Figure 2.

Phylogenetic trees of the innate immune signaling adaptors and diagrams of their protein structures. The fish protein names are highlighted in blue (Dr [Danio rerio]) or green (Fr [Takifugu rubripes] and Tn [Tetraodon nigroviridis]). The numbers in the tree indicate the bootstrap values. Scale: interval of 0.1 amino acid substitutions. Hs, Homo sapiens, Mm, Mus musculus. Protein domains are shown as boxes based on identification by Pfam [55] or Smart [56]. Some domains were not recognized by these programs, although manual inspection indicated clear conservation of the domain within the protein family. These domains are also shown as boxes in the diagrams. The identities of the domains are listed at the bottom. Scale bar = 100 amino acids. The Tetraodon version of the Ikap (IKK [Inhibitor of nuclear factor-κB kinase] complex associated protein) gene contains two full repeats of the IKI3 domain. It is not clear whether this prediction is due to an error in the genome assembly or whether the gene does indeed contain an internal duplication covering the whole length of the gene found in other species. The two halves of the predicted gene were treated as separate peptides in the phylogenetic tree and the diagram.