Positive selection in loops and turns within ancient protein domains. (A, C, and E) Ribbon diagrams show annotated structural prediction models of mouse proteins, generated automatically by FREEDA and visualized in PyMOL without manual modifications. Residues with the highest probability of having evolved under positive selection are colored magenta, and a subset of these is shown in snippets of the multiple sequence alignments in Murinae. (B, D, and F) Dark gray: highly conserved residues; gray: less conserved residues; white: non-synonymous substitutions. (A and B) MIS18β (MmMIS18β) shows the Yippee domain (orange) and two CXXC motifs (labeled by the user within the GUI, gray and yellow). The label for CXXC motif 1 is not visible to accommodate labeling of the R76 residue. The two CXXC motifs are enlarged with the R76 residue (magenta) within motif 1. (C and D) AURKC (MmAURKC) shows the protein kinase domain (orange) and activation loop (labeled by the user within the GUI, gray). A loop within the protein kinase domain is enlarged, with N150 shown in the multiple sequence alignment. (E and F) CENP-O (MmCENP-O) shows the C-terminal RWD domain (labeled by the user within the GUI, gray). The most likely adaptive residues of C-terminal RWD domain are shown in the multiple sequence alignment.