Bioinformatics Advance Access originally published online on May 27, 2004
Bioinformatics 2004 20(16):2787-2791; doi:10.1093/bioinformatics/bth330
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Bioinformatics vol. 20 issue 16 © Oxford University Press 2004; all rights reserved.
BacTregulators: a database of transcriptional regulators in bacteria and archaea
1 Department of Plant Biochemistry and Molecular and Cellular Biology, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, E-18008 Granada, Spain and 2 Bioinformatics, Hospital Universitario Virgen de las Nieves, E-18014 Granada, Spain
Received on February 23, 2004; revised on April 27, 2004; accepted on May 10, 2004
Advance Access Publication May 27, 2004
Motivation: The BacTregulators database is intended to collect and to integrate information on proteins belonging to defined families of transcriptional regulators in prokaryotes.
Results: The BacTregulators database currently contains data on two families of transcriptional regulators: AraC-XylS and TetR. The proteins included in the BacTregulators database have been identified by screening 123 genomes from archaea and bacteria and the SWISS-PROT and TrEMBL databases with profiles defining each family. As the result of an integration process, we have included 1326 different protein sequences from the AraC-XylS family and 1487 different protein sequences from the TetR family. The definition of an entry in BacTregulators is based on protein sequence, source organism, genome element and position in this genome element. The BacTregulators site allows the user to retrieve protein sequences, functional features and experimental evidence supporting the functions, references and the three-dimensional structure of the regulator when available. BacTregulators supplies an innovative tool that allows the researcher to obtain an integrated report that shows the data corresponding to other entries which are related by sequence similarity to the query entry. BacTregulators detects and classifies the regulators belonging to AraC-XylS and TetR families present in prokaryotic genomes, and thus contributes to a more accurate annotation of regulators in genomes. The information collected on each protein in the family can be useful to characterize a new regulator or compile information on the biological properties of a known regulator.
Availability: The BacTregulators is available at www.bactregulators.org
Supplementary information: www.bactregulators.org/supplementary/
Contact: rtobes{at}bioinformatica.org
* To whom correspondence should be addressed.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
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