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Research Journal of Biological Sciences

Year: 2010  |  Volume: 5  |  Issue: 6  |  Page No.: 404 - 413

Protein Function Extrapolation via Inventorical Clustering and Predictive Comparative Analysis of Sequence Structure Function Relationships of a Burkholderia pseudomallei ATP Binding Protein

Mohd Firdaus-Raih, Roohaida Othman and Rahmah Mohamed

Abstract

The tropical soil pathogen Burkholderia pseudomallei is known to secrete a variety of extracellular virulence factors and is resistant to a wide range of antibiotics. ATP Binding Cassette (ABC) transport systems typically consist of three proteins encoded by genes in the same operon or neighboring operons. This functionally diverse protein super family typically carry out vector driven transport across cell membranes. The studies have identified an open reading frame that was predicted to code for an ATP binding protein in B. pseudomallei. A whole genome inventorization and function classification by sequence similarity clustering was done by comparison of ABC transporters from three completed genomes. The predicted protein sequence of the ATP binding domain was successfully modelled onto the crystal structure of an ATP binding subunit for the histidine permease of Salmonella typhimurium. The putative ATP binding site was identified and the model deemed to be functionally viable from a structural-mechanics point of view. We have also detected two highly conserved residues which appear to be independent of the known motifs associated with the ATP binding subunit. This integrated process was able to identify and infer function to an ABC domain from B. pseudomallei despite low target template sequence identity (26.4%). This approach enabled ABC transporters with varying functions to be classified predictively.

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