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* Sigma-54 interaction domain signatures *
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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.
 - 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.
 - 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.

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.

-Consensus pattern: [LIVMFY](3)-x-G-[DE]-[ST]-G-[ST]-G-K-x(2)-[LIVMFY]
-Sequences known to belong to this class detected by the pattern: A majority.
-Other sequence(s) detected in SWISS-PROT: NONE.

-Consensus pattern: G-x-[LIVMF]-x(2)-A-[DNEQASH]-[GNEK]-G-[STI]-[LIVMFY](3)-D-
                    E-[LIVM]
-Sequences known to belong to this class detected by the pattern: A majority.
-Other sequence(s) detected in SWISS-PROT: NONE.

-Consensus pattern: [FYW]-P-[GS]-N-[LIVM]-R-[EQ]-L-x-[NHAT]
-Sequences known to belong to this class detected by the pattern: Almost   all
 of these proteins.
-Other sequence(s) detected in SWISS-PROT: NONE.

-Last update: June 1994 / Patterns and text revised.

[ 1] Morrett E., Segovia L.
     J. Bacteriol. 175:6067-6074(1993).
[ 2] Austin S., Kundrot C., Dixon R.
     Nucleic Acids Res. 19:2281-2287(1991).
[ 3] Albright L.M., Huala E., Ausubel F.M.
     Annu. Rev. Genet. 23:311-336(1989).
[ 4] Austin S., Dixon R.
     EMBO J. 11:2219-2228(1992).