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