Some bacterial regulatory proteins activate the expression of genes from promoters recognized by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent [1,2] interaction with sigma-54. This domain has been found in the proteins listed below:

• acoR from Alcaligenes eutrophus, an activator of the acetoin catabolism operon acoXABC.
• algB from Pseudomonas aeruginosa, an activator of alginate biosynthetic gene algD.
• dctD from Rhizobium, an activator of dctA, the C4-dicarboxylate transport protein.
• dhaR from Citrobacter freundii, a regulator of the dha operon for glycerol utilization.
• fhlA from Escherichia coli, an activator of the formate dehydrogenase H and hydrogenase III structural genes.
• flbD from Caulobacter crescentus, an activator of flagellar genes.
• hoxA from Alcaligenes eutrophus, an activator of the hydrogenase operon.
• hrpS from Pseudomonas syringae, an activator of hprD as well as other hrp loci involved in plant pathogenicity.
• hupR1 from Rhodobacter capsulatus, an activator of the [NiFe] hydrogenase genes hupSL.
• hydG from Escherichia coli and Salmonella typhimurium, an activator of the hydrogenase activity.
• levR from Bacillus subtilis, which regulates the expression of the levanase operon (levDEFG and sacC).
• nifA (as well as anfA and vnfA) from various bacteria, an activator of the nif nitrogen-fixing operon.
• ntrC, from various bacteria, an activator of nitrogen assimilatory genes such as that for glutamine synthetase (glnA) or of the nif operon.
• pgtA from Salmonella typhimurium, the activator of the inducible phospho- glycerate transport system.
• pilR from Pseudomonas aeruginosa, an activator of pilin gene transcription.
• rocR from Bacillus subtilis, an activator of genes for arginine utilization
• tyrR from Escherichia coli, involved in the transcriptional regulation of aromatic amino-acid biosynthesis and transport.
• wtsA, from Erwinia stewartii, an activator of plant pathogenicity gene wtsB.
• xylR from Pseudomonas putida, the activator of the tol plasmid xylene catabolism operon xylCAB and of xylS.
• Escherichia coli hypothetical protein yfhA.
• Escherichia coli hypothetical protein yhgB.

About half of these proteins (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [3] 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 [4]. 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; we have developed signature patterns for both motifs. Other regions of the domain are also conserved. We have selected one of them, located in the C-terminal section, as a third signature pattern.