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PR00045

Identifier
SIGMA54FCT  [View Relations]  [View Alignment]  
Accession
PR00045
No. of Motifs
4
Creation Date
25-MAY-1993  (UPDATE 07-JUN-1999)
Title
Sigma-54 factor signature
Database References

PROSITE; PS00717 SIGMA54_1; PS00718 SIGMA54_2
BLOCKS; BL00717
PFAM; PF00309 Sigma54_factors
INTERPRO; IPR000394
Literature References
1. SASSE-DWIGHT, S. AND GRALLA, J.D.
Role of the eukaryotic type functional domains found in prokaryotic
enhancer receptor factor sigma 54.
CELL 62(5) 945-954 (1990).
 
2. DEBARBOUILLE, M., MARTIN-VERSTRAETE, I., KUNST, F. AND RAPOPORT, G.
The Bacillus subtilis sigL gene encodes an equivalent of sigma 54 from Gram
negative bacteria.
PROC.NATL.ACAD.SCI.U.S.A. 88(20) 9092-9096 (1991).
 
3. BRUN, Y.V. AND SHAPIRO, L.
A temporally controlled sigma factor is required for polar morphogenesis
and normal cell division in caulobacter.
GENES DEV. 6 2395-2408 (1992).
 
4. INOUYE, S., YAMADA, M., NAKAZAWA, A. AND NAKAZAWA, T.
Cloning and sequence analysis of the ntrA (rpoN) gene of Pseudomonas 
putida.
GENE 85 145-152 (1989).

Documentation
Sigma factors are bacterial transcription factors that promote the binding 
of RNA polymerase to promoters containing their recognition sites. This 
binding is facilitated by 2 leucine zipper regions [1], which help to
position the polymerase-sigma factor complex over the correct DNA region.
This region is then `melted' by the acidic domain of the sigma factor,
allowing transcription to take place.
 
Most bacteria express a multiplicity of sigma factors. Two of these,
sigma-70 (generally known as the major or primary sigma factor) and 
sigma-54, direct the transcription of a wide variety of genes: the others
(known as alternative sigma factors) are required for the transcription of 
specific subsets of genes. 
 
Sigma-54 differs from sigma-70 in that it allows regulation of gene
expression by remotely-bound enhancer molecules upstream from the promoter.
These enhancers are often phosphorylated by a sensor protein before they
can activate transcription. Binding of the enhancers activates the pre-
bound polymerase-sigma factor complex, which then `melts' the DNA at the
transcriptional start site, allowing transcriptional activation. Thus the
RNA polymerase-sigma-54 complex acts as a receptor complex for receipt of
the melting signal from the remotely-bound activator.
 
Genes that are activated by sigma-54 are, in general, involved in nitrogen
source assimilation [2] in Gram-negative bacteria, although genes involved
in forming the structure of flagellae [3] and degradation of toluene and
xylenes [4] have also been found to require the presence of sigma-54. The
main feature of these genes is that they lack the usual -10 and -35
sequences recognised by factor 70, but have strongly conserved -12 and
-24 sequences.
 
SIGMA54FCT is a 4-element fingerprint that provides a signature for the 
sigma-54 proteins. The fingerprint was derived from an initial alignment
of 5 sequences: motif 2 spans the ATP-binding region (the so-called P-loop)
(cf. PROSITE pattern SIGMA54_1 (PS00717)), and motif 4 encodes a second
ATP-binding region (cf. PROSITE pattern SIGMA54_2 (PS00718)). Two
iterations on OWL19.1 were required to reach convergence, at which point
a true set comprising 16 sequences was identified. Several partial matches
were also found that lack matches with motif 3. 
 
