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