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