Quantitative sequence-function relationships in proteins based on gene ontology |
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| Authors: | Vineet Sangar Daniel J Blankenberg Naomi Altman Arthur M Lesk |
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| Institution: | (1) Department of Biochemistry and Molecular Biology, Center of Computational Biology and Genomics, The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA;(2) Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA |
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| Abstract: | Background The relationship between divergence of amino-acid sequence and divergence of function among homologous proteins is complex.
The assumption that homologs share function – the basis of transfer of annotations in databases – must therefore be regarded
with caution. Here, we present a quantitative study of sequence and function divergence, based on the Gene Ontology classification
of function. We determined the relationship between sequence divergence and function divergence in 6828 protein families from
the PFAM database. Within families there is a broad range of sequence similarity from very closely related proteins – for
instance, orthologs in different mammals – to very distantly-related proteins at the limit of reliable recognition of homology. |
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