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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.
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