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In silico identification and characterization of novel drug targets and outer membrane proteins in the fish pathogen Edwardsiella tarda

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Author(s): Mohammed Neema | Iddya Karunasagar | Indrani Karunasagar

Journal: Open Access Bioinformatics
ISSN 1179-2701

Volume: 2011;
Issue: default;
Start page: 37;
Date: 2011;
Original page

ABSTRACT
Mohammed Neema, Iddya Karunasagar, Indrani KarunasagarUNESCO Microbial Resource Centre for Marine Biotechnology, Department of Fishery Microbiology, Karnataka Veterinary Animal and Fisheries Sciences University, College of Fisheries, Mangalore, Karnataka, IndiaAbstract: The complete genome of the fish pathogen Edwardsiella tarda and the host Danio rerio (zebrafish) was subjected to subtractive genome analysis with the objective of identifying potential drug targets and vaccine candidates. The homologous proteins were excluded to prevent any chance of cytotoxic cross-reaction with the host. The nonparalogous proteins were analyzed for sequence homology with the Database of Essential Genes to determine the essentiality of the proteins for the bacteria. These essential proteins were further analyzed to predict the metabolic pathways in which they were involved. Cellular localization analysis was carried out to determine the possibility of the protein being present in the outer membrane. Outer membrane proteins may play an important role in the interaction with hosts and in bacterial pathogenicity. The study identified 171 of 3986 proteins as potential drug targets. The study also identified seven novel outer membrane proteins.Keywords: subtractive genomics, CD-HIT, DEG, KEGG, homology modelling, Edwardsiella tarda, OMPs
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