Amino acid substitution during functionally constrained divergent evolution of protein sequences
نویسندگان
چکیده
منابع مشابه
Amino acid substitution matrices from protein blocks.
Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more t...
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We derive an analytic expression for site-specific stationary distributions of amino acids from the structurally constrained neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that we obtain have a Boltzmann-like shape, and their effective temperature parameter, measuring the limit of divergent evolutionary changes at a given site, can ...
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Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids being exchanged. Recent developments have shown that models which allow for amino acid pairs to have independent rates of substitution offer improved fit over single rate model...
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متن کاملAmino Acid Substitution Scores
GNPKVKAH Here we discuss standard ways of assigning a score to each amino acid pair, i.e., to each possible column of a gap-free pairwise protein alignment. Examples of such scoring matrices include the PAM30, PAM70, BLOSUM80, BLOSUM62 and BLOSUM45 matrices that are available on NCBI’s blastp server. Such scores are appropriate for comparing two sequences about which we have no other informatio...
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ژورنال
عنوان ژورنال: "Protein Engineering, Design and Selection"
سال: 1994
ISSN: 1741-0126,1741-0134
DOI: 10.1093/protein/7.11.1323