HHsearch alignment for GI: 254780289 and conserved domain: TIGR02950

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family; InterPro: IPR014296 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 family of RNA polymerase sigma factors is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors, as two proteins from this family are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these do not apparently represent the same two sigma factors in each species). One of these proteins is designated as SigM in B. subtilis (SP: SIGM_BACSU) and is activated by various stressors , .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=91.97  E-value=0.62  Score=26.32  Aligned_cols=77  Identities=18%  Similarity=0.210  Sum_probs=59.6

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             04756238988998999999999999999973299889999999818798674688999899667899999999999998
Q gi|254780289|r  587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK  666 (682)
Q Consensus       587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~  666 (682)
T Consensus        81 ~~~~~~~l~~~~~pE~~~~~K~~~e~~~~~l~~Lpe~yr~vl~Lr~----~~efSYkEia~~~n~sl~~vK~~LfRaR~e  156 (162)
T TIGR02950        81 LIGELELLDPVESPEHELLIKEELEELTKHLSSLPENYRTVLLLRE----FKEFSYKEIAELLNLSLAKVKSELFRARKE  156 (162)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             2000131276441089999999999999998527087656567543----126688899998456022100444487799


Q ss_pred             H
Q ss_conf             3
Q gi|254780289|r  667 L  667 (682)
Q Consensus       667 l  667 (682)
T Consensus       157 L  157 (162)
T TIGR02950       157 L  157 (162)
T ss_pred             H
T ss_conf             9