Pseudochrobactrum glaciei sp. nov., isolated from sea ice collected from Peter the Great Bay of the Sea of Japan.
ABSTRACT An aerobic, Gram-negative, non-pigmented, non-motile bacterium, KMM 3858(T), was isolated from a sea-ice sample collected from Peter the Great Bay of the Sea of Japan, Russia, and subjected to a phenotypic and phylogenetic study. Comparative analyses based on the 16S rRNA and recA gene sequences placed strain KMM 3858(T) within the genus Pseudochrobactrum. The major chemotaxonomic characteristics were found to be the presence of phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminolipid and phosphatidylcholine, major fatty acids C(18 : 1)omega7c and C(19 : 0) cyclo, and ubiquinone Q-10, confirming the affiliation of strain KMM 3858(T) to the genus Pseudochrobactrum. On the basis of the phylogenetic analysis and the physiological and biochemical characterization, strain KMM 3858(T) should be classified as representing a novel species of the genus Pseudochrobactrum, for which the name Pseudochrobactrum glaciei sp. nov. is proposed. The type strain is strain Pi26(T) (=KMM 3858(T)=NRIC 0733(T)=JCM 15115(T)).
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ABSTRACT: We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).Molecular Biology and Evolution 09/2007; 24(8):1596-9. · 10.35 Impact Factor
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ABSTRACT: We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices.Proceedings of the National Academy of Sciences 05/1988; 85(8):2444-8. · 9.74 Impact Factor
- Journal of Bacteriology 08/1953; 66(1):24-6. · 3.19 Impact Factor