An update on SPTR37_9f identified a true set of 34 sequences, and 3
partial matches.
Summary Information
  34 codes involving  4 elements
3 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
434343434
33303
20000
1234
True Positives
O08352        O24775        O30651        O32343        
O54393 O66858 O69080 O69778
O84615 O86452 Q59085 Q59751
RP54_ACICA RP54_ALCEU RP54_AZOCA RP54_AZOVI
RP54_BACSU RP54_BRAJA RP54_CAUCR RP54_ECOLI
RP54_HELPY RP54_KLEPN RP54_PSEAE RP54_PSEPU
RP54_RHILP RP54_RHIME RP54_RHISN RP54_RHOSH
RP54_SALTY RP54_THIFE RP54_VIBAN RP54_XANCV
RP55_BRAJA RP55_RHIME
True Positive Partials
Codes involving 3 elements
O51406 RP54_RHOCA RP54_TREPA
Sequence Titles
O08352      RNA POLYMERASE SIGMA-54 FACTOR - LISTERIA MONOCYTOGENES. 
O24775 RNA POLYMERASE SIGMA-54 FACTOR - VIBRIO ALGINOLYTICUS.
O30651 SIGMA54 - VIBRIO CHOLERAE.
O32343 RNA POLYMERASE SIGMA-54 FACTOR - CAULOBACTER CRESCENTUS.
O54393 RNA POLYMERASE SIGMA-54 FACTOR - MYXOCOCCUS XANTHUS.
O66858 RNA POLYMERASE SIGMA FACTOR RPON - AQUIFEX AEOLICUS.
O69080 RNA POLYMERASE SUBUNIT SIGMA-54 - PLANCTOMYCES LIMNOPHILUS.
O69778 RNA POLYMERASE SIGMA-54 FACTOR - RHIZOBIUM ETLI.
O84615 RNA POLYMERASE SIGMA-54 - CHLAMYDIA TRACHOMATIS.
O86452 RNA POLYMERASE SIGMA-54 FACTOR - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA).
Q59085 RNA POLYMERASE SIGMA-54 FACTOR - AZOSPIRILLUM BRASILENSE.
Q59751 RNA POLYMERASE SIGMA-54 FACTOR - RHIZOBIUM MELILOTI.
RP54_ACICA RNA POLYMERASE SIGMA-54 FACTOR - ACINETOBACTER CALCOACETICUS.
RP54_ALCEU RNA POLYMERASE SIGMA-54 FACTOR - ALCALIGENES EUTROPHUS.
RP54_AZOCA RNA POLYMERASE SIGMA-54 FACTOR - AZORHIZOBIUM CAULINODANS.
RP54_AZOVI RNA POLYMERASE SIGMA-54 FACTOR - AZOTOBACTER VINELANDII.
RP54_BACSU RNA POLYMERASE SIGMA-54 FACTOR - BACILLUS SUBTILIS.
RP54_BRAJA RNA POLYMERASE SIGMA-54 FACTOR 1 - BRADYRHIZOBIUM JAPONICUM.
RP54_CAUCR RNA POLYMERASE SIGMA-54 FACTOR - CAULOBACTER CRESCENTUS.
RP54_ECOLI RNA POLYMERASE SIGMA-54 FACTOR - ESCHERICHIA COLI.
RP54_HELPY RNA POLYMERASE SIGMA-54 FACTOR - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
RP54_KLEPN RNA POLYMERASE SIGMA-54 FACTOR - KLEBSIELLA PNEUMONIAE.
RP54_PSEAE RNA POLYMERASE SIGMA-54 FACTOR - PSEUDOMONAS AERUGINOSA.
RP54_PSEPU RNA POLYMERASE SIGMA-54 FACTOR - PSEUDOMONAS PUTIDA.
RP54_RHILP RNA POLYMERASE SIGMA-54 FACTOR - RHIZOBIUM LEGUMINOSARUM (BIOVAR PHASEOLI).
RP54_RHIME RNA POLYMERASE SIGMA-54 FACTOR (VERSION 1) - RHIZOBIUM MELILOTI.
RP54_RHISN RNA POLYMERASE SIGMA-54 FACTOR - RHIZOBIUM SP. (STRAIN NGR234).
RP54_RHOSH RNA POLYMERASE SIGMA-54 FACTOR - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
RP54_SALTY RNA POLYMERASE SIGMA-54 FACTOR - SALMONELLA TYPHIMURIUM.
RP54_THIFE RNA POLYMERASE SIGMA-54 FACTOR - THIOBACILLUS FERROOXIDANS.
RP54_VIBAN RNA POLYMERASE SIGMA-54 FACTOR - VIBRIO ANGUILLARUM.
RP54_XANCV RNA POLYMERASE SIGMA-54 FACTOR - XANTHOMONAS CAMPESTRIS (PV. VESICATORIA).
RP55_BRAJA RNA POLYMERASE SIGMA-54 FACTOR 2 - BRADYRHIZOBIUM JAPONICUM.
RP55_RHIME RNA POLYMERASE SIGMA-54 FACTOR (VERSION 2) - RHIZOBIUM MELILOTI.

