Chromo domain comparison between selected Su(var)3-9, HP1 and Polycomb proteins. A. Alignment of consensus sequences. Absolute identical residues are black boxed, 75–99%-identical ones are dark grey boxed and 74–50% identical amino acid positions are light grey boxed for each class of orthologues. Functionally important residues are marked by a filled triangle (methyl lysine recognition), a filled quad (histone H3K9/K27 side chain or backbone recognition) or a filled circle (recognition of the lysine 2 of the H3 peptide) according to Nielsen et al. . An arginine (position 43 of the alignment, marked with an empty circle), which is specifically conserved in Polycomb proteins, is important for preference of H3K27me against H3K9me . Determined secondary structures of HP1  and Clr4p  are given beneath the alignment. B. Numbers of identical consensus residues between Su(var)3-9, HP1 and Polycomb chromo domains. C. Unrooted neighbour joining tree of selected Su(var)3-9, HP1 and Polycomb chromo domains from vertebrates and insects. Only species which have orthologues of all three proteins are included. Abbreviations: Aga, Anopheles gambiae; Ame, Apis mellifera; Dme, Drosophila melanogaster; Dps, Drosophila pseudoobscura; Dre, Danio rerio; Hsa, Homo sapiens; Mmu, Mus musculus; Xla, Xenopus laevis.