>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=98.55 E-value=5.2e-06 Score=59.67 Aligned_cols=181 Identities=21% Similarity=0.280 Sum_probs=123.5 Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH Q ss_conf 99999999982859999999994307787565555799998889999998889989862185345689997577899999 Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113 (302) Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I 113 (302) T Consensus 8 D~~Lv~RVQ-rG~k~AF~lLV~KYQ~kv~~Lv~Ryv~~~~e~~DVAQe~FvkAYRAl~~FRGd--saFYTWLy------- 77 (192) T TIGR02939 8 DLELVERVQ-RGEKQAFDLLVRKYQHKVVSLVGRYVRDSEEVEDVAQEAFVKAYRALASFRGD--SAFYTWLY------- 77 (192) T ss_pred HHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHCCCCHHHHHHHHHHHHHCCCCCC--HHHHHHHH------- T ss_conf 289988873-32235677788999999999998761481003401477899999751235551--36789999------- Q ss_pred HHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCC Q ss_conf 98532024600110230035899999999788786624478882467788861898321100000012234335520232 Q gi|254780611|r 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193 (302) Q Consensus 114 ~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~ 193 (302) T Consensus 78 -----------RIa-----------vNTAKNyLV---aq~Rr~p~~d------g~~~e---------------------- 104 (192) T TIGR02939 78 -----------RIA-----------VNTAKNYLV---AQGRRPPTSD------GVEAE---------------------- 104 (192) T ss_pred -----------HHH-----------HHHHHHHHH---HCCCCCCCCC------CCCCH---------------------- T ss_conf -----------999-----------988777664---2479887445------67604---------------------- Q ss_pred CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 34532000001235687056556666666777999999621999999999998278888898999999778999999999 Q gi|254780611|r 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273 (302) Q Consensus 194 d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302) T Consensus 105 dAE~F~~a~~Lr-~~~tPE~~ll----~~el~~~v~~a~~aLPE~Lr~Ai~LREl--eGLSYe~IA~~MdCPvGTVRSRI 177 (192) T TIGR02939 105 DAEQFEEADALR-DIDTPERLLL----SRELEQTVNKALEALPEDLRTAITLREL--EGLSYEDIAEIMDCPVGTVRSRI 177 (192) T ss_pred HHHCCCCCCCCC-CCCCHHHHHH----HHHHHHHHHHHHHHCCHHHHHHHHHHHC--CCCCHHHHHHHCCCCCCCCCCHH T ss_conf 331200267665-5666167999----9999999999986172678745446512--68787888733069988621146 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 999999999999740 Q gi|254780611|r 274 ARAFKKVQESIQKQV 288 (302) Q Consensus 274 ~~AL~kLR~~l~~~~ 288 (302) T Consensus 178 FRA----REAi~~~l 188 (192) T TIGR02939 178 FRA----REAIAKRL 188 (192) T ss_pred HHH----HHHHHHHH T ss_conf 775----89999862

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02939