Eukaryotic linear motif resource (ELM)

Eukaryotic linear motif resource (ELM) predicts and catalogs functional short linear motifs (SLiMs) in eukaryotic proteins to support analysis of regulatory sites involved in intracellular signaling, protein turnover, localization, and post-translational modifications such as phosphorylation, acetylation, and glycosylation.

Key Features:

• Annotated motif database: Contains over 1800 annotated motif instances across 170 distinct functional classes, including approximately 500 new instances and 24 newly identified classes.
• Motif prediction and discovery: Identifies known and candidate novel linear motifs in user-submitted protein sequences.
• Contextual filtering: Integrates protein domain, structural information, native disorder, cellular context, and taxonomic range to reduce false positives in motif prediction.
• Instance mapping (PHI-BLAST): Implements an Instance Mapper protocol based on PHI-BLAST to map motif instances from homologous proteins for comparative evaluation.
• Cross-references: Provides links to related annotations and external databases for integration with protein structures and literature.
• Focus on SLiMs independent of tertiary structure: Emphasizes short linear motifs that function independently of protein tertiary structure.

Scientific Applications:

• Regulatory site analysis: Analyze and catalog regulatory SLiMs involved in signaling, localization, and protein turnover in eukaryotic proteins.
• Post-translational modification studies: Identify and investigate motifs associated with phosphorylation, acetylation, glycosylation, and other PTMs.
• Comparative motif conservation: Map motif occurrences across homologous proteins to assess conservation and prioritize candidates for experimental validation.
• Proteome-scale motif discovery: Survey eukaryotic proteomes to discover potential new motif classes and expand motif repertoires.

Methodology:

Motif annotation and prediction coupled with integration of protein domain, structural, disorder, cellular context, and taxonomic-range filters; Instance Mapper protocol uses PHI-BLAST to map motif instances in homologous proteins.