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* Bacterial regulatory proteins, luxR family signature *
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The many bacterial transcription regulation proteins which bind DNA  through a
'helix-turn-helix' motif can  be  classified into subfamilies  on the basis of
sequence similarities.  One of these subfamilies  groups  together [1,2,3] the
following proteins  (references  are  only  provided  for  recently determined
sequences):

 - bvgA; Bordetella pertussis; plays a role in virulence.
 - comA; Bacillus subtilis; plays a role in the expression of  late-expressing
   competence genes.
 - degU; Bacillus subtilis; activates extracellular proteases genes.
 - evgA; Escherichia coli.
 - expR; Erwinia carotovora; acts in  virulence (soft rot disease) through the
   activation of genes for plant tissue macerating enzymes.
 - fimZ; Escherichia coli and Salmonella typhimurium.
 - fixJ; Rhizobiaceae; induces the expression of nifA and fixN.
 - gerE; Bacillus subtilis; regulation of spore formation.
 - gacA; Pseudomonas fluorescens;  involved  in  the  regulation  of secondary
   metabolism.
 - glpR; Pseudomonas aeruginosa;  activates  genes of the  glycerol  metabolic
   pathway.
 - lasR; Pseudomonas aeruginosa; activates the elastase gene (lasB).
 - luxR; Vibrio fischeri; activates the bioluminescence operon.
 - malT; Escherichia coli; activates  the maltose  operon.  MalT binds ATP and
   maltotriose.
 - narL and narP; Escherichia coli; activate the nitrate reductase operon.
 - nodW, Rhizobiaceae; probably regulates the transcription of genes  involved
   in the nodulation process.
 - rcsA, Enterobacteria; activates genes for capsular polysaccharide synthesis.
 - rcsB; Enterobacteria; involved in the regulation of capsular polysaccharide
   synthesis.
 - rhiR, Rhizobiaceae; activates the rhiABC operon.
 - sdiA; Escherichia coli; activates the ftsQAZ operon.
 - traR; Agrobacterium tumefaciens;  involved  in the regulation of Ti plasmid
   transfer.
 - uhpA; Escherichia coli and Salmonella typhimurium; activates  the uhpT gene
   for hexose phosphate transport.
 - uvrY, an Escherichia coli hypothetical protein.
 - A hypothetical transcriptional regulator  encoded  downstream of  the trpAB
   genes in Pseudomonas aeruginosa.

The size of these proteins range from 74 amino acids (gerE) to 901 (malT), but
the majority  of  them  have  from  190  to  230 residues. On the basis of the
mechanism by which they are activated they can be classified into two classes:

 - A  class of regulators which belong to a two-component sensory transduction
   system where the protein  is activated by its phosphorylation, generally on
   an aspartate  residue,  by a transmembrane kinase. The proteins that belong
   to this  class  are:  bvgA, comA, degU, evgA, fimZ, fixJ, gacA, glpR, narL,
   narP, nodW, rcsB and uhpA.
 - A  class  of  regulators  which  is activated when bound to the autoinducer
   molecule N-(3-oxohexanoyl)-L-homoserine  lactone  (OHHL)  [4]. The proteins
   that belong to this class are: expR, luxR and traR.

The 'helix-turn-helix' DNA-binding  motif  of these proteins is located in the
C-terminal section  of the sequences.  The pattern  we  use  to  detect  these
proteins starts  three residues downstream of the N-terminal  extremity of the
helix-turn-helix motif  and  extend  five  residues upstream of its C-terminal
extremity.

-Consensus pattern: [GDC]-x(2)-[NSTAV]-x(2)-[IV]-[GSTA]-x(2)-[LIVMFYWC]-x-
                    [LIVMFYWCR]-x(3)-[NST]-[LIVM]-x(5)-[NRHSA]-[LIVMTA]-x(2)-K
-Sequences known to belong to this class detected by the pattern: ALL,  except
 for traR.
-Other sequence(s) detected in SWISS-PROT: NONE.
-Last update: June 1994 / Pattern and text revised.

[ 1] Henikoff S., Wallace J.C., Brown J.P.
     Meth. Enzymol. 183:111-132(1990).
[ 2] Stout V., Torres-Cabassa A., Maurizi M.R., Gutnick D., Gottesman S.
     J. Bacteriol. 173:1738-1747(1991).
[ 3] Kahn D., Ditta G.
     Mol. Microbiol. 5:987-997(1991).
[ 4] Swift S., Winson M.K., Chan P.F., Bainton N.J., Birdsall M.,
     Reeves P.J., Rees C.E.D., Chhabra S.R., Hill P.J., Throup J.P.,
     Bycroft B.W., Salmond G.P.C., Williams P., Stewart G.S.A.B.
     Mol. Microbiol. 10:511-520(1993).