Figure 7

Unrooted phylogenetic tree (radial view) of the TyrP family of transport proteins. A multiple alignment was obtained by input of the indicated sequences into the ClustalW program (version 1.4). Manual alignment adjustments were made with the assistance of the BioEdit multiple alignment tool of Hall [61]. The refined multiple alignment was used as input for generation of a phylogenetic tree using the program packages PHYLIP [62] and PHYLO_WIN [63]. The neigbor-joining and Fitch programs were used to obtain distance-based trees. The distance matrix was obtained using Protdist with a Dayhoff PAM matrix. The Seqboot and Consense programs were then used to assess the statistical strength of the tree using bootstrap resampling. Neighbor-joining (shown) and Fitch trees yielded similar clusters and arrangement of taxa within them. Bootstrap values of 1,000 per 1,000 iterations (indicated with blue circles) supported the major nodes, one of which contains all of the chlamydial proteins. The experimentally documented E. coli proteins TyrP (tyrosine transport), Mtr (high-affinity tryptophan transport) and TraB (low-affinity tryptophan transport) are highlighted in yellow. See Table 2 for organism acronyms and gene identification numbers. In contrast to the two paralogs of tyrP present in C. pneumoniae CWLO29, as shown, some intra-species variation occurs in that C. pneumoniae J138 has only a single tyrP gene, and a small hypothetical gene is inserted between the two paralog tyrP genes of C. pneumoniae AR39.