PRODORIC: prokaryotic database of gene regulation

Abstract

The database PRODORIC aims to systematically organize information on prokaryotic gene expression, and to integrate this information into regulatory networks. The present version focuses on pathogenic bacteria such as Pseudomonas aeruginosa. PRODORIC links data on environmental stimuli with trans-acting transcription factors, cis-acting promoter elements and regulon definition. Interactive graphical representations of operon, gene and promoter structures including regulator-binding sites, transcriptional and translational start sites, supplemented with information on regulatory proteins are available at varying levels of detail. The data collection provided is based on exhaustive analyses of scientific literature and computational sequence prediction. Included within PRODORIC are tools to define and predict regulator binding sites. It is accessible at http://prodoric.tu-bs.de.

Figure 1

Schematic overview of the relational model core of the database structure, which describes protein--site- and protein--protein-interactions. Boxes in light grey refer to the corresponding genome sequence.

Figure 1

Weight matrix representations and resulting IUPAC consensi of the fumarate and nitrate reduction regulatory protein (Fnr) binding site and comparison between different species. (A) P. aeruginosa, (B) E. coli and (C) B. subtilis. The orthologous protein in P. aeruginosa is Anr (arginine fermentation and nitrate respiration regulator).