HHsearch alignment for GI: 254780289 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=418.99  Aligned_cols=252  Identities=28%  Similarity=0.429  Sum_probs=216.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             33222221126889999998765332112468999875557899988752235677788754436799998874385457
Q gi|254780289|r  414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG  493 (682)
Q Consensus       414 ~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g  493 (682)
T Consensus         8 ~~vn~~P~L~~EEE~~LA~r~r~~~D--l~AA~~Lv~SHLRfVv~iArgY~GYGL~~aDLIQEGNIGLMkAVkRFdP~~G   85 (279)
T TIGR02392         8 RAVNRIPMLTAEEEQELAKRLREEGD--LDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERG   85 (279)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHCCC--HHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99971789998899999998654237--7899987466247875532036777744244342222665533442178987


Q ss_pred             CEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHH-HHHHHHHHHC-CCCCCH---HHHHHHCCCCHHHHHHHH-
Q ss_conf             3120102898999999999722870461420588989999-9999987760-889997---899987099989999999-
Q gi|254780289|r  494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV-RTARRMSNKI-KREPTP---EEIAKKLAMPVEGVRKVL-  567 (682)
Q Consensus       494 ~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~-~~~~~~~~~~-~~~~~~---~~~a~~~~~~~~~~~~~~-  567 (682)
T Consensus        86 vRLvSfAvHWIkAeIHEyILrnWRlVKvATTkaQrKLFFNLRk~K~ki~~l~~gw~~~~e~~~~A~~L~V~~~eV~eMe~  165 (279)
T TIGR02392        86 VRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKKITRLQDGWLNPEEVEAIAEELGVSEEEVLEMES  165 (279)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             22047888999999866899755598885277678887658889998631015798989999999763898889988751


Q ss_pred             HHHCCCCCCCCCCCCCCCC-----EEEEEECCCCCCCHHHHHHHHH----HHHHHHHHHHCCCHHHHHHHHHHHCCCCCC
Q ss_conf             8608987553635889986-----0475623898899899999999----999999997329988999999981879867
Q gi|254780289|r  568 KITKEPISLETPIGDEDTS-----HLGDFIEDKNAVSPLDSAIQAN----LRETTTRVLASLTPREERVLRMRFGIGMNT  638 (682)
Q Consensus       568 ~~~~~~~sl~~~~~~~~~~-----~~~~~~~d~~~~~~~~~~~~~~----~~~~~~~~l~~l~~re~~v~~~r~g~~~~~  638 (682)
T Consensus       166 RlsG~D~~L~~~~~~~~~~~~~~~~~~~yL~D~~~~~~~~~l~~~~~~~~~~~~L~~AL~~Ld~RsR~I~~~Rw--L~d~  243 (279)
T TIGR02392       166 RLSGRDISLNASIDDDEDDGGSDFAPIAYLADKATSDPEATLEEEQWEELQTQKLANALESLDARSRRIIEARW--LDDD  243 (279)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCC
T ss_conf             45537733478876553456311457886304777788899999899999999999998852288799998730--2788


Q ss_pred             -CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             -4688999899667899999999999998329
Q gi|254780289|r  639 -DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH  669 (682)
Q Consensus       639 -~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~  669 (682)
T Consensus       244 ~~~TL~~LA~eygvSaERiRQiE~~Am~K~k~  275 (279)
T TIGR02392       244 GKLTLHELAAEYGVSAERIRQIEKNAMKKLKA  275 (279)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             99647899988487466799999999999999