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MBE Advance Access originally published online on May 3, 2006
Molecular Biology and Evolution 2006 23(7):1406-1413; doi:10.1093/molbev/msl002
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Prediction of Function Divergence in Protein Families Using the Substitution Rate Variation Parameter Alpha

Saraswathi Abhiman, Carsten O. Daub and Erik L. L. Sonnhammer

Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden

E-mail: Abhiman.Saraswathi{at}cgb.ki.se.

Protein families typically embody a range of related functions and may thus be decomposed into subfamilies with, for example, distinct substrate specificities. Detection of functionally divergent subfamilies is possible by methods for recognizing branches of adaptive evolution in a gene tree. As the number of genome sequences is growing rapidly, it is highly desirable to automatically detect subfamily function divergence.

To this end, we here introduce a method for large-scale prediction of function divergence within protein families. It is called the alpha shift measure (ASM) as it is based on detecting a shift in the shape parameter (alpha [{alpha}]) of the substitution rate gamma distribution. Four different methods for estimating {alpha} were investigated. We benchmarked the accuracy of ASM using function annotation from Enzyme Commission numbers within Pfam protein families divided into subfamilies by the automatic tree-based method BETE.

In a test using 563 subfamily pairs in 162 families, ASM outperformed functional site-based methods using rate or conservation shifting (rate shift measure [RSM] and conservation shift measure [CSM]). The best results were obtained using the "GZ-Gamma" method for estimating {alpha}. By combining ASM with RSM and CSM using linear discriminant analysis, the prediction accuracy was further improved.

Key Words: protein evolution • adaptive evolution • enzyme • protein function • protein subfamily • substitution rates • gamma distribution • alpha parameter • function shift


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