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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
Yadav V, Yadav D, Singh Yadav KD., In silico analysis of α-L-rhamnosidase protein sequences from different source organisms. Onl J Bioinform, 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.