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A Phylogenetic Approach for Assigning Function of Hypothetical Proteins in photorhabdus luminescens Subsp. laumondii TT01 Genome | OMICS International | Abstract
ISSN: 0974-7230

Journal of Computer Science & Systems Biology
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Research Article

A Phylogenetic Approach for Assigning Function of Hypothetical Proteins in photorhabdus luminescens Subsp. laumondii TT01 Genome

Razia M1, Karthik Raja R1, Padmanaban K1, Sivaramakrishnan S1 and Chellapandi P2*

1Department of Biotechnology, Bharathidasan University, Tiruchirappalli-620024, Tamilnadu, India

2Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli-620024, Tamilnadu, India

*Corresponding Author:
Dr. Chellapandi P
Department of Bioinformatics
School of Life Sciences
Bharathidasan University
Tiruchirappalli- 620024, Tamilnadu, India
Tel: +91-431-2407071
Fax: +91-431-2407045
E-mail : [email protected]

Received Date: January 19, 2010; Accepted Date: February 08, 2010; Published Date: February 08, 2010

Citation: Razia M, Raja KR, Padmanaban K, Sivaramakrishnan S, Chellapandi P (2010) A Phylogenetic Approach for Assigning Function of Hypothetical Proteins in Photorhabdus luminescens Subsp. laumondii TT01 Genome. J Comput Sci Syst Biol 3:021-029. doi: 10.4172/jcsb.1000051

Copyright: © 2009 Razia M, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

Polyketides are larger family of structurally diverse natural products with a broad range of biological activity. The occurrence of polyketide synthase gene family/cluster in bacteria is capable to synthesis the polyketides. In this study, sequence and structural similarities of some hypothetical proteins of Photorhabdus luminescens subsp. laumondii TT01 analyzed to assign the functional relationship with polyketide synthases (PKSs) using bioinformatics tools. Many hypothetical proteins of this organism have shown homologies to PKS family on which a significant homolog found to be located at genomic region 2247626-2249476 bp in chromosome 1 carrying identical function. On searching motif and domain, it showed a strong similarity to ketoacyl (KA) synthase I and then to acyl carrier protein. The ketosynthaseacyltransferasedidomain module 5 (2HG4) of Saccharopolyspora erythraea found as a good ortholog and the best template for modeling 3D structure from the sequences of hypothetical proteins. ProFunc and Castp servers used to annotate the structure-function relationship of protein models. The structural aspects at primary and secondary levels also showed a close resemblance to KA synthase. Phylogenetic analysis of this sequence and protein model ensured its function would be -KA synthase showing the functional reliability like ketosynthase, and it has evolutionary relationship with soil bacteria. There was a horizontal gene transfer event to acquire this domain in P.luminescence genome. Consequently, an abundance of PKS gene in the genome of entomopathogenic bacteria will obviously helpful to protect its host nematode from other pathological pervasiveness.

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