HHsearch alignment for GI: 254780611 and conserved domain: TIGR02392
>TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759 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 proteobacterial clade of sigma factors called RpoH. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat.
Probab=100.00 E-value=0 Score=543.43 Aligned_cols=272 Identities=49% Similarity=0.803 Sum_probs=260.0
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 05999999840799999899999999999828599999999943077875655557999988899999988899898621
Q gi|254780611|r 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93 (302)
Q Consensus 14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kF 93 (302)
T Consensus 1 g~L~~Yi~~vn~~P~L~~EEE~~LA~r~r~~~Dl~AA~~Lv~SHLRfVv~iArgY~GYGL~~aDLIQEGNIGLMkAVkRF 80 (279)
T TIGR02392 1 GSLDAYIRAVNRIPMLTAEEEQELAKRLREEGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80 (279)
T ss_pred CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 97788999997178999889999999865423778999874662478755320367777442443422226655334421
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCC
Q ss_conf 85345689997577899999985320246001102300358999999997887866244788824677888618983211
Q gi|254780611|r 94 DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173 (302)
Q Consensus 94 Dp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v 173 (302)
T Consensus 81 dP~~GvRLvSfAvHWIkAeIHEyILrnWRlVKvATTkaQrKLFFNLRk~K~ki~~l~~gw~~~~e~~~~A~~L~V~~~eV 160 (279)
T TIGR02392 81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKKITRLQDGWLNPEEVEAIAEELGVSEEEV 160 (279)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
T ss_conf 78987220478889999998668997555988852776788876588899986310157989899999997638988899
Q ss_pred CCCCCCCCC-CCCHHHHCCCCCCCCC---CHHCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHC
Q ss_conf 000000122-3433552023234532---000001235-68705655666666677799999962199999999999827
Q gi|254780611|r 174 ISMNCRLAG-DESLNALINSSDKNSS---QWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248 (302)
Q Consensus 174 ~~l~~~~~~-~~SLd~~i~~~d~~~~---~~~d~l~~~-~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~ 248 (302)
T Consensus 161 ~eMe~RlsG~D~~L~~~~~~~~~~~~~~~~~~~yL~D~~~~~~~~~l~~~~~~~~~~~~L~~AL~~Ld~RsR~I~~~RwL 240 (279)
T TIGR02392 161 LEMESRLSGRDISLNASIDDDEDDGGSDFAPIAYLADKATSDPEATLEEEQWEELQTQKLANALESLDARSRRIIEARWL 240 (279)
T ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 88751455377334788765534563114578863047777888999998999999999999988522887999987302
Q ss_pred CCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 888-8898999999778999999999999999999999
Q gi|254780611|r 249 QEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302)
Q Consensus 249 ~~~-~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302)
T Consensus 241 ~d~~~~TL~~LA~eygvSaERiRQiE~~Am~K~k~~~~ 278 (279)
T TIGR02392 241 DDDGKLTLHELAAEYGVSAERIRQIEKNAMKKLKAALA 278 (279)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 78899647899988487466799999999999999841