FIG 5.

DNase I footprinting of VpsR with and without c-di-GMP at P_rbmA, P_rbmF, and P_vpsU. (A) DNase I footprints of the template strand were obtained using DNA alone or DNA incubated with VpsR without or with 50 μM c-di-GMP as indicated. VpsR protection is indicated to the right of each image with a dotted line. (B) Sequences of determined VpsR protection sites at P_rbmA, P_rbmF, P_vpsU, and P_vpsL aligned to indicate sequence similarity. The consensus sequence underneath was determined from the presence of a base in at least 3 out of the 4 binding sites. A previously reported Logo sequence (30) is shown for comparison.