PIRSF whole-protein classification database

PIRSF whole-protein classification database classifies protein sequences by whole-protein evolutionary relationships to support functional and structural annotation of proteins.

Key Features:

• Hierarchical Classification: Employs a network-based hierarchy organizing sequences into superfamilies and subfamilies that reflect evolutionary lineage.
• Whole-Protein Focus: Classifies entire proteins rather than individual domains, enabling annotation of proteins lacking distinct domains.
• Homology and Homeomorphism Identification: Identifies homologous family members sharing common ancestry and homeomorphic members exhibiting full-length sequence similarity and shared domain architecture.
• Curated Datasets: Maintains preliminary clusters and curated families, with curated families annotated with family names, membership lists, parent–child relationships, domain architectures, optional descriptions, and bibliographies.
• Sequence-Level Analyses: Produces multiple sequence alignments and phylogenetic trees for curated families and records membership statistics and cross-references to other databases.
• UniProtKB Clustering: Clusters UniProtKB sequences into non-overlapping groups that reflect evolutionary history.

Scientific Applications:

• Phylogenetic Analysis: Facilitates analysis of phylogenetic profiles and evolutionary relationships among proteins.
• Functional Insights: Supports identification of functional convergence and divergence across protein families and annotation of generic biochemical functions and specific biological roles.
• Structural Relationships: Reveals relationships among homeomorphic families, domains, and structural classes to inform structural biology.

Methodology:

Clusters UniProtKB sequences into non-overlapping groups, builds a network hierarchy of superfamilies and subfamilies, identifies homologous and homeomorphic family members, and generates multiple sequence alignments and phylogenetic trees for curated families.