Sigma factors [1] are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes: the sigma-54 and sigma-70 families. The sigma-70 family has many different sigma factors (see the relevant entry <PDOC00592>). The sigma-54 family consists exclusively of sigma-54 factor [2,3] required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10,-35 sequences recognized by the major sigma factors. The sigma-54 factor is also characterized by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences.

Structurally sigma-54 factors consist of three distinct regions:

• A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif.
• A region of variable length which is not well conserved.
• A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known.

We developed two signature patterns for this family of sigma factors. The first starts two residues before the N-terminal extremity of the helix-turn-helix region and ends two residues before its C-terminal extremity. The second is the conserved octapeptide. A profile has also been designed that covers the whole C-terminal region.