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  • Title: [Graphic identification of conservative and variable segments in the amino acid sequences of homologous proteins].
    Author: Kostetskiĭ PV, Vladimirova RR.
    Journal: Bioorg Khim; 1989 Nov; 15(11):1573-6. PubMed ID: 2624595.
    Abstract:
    An algorithm is presented for localizing variable and constant regions in homologous protein sequences. A set of aligned protein sequences is divided into two groups consisting of m and n sequences. Each group contains sequences of most related species. Value of the position dissimilarity of proteins from different groups of m and n sequences is defined as a number of failures to coincide in comparison with all possible mXn pairs of amino acid residues in the position (each from different group) divided by mXn. The position dissimilarity value of m protein sequences within a group is defined as the number of failures to coincide in comparison with all possible mX X(m-1)/2 pairs of amino acid residues divided by mX(m-1)/2. Ten position average of dissimilarity values is plotted vs. the first position number. Area of the figure included between the profile of dissimilarity values and its mean value line characterizes the overall irregularity of amino acid substitutions along the protein sequences. If the area value is greater than the average area for 1000 random profile by more than two standard deviation units, the profile extrema containing the "surplus" of area are cut off. The cut off stretches are likely to be variable and constant regions. In case of "between groups" comparisons it is found that the overall irregularity of amino acid substitutions is very high for all considered families of proteins; phospholipases A2, aspartate aminotransferases, alpha-subunits of Na+,K(+)-ATPase, L- and M-subunits of photosynthetic bacteria photoreaction centre, human rhodopsins.
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