Phylogenetic tree of streptococcal and staphylococcal SAgs and SSL nucleotide sequences. The phylogenetic tree was constructed using the Bayesian MCMC method, with 100,000 generations. The resultant potential scale reduction factor was 1.078. Essentially the same result was obtained by changing the number of generations and by using the amino acid evolution model (data not shown). The nucleotide sequences used for alignment are shown in Additional file9. The resulting phylogenetic tree was composed of three clades, with clade I including only streptococcal SAgs, clade II including only staphylococcal SSLs, and clade III including SAgs from both species. Orthologous gene products, including SpeG and SMEZ in clade I, SSL-like proteins in clade II and SElW in clade III, are emphasized.