HHsearch alignment for GI: 254780351 and conserved domain: TIGR00331

>TIGR00331 hrcA heat-inducible transcription repressor HrcA; InterPro: IPR002571 In response to elevated temperature, both prokaryotic and eukaryotic cells increase expression of a small family of chaperones. The regulatory network that functions to control the transcription of the heat shock genes in bacteria includes unique structural motifs in the promoter region of these genes and the expression of alternate sigma factors. One of the conserved structural motifs, the inverted repeat CIRCE element, is found in the 5' region of many heat shock operons . For Bacillus subtilis three classes of heat shock genes regulated by different mechanisms have been described. Regulation of class I heat shock genes (dnaK and groE operons) involves an inverted repeat (CIRCE element) which most probably serves as an operator for a repressor .; GO: 0006355 regulation of transcription DNA-dependent.
Probab=92.33  E-value=0.92  Score=24.80  Aligned_cols=82  Identities=15%  Similarity=0.138  Sum_probs=57.7

Q ss_pred             CCCCCHHHHHHH--HCCCCCHHHHHHHHHHHCCCEEEEECCCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             179688999998--547710567999999977887886361007105644578899999999999999999998534999
Q gi|254780351|r   68 DLELTAGELRSR--GYYLGSNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAETISQLYQRHIESIDKVGGLS  145 (171)
Q Consensus        68 ~~~~t~~eLa~~--l~i~~~tvs~~i~~Le~~G~i~r~~~~~D~R~~~i~LT~~G~~~~~~~~~~~~~~~~~l~~~~~ls  145 (171)
T Consensus        19 ~~PVGSk~L~~~~~l~~SSATIRN~Ma~LE~~Gfi~k~HtSsGR-----iPt~~GYRyYVd----------~l~~~~~~~   83 (343)
T TIGR00331        19 GEPVGSKTLLEKYNLGLSSATIRNDMADLEELGFIEKPHTSSGR-----IPTDKGYRYYVD----------HLLKVDSLT   83 (343)
T ss_pred             CCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCC-----CHHHHHHHHHHH----------HHCCCCCCC
T ss_conf             89620476775617999970365779998750220047415787-----522300689999----------744788878


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999999999999985
Q gi|254780351|r  146 VDDFIAMNKLLQRLNRFWG  164 (171)
Q Consensus       146 ~ee~~~l~~~L~rler~~~  164 (171)
T Consensus        84 ~~e~~~I~~~~~~~~~~~~  102 (343)
T TIGR00331        84 EEEKRRIQNQLLQERFELE  102 (343)
T ss_pred             HHHHHHHHHHHHHHHCCHH
T ss_conf             7899999998635312402