Protein Domains and Motifs
The protein family concept was thought of at a time when very few protein structures and sequences were known. Currently in protein science it is known that many proteins have multiple independent structural and functional units and different domains in a protein have evolved independently due to evolutionary shuffling. Because of this, recently there has been a change of focus on families of protein domains. Functional constraints have allowed for the rate of evolution among proteins to vary. Regions of proteins that are functionally constrained have evolved more slowly than unconstrained regions (eg.surface loops) which in turn give rise to blocks of conserved sequence when the sequences of protein families are compared. These blocks are commonly referred to as motifs.
Evolution of Protein Families
Protein families arise in two ways; 1) The parent species separates into two genetically different species. Each species of protein independently accumulates variations via mutations therefore gives rise to a family of orthologous proteins with conserved sequence motifs. 2) Gene duplication can create a second copy of a gene (paralog). The original gene is able to still perform its function and now the duplicated gene is able to diverge and acquire new functions via mutation.
Importance of Protein Families
Identification of protein families is essential to phylogenetic analysis, functional annotation and exploration of protein function diversity in a given phylogenetic branch.