Localizome

Localizome predicts transmembrane helix number and topology of eukaryotic proteins to support protein topology and subcellular localization analyses.

Key Features:

• Pfam integration: Detects Pfam domains in eukaryotic protein sequences using the hmmpfam tool.
• TM helix prediction (Phobius): Predicts transmembrane helices and topology using the Phobius algorithm.
• LocaloDom curated database: Cross-references predictions with LocaloDom, a database of TM topologies and TM helix numbers constructed by combining Pfam domains with Swiss-Prot annotations and Phobius predictions.
• Correction mechanism: Adjusts combined domain and topology results to conform to rules encoded in LocaloDom.
• Performance metrics: Reports accuracy and coverage metrics, including 99% accuracy and 75% coverage for soluble proteins, and 96% accuracy and 68% coverage for transmembrane protein domain regions.

Scientific Applications:

• Subcellular localization analysis: Provides topology information useful for studies of protein localization in eukaryotic cells.
• Membrane protein annotation: Supplies TM helix number and topology data for annotation and functional interpretation of soluble and membrane proteins.

Methodology:

Pfam domains are detected with hmmpfam, TM helices and topology are predicted with Phobius, predictions are cross-referenced against the LocaloDom database (built from Pfam, Swiss-Prot annotations, and Phobius predictions), and combined results are corrected to follow rules in LocaloDom.