HHsearch alignment for GI: 254780611 and conserved domain: PRK05911

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed.
Probab=100.00  E-value=0  Score=415.83  Aligned_cols=244  Identities=20%  Similarity=0.270  Sum_probs=202.6

Q ss_pred             CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf             98999999999998285999999999430778756555579---999888999999888998986218534568999757
Q gi|254780611|r   30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM  106 (302)
Q Consensus        30 t~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~---~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~  106 (302)
T Consensus         5 ~~~~~~~lw~~y~~~~d~~ar~~LI~~nLrLV~~iA~r~~~~~p~~v~~~DLiQeG~iGLi~AiekFDp~kG~rFsTYA~   84 (257)
T PRK05911          5 KTQNIAETWQLYWETQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL   84 (257)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
T ss_conf             06789999999988399999999999839999999999864699999889999999999999998329866999488769


Q ss_pred             HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC--CCC
Q ss_conf             789999998532024600110230035899999999788786624478882467788861898321100000012--234
Q gi|254780611|r  107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDE  184 (302)
Q Consensus       107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~--~~~  184 (302)
T Consensus        85 ~wIr~aI~~~lr~~~~---lpr~~-----~~~~~ki~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~  156 (257)
T PRK05911         85 FLIKAAIIDDLRKQDW---VPRSV-----HQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALIL  156 (257)
T ss_pred             HHHHHHHHHHHHHCCC---CCHHH-----HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEE
T ss_conf             9989999999987162---55799-----999999999999999986889999999988397999999999853552223


Q ss_pred             CHHHHCCCC--CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf             335520232--345320000012356870565566666667779999996219999999999982788888989999997
Q gi|254780611|r  185 SLNALINSS--DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF  262 (302)
Q Consensus       185 SLd~~i~~~--d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~l  262 (302)
T Consensus       157 sl~~~~~~~~d~~~~~~l~d~i~d~~~~~~~~---~~~~~~~~~~L~~al~~L~erEr~Ii~lry~e~--~Tl~EIg~~l  231 (257)
T PRK05911        157 SLNEEFPSQSDDEAGLALEERIADERAETGYD---VVDKKEFSSILANAILALEEKERKVMALYYYEE--LVLKEIGKIL  231 (257)
T ss_pred             CCCCCCCCCCCCCCCCCHHHHCCCCCCCCHHH---HHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC--CCHHHHHHHH
T ss_conf             05788887888876530777467988899899---999999999999998658999999999874898--7899999897


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             789999999999999999999997
Q gi|254780611|r  263 EVSRERVRQIEARAFKKVQESIQK  286 (302)
Q Consensus       263 giS~eRVrQI~~~AL~kLR~~l~~  286 (302)
T Consensus       232 gvS~eRVrQi~~~AL~kLR~~L~a  255 (257)
T PRK05911        232 GVSESRVSQIHSKALLKLRAALSA  255 (257)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             988999999999999999999986