Figure 2

Phylogenetic tree of 186 annotated CIR and selected YIR proteins. Sequences of 186 CIR-BIR-YIR conserved domains of the putative CIR proteins and 14 different putative conserved domains of YIRs representing different YIR subfamily proteins were aligned using ClustalW2 [40] and a maximum likelihood tree was calculated using PhyML [41]. The cir subfamilies, indicated by the unrooted phylogenetic tree, are highlighted by different colours. Subfamily 1 (purple) and subfamily 2 (cyan) consist of CIR proteins very similar to well known YIR and BIR proteins of the PIR superfamily [20]. The remaining CIR proteins were more divergent, often due to highly variable insertions within the CIR-BIR-YIR conserved domain. These sequences were finally not assigned to any subfamily. The phylogenetic tree indicated that the YIR proteins cluster only with subfamily 2 and neither with subfamily 1 nor the large CIR proteins. The putative YIR domains are indicated by blue circles. The scale bar represents 0.5 substitutions per amino acid position. Black hexagons mark major branches with more than 95% support, the grey hexagon labels the minor branch with 92% support. See in Additional file 3 for identification of the individual proteins in each branch.