Alignment of the Caenorhabditis protist-type lysozyme amino acid sequences. The figure only shows the top quarter of the alignment. The complete alignment is given in Additional file 1. In both cases, black lines at the beginning of the alignment denote the inferred signal peptides. Alignment 4 (see methods and results) includes all taxa and the entire protein sequences. Vertical black lines with arrows below the alignment indicate the regions used for specific DNA sequence analysis of all protist-type lysozymes (alignment 5). Vertical black lines with arrows above the alignment indicate those regions analyzed for the clade 1 lysozymes (alignments 6 and 7 for protein and DNA sequences, respectively). Clade 2 lysozyme analysis was based on complete sequences (alignments 8 and 9 for protein and DNA sequences, respectively). Note that all alignments are subsets of alignment 4, i.e. the position of indels is identical. The red box and arrow indicate the sequence position, which was inferred to be under positive selection for the clade 1 lysozymes.
Schulenburg and Boehnisch BMC Evolutionary Biology 2008 8:114 doi:10.1186/1471-2148-8-114