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