RRE-Finder

RRE-Finder identifies Ribosomally Synthesized and Post-translationally Modified Peptide (RiPP) recognition elements (RREs) in protein sequences to enable discovery and analysis of RRE-dependent RiPP biosynthetic pathways.

Key Features:

• Class-Independent Discovery: Identifies RRE domains with high sensitivity across diverse RiPP biosynthetic gene clusters (BGCs).
• Precision Mode: Reports high-confidence RREs and, when applied to UniProtKB, retrieved over 30,000 high-confidence RREs spanning all characterized RRE-dependent RiPP classes.
• Exploratory Mode: Identifies putative RREs and novel RiPP gene cluster architectures to assist discovery of new RiPP classes.
• RRE:Precursor Interaction Analysis: Enables analysis and prediction of RRE:precursor peptide interactions, reflecting the high affinity and specificity of these complexes.
• Evolutionary Insights: Provides sequence data used to explore potential evolutionary origins and diversification of the RRE domain.

Scientific Applications:

• RiPP Biosynthetic Diversity Exploration: Enables large-scale surveys of RRE-dependent RiPPs across genomes and protein databases.
• Novel RiPP Class Discovery: Supports identification of new RiPP classes and novel gene cluster architectures.
• Biochemical Studies of Peptide Maturation: Supplies RRE sequence datasets to support biochemical characterization of precursor peptide binding and post-translational modification enzymes.
• Biotechnology: Informs engineering of RRE:precursor interactions for biotechnological applications.

Methodology:

Accepts protein input in .fasta and .genbank formats, accepts antiSMASH output via a .final.gbk file with the '--antismash ripp' option, and Precision Mode was applied to UniProtKB to retrieve over 30,000 high-confidence RREs.