InterPro, progress and status in 2005

Abstract

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis

“…Every predicted gene was annotated using Double Affine Smith-Waterman alignments (http://www.timelogic.com/) with Swissprot and KEGG proteins. Protein domains were predicted using InterProScan 46,47 against various domain libraries (Prints, Prosite, PFAM, ProDom, SMART). Individual annotations have then been summarized according to Gene Ontology 48 , KOGs 18 and KEGG metabolic pathways 49 .…”

Fungal Genomic Annotation

“…Comparison with the specialized databases (e.g,, KEGG (Kanehisa et al 2004)) and functional classification allows one to map the predicted proteins onto metabolic pathways, Gene Ontology and KOG (Tatusov et al 2003) categories provide the user with multiple entry points into the annotation data. Although implementation of these steps varies, most of the pipeline utilizes Blast or Smith-Waterman searches to find all potential homologs, InterProScan (Mulder et al 2005) or various domain-search methods to predict domains, and public software (e.g., TMHMM (www.cbs.dtu.dk/services/TMHMM/), SignalP (Bendtsen et al 2004), and TargetP (Emanuelsson et al 2000)) for more specialized analysis.…”

“…For all genomes housed at MIPS the automated functional annotation system Pedant ) is used. The Pedant system performs Blast against known proteins from GenBank and the Funcat database , as well as predicting domains using Interpro (Mulder et al 2005) and other domain-specific databases. For the genomes S. cerevisiae, N. crassa, Ustilago myadis and Magnaporthe grisea, MIPS performs in-depth manual curation and verification of both gene structure (provided by the sequencing centers) and gene function.…”

Reconstructing protein complexes: From proteomics to systems biology

“…It is relatively simple to compare the frequency of any such tag to that expected within a random selection of proteins from the genome. There is a range of possible sources for these, but most of the commonly used annotations can be obtained directly through the InterPro database [10]. It is also useful to consider domains that are missing from the complex.…”