HHsearch alignment for GI: 254780611 and conserved domain: PRK07405

>PRK07405 RNA polymerase sigma factor SigD; Validated.
Probab=100.00  E-value=0  Score=513.91  Aligned_cols=265  Identities=25%  Similarity=0.457  Sum_probs=233.9

Q ss_pred             CCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH---------------------------------------HCCHHH
Q ss_conf             55874059999998407999998999999999998---------------------------------------285999
Q gi|254780611|r    9 IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------------------HGDLSA   49 (302)
Q Consensus         9 ~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~---------------------------------------~gd~~A   49 (302)
T Consensus         4 ~~~~~d~~~~Yl~ei~~~~LLt~eeE~~la~~i~~~~~~~~~~~~l~~~~~~~~~~~~~a~a~~~~~~~l~~~~~~g~~A   83 (318)
T PRK07405          4 AKTATDLVRTYLREIGRVPLLTHEEEILYGKQVQRLMALQEIRESLAEELGREPSDLEWAKAAKLSEEELRRAIAEGEAA   83 (318)
T ss_pred             CCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             87898759999998177679999999999999999988899999999871678746788876045689999987627999


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC
Q ss_conf             99999943077875655557999988899999988899898621853456899975778999999853202460011023
Q gi|254780611|r   50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT  129 (302)
Q Consensus        50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~  129 (302)
T Consensus        84 ~~~lv~~NLRLVv~iAk~y~~~gl~~~DLIQEGniGLi~AvekFDp~rG~rFSTYA~wWIrq~I~r~i~~~~r~IRlP~~  163 (318)
T PRK07405         84 KRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIH  163 (318)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf             99999981999999998665799798899998689999999970976598022200999999999999976985168778


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC
Q ss_conf             00358999999997887866244788824677888618983211000000122343355202323453200000123568
Q gi|254780611|r  130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD  209 (302)
Q Consensus       130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~  209 (302)
T Consensus       164 ~~~-----~~~ki~~~~~~L~~~lGr~Pt~~EIAe~lgi~~e~V~~~l~~~~~~~SLD~~v~d~--~~~~l~dll~D~~~  236 (318)
T PRK07405        164 ITE-----KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDN--QDTELGELLEDDGA  236 (318)
T ss_pred             HHH-----HHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCC--CCCHHHHHHCCCCC
T ss_conf             999-----99999999999998718986489999885999999999999807886768888999--86405667547889


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             7056556666666777999999621999999999998278--88889899999977899999999999999999999
Q gi|254780611|r  210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI  284 (302)
Q Consensus       210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l  284 (302)
T Consensus       237 ~pe~~~~----~~~l~~~L~~~L~~L~eREr~II~lRfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~~~  309 (318)
T PRK07405        237 SPEDFAT----QSSLRRDLERLMADLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKRK  309 (318)
T ss_pred             CHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             8799999----999999999999629998999999980778989747999998979599999999999999998728