Pii: S0378-1119(02)00401-8

SET-domain (SET: Su(var)3-9, E(z) and Trithorax)-containing proteins were collected through sequence searches of the available databases. After removing redundancies, the proteins belonging to three families, SU(VAR)3-9, E(Z) and TRITHORAX, were selected. Analysis of the relationship between the different members is based on pairwise alignment, compilation, and comparison of their SETdomains. The level of homology of the SET-domains defined the distribution of the proteins into families and into clades within the families. The architecture of the entire protein supported the distribution pattern built upon SET-domain similarity. Parallel cladistic and proteinarchitecture analyses outlined two plausible criteria for predicting function. q 2002 Published by Elsevier Science B.V.