>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS; InterPro: IPR012761 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. 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. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second principal sigma factor at that time.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.

Probab=98.80  E-value=3.6e-08  Score=83.47  Aligned_cols=124  Identities=21%  Similarity=0.154  Sum_probs=93.2

Q ss_pred             CCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH------------HHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             77772899999985697688978899999999988------------999999987282389999999987311710367
Q gi|254780289|r  115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG------------RAMMMASLCESPLTFQALIIWRDELNDGTTLLR  182 (682)
Q Consensus       115 ~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G------------~~~i~~al~~~P~ti~~il~~~e~i~~ge~~Lr  182 (682)
T Consensus         9 ~~~~D~~Q~YL~eIg~~PLLt~~EE~~~Arra~~GD~eAR~~MIE~NLRLVV~IAk~Y~nRGlpLlDLIEEGNLGLm~Av   88 (292)
T TIGR02394         9 TRVADVTQLYLREIGFKPLLTAEEELAYARRALAGDFEARKKMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAV   88 (292)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             23302688878886015588988999998886507888988877640126767864404765145777765335665421


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHH
Q ss_conf             87642101354333333343333321100011100010000000012210000111
Q gi|254780289|r  183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK  238 (682)
Q Consensus       183 dIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~  238 (682)
T Consensus        89 EKFDPeRGFRFSTYATWWIRQtIERAIMNQaRTiRLPvHV~kELNv~LRa~r~L~~  144 (292)
T TIGR02394        89 EKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVVKELNVYLRAARQLEK  144 (292)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEECCHHHHHHHHHHHHHHHHHHH
T ss_conf             04588999844301113665327865313544110531434677799998887655