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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.