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Molecular Biology and Evolution, Vol 9, 152-167, Copyright © 1992 by Society for Molecular Biology and Evolution

ORIGINAL ARTICLE

Significant similarity and dissimilarity in homologous proteins

S Karlin, V Brendel and P Bucher
Department of Mathematics, Stanford University, California 94305.

Common practice emphasizes significant sequence similarities between different members of protein families. These similarities presumably reflect on evolutionary conservation of structurally and functionally essential residues. The nonconserved regions, on the other hand, may be either selectively neutral or differentiated. We propose several distributional sequence statistics (e.g., clustering of charged residues, compositional biases, and repetitive patterns) as indicators of differentiation events. These ideas are illustrated with various examples, including comparisons among G protein-coupled receptors, herpesvirus proteins, and GTPase-activating proteins.
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