HHsearch alignment for GI: 254780611 and conserved domain: PRK05658

>PRK05658 RNA polymerase sigma factor RpoD; Validated.
Probab=100.00  E-value=0  Score=502.02  Aligned_cols=254  Identities=27%  Similarity=0.438  Sum_probs=217.3

Q ss_pred             HHCCCCCCHHHHHHHHHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             407999998999999999998285---99999999943077875655557999988899999988899898621853456
Q gi|254780611|r   23 IRKIPMLEKQEEYVLAKRYREHGD---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF   99 (302)
Q Consensus        23 i~~~~~Lt~eee~~l~~~~~~~gd---~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~   99 (302)
T Consensus       354 ie~~~gl~i~elK~i~r~I~~-Ge~~a~~AKkeMiEANLRLVISIAKKYtNRGLqFLDLIQEGNiGLMkAVdKFeyrrGy  432 (620)
T PRK05658        354 IEEETGLTIEELKEINRQISK-GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY  432 (620)
T ss_pred             HHHHHCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHCCCCCCC
T ss_conf             999849799999999999999-8777899999999861899999999831489987899874407999999862845597


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             89997577899999985320246001102300358999999997887866244788824677888618983211000000
Q gi|254780611|r  100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR  179 (302)
Q Consensus       100 ~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~  179 (302)
T Consensus       433 KFSTYATWWIRQAITRaIaDqaRTIRiPVHmi-----etinkl~r~~r~l~qe~Grept~eEia~~~~~~~~kvr~vlki  507 (620)
T PRK05658        433 KFSTYATWWIRQAITRSIADQARTIRIPVHMI-----ETINKLNRISRQMLQEMGREPTPEELAERLGMPEDKVRKVLKI  507 (620)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHH-----HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             13577999999999999986177401518899-----9999999999999998289999999998949899999999986


Q ss_pred             CCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCC--CCCHHH
Q ss_conf             122343355202323453200000123568705655666666677799999962199999999999827888--889899
Q gi|254780611|r  180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLEN  257 (302)
Q Consensus       180 ~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~--~~Tl~E  257 (302)
T Consensus       508 ~~epiSle~pig~~--~ds~lgdfied~~~~~p~---~~~~~~~l~~~~~~vl~~Lt~rE~~vl~~RfGi~~~~~~TLee  582 (620)
T PRK05658        508 AKEPISLETPIGDD--EDSHLGDFIEDKNAELPI---DAATQESLREQTTDVLASLTPREAKVLRMRFGIDMNTDHTLEE  582 (620)
T ss_pred             CCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCHH---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHH
T ss_conf             48980243887888--876400101689999879---9999999999999998479999999999957999999678999


Q ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999977899999999999999999999974
Q gi|254780611|r  258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ  287 (302)
Q Consensus       258 Ia~~lgiS~eRVrQI~~~AL~kLR~~l~~~  287 (302)
T Consensus       583 vg~~f~vtRERiRQIEakalrklrhp~r~~  612 (620)
T PRK05658        583 VGKQFDVTRERIRQIEAKALRKLRHPSRSR  612 (620)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHCCCCHHH
T ss_conf             998829768989999999999856872578