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