HHsearch alignment for GI: 254780611 and conserved domain: PRK09210

>PRK09210 RNA polymerase sigma factor RpoD; Validated.
Probab=100.00  E-value=0  Score=528.39  Aligned_cols=266  Identities=29%  Similarity=0.457  Sum_probs=234.7

Q ss_pred             CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             87405999999840799999899999999999828599999999943077875655557999988899999988899898
Q gi|254780611|r   11 NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV   90 (302)
Q Consensus        11 ~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai   90 (302)
T Consensus        94 ~~~d~v~~YL~eI~~~pLLt~eEE~~La~r~~-~GD~~Ar~~Li~aNLRLVVsIAkkY~~~Gl~l~DLIQEGNiGLmkAV  172 (368)
T PRK09210         94 KINDPVRMYLKEIGRVPLLTAEEEIELAKRIE-EGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAV  172 (368)
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             55858999999956788999999999999988-15799999999983899999998666899898999998679999999


Q ss_pred             HHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCC
Q ss_conf             62185345689997577899999985320246001102300358999999997887866244788824677888618983
Q gi|254780611|r   91 KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE  170 (302)
Q Consensus        91 ~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~  170 (302)
T Consensus       173 eKFDp~rG~RFSTYA~WWIRqaI~raI~~q~r~IRiPvh~~e-----~~~kl~r~~r~L~q~lGrePt~eEIA~~lgi~~  247 (368)
T PRK09210        173 EKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE-----TINKLIRVQRQLLQELGRDPTPEEIAEEMDMPP  247 (368)
T ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCH
T ss_conf             972987799533466999999999999982785135424999-----999999999999998389998899998949989


Q ss_pred             CCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC
Q ss_conf             21100000012234335520232345320000012356870565566666667779999996219999999999982788
Q gi|254780611|r  171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE  250 (302)
Q Consensus       171 ~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~  250 (302)
T Consensus       248 e~V~~i~~~~~~~~SLd~pvg~e--~~s~l~d~i~D~~~~~p~e---~~~~~~l~~~l~~~L~~L~~REr~Il~~RfGL~  322 (368)
T PRK09210        248 EKVREILKIAQEPVSLETPIGEE--DDSHLGDFIEDQDATSPAD---HAAYELLKEQLEEVLDTLTDREENVLRLRFGLD  322 (368)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCC--CCCHHHHHHCCCCCCCHHH---HHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf             99999998538885668867887--7552875524899999899---999999999999998179999999999975999


Q ss_pred             --CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             --8889899999977899999999999999999999974
Q gi|254780611|r  251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ  287 (302)
Q Consensus       251 --~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~  287 (302)
T Consensus       323 ~~~~~TLeEIg~~lgvSRERVRQIE~kAL~KLR~~~~~~  361 (368)
T PRK09210        323 DGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK  361 (368)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHH
T ss_conf             689614999998969798999999999999976736878