InterPro as a new tool for complete genome analysis: An example of comparative analysis

InterPro, an integrated documentation resource for protein families, protein domains, and functional sites, was developed to amalgamate the individual efforts of the PROSITE, PRINTS, Pfam, and ProDom databases. InterPro can be used for the computational functional classification of newly determined amino acid sequences that lack biochemical characterization and for comparative genome analysis. InterPro contains over 3500 entries for more than 1 000 000 hits in SWISS-PROT and TrEMBL. The database is accessible for text-and sequence-based searches at http://www.ebi.ac.uk/interpro/. InterPro was used for the complete analysis of the proteome of the pathogenic microorganism Mycobacterium tuberculosis and the comparison with the predicted protein-coding sequences of the complete genomes of Bacillus subtilis and Escherichia coli. It was found that 64.8% of proteins in the proteome of M. tuberculosis matched InterPro entries and can be classified by their functions. The comparison with B. subtilis and E. coli provided information on the most common protein families and domains and on the most highly represented protein families in each organism. Thus, InterPro is a useful tool for general comparison of complete proteomes and their compositions.