HHsearch alignment for GI: 254780611 and conserved domain: TIGR02952

>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family; InterPro: IPR014298 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 group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=99.25  E-value=2.7e-10  Score=88.38  Aligned_cols=169  Identities=15%  Similarity=0.217  Sum_probs=120.0

Q ss_pred             HHHHHHHCCHHHHHHHHHHHHHHH-HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             999998285999999999430778-7565555799998889999998889989862185345689997577899999985
Q gi|254780611|r   38 AKRYREHGDLSAAHRLVTSHLRLV-VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY  116 (302)
Q Consensus        38 ~~~~~~~gd~~Ar~~Li~~nlrlV-~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~  116 (302)
T Consensus         2 l~~a~-~~e~~Afa~lye~Y~~~vYrYI~yrv-g~~~tAEDL~s~vF~~~L~~i~~f~~~~~t~f~~WLf~iA~N~v~Dy   79 (171)
T TIGR02952         2 LERAQ-EKEEDAFARLYETYSDKVYRYIYYRV-GDKYTAEDLTSEVFLRVLRKIDSFKEQKNTDFEAWLFTIARNVVADY   79 (171)
T ss_pred             CHHHH-HHHHHHHHHHHHHHHHHHHHHHEEEE-CCEEEHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             03577-67699999998987256662101312-88531146478999999731221012578772247899999999988


Q ss_pred             HHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC
Q ss_conf             32024600110230035899999999788786624478882467788861898321100000012234335520232345
Q gi|254780611|r  117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN  196 (302)
Q Consensus       117 i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~  196 (302)
T Consensus        80 fr~~~r~---------------------------------~-------------------------~~~~~~~~------   95 (171)
T TIGR02952        80 FRKSKRR---------------------------------P-------------------------LLSLDVVK------   95 (171)
T ss_pred             HHCCCCC---------------------------------C-------------------------CCCHHHHH------
T ss_conf             5113455---------------------------------2-------------------------10099989------


Q ss_pred             CCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             32000001235687056556666666777999999621999999999998278888898999999778999999999999
Q gi|254780611|r  197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA  276 (302)
Q Consensus       197 ~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A  276 (302)
T Consensus        96 ------~l~~~e~~P~e~~----~~~~~n~~L~~a~~~L~p~qq~viaLrF~~~--L~~~EvA~ilGk~~gavk~Lq~rA  163 (171)
T TIGR02952        96 ------ELLSAEPSPEEAV----LKELANEKLLEAVKKLTPKQQEVIALRFAQN--LPIAEVARILGKTEGAVKALQFRA  163 (171)
T ss_pred             ------HHHHCCCCHHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHCCC--CCHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             ------8873489817899----9888899999999610832312033321168--838789987268974689999999


Q ss_pred             HHHHHHHH
Q ss_conf             99999999
Q gi|254780611|r  277 FKKVQESI  284 (302)
Q Consensus       277 L~kLR~~l  284 (302)
T Consensus       164 v~~L~r~l  171 (171)
T TIGR02952       164 VKKLARQL  171 (171)
T ss_pred             HHHHHHHC
T ss_conf             99987309