In Silico Characterization of Pectate Lyase Protein Sequences from Different Source OrganismsReport as inadecuate

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Enzyme ResearchVolume 2010 2010, Article ID 950230, 11 pages

Research Article

Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur 273 009, India

School of Biotechnology, B.H.U, Varanasi 221 005, India

Environmental Biotechnology Division, National Environmental Engineering Research Institute, Nehru Marg, Nagpur, Maharashtra 440 020, India

Received 21 June 2010; Accepted 15 August 2010

Academic Editor: Leszek Kleczkowski

Copyright © 2010 Amit Kumar Dubey et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


A total of 121 protein sequences of pectate lyases were subjected to homology search, multiple sequence alignment, phylogenetic tree construction, and motif analysis. The phylogenetic tree constructed revealed different clusters based on different source organisms representing bacterial, fungal, plant, and nematode pectate lyases. The multiple accessions of bacterial, fungal, nematode, and plant pectate lyase protein sequences were placed closely revealing a sequence level similarity. The multiple sequence alignment of these pectate lyase protein sequences from different source organisms showed conserved regions at different stretches with maximum homology from amino acid residues 439–467, 715–816, and 829–910 which could be used for designing degenerate primers or probes specific for pectate lyases. The motif analysis revealed a conserved Pec_Lyase_C domain uniformly observed in all pectate lyases irrespective of variable sources suggesting its possible role in structural and enzymatic functions.

Author: Amit Kumar Dubey, Sangeeta Yadav, Manish Kumar, Vinay Kumar Singh, Bijaya Ketan Sarangi, and Dinesh Yadav



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