<p>Some bacterial regulatory proteins activate the expression of genes frompromoters recognised by core RNA polymerase associated with the alternativesigma-54 factor. These have a conserved domain of about 230 residues involvedin the ATP-dependent [<cite idref="PUB00002228"/>, <cite idref="PUB00004389"/>] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [<cite idref="PUB00000103"/>] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction [<cite idref="PUB00001221"/>]. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.</p>