HHsearch alignment for GI: 254780611 and conserved domain: PRK07406

>PRK07406 RNA polymerase sigma factor RpoD; Validated.
Probab=100.00  E-value=0  Score=509.14  Aligned_cols=265  Identities=28%  Similarity=0.463  Sum_probs=232.6

Q ss_pred             CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH---------------------------------------HCCHHHHHH
Q ss_conf             74059999998407999998999999999998---------------------------------------285999999
Q gi|254780611|r   12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------------------HGDLSAAHR   52 (302)
Q Consensus        12 ~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~---------------------------------------~gd~~Ar~~   52 (302)
T Consensus        73 t~D~vr~YL~eIg~~~LLt~~eEi~La~~i~~~~~le~~~~~l~~~~~~~p~~~ewa~~~~~~~~~l~~~~~~g~~Ar~~  152 (385)
T PRK07406         73 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGHFPSVEEWAELVDMPLPKFRRRLMLGRRAKEK  152 (385)
T ss_pred             CCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf             88849999986277679999999999999999999999999988741665427999988088889999999879999999


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHH
Q ss_conf             99943077875655557999988899999988899898621853456899975778999999853202460011023003
Q gi|254780611|r   53 LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ  132 (302)
Q Consensus        53 Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~  132 (302)
T Consensus       153 LI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniGLirAvEKFDp~rG~RFSTYA~WWIRqaI~RaI~~~sr~IRlP~h~~-  231 (385)
T PRK07406        153 MVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLY-  231 (385)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEHHHHHHHHHHHHHHHHCCCEECCHHHHH-
T ss_conf             9999899999999865689989889999858999999998196548822110299999999999997386120208999-


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCH
Q ss_conf             58999999997887866244788824677888618983211000000122343355202323453200000123568705
Q gi|254780611|r  133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE  212 (302)
Q Consensus       133 r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~  212 (302)
T Consensus       232 ----e~l~ki~k~~~~L~~~lGr~Pt~eEIA~~l~i~~e~v~~~~~~~~~~vSLD~pvg~~~--ds~l~D~i~~d~~~pe  305 (385)
T PRK07406        232 ----ETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEE--DSRLGDFIEADGETPE  305 (385)
T ss_pred             ----HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCC--CCCHHHHHHCCCCCHH
T ss_conf             ----9999999999999987089986999999939999999999985489865458888765--3318889863599999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             65566666667779999996219999999999982788--8889899999977899999999999999999999974
Q gi|254780611|r  213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ  287 (302)
Q Consensus       213 ~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~  287 (302)
T Consensus       306 ~~~----~~~~lr~~L~~~L~~L~eREr~II~lRfGL~dg~~~TL~EIg~~lgISRERVRQIE~rAL~KLR~p~r~~  378 (385)
T PRK07406        306 DDV----SKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNS  378 (385)
T ss_pred             HHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHH
T ss_conf             999----9999999999998649999999999975899999646999998979599999999999999967717789