HHsearch alignment for GI: 254780289 and conserved domain: TIGR02859

>TIGR02859 spore_sigH RNA polymerase sigma-H factor; InterPro: IPR014218 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 , . Members of this entry represent the RNA polymerase sigma-H factor required for sporulation in endospore-forming bacteria. These proteins are also called Sigma-30 and SigH. Related sequences exist in Listeria, but as Listeria does not form spores the role of these related sigma factors in that genus is in doubt.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=98.78  E-value=2e-07  Score=77.61  Aligned_cols=182  Identities=26%  Similarity=0.365  Sum_probs=150.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf             99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r  428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA  507 (682)
Q Consensus       428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~  507 (682)
T Consensus         7 ~~~~~~~~~G~~---~a~~~~i~~y~~fv~ak~~~yfl~Gad~edi~qeGmiGlyka~rd~~~~~l~sf~afaelC~trq   83 (198)
T TIGR02859         7 EEIVELAREGDE---KALEYLIEKYKNFVKAKARSYFLVGADKEDIIQEGMIGLYKAIRDYKEDKLSSFKAFAELCVTRQ   83 (198)
T ss_pred             HHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999970118---89999999999998775311013206456566611689999997531567899999999999999


Q ss_pred             HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC-CCCC
Q ss_conf             999997228704614205889899999999987760889997899987099989999999860898755363588-9986
Q gi|254780289|r  508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTS  586 (682)
Q Consensus       508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~-~~~~  586 (682)
T Consensus        84 iitaiktatrqkhiPln-----------------------------------------------~y~sl~kPiy~~~sdr  116 (198)
T TIGR02859        84 IITAIKTATRQKHIPLN-----------------------------------------------SYVSLNKPIYDEESDR  116 (198)
T ss_pred             HHHHHHHHHHHCCCCCH-----------------------------------------------HHEECCCCCCCCCCHH
T ss_conf             99998876520246520-----------------------------------------------0000256525452014


Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             047562389889989999999999999999732-9988999999981879867468899989966789999999999999
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR  665 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~-l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~  665 (682)
T Consensus       117 tl~d~~~~~~~~dP~~l~i~~e~~~~~~~~~~~~ls~le~~vl~~yl---~G--~~yqei~~~l~r---~~ksidn-alq  187 (198)
T TIGR02859       117 TLLDVVSEAKVADPEELIISKEEYEKIESKLEELLSDLELKVLVLYL---DG--KSYQEIAEDLNR---HVKSIDN-ALQ  187 (198)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---CC--CHHHHHHHHHHH---HHHHHHH-HHH
T ss_conf             79998854432252777631688999999999999999999999984---57--407889988645---6678999-999


Q ss_pred             HHC
Q ss_conf             832
Q gi|254780289|r  666 KLK  668 (682)
Q Consensus       666 ~l~  668 (682)
T Consensus       188 rvk  190 (198)
T TIGR02859       188 RVK  190 (198)
T ss_pred             HHH
T ss_conf             999