Pro54DB: a database for experimentally verified sigma-54 promoters

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Sigma54 (σ54) promoters regulate essential prokaryotic genes involved in carbon/nitrogen metabolism and environmental responses.
• Understanding σ54 promoter mechanisms is key for gene transcription regulation and identifying uncharacterized genes.

Purpose of the Study:

• To create Pro54DB, an accessible, interactive, and extensible database for σ54 promoter information.
• To consolidate experimental findings on σ54 promoters for enhanced research utility.

Main Methods:

• Manual curation of σ54 promoter data from scientific literature.
• Data extraction and organization into a centralized database.

Main Results:

• Pro54DB currently contains 210 experimentally confirmed σ54 promoters.
• The database includes 297 regulated genes across 43 prokaryotic species.
• Data is sourced from 133 publications, ensuring comprehensive coverage.

Conclusions:

• Pro54DB serves as a valuable resource for researchers in bioinformatics and molecular biology.
• The database facilitates a deeper understanding of prokaryotic gene regulation by σ54 promoters.