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Nucleic Acids Research Advance Access originally published online on November 29, 2006
Nucleic Acids Research 2007 35(Database issue):D271-D273; doi:10.1093/nar/gkl949
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Nucleic Acids Research, 2007, Vol. 35, Database issue D271-D273
Published by Oxford University Press 2006
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

Sentra: a database of signal transduction proteins for comparative genome analysis

Mark D'Souza1,2,*, Elizabeth M. Glass1,2, Mustafa H. Syed1, Yi Zhang1, Alexis Rodriguez1, Natalia Maltsev1,2 and Michael Y. Galperin3,*

1 Computational Biology Group, Mathematics and Computer Science Division, Argonne National Laboratory Argonne, IL 60439, USA 2 Computation Institute, University of Chicago Chicago, IL 60637, USA 3 National Center for Biotechnology Information, National Library of Medicine MSC3830, National Institutes of Health, Bethesda, MD 20894, USA

*To whom correspondence should be addressed. Tel: +1 630 252 5195; Fax: +1 630 252 5986; Email: dsouza{at}mcs.anl.gov

Received September 14, 2006. Revised October 18, 2006. Accepted October 20, 2006.

Sentra (http://compbio.mcs.anl.gov/sentra), a database of signal transduction proteins encoded in completely sequenced prokaryotic genomes, has been updated to reflect recent advances in understanding signal transduction events on a whole-genome scale. Sentra consists of two principal components, a manually curated list of signal transduction proteins in 202 completely sequenced prokaryotic genomes and an automatically generated listing of predicted signaling proteins in 235 sequenced genomes that are awaiting manual curation. In addition to two-component histidine kinases and response regulators, the database now lists manually curated Ser/Thr/Tyr protein kinases and protein phosphatases, as well as adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases, as defined in several recent reviews. All entries in Sentra are extensively annotated with relevant information from public databases (e.g. UniProt, KEGG, PDB and NCBI). Sentra's infrastructure was redesigned to support interactive cross-genome comparisons of signal transduction capabilities of prokaryotic organisms from a taxonomic and phenotypic perspective and in the framework of signal transduction pathways from KEGG. Sentra leverages the PUMA2 system to support interactive analysis and annotation of signal transduction proteins by the users.

*Correspondence may also be addressed to Michael Y. Galperin. Tel: +1 301 435 5910; Fax: +1 301 435 7793; Email: galperin{at}ncbi.nlm.nih.gov


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