>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=100.00 E-value=0 Score=547.16 Aligned_cols=273 Identities=30% Similarity=0.473 Sum_probs=242.9 Q ss_pred CCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 45587405999999840799999899999999999828599999999943077875655557999988899999988899 Q gi|254780611|r 8 IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87 (302) Q Consensus 8 ~~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi 87 (302) T Consensus 7 ~~~~~~D~~Q~YL~eIg~~PLLt~~EE~~~Arra~-~GD~eAR~~MIE~NLRLVV~IAk~Y~nRGlpLlDLIEEGNLGLm 85 (292) T TIGR02394 7 TETRVADVTQLYLREIGFKPLLTAEEELAYARRAL-AGDFEARKKMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLM 85 (292) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHCHHHHHHHHHCCCCCCHHHHHHHHHHHHHH T ss_conf 22233026888788860155889889999988865-07888988877640126767864404765145777765335665 Q ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHH Q ss_conf 8986218534568999757789999998532024600110230035899999999788786624478---8824677888 Q gi|254780611|r 88 QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL---KPEQVVAIAK 164 (302) Q Consensus 88 ~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~---~~~~~~eiA~ 164 (302) T Consensus 86 ~AvEKFDPeRGFRFSTYATWWIRQtIERAIMNQaRTiRLPvHV~-kEL-Nv~LRa~r~L~~ns~~~~E~~~EpS~eeiA~ 163 (292) T TIGR02394 86 HAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVV-KEL-NVYLRAARQLEKNSAKLDEEEREPSVEEIAE 163 (292) T ss_pred HHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEECCHHHH-HHH-HHHHHHHHHHHHHHHHCCCCCCCCCHHHHHH T ss_conf 42104588999844301113665327865313544110531434-677-7999988876556763373357788789998 Q ss_pred HCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH Q ss_conf 61898321100000012234335520232345320000012356870565566666667779999996219999999999 Q gi|254780611|r 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244 (302) Q Consensus 165 ~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~ 244 (302) T Consensus 164 ~~~kpvedv~~~L~Lne~~~S~D~Pl~~D-~n~~Sl~d~~ADe~~~~P~~~~---~~~~l~~~~~~~L~~Lne~~R~V~~ 239 (292) T TIGR02394 164 LLDKPVEDVSKVLALNERIASLDAPLDED-SNSKSLLDTIADEQSIDPESLV---QNDDLKQLIEAWLAELNERQREVLA 239 (292) T ss_pred HHCCCHHHHHHHHHHCCCCEEEECCCCCC-CCCHHHHHCCCCCCCCCHHHHH---HHHHHHHHHHHHHHHHCHHHHEEHH T ss_conf 83898889999984179952530577877-4301210004788877807642---1899999999988610632112101 Q ss_pred HHHCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 98278--88889899999977899999999999999999999974 Q gi|254780611|r 245 ARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 245 ~ry~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 240 rRFGL~g~E~~TLE~va~~~gLTRERvRQIQ~eaL~~Lr~~L~~~ 284 (292) T TIGR02394 240 RRFGLRGYEKATLEEVAKELGLTRERVRQIQVEALKKLRRILERK 284 (292) T ss_pred HHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 003766542666999998728810478998899999999999864

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02394