HHsearch alignment for GI: 254780611 and conserved domain: PRK12537
>PRK12537 RNA polymerase sigma factor; Provisional.
Probab=99.71 E-value=1.5e-15 Score=123.53 Aligned_cols=177 Identities=11% Similarity=0.116 Sum_probs=122.8
Q ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
Q ss_conf 89999999999982859999999994307787565555799998889999998889989862185345689997577899
Q gi|254780611|r 31 KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110 (302)
Q Consensus 31 ~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr 110 (302)
T Consensus 7 p~d~e~ll~~~~-~GD~~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDivQe~Fl~~~~~~~~~~~~~~-~~~~WL~~Iar 84 (184)
T PRK12537 7 PFDYEACLQACA-RGERRALQRLYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTKAASFDAARG-SARGWIYSVTR 84 (184)
T ss_pred CCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCC-CHHHHHHHHHH
T ss_conf 999999999999-5889999999999999999999999299999999999999999986041684426-39999999999
Q ss_pred HHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHC
Q ss_conf 99998532024600110230035899999999788786624478882467788861898321100000012234335520
Q gi|254780611|r 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190 (302)
Q Consensus 111 ~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i 190 (302)
T Consensus 85 n~~~~~lR~~~r~~-----------------------------~~~~~--------------------------~~~~-~ 108 (184)
T PRK12537 85 HLALNTLRDTRREV-----------------------------VLDDD--------------------------ASEQ-A 108 (184)
T ss_pred HHHHHHHHHHCCCC-----------------------------CCCCH--------------------------HHHH-C
T ss_conf 99999999850656-----------------------------66510--------------------------0210-1
Q ss_pred CCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf 23234532000001235687056556666666777999999621999999999998278888898999999778999999
Q gi|254780611|r 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270 (302)
Q Consensus 191 ~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVr 270 (302)
T Consensus 109 ~---~~----------~~~~~~~----~~~~~~~~~~l~~~l~~L~~~~r~~i~l~~~eg--~s~~EIA~~l~is~~TVk 169 (184)
T PRK12537 109 T---AQ----------GWQEIID----DFDLWVNSGKIHRCLEQLEPARRNCILHAYVDG--CSHAEIAQRLGAPLGTVK 169 (184)
T ss_pred C---CC----------CCCCCCC----HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHH
T ss_conf 3---46----------7777556----798999999999999809998999999988439--999999999892999999
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99999999999999
Q gi|254780611|r 271 QIEARAFKKVQESI 284 (302)
Q Consensus 271 QI~~~AL~kLR~~l 284 (302)
T Consensus 170 ~rl~rA~~~LR~~L 183 (184)
T PRK12537 170 AWIKRSLKALRECM 183 (184)
T ss_pred HHHHHHHHHHHHHC
T ss_conf 99999999999872