>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=646.57 Aligned_cols=231 Identities=45% Similarity=0.742 Sum_probs=226.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECC Q ss_conf 46899987555789998875223567778875443679999887438545731201028989999999997228704614 Q gi|254780289|r 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522 (682) Q Consensus 443 ~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~ 522 (682) T Consensus 46 eAR~~MIE~NLRLVV~IAk~Y~nRGlpLlDLIEEGNLGLm~AvEKFDPeRGFRFSTYATWWIRQtIERAIMNQaRTiRLP 125 (292) T TIGR02394 46 EARKKMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLP 125 (292) T ss_pred HHHHHHHHHHCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEECC T ss_conf 89888776401267678644047651457777653356654210458899984430111366532786531354411053 Q ss_pred CHHHHHHHHHHHHHHHHHH---HCC---CCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC-CCEEEEEECCC Q ss_conf 2058898999999999877---608---8999789998709998999999986089875536358899-86047562389 Q gi|254780289|r 523 VHMRDKIHKVVRTARRMSN---KIK---REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDK 595 (682) Q Consensus 523 ~~~~~~~~~~~~~~~~~~~---~~~---~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~-~~~~~~~~~d~ 595 (682) T Consensus 126 vHV~kELNv~LRa~r~L~~ns~~~~E~~~EpS~eeiA~~~~kpvedv~~~L~Lne~~~S~D~Pl~~D~n~~Sl~d~~ADe 205 (292) T TIGR02394 126 VHVVKELNVYLRAARQLEKNSAKLDEEEREPSVEEIAELLDKPVEDVSKVLALNERIASLDAPLDEDSNSKSLLDTIADE 205 (292) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHCCCCC T ss_conf 14346777999988876556763373357788789998838988899999841799525305778774301210004788 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHH Q ss_conf 889989999999999999999732998899999998187986746889998996678999999999999983296777 Q gi|254780289|r 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673 (682) Q Consensus 596 ~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~ 673 (682) T Consensus 206 ~~~~P~~~~~~~~l~~~~~~~L~~Lne~~R~V~~rRFGL~g~E~~TLE~va~~~gLTRERvRQIQ~eaL~~Lr~~L~~ 283 (292) T TIGR02394 206 QSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLRGYEKATLEEVAKELGLTRERVRQIQVEALKKLRRILER 283 (292) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHCHHHHEEHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 877807642189999999998861063211210100376654266699999872881047899889999999999986

HHsearch alignment for GI: 254780289 and conserved domain: TIGR02394