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