O51406 RNA POLYMERASE SIGMA-54 FACTOR (NTRA) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
RP54_RHOCA RNA POLYMERASE SIGMA-54 FACTOR - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
RP54_TREPA RNA POLYMERASE SIGMA-54 FACTOR - TREPONEMA PALLIDUM.
Scan History
OWL19_1    2  100  NSINGLE    
OWL26_0 1 180 NSINGLE
SPTR37_9f 2 71 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
DPVGVAAKDLRDCLLIQL RP54_SALTY 186 186 -
DPPGVFARTLGECLAIQL RP54_RHIME 214 214 -
DPVGVAAKDLRDCLLVQL RP54_KLEPN 186 186 -
DPPGVGARNAAECLALQL RP54_ALCEU 205 205 -
EPAGIGARSLQECILLQL RP54_BACSU 146 146 -

Motif 2 width=13
Element Seqn Id St Int Rpt
LHESTVSRAIKGK RP54_BACSU 334 170 -
MHESTVSRVTSNK RP54_RHIME 403 171 -
MHESTISRVTTQK RP54_SALTY 376 172 -
MHESTISRVTTQK RP54_KLEPN 376 172 -
LHESTISRVTTNK RP54_ALCEU 393 170 -

Motif 3 width=12
Element Seqn Id St Int Rpt
TPRGLFELKYFF RP54_RHIME 419 3 -
SPRGIFELKYFF RP54_SALTY 392 3 -
SPRGIFELKYFF RP54_KLEPN 392 3 -
TPMGTFELKYFF RP54_ALCEU 409 3 -
TPYGLFEMKLFF RP54_BACSU 350 3 -

Motif 4 width=19
Element Seqn Id St Int Rpt
GVDIARRTVAKYREAMSIP RP54_RHIME 478 47 -
GIMVARRTVAKYRESLSIP RP54_SALTY 450 46 -
GIMVARRTVAKYRESLSIP RP54_KLEPN 450 46 -
GFVVARRTVAKYREALKIP RP54_ALCEU 467 46 -
GIQISRRTVAKYRDQMNIP RP54_BACSU 409 47 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
DPPGVFARTLGECLAIQL Q59751 214 214 -
DPPGVFARTLGECLAIQL RP54_RHIME 214 214 -
DPPGVFARSLAECLAIQL RP54_RHILP 223 223 -
DPPGIFARSLKECLAIQL Q59085 231 231 -
EPAGIGARNLRECLLLQL RP54_PSEAE 206 206 -
EPAGVGARNLGECLLLQL RP54_PSEPU 206 206 -
EPAGIGARDLRECLLLQL O86452 211 211 -
DPPGVFARTLGECLGLQL RP55_RHIME 215 215 -
DPPGIFARSLGECLEIQL O69778 183 183 -
DPPGVCARNLSECLAIQL RP55_BRAJA 225 225 -
DPLGVASRNLQECLLLQL O24775 200 200 -
EPVGVFARDVRECLALQL O32343 202 202 -
EPVGVFARDVRECLALQL RP54_CAUCR 202 202 -
DPPGVCARNLRECLAIQL RP54_BRAJA 177 177 -
EPAGIAARDLSESLLLQL RP54_AZOVI 211 211 -
DPVGVAAKDLRDCLLIQL RP54_ECOLI 186 186 -
DPPGVFARTLSECLAIQL RP54_RHISN 216 216 -
DPVGVAAKDLRDCLLIQL RP54_SALTY 186 186 -
DPPGVGARNLSECLLLQL RP54_THIFE 186 186 -
EPSGVGARSLSECLALQL RP54_AZOCA 213 213 -
EPIGIGARSLAECLFVQI RP54_ACICA 194 194 -
DPVGVAAKDLRDCLLVQL RP54_KLEPN 186 186 -
DPPGVGARNAAECLALQL RP54_ALCEU 205 205 -
DPLGVASVNLQDCLLLQL RP54_VIBAN 197 197 -
DPFGVASLNLQDCLLLQL O30651 198 198 -
DPRGCGARDLQECLLIQL O54393 214 214 -
DPVGVGARTLGECLALQL RP54_XANCV 188 188 -
EPAGIGARSLQECILLQL RP54_BACSU 146 146 -
EPAGVGARDAKECLLLQL O69080 206 206 -
EPAGLFARSLAECLALQL RP54_RHOSH 148 148 -
EPAGVGARDARECILLQI O08352 155 155 -
EPLGVCSKDVWEFLELQI O66858 135 135 -
HPLGVGAPSLQSYWVSLL O84615 136 136 -
NPAGIGAKDVKESFLFQL RP54_HELPY 143 143 -

