PIRSF Family Classification System for Protein Functional and Evolutionary Analysis

By Anastasia N. Nikolskaya, C. Arighi, Hongzhan Huang, W. C. Barker, Cathy H. Wu. 2006

91 citations recorded by the source corpus.

The PIRSF protein classification system (http://pir.georgetown.edu/pirsf/) reflects evolutionary relationships of full-length proteins and domains. The primary PIRSF classification unit is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). PIRSF families are curated systematically based on literature review and integrative sequence and functional analysis, including sequence and structure similarity, domain architecture, functional association, genome context, and phyletic pattern. The results of classification and expert annotation are summarized in PIRSF family reports with graphical viewers for taxonomic distribution, domain architecture, family hierarchy, and multiple alignment and phylogenetic tree. The PIRSF system provides a comprehensive resource for bioinformatics analysis and comparative studies of protein function and evolution. Domain or fold-based searches allow identification of evolutionarily related protein families sharing domains or structural folds. Functional convergence and functional divergence are revealed by the relationships between protein classification and curated family functions. The taxonomic distribution allows the identification of lineage-specific or broadly conserved protein families and can reveal horizontal gene transfer. Here we demonstrate, with illustrative examples, how to use the web-based PIRSF system as a tool for functional and evolutionary studies of protein families.

Subfields: Molecular Biology

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Citations in the corpus

UniProt: the universal protein knowledgebase (2016, methodology): “InterPro integrates signatures from the HAMAP (19) and PIRSF (20) projects within the UniProt Consortium.”
MicrobesOnline: an integrated portal for comparative and functional genomics (2009, methodology): “FastBLAST and FastHMM (13) are used to search against the TIGRFAM (14), Superfamily (15), SMART (16), Pfam (17), Panther (18), PirSF (19), Gene3D (20), COG (21), PDB (22) and UniProt (23) databases.”
Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation (2011, background): “For example, for hierarchical protein family classification [6] and functional annotation one may choose a larger or smaller set of representative proteomes depending on the phyletic distribution of the protein family members and sequence variation.”
InterPro in 2022 (2022, unknown): “It is now also available for PANTHER, PIRSF, SFLD and TIGRFAMs signatures.”
The InterPro protein families database: the classification resource after 15 years (2014, background): “From an initial core of four source databases (Pfam (1), PRINTS (2), PROSITE (3) and ProDom (4)), InterPro has expanded, so that it now integrates signatures from seven additional repositories: CATH-Gene3D (5), HAMAP (6), PANTHER (7), PIRSF (8), SMART (9), SUPERFAMILY (10) and TIGRFAMs (11).”
InterPro in 2011: new developments in the family and domain prediction database (2011, methodology): “The InterPro database integrates predictive models, or signatures, from multiple, diverse source repositories: Pfam (1), PRINTS (2), PROSITE (3), SMART (4), ProDom (5), PIRSF (6), SUPERFAMILY (7), PANTHER (8), CATHGene3D (9), TIGRFAMs (10) and HAMAP (11).”
InterPro: the integrative protein signature database (2008, unknown): “Since then, six other member databases have also joined and their data has been integrated: SMART (6), TIGRFAMs (7), PIRSF ( 8 ), SUPERFAMILY (9), PANTHER (10) and Gene3D (11).”
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018, methodology): “Launched in 1999, InterPro is derived from 14 different specialist member databases: CATH-Gene3D (2), the Conserved Do-mains Database (CDD) (3), HAMAP (4), PANTHER (5), Pfam (6), PIRSF (7), PRINTS (8), ProDom (9), PROSITE Patterns (10), PROSITE Profiles (10), SMART (11), the Structure–Function Linka”