Abstract
Provalidator is a web-based tool that facilitates the design and validation of generalized profiles of protein families in prokaryotes. This tool combines the nearly full automation of profile building with a search for family members in all available databases. The tool is useful for assigning a given protein to a specific family, and is also useful for genome mining in annotated prokaryotic genomes. The tool is freely available at http://www.bactregulators.org. As proof of concept we constructed a profile that best defines the MerR family of transcriptional regulators. The profile created includes functional residues that are part of the helix-turn-helix DNA binding domain and accessory elements defined as wings 1 and 2, suggesting that members of the MerR family of regulators may exhibit conserved 3D structure in the region that defines the family profile. The profile defined for MerR was used to search for members of this family in the Swiss-Prot and TrEMBL databases, and also to identify members of the family in the genome of Pseudomonas putida. One of these identified regulators was found to be involved in zinc tolerance, showing the usefulness of identifying family members and assigning phenotypes.
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