Phylogenetic analysis of the amino acid sequence of the hydrophobic domains of the Cpn 1054 gene family obtained from C. pneumoniae CWL029. Hydrophobic domains of Cpn186, 284, 285, 829, and 830 are included in this figure as outliers. The outliers represent candidate Inc proteins that contain a bilobed hydrophobic domain similar to that encoded by Cpn 1054 gene family members, but that share no obvious amino acid similarity with family members. Multiple sequence alignments were performed and analyzed using CLUSTALW and PAUP* programs. Distance matrices were inferred by neighbor-joining to estimate evolutionary distances. Bootstrap values (based on 1000 replicates) are represented at each node. Scale bar indicates 0.1 change per nucleotide.