Use and Importance of Protein Families
As the total number of sequenced proteins increases and interest expands in proteome analysis, there is an ongoing effort to organize proteins into families and to describe their component domains and motifs. Reliable identification of protein families is critical to phylogenetic analysis, functional annotation, and the exploration of diversity of protein function in a given phylogenetic branch. The Enzyme Function Initiative (EFI) is using protein families and superfamilies as the basis for development of a sequence/structure-based strategy for large scale functional assignment of enzymes of unknown function.
The algorithmic means for establishing protein families on a large scale are based on a notion of similarity. Most of the time the only similarity we have access to is sequence similarity.
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