Fig. 4.

Alignments of chromo domains in dictyostelid and protostelid Skipper retrotransposons. Alignments were generated with ClustalX. Shading is to a 50 % consensus and was generated with BoxShade. Black boxes indicate invariant amino acids, and gray boxes represent similar amino acids. The corresponding sequences of the chromo domain (CHD) and the “shadow” chromo domain (CSD) of D. discoideum heterochromatin protein 1 (HcpA) [38] are shown for comparison. Red dots depict aromatic cage residues present in canonical chromo domains [39]. The alignment is separated into retrotransposons containing canonical (group I) chromo domains (Skipper-1 elements) and group II chromo domains (Skipper-2 elements) in which the first and third aromatic amino acid of the cage are diverged (indicated by open circles). Dd: Dictyostelium discoideum; Dp: D. purpureum; Dl: D. lacteum; Pp: Polysphondylium pallidum; Df: D. fasciculatum; Pf: Protostelium fungivorum