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Bioinformatics Advance Access originally published online on March 16, 2006
Bioinformatics 2006 22(11):1297-1301; doi:10.1093/bioinformatics/btl096
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Published by Oxford University Press 2006
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion

Kira S. Makarova 1, Eugene V. Koonin 1, Robert Haselkorn 2 and Michael Y. Galperin 1,*

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
2 Department of Molecular Genetics and Cell Biology, University of Chicago Chicago, IL 60637, USA

*To whom correspondence should be addressed.

The cyanobacterium Anabaena (Nostoc) PCC 7120 responds to starvation for nitrogen compounds by differentiating approximately every 10th cell in the filament into nitrogen-fixing cells called heterocysts. Heterocyst formation is subject to complex regulation, which involves an unusual response regulator PatA that contains a CheY-like phosphoacceptor (receiver, REC) domain at its C-terminus. PatA-like response regulators are widespread in cyanobacteria; one of them regulates phototaxis in Synechocystis PCC 6803. Sequence analysis of PatA revealed, in addition to the REC domain, a previously undetected, conserved domain, which we named PATAN (after PatA N-terminus), and a potential helix–turn–helix (HTH) domain. PATAN domains are encoded in a variety of environmental bacteria and archaea, often in several copies per genome, and are typically associated with REC, Roadblock and other signal transduction domains, or with DNA-binding HTH domains. Many PATAN domains contain insertions of a small additional domain, termed {alpha}-clip, which is predicted to form a four-helix bundle. PATAN domains appear to participate in protein–protein interactions that regulate gliding motility and processes of cell development and differentiation in cyanobacteria and some proteobacteria, such as Myxococcus xanthus and Geobacter sulfurreducens.

Contact: galperin{at}ncbi.nlm.nih.gov

Supplementary information: http://www.ncbi.nlm.nih.gov/Complete_Genomes/SigCensus/PATAN.html

Received on February 18, 2006; revised on March 9, 2006; accepted on March 10, 2006

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