Phylogenetic trees showing the relationships between the five duplicated gene cluster regions. (a) Neighbor-joining phylogenetic tree of all available protein sequences of the ATP/GTP-binding protein family (family D in Table 2) with the protein ortholog of Streptomyces coelicolor as the outgroup. This tree is representative of all the trees drawn using the six most conserved proteins in these regions as well as using the protein ortholog of Corynebacterium diphtheriae as the outgroup. (b) Neighbor-joining phylogenetic tree of all six conserved proteins from the M. tuberculosis gene clusters combined into one protein per region. The combined protein of C. diphtheriae was used as the outgroup. (c) Neighbor-joining phylogenetic tree of the ESAT-6 and CFP-10 protein families combined (family G and H), using the combined protein of C. diphtheriae as the outgroup.