HHsearch alignment for GI: 254780289 and conserved domain: TIGR02846
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209 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 , . The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homologue sigma-E (sigma-29, see IPR014200 from INTERPRO), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note: that in Bacillus subtilis (and apparently also in Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=99.96 E-value=2.1e-28 Score=243.13 Aligned_cols=192 Identities=30% Similarity=0.447 Sum_probs=166.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682)
Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682)
T Consensus 30 Ls~~eE~~YL~~l~~GD~---~Ar~~LiErNLRLVAHiVKKf~~~G~~~dDLISIGTiGLIKAidsf~~~KGt~LATYAA 106 (228)
T TIGR02846 30 LSEEEEKKYLERLKEGDE---EARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPEKGTRLATYAA 106 (228)
T ss_pred CCHHHHHHHHHHHHHHHH---HHHHHHHHHCCCEEEEEEECCCCCCCCCCCHHCCCCHHEECCEECCCCCCCCHHHHHHH
T ss_conf 986689999999873159---99999776333000215651178874100001002201000110224787731566786
Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682)
Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682)
T Consensus 107 rCiENEILM~lR~~----------------------------------------------------KK~k~eV~L~DPIG 134 (228)
T TIGR02846 107 RCIENEILMHLRAL----------------------------------------------------KKTKGEVSLQDPIG 134 (228)
T ss_pred HHHHHHHHHHHHHC----------------------------------------------------CCCCCCEEECCCCC
T ss_conf 65347899999743----------------------------------------------------67478332107888
Q ss_pred CCCC---CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf 8998---60475623898899899999999999999997-3299889999999818798674688999899667899999
Q gi|254780289|r 582 DEDT---SHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657 (682)
Q Consensus 582 ~~~~---~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l-~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~r 657 (682)
T Consensus 135 ~DKEGNEIsL~DiL~~~~d~v~-e~v~~~~~~~~l~~~~~~~L~~rE~~vi~~RyGL~~~~~~tQREIA~~LgISRSYVS 213 (228)
T TIGR02846 135 VDKEGNEISLIDILGSDEDSVI-EQVEKKLEIKKLYKKLNSVLKGREREVIEMRYGLKDGREKTQREIAKILGISRSYVS 213 (228)
T ss_pred CCCCCCEEEEEECCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCHHHH
T ss_conf 6767642300000168873168-888864459999999998740888999987436688895417899877086500454
Q ss_pred HHHHHHHHHHCC
Q ss_conf 999999998329
Q gi|254780289|r 658 QIEAKAIRKLKH 669 (682)
Q Consensus 658 qi~~~a~~~l~~ 669 (682)
T Consensus 214 RIEK~Al~Kl~~ 225 (228)
T TIGR02846 214 RIEKKALKKLYK 225 (228)
T ss_pred HHHHHHHHHHHH
T ss_conf 888999999986