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OJBTM
Online Journal of Bioinformatics ©
Volume 11 (2): 293-301, 2010
In silico analysis of α-L-rhamnosidase
protein sequences from different source organisms.
Vinita
Yadav1*, Dinesh Yadav2 and Kapil Deo Singh Yadav1
1Department(s) of Chemistry and 2Biotechnology,
DDU Gorakhpur University, Gorakhpur, India
ABSTRACT
Yadav V, Yadav D,
Singh Yadav KD., In silico analysis of α-L-rhamnosidase
protein sequences from different source organisms. Online J Bioinformatics, 11 (2): 293, 2010. A total of 64 protein sequences of α-L-rhamnosidase
representing different source organisms available in GenBank
were downloaded and in silico characterized for homology search, multiple
sequence alignment, domain analysis and phylogenetic
tree construction to reveal sequence level similarity. Two major clusters
representing bacterial and fungal α-L-rhamnosidase
were observed. The multiple accessions of different bacterial and fungal
sources formed clusters revealing a sequence level similarity. The multiple
sequence alignment of α-L-rhamnosidase protein
sequences from different source organisms showed conserved regions at different
stretches indicating homology at sequence level. A total of seven motifs were
observed in MEME which showed similarity with Bacrhamnosid
family belonging to clan six hairpin glycosidase hydrolases
super family which is conserved in all the fungal and bacterial α-L-rhamnosidase protein sequences. One of the motifs showed
similarity with Bac_rhamnoside_N domain belonging to
clan galactose-binding domain-like superfamily. The presence of such motifs is indicative of
its structural organization with six helical hairpins and β-sandwich
domain involved in carbohydrate recognition.
Key words: α-L-rhamnosidase,
MEME, Multiple sequence alignment, domain analysis, dendrogram.