Figure 1

Profiles of the Pho boxes constructed by phylogenetic footprinting. A. Multiple sequence alignments of the DNA binding domains of the SphR sequences of 16 sequenced cyanobacteria and that of the PhoB of E. coli, generated by the ClustalX program. The red dots show the positions in PhoB sequence of E. coli that are in direct contact with the Pho boxes of the DNA sequence in the crystal structure of PhoB-DNA complex. B. Phylogenetic relationships of SphR of the 16 genomes in our analyses. The tree was generated using the neighbor-joining method based on the multiple sequence alignments by the ClustalX program using the default settings, and is rooted at PhoB of E. coli K12. Scale bar, substitutions per position. C. Logo representation of the profile of the putative two tandem repeats of Pho boxes plus the linker found by phylogenetic footprinting. D. Logo representation of the profile of the combined putative Pho boxes of the two tandem repeats shown in panel (C). Logos were generated by the Weblogo server [32].