Figure 3

Phylogenetic relationships of concatenated protein sequences of RcGTA-like genes 12-15 from bacteriophages and bacteria. Amino acid sequences were aligned using Clustal X2 [31] and phylogenetic analysis was performed using the Mega 4.0 software [32]. Neighbor-joining tree was constructed using the minimum evolution distance with default parameters. Bootstrap resamplings were performed for 1,000 replications and the values (> 50%) for major branches were shown on the edge of the circular tree, except one in the center indicated by an arrow. Highly supported major subclusters were separated by dashed lines. The numbers in the end of names of bacteria (P. denitrificans PD1222, R. sphaeroides ATCC 17025 and O. carboxidovorans OM5) indicate multiple RcGTA-like elements in one bacterial genome. The four gene clusters in group II only contain RcGTA-like genes 12 to 15. Both PD1222 and ATCC 17025 also contain a complete RcGTA-like gene cluster (in group I). The scale bar represents 0.2 amino acid substitutions per site.