SitEx

SitEx maps relationships between protein functional sites and exon-intron architecture to elucidate gene function, origin, and evolution.

Key Features:

• Functional Site Mapping: Contains data on 9,994 functional-site amino acid positions across 2,021 proteins from proteomes of 17 different organisms.
• Integration with BLAST: Incorporates BLAST to perform sequence similarity searches between a query protein and polypeptides encoded by individual exons stored in SitEx.
• Structural Analysis via 3DExonScan: Implements 3DExonScan to search for structural similarities between a given protein and polypeptides using superimposition techniques.
• Coding Feature Analysis: Analyzes coding features related to functional sites with respect to exon structure to identify exons involved in shuffling during protein evolution.
• Protein-Engineering Applications: Supports design and hypothesis testing for protein-engineering experiments by linking gene-exon structure to protein functional sites.

Scientific Applications:

• Gene-structure vs. protein-function analysis: Investigating the relationship between exon-intron organization and the location of functional sites within proteins.
• Evolutionary analysis: Tracing evolutionary processes that shape protein structures and functions by comparing functional site localization and exon arrangements.
• Protein engineering experiment design: Designing and prioritizing modifications to proteins for therapeutic or industrial applications based on exon-linked functional site information.

Methodology:

Sequence similarity searches using BLAST against polypeptides encoded by individual exons and structural comparisons via 3DExonScan employing superimposition techniques.