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Bioinformatics Advance Access originally published online on September 12, 2007
Bioinformatics 2007 23(19):2518-2521; doi:10.1093/bioinformatics/btm384
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes

Kirill Borziak and Igor B. Zhulin *

Joint Institute for Computational Sciences, The University of Tennessee – Oak Ridge National Laboratory, Oak Ridge, TN 37831-6173, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Sensory domains that are conserved among Bacteria, Archaea and Eucarya are important detectors of common signals detected by living cells. Due to their high sequence divergence, sensory domains are difficult to identify. We systematically look for novel sensory domains using sensitive profile-based searches initiated with regions of signal transduction proteins where no known domains can be identified by current domain models.

Results: Using profile searches followed by multiple sequence alignment, structure prediction and domain architecture analysis, we have identified a novel sensory domain termed FIST, which is present in signal transduction proteins from Bacteria, Archaea and Eucarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids.

Contact: joulineib{at}ornl.gov

Supplementary information: http://genomics.ornl.gov/research/pubs/fist

Associate Editor: Alex Bateman

Received on May 22, 2007; revised on July 15, 2007; accepted on July 17, 2007

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