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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. 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.
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