Zebra2

Zebra2 identifies subfamily-specific and conserved positions within protein superfamilies to reveal determinants of functional diversity, including catalytic and structural residues.

Key Features:

• Automated detection: Searches for subfamily-specific and conserved positions across protein superfamilies and integrates with Mustguseal, which automatically collects and superimposes large sets of functionally diverse homologs exhibiting high structural similarity but low sequence identity.
• Multi-level results organization: Organizes results into distinct information levels, including a Sequence Similarity Network, sequence- and 3D-structure-based analyses of conservation and variability, and detailed annotations integrating data from external databases.
• Sequence- and structure-based analysis: Provides interfaces for analyzing conservation and variability using both multiple sequence alignments and 3D structural superpositions.
• Detailed annotation integration: Aggregates comprehensive protein annotations with links to external resources and databases.
• Functional diversity analysis: Enables systematic analysis of evolutionarily related proteins that perform different functions within a shared 3D structure to identify common and subfamily-specific patterns associated with function-related structural elements.
• Statistical assessment and classification: Supports selection of alignment columns, parameter definition for scoring and statistical assessment of positions, and both automatic and manual classification of proteins into functional subfamilies.
• Rational design and directed evolution support: Identifies hot-spots for rational design and helps prepare focused libraries for directed evolution experiments.

Scientific Applications:

• Protein superfamily analysis: Conducts systematic analyses of protein superfamilies to elucidate sources of functional diversity.
• Residue identification for engineering: Identifies conserved and subfamily-specific residues to inform protein engineering and design strategies.
• Target structural element characterization: Pinpoints critical structural elements and residues that can guide rational drug design and functional studies.

Methodology:

Mustguseal automatically collects and superimposes functionally diverse homologs with high structural similarity and low sequence identity; users select columns from a multiple sequence alignment to propose subfamily classifications and estimate statistical significance; parameters are defined to enhance scoring and statistical assessment; the tool supports automatic or manual classification of proteins into functional subfamilies.