Predicted Prokaryotic Regulatory Proteins (P2RP)

Predicted Prokaryotic Regulatory Proteins (P2RP) predicts regulatory proteins (RPs) in prokaryotic sequences by scanning amino acid or genomic DNA sequences for DNA-binding and two-component system (TCS) domains and classifying them into regulatory protein families.

Key Features:

• Input types: Accepts amino acid and genomic DNA sequences for analysis.
• Domain scanning: Scans sequences for DNA-binding domains and Two-Component System (TCS) domains characteristic of regulatory proteins.
• Identification of regulatory proteins: Detects potential regulatory proteins (RPs) based on presence of characteristic domains.
• Annotation and classification: Categorizes predicted RPs into families and annotates sequence features and functional domains.
• Pipeline integration: Produces structured annotations intended for incorporation into genome annotation and re-annotation pipelines.

Scientific Applications:

• Genomic research: Facilitates identification of potential regulatory proteins in novel prokaryotic sequence data.
• Comparative genomics: Enables standardization and comparison of RP annotations across prokaryotic genomes.
• Functional genomics: Supports functional characterization of regulatory proteins and their roles in cellular responses.

Methodology:

P2RP employs an integrated software pipeline that accepts amino acid or genomic DNA input, scans for DNA-binding and TCS domains, and performs classification and detailed annotation of predicted regulatory proteins.