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. With regards to sequence similarity, sigma factors can be grouped into two classes: the sigma-54 and sigma-70 families. The sigma-70 family includes, in addition to the primary sigma factor, a wide variety of sigma factors. It also includes a divergent subfamily [2] that regulates gene encoding for proteins with extracytoplasmic function. The proteins that are currently known to belong to this sigma factor subfamily, known as ECF, are:

• algU, from Pseudomonas aeruginosa, which regulates genes for extracellular alginate biosynthesis.
• carQ, from Myxococcus xanthus, which is involved in the regulation of the light induced biosynthesis of membrane-localized carotenoids.
• cnrH, from Alcaligenes eutrophus plasmid pMOL28, which regulates the genes for a membrane-located efflux system that confers resistance to nickel and cobalt.
• fecI, from Escherichia coli, which regulates the fec genes for periplasmic iron dicitrate transport.
• hrpL, from Pseudomonas syringae, which is involved in the activation of hrp loci genes which are involved in plant pathogenicity.
• rpoE, from Escherichia coli, Salmonella typhimurium and Haemophilus influenzae. RpoE is involved in heat shock and oxidative stress response; it is believed to control protein processing in the extracytoplasmic compartment.
• rfaY, from Xanthomonas campestris, which is involved in lipopolysaccharide biosynthesis and pathogenicity.
• sigE, from Streptococcus coelicolor, which is involved in the transcription of the dagA gene coding for an extracellular agar-degrading enzyme.
• sigV, a Bacillus subtilis sigma factor.
• sigX, a Bacillus subtilis sigma factor.
• sigY, a Bacillus subtilis sigma factor.
• sigZ, a Bacillus subtilis sigma factor.
• HI1459, a hypothetical Haemophilus influenzae sigma factor.

As a signature pattern for the ECF subfamily we chose the region that corresponds to subdomain 2.2 in classical sigma-70 factors [3]; this region seems to be involved in the binding of the sigma factor to the core RNA polymerase.