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