©1996-2012 All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publications. This article may be copied once but may not be, reproduced or re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements (DEST) for the Higher Education Research Data Collection (Australia). Linking:To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.
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
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.