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Volume 7


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In Silico Biology 7, 0026 (2007); ©2007, Bioinformation Systems e.V.  



Genome-wide prediction and annotation of Burkholderia pseudomallei AraC/XylS family transcription regulator

Boon-San Lim1, Chan-Eng Chong1, Zulkeflie Zamrod1, Sheila Nathan1, 2* and Rahmah Mohamed1, 2

1 School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
2 Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, 43600 Bangi, Selangor, Malaysia


* Corresponding author
  Email: sheila@pkrisc.cc.ukm.my


Edited by H. Michael; received November 02, 2006; revised April 17, 2007; accepted April 25, 2007; published June 16, 2007


Abstract

Many members of the AraC/XylS family transcription regulator have been proven to play a critical role in regulating bacterial virulence factors in response to environmental stress. By using the Hidden Markov Model (HMM) profile built from the alignment of a 99 amino acid conserved domain sequence of 273 AraC/XylS family transcription regulators, we detected a total of 45 AraC/XylS family transcription regulators in the genome of the Gram-negative pathogen, Burkholderia pseudomallei. Further in silico analysis of each detected AraC/XylS family transcription regulatory protein and its neighboring genes allowed us to make a first-order guess on the role of some of these transcription regulators in regulating important virulence factors such as those involved in three type III secretion systems and biosynthesis of pyochelin, exopolysaccharide (EPS) and phospholipase C. This paper has demonstrated an efficient and systematic genome-wide scale prediction of the AraC/XylS family that can be applied to other protein families.


Keywords: raC/XylS, α-helix-turn-α-helix, hidden Markov model, Burkholderia pseudomallei