RadicalSAM.org

RadicalSAM.org maps sequence-function relationships across the radical S-adenosylmethionine (radical SAM) superfamily to support discovery and annotation of enzymatic activities and metabolic functions among approximately 700,000 UniProt entries.

Key Features:

• Sequence-function mapping: Maps and interprets sequence-function space within the radical SAM superfamily using genomic enzymology approaches.
• Sequence similarity networks (SSNs): Constructs and analyzes SSNs to identify isofunctional groups among radical SAM enzymes.
• Genome neighborhood diagrams (GNDs): Generates GNDs to provide genomic context for bacterial, archaeal, and fungal members and leverages gene co-localization for functional inference.
• Annotation integration: Integrates experimentally verified annotations to refine functional predictions for uncharacterized enzymes.
• Targeting uncharacterized members: Prioritizes and examines uncharacterized radical SAM enzymes cataloged in UniProt for functional discovery.

Scientific Applications:

• Discovery of enzymatic activities: Facilitates identification of novel radical SAM enzymatic activities and associated metabolic roles.
• Functional annotation: Supports annotation of uncharacterized radical SAM family members in UniProt.
• Experimental guidance: Informs selection of candidate enzymes and genomic contexts for experimental validation.
• Comparative genomic analysis: Enables comparative analysis of genomic neighborhoods across bacterial, archaeal, and fungal genomes to infer function.

Methodology:

Computational methods explicitly include application of genomic enzymology strategies to UniProt radical SAM sequences, construction and analysis of sequence similarity networks (SSNs) to identify isofunctional groups, and generation of genome neighborhood diagrams (GNDs) for bacterial, archaeal, and fungal genomes.