HHsearch alignment for GI: 254780611 and conserved domain: COG1595

>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription].
Probab=99.45  E-value=2.7e-11  Score=95.04  Aligned_cols=170  Identities=16%  Similarity=0.183  Sum_probs=121.6

Q ss_pred             HHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             82859999999994307787565555799998889999998889989862185345689997577899999985320246
Q gi|254780611|r   43 EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS  122 (302)
Q Consensus        43 ~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~  122 (302)
T Consensus        10 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~r   87 (182)
T COG1595          10 LRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRKR   87 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHC-CC-CCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             875178899999999999999999996884309999999999999733311-67-8878999999999999999997610


Q ss_pred             CHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHC
Q ss_conf             00110230035899999999788786624478882467788861898321100000012234335520232345320000
Q gi|254780611|r  123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD  202 (302)
Q Consensus       123 ~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d  202 (302)
T Consensus        88 ----------------------~~~~~~~~~------------------------~-----~------~-----------   99 (182)
T COG1595          88 ----------------------RRARVEEAD------------------------L-----L------P-----------   99 (182)
T ss_pred             ----------------------HCCHHHHCC------------------------C-----C------C-----------
T ss_conf             ----------------------132001000------------------------2-----4------5-----------


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf             01235687056556666666777999999621999999999998278888898999999778999999999999999999
Q gi|254780611|r  203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE  282 (302)
Q Consensus       203 ~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~  282 (302)
T Consensus       100 --~~~~~~~~~~--~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~g--ls~~EIA~~l~i~~~tVks~l~ra~~~l~~  173 (182)
T COG1595         100 --EEADPAPDLA--ELLLAEEELERLRRALARLPPRQREAFLLRYLEG--LSYEEIAEILGISVGTVKSRLHRARKKLRE  173 (182)
T ss_pred             --CCCCCCCHHH--HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             --4345670267--8887678999999999839999999999999859--999999989599999999999999999999


Q ss_pred             HHHHHH
Q ss_conf             999740
Q gi|254780611|r  283 SIQKQV  288 (302)
Q Consensus       283 ~l~~~~  288 (302)
T Consensus       174 ~l~~~~  179 (182)
T COG1595         174 QLEEAG  179 (182)
T ss_pred             HHHHHC
T ss_conf             875501