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OJBTM
Online Journal of Bioinformatics ©
Volume
13(1):156-166, 2012
In Silico characterization of glycosidase protein sequences
from bacterial sources.
Vinita Yadav and Kapil Deo Singh Yadav
Department of Chemistry, Deen Dayal Upadhyaya
Gorakhpur University, Gorakhpur. India
ABSTRACT
Yadav V, Yadav KDS.,
In Silico characterization of glycosidase protein
sequences from bacterial sources. Online J Bioinform, 13
(1):156-166, 2012. Protein sequences of different glycosidases from bacterial sources located at the European
Bioinformatics Institute (http://www.ebi.ac.uk/Databases/ enzymes.html) database were downloaded for in silico characterization at sequence
level. Homology was deduced between 55 bacterial glycosidases
by multiple sequence alignment, phylogenetic
construction and motif analysis. Multiple sequence alignment of the glycosidase
protein sequences showed conserved regions at different stretches suggesting
significant similarity at sequence level. The phylogenetic
tree of glycosidase protein sequences revealed two major clusters. From the
ancestral sequence inference, it is observed that conserved amino acid residues
are the part of active site as catalytic residue or binding site. The MEME
suite results revealed three motifs, out of which two motifs have significant
similarity with tim barrel
fold and one have similarity with b-jelly roll
fold. The tim barrel fold is more common than b-jelly roll fold among all the 55
glycosidase protein sequences from bacterial sources.
Keywords: Glycosidases, in silico, multiple sequence alignment, ancestral
inference, motifs, tim barrel
fold.