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