Evolutionary classification

The evolutionary classification has a rational basis, since, to date, the catalytic mechanisms for most peptidases have been established, and the elucidation of their amino acid sequences is progressing rapidly. This classification has the major advantage of fitting well with the catalytic types, but allows no prediction about the types of reaction being catalyzed. For example, some families contain endo- and exopeptidases, e.g., SB-S8, SC-S9 and CA-Cl. Other families exhibit a single type of specificity, e.g., all families in clan MB are endopeptidases, family MC-M14 is almost exclusively composed of carboxypeptidases, and family MF-M17 is composed of aminopeptidases. Furthermore, the same enzyme specificity can sometimes be found in more than one family, e.g., D-Ala-D-Ala carboxypeptidases are found in four different families (SE-S11, SE-S12, SE-S13, and MD-M15). 

Dietmann, S., et al., A fully automatic evolutionary classification of protein folds Dali Domain Dictionary version 3. Nucleic Acids Res, 2001. 29(1) p. 55-7. 

Table 12.5-2. Evolutionary classification of peptidases into families and clans based on primary and teriary structure.

Since the publication over a quarter of a century ago of my original paper Philosophical Foundations of Classical Evolutionary Classification, I have become increasingly interested in systems of explanation in science and especially in evolutionary biology (see Bock, 1978, 1981, 1988, 1991, 1992, 2000 Szalay and Bock, 1991). This was prompted by concerns in 1974 when I introduced into systematics Popper s ideas that the nature of explanation and the methods of testing theoretical statements in classification and phylogeny do not fit easily or at all into the Popperian mold. 

Bock, W.J., Philosophical foundations of classical evolutionary classification, Syst. Zoo/., 22, 375-392, 1974. 

Bock, W.J.. Foundations and methods of evolutionary classification, in Major Patterns in Vertebrate Evolution, Hecht, M.K., Goody, P.C., and Hecht B.M., Eds., NATO Advanced Study Institute, Series A, Plenum, New York, 1977, pp. 851-895. 

Bock, W.J., Functional-adaptive analysis in evolutionary classification. Am. Zool., 21, 5-20, 1981. 

Darwin, Charles, 1 classification, 54 embryology, 263 evolutionary classification, 49 idea of evolution, 9 subjective view of species, 9 theories, 50-51, 52, 63 theory of descent, 70 theory of evolution, 80,149, 182 Data matrix... 

Additionally, there are a number of MMPs, which do not fit exactly in this classification but are ordered with regard to structural similarities, evolutionary classification, or differential expression (Chang and Werb 2001 Ra and Parks 2007). 

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