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