HHsearch alignment for GI: 254780611 and conserved domain: COG0568

>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription].
Probab=100.00  E-value=0  Score=482.39  Aligned_cols=266  Identities=38%  Similarity=0.576  Sum_probs=237.9

Q ss_pred             CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             87405999999840799999899999999999828-59999999994307787565555799998889999998889989
Q gi|254780611|r   11 NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG-DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA   89 (302)
Q Consensus        11 ~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~g-d~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~A   89 (302)
T Consensus        64 ~~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkA  143 (342)
T COG0568          64 RPAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKA  143 (342)
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCCHHHHHH
T ss_conf             13456889998876400159789999999998588559999999999889999999986337986889885250999999


Q ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCC
Q ss_conf             86218534568999757789999998532024600110230035899999999788786624478882467788861898
Q gi|254780611|r   90 VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS  169 (302)
Q Consensus        90 i~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis  169 (302)
T Consensus       144 VekFdp~rG~kFsTYA~wWIrqaI~raI~~q~rtIRipvh--~~e~~nkl~r~~r~l~q~---~~r~p~~eeia~~l~~~  218 (342)
T COG0568         144 VEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVH--QVELINKLRRVKRELLQE---LGREPTPEEIAEELGVS  218 (342)
T ss_pred             HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHH--HHHHHHHHHHHHHHHHHH---HCCCCCHHHHHHHHCCC
T ss_conf             9962966687211099999999999999974234657699--999999999999999998---45899799999995999


Q ss_pred             CCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHH
Q ss_conf             3211000000122343355202323453200000123568-7056556666666777999999621-9999999999982
Q gi|254780611|r  170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARR  247 (302)
Q Consensus       170 ~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~-~~~~~~~e~~e~~~~~~~L~~~l~~-L~~rEr~II~~ry  247 (302)
T Consensus       219 ~~~V~~m~~~~~~~~SLd~~ig~ded~--~l~d~leD~~~~~p~~~~~~~----~~~~~~~~~L~~~Lt~rE~~Vi~~R~  292 (342)
T COG0568         219 PDKVREMLKRASEPISLDTPIGDDEDS--ELGDFLEDDKSVSPEDAVERE----SLKEDLNEVLAEALTERERRVIRLRF  292 (342)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCC--HHHHHHHCCCCCCHHHHHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             999999998653676767848888520--788876426878989999988----89999999987159999999999995


Q ss_pred             CC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             78--88889899999977899999999999999999999974
Q gi|254780611|r  248 LQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ  287 (302)
Q Consensus       248 ~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~  287 (302)
T Consensus       293 gl~~~~~~TLeevg~~~~vsrERvRQIE~kAl~KLr~~~~~~  334 (342)
T COG0568         293 GLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERS  334 (342)
T ss_pred             CCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             567999551999998959869999999999999998706322