Motif 2 width=13
Element Seqn Id St Int Rpt
MHESTISRVTTQK RP54_ECOLI 376 172 -
MHESTVSRVTSNK RP54_RHISN 405 171 -
MHESTVSRVTSNK Q59751 403 171 -
MHESTVSRVTSNK RP54_RHIME 403 171 -
MHESTVSRVTSNK RP54_RHILP 408 167 -
MHESTVSRVTTNK Q59085 419 170 -
MHESTISRVTTQK RP54_PSEAE 396 172 -
MHESTISRVTTQK RP54_PSEPU 396 172 -
MHESTISRVTTQK O86452 401 172 -
MHESTVSRVTSNK RP55_RHIME 404 171 -
MHESTVSRVTSNK O69778 372 171 -
MHESTVSRVTANK RP55_BRAJA 413 170 -
MHESTISRVTTQK O24775 388 170 -
MHESTVSRVTSNK O32343 390 170 -
MHESTVSRVTSNK RP54_CAUCR 390 170 -
MHESTVSRVTANK RP54_BRAJA 365 170 -
MHESTISRVTTQK RP54_AZOVI 401 172 -
MHESTISRVTTQK RP54_SALTY 376 172 -
MHESTVSRVTNQK RP54_THIFE 375 171 -
MHESTVSRVTSNK RP54_AZOCA 401 170 -
LHESTVSRVTTNK RP54_ACICA 383 171 -
MHESTISRVTTQK RP54_KLEPN 376 172 -
LHESTISRVTTNK RP54_ALCEU 393 170 -
MHESTISRVTTQK RP54_VIBAN 385 170 -
MHESTISRVTTQK O30651 386 170 -
MHESTVSRVTTSK O54393 404 172 -
LHESTISRAIARK RP54_XANCV 378 172 -
LHESTVSRAIKGK RP54_BACSU 334 170 -
VHVTTVSRAVDDK O69080 395 171 -
LHPSTISRATATR RP54_RHOSH 329 163 -
VHESTVSRAVNGK O08352 342 169 -
IHESTLSRIVNSK O66858 303 150 -
LHEATVCRAIDNK O84615 324 170 -
HSVSTISRAISNK RP54_HELPY 311 150 -

