HHsearch alignment for GI: 254780289 and conserved domain: PRK05658
>PRK05658 RNA polymerase sigma factor RpoD; Validated.
Probab=97.10 E-value=0.0011 Score=48.14 Aligned_cols=229 Identities=19% Similarity=0.234 Sum_probs=94.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHCCCHHHHHHHCCCCCCCHHHHH
Q ss_conf 9999999999998621005778878999999999999999999--------99999712535777763167768989999
Q gi|254780289|r 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL--------LRLAQSYGIKRDVFLERHQGRELDPHWVS 385 (682)
Q Consensus 314 ~~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L--------~rl~~k~~i~R~~Fi~~f~gnEt~~~wl~ 385 (682)
T Consensus 344 I~~~q~kL~~ie~~~gl~i~elK~i~r~I~~Ge~~a~~AKkeMiEANLRLVISIAKKYtNRGLqFLDLIQ--EGNiGLMk 421 (620)
T PRK05658 344 IQRLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ--EGNIGLMK 421 (620)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH--HCCHHHHH
T ss_conf 9999999999999849799999999999999877789999999986189999999983148998789987--44079999
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHH
Q ss_conf 9861355106765543456776532-233332222211268899999987653321124-----------6899987555
Q gi|254780289|r 386 YAKDFPEGEWKNFVACEVDSILKIR-NEIKSISVETGISISEFRHIVSMVRKGECEASI-----------AKKEMVEANL 453 (682)
Q Consensus 386 ~~~~~~~~~~~~~l~~~~~eI~~~q-~kL~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~-----------AK~~l~~anl 453 (682)
T Consensus 422 AVdKFeyrrGyKFSTYATWWIRQAITRaIaDqaRTIRiPVHmietinkl~r~~r~l~qe~Grept~eEia~~~~~~~~kv 501 (620)
T PRK05658 422 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERLGMPEDKV 501 (620)
T ss_pred HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHH
T ss_conf 99862845597135779999999999999861774015188999999999999999998289999999998949899999
Q ss_pred HHHHHHