HHsearch alignment for GI: 254780611 and conserved domain: PRK12529

>PRK12529 RNA polymerase sigma factor; Provisional.
Probab=98.94  E-value=1.7e-07  Score=69.59  Aligned_cols=165  Identities=13%  Similarity=0.118  Sum_probs=102.0

Q ss_pred             HCCHHHHHHHHHHHHHHH-HHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             285999999999430778-75655557999-9888999999888998986218534568999757789999998532024
Q gi|254780611|r   44 HGDLSAAHRLVTSHLRLV-VKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW  121 (302)
Q Consensus        44 ~gd~~Ar~~Li~~nlrlV-~~iA~~y~~~g-~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~  121 (302)
T Consensus         9 ~~D~~a~~~Ly~~h~~~L~~~l~~Rl~~~~~~~AeDl~QDvFlrl~~~~~~~~~~~i~~p~a~L~rIA~Nl~id------   82 (178)
T PRK12529          9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVS------   82 (178)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH------
T ss_conf             44799999999999999999999982899835469999999999997344456432334899999999999999------


Q ss_pred             CCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHH
Q ss_conf             60011023003589999999978878662447888246778886189832110000001223433552023234532000
Q gi|254780611|r  122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ  201 (302)
Q Consensus       122 ~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~  201 (302)
T Consensus        83 ----------------~~Rr~~~~~~~----------le~~------------------------~--------------   98 (178)
T PRK12529         83 ----------------WRRRQSLELAW----------LEAL------------------------A--------------   98 (178)
T ss_pred             ----------------HHHHHHHHHHH----------HHHH------------------------H--------------
T ss_conf             ----------------99988889878----------9988------------------------6--------------


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             00123568705655666666677799999962199999999999827888889899999977899999999999999999
Q gi|254780611|r  202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ  281 (302)
Q Consensus       202 d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR  281 (302)
T Consensus        99 ~~~~~~~pspE~~~~~~----e~l~~l~~al~~Lp~r~R~vF~L~r~eG--ls~~EIAe~LgiS~~tV~~~l~rAl~~C~  172 (178)
T PRK12529         99 TLPEPLHPSPEQQSVIL----ETLHEIDALLDTLRPRVKQAFLMATLDG--MKQKDIAQALDIALPTVKKYIHQAYVTCL  172 (178)
T ss_pred             CCCCCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             47866689989999999----9999999998569978889987998829--99999999989599999999999999999


Q ss_pred             HHH
Q ss_conf             999
Q gi|254780611|r  282 ESI  284 (302)
Q Consensus       282 ~~l  284 (302)
T Consensus       173 ~~~  175 (178)
T PRK12529        173 SLM  175 (178)
T ss_pred             HHC
T ss_conf             867