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Figure 1 | BMC Bioinformatics

Figure 1

From: Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores

Figure 1

Aging properties of amino acids. Protein sequences are considered as systems, which components are amino acids. Over time, either amino acids are conserved (similarity of a residue with its descendant is that of identity, diagonal term of a substitution matrix) or modified due to random DNA mutations. Similarity decreases therefore with time, since no similarity is higher than that of identity. When the similarity falls below a threshold that is necessary for the residue to operate according to a standard (functional conservation), the component is damaged. (A) Score distribution corresponding to valine substitution. In this case, the score distribution is exponential, suggesting that valine (V) is a non-aging component. Based on BLOSUM62, residues of this type are V, F, P, W, Y, E, G, H, I, L, K, R, N, D and C (B) Score distribution corresponding to threonine substitution. The score distribution shows a peak, indicating a probable accelerated process of aging (functional damage) when the residue is substituted by random mutation in some other amino acids. Based on BLOSUM62, residues of this type are T, S, M, A and Q. (C) Score distribution in the BLOSUM62 similarity matrix. The complete distribution in the BLOSUM62 matrix is exponential (0.287.exp(-0.287.(s+4))), supporting a general model of amino acids as nonaging components. The exponential law for positive scores is characterized by the same parameter (╬╗' = 0.287). The original residue is termed i; its descent is termed j.

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