>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE; InterPro: IPR014286 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 RpoE. These proteins are variously annotated as sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.

Probab=94.17 E-value=0.52 Score=26.96 Aligned_cols=159 Identities=19% Similarity=0.276 Sum_probs=120.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682) T Consensus 9 ~~Lv~RVQrG~k---~AF~lLV~KYQ~kv~~Lv~Ryv~~~~e~~DVAQe~FvkAYRAl~~FRGd-----saFYTWLyRIa 80 (192) T TIGR02939 9 LELVERVQRGEK---QAFDLLVRKYQHKVVSLVGRYVRDSEEVEDVAQEAFVKAYRALASFRGD-----SAFYTWLYRIA 80 (192) T ss_pred HHHHHHHHCCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHCCCCHHHHHHHHHHHHHCCCCCC-----HHHHHHHHHHH T ss_conf 899888733223---5677788999999999998761481003401477899999751235551-----36789999999 Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHH-HHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 99999722870461420588989999999998776088999789-99870999899999998608987553635889986 Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE-IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586 (682) Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~ 586 (682) T Consensus 81 vN-------------------------TAKNyLVaq~Rr~p~~dg~------------------------~--~edAE~F 109 (192) T TIGR02939 81 VN-------------------------TAKNYLVAQGRRPPTSDGV------------------------E--AEDAEQF 109 (192) T ss_pred HH-------------------------HHHHHHHHCCCCCCCCCCC------------------------C--CHHHHCC T ss_conf 98-------------------------8777664247988744567------------------------6--0433120 Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCC Q ss_conf 04756238988998999999999999999973299889999999818798674688999899667 Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651 (682) Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~ 651 (682) T Consensus 110 ~~a~~Lr--~~~tPE~~ll~~el~~~v~~a~~aLPE~Lr~Ai~LRE----leGLSYe~IA~~MdC 168 (192) T TIGR02939 110 EEADALR--DIDTPERLLLSRELEQTVNKALEALPEDLRTAITLRE----LEGLSYEDIAEIMDC 168 (192) T ss_pred CCCCCCC--CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----CCCCCHHHHHHHCCC T ss_conf 0267665--5666167999999999999998617267874544651----268787888733069

HHsearch alignment for GI: 254780289 and conserved domain: TIGR02939