorly characterized bacterial phylum Acidobacteria originated from precursors belonging to the phylum Bacteroidetes. Members of the Acidobacteria and Bacteroidetes display similar functional capabilities and specialize on degradation of plant-derived organic matter. Several proposed lateral gene transfers between the Acidobacteria and Bacteroidetes occurred presumably during specialization of these bacteria for their environments.

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Section: Methods and Algorithmsmentioning

confidence: 99%

Lateral gene transfer between the Bacteroidetes and Acidobacteria: The case of α‐l‐rhamnosidases

Naumoff

Dedysh

2012

FEBS Letters

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“…Planctomycetal or experimentally-characterized bacterial proteins were preferred if available. At the next stage the obtained PL17 T proteins were used as queries for the BLAST search, all revealed proteins were analyzed by PSI Protein Classifier [31] in order to detect proteins, which are deposited in the CAZy database. The most similar sequences were selected based on the BLAST search results.…”

Section: Methodsmentioning

confidence: 99%

Frigoriglobus tundricola gen. nov., sp. nov., a psychrotolerant cellulolytic planctomycete of the family Gemmataceae from a littoral tundra wetland

Kulichevskaya

Ivanova

Naumoff

et al. 2020

Systematic and Applied Microbiology

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Planctomycetes of the family Gemmataceae are characterized by large genome sizes and cosmopolitan distribution in freshwater and terrestrial environments but their ecological functions remain poorly understood. In this study, we characterized a novel representative of this family, strain PL17 T , which was isolated from a littoral tundra wetland and was capable of growth on xylan and cellulose. Cells of this isolate were represented by pink-pigmented spheres that multiplied by budding and occurred singly or in short chains and aggregates. Strain PL17 T was obligately aerobic, mildly acidophilic chemoorganotrophic bacterium, which displayed good tolerance of low temperatures. The major fatty acids were C 18:0 , C 16:1 ω 5 , and βOH-C 16:1 ; the major polar lipid was trimethylornithine. The genome of strain PL17 T consisted of a 9.83 Mb chromosome and a 24.69 kb plasmid. The G + C contents of the chromosomal and plasmid DNA were 67.4 and 62.3 mol%, respectively. Over 8900 potential protein-coding genes were identified in the genome including a putative cellulase that contains a domain from the GH5 family of glycoside hydrolases. The genome of strain PL17 T contained one linked and one unlinked rRNA operons with 16S rRNA gene sequences displaying 94.5% similarity to that in Gemmata obscuriglobus UQM2246 T . Based on the results of comparative phenotypic, chemotaxonomic and phylogenomic analyses, we propose to classify strain PL17 T (= CECT 9407 T = VKM B-3467 T ) as representing a novel genus and species of the family Gemmataceae , Frigoriglobus tundricola gen. nov., sp. nov.

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Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040

Funane

Kawabata

Suzuki

et al. 2011

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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PSI protein classifier: A new program automating PSI-BLAST search results

Cited by 14 publications

References 44 publications

Lateral gene transfer between the Bacteroidetes and Acidobacteria: The case of α‐l‐rhamnosidases

Lateral gene transfer between the Bacteroidetes and Acidobacteria: The case of α‐l‐rhamnosidases

Frigoriglobus tundricola gen. nov., sp. nov., a psychrotolerant cellulolytic planctomycete of the family Gemmataceae from a littoral tundra wetland

Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040

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