Motif 3 width=12
Element Seqn Id St Int Rpt
TPRGLFELKYFF RP54_RHISN 421 3 -
TPRGLFELKYFF Q59751 419 3 -
TPRGLFELKYFF RP54_RHILP 424 3 -
TPRGVFELKYFF Q59085 435 3 -
TPRGIFELKYFF RP54_PSEAE 412 3 -
TPRGIYELKYFF RP54_PSEPU 412 3 -
TPRGIYELKYFF O86452 417 3 -
TPRGLYELKYFF RP55_RHIME 420 3 -
TPRGVFELKYFF O69778 388 3 -
TNRGTFELKYFF RP55_BRAJA 429 3 -
TPRGIFELKYFF O24775 404 3 -
TPRGVFELKFFF O32343 406 3 -
TPRGVFELKFFF RP54_CAUCR 406 3 -
TNRGTFELKYFF RP54_BRAJA 381 3 -
TPRGIYELKYFF RP54_AZOVI 417 3 -
SPRGIFELKYFF RP54_ECOLI 392 3 -
SPRGIFELKYFF RP54_SALTY 392 3 -
TPRGLFELKYFF RP54_RHIME 419 3 -
TPRGLYEFKYFF RP54_THIFE 391 3 -
TPRGVLEMKFFF RP54_AZOCA 417 3 -
TPRGLFELKYFF RP54_ACICA 399 3 -
SPRGIFELKYFF RP54_KLEPN 392 3 -
TPMGTFELKYFF RP54_ALCEU 409 3 -
TPRGIFELKYFF RP54_VIBAN 401 3 -
TPRGIFELKYFF O30651 402 3 -
TPQGIFELKYFF O54393 420 3 -
TPRGTIALRAFF RP54_XANCV 394 3 -
TPYGLFEMKLFF RP54_BACSU 350 3 -
TPRGLFPLKRFF O69080 411 3 -
TPRGLIPLRAFF RP54_RHOSH 345 3 -
TTNGVYELKRFF O08352 358 3 -
TPVGTYSLRTFF O66858 319 3 -
TPVGLLPMRSLF O84615 340 3 -
CERGVFPIKHFF RP54_HELPY 327 3 -

Motif 4 width=19
Element Seqn Id St Int Rpt
GIPCARRTVAKYRSQLNIL O84615 394 42 -
GVDIARRTVAKYREAMNIP RP54_RHISN 480 47 -
GVDIARRTVAKYREAMSIP Q59751 478 47 -
GVDIARRTVAKYREAMSIP RP54_RHIME 478 47 -
GIDLARRTVAKYREAMNIA RP54_RHILP 484 48 -
GIDIARRTVAKYREAMRIP Q59085 494 47 -
GIQVARRTVAKYRESLGIA RP54_PSEAE 470 46 -
GIQVARRTVAKYRESLGIA RP54_PSEPU 470 46 -
GIQVARRTVAKYRESLGIA O86452 475 46 -
GVDIARRTVAKYREAMHIP RP55_RHIME 479 47 -
GVDIARRTVAKYREAMRIP O69778 447 47 -
GIDIARRTVAKYREAMRIP RP55_BRAJA 488 47 -
GIQVARRTIAKYRESLGIA O24775 462 46 -
GVDIARRTVAKYREAMRIP O32343 466 48 -
GVDIARRTVAKYREAMRIP RP54_CAUCR 466 48 -
GIDIARRTVAKYREAMRIR RP54_BRAJA 440 47 -
GIQVARRTVAKYRESLSIA RP54_AZOVI 475 46 -
GIMVARRTVAKYRESLSIP RP54_ECOLI 450 46 -
GIMVARRTVAKYRESLSIP RP54_SALTY 450 46 -
GIQIARRTVAKYREAANVP RP54_THIFE 449 46 -
GIDIARRTVAKYRESMNIP RP54_AZOCA 476 47 -
GIDVARRTVAKYRESLHIP RP54_ACICA 457 46 -
GIMVARRTVAKYRESLSIP RP54_KLEPN 450 46 -
GFVVARRTVAKYREALKIP RP54_ALCEU 467 46 -
GIQVARRTIAKYRESLGIA RP54_VIBAN 459 46 -
GIQVARRTIAKYRESLGIA O30651 460 46 -
GTEIARRTVAKYREVLGIL O54393 478 46 -
GVPVARRTVAKYREAMNIS RP54_XANCV 452 46 -
GIQISRRTVAKYRDQMNIP RP54_BACSU 409 47 -
GFNLARRTVTKYRKALNIP O69080 469 46 -
GAVLARRTVTKYRETLGIP RP54_RHOSH 404 47 -
EIQVSRRAIAKYRLELNIP O08352 421 51 -
GFKVARRTVAKYREMLGIP O66858 373 42 -
HLKMVRRTITKYRQLLNIA RP54_HELPY 383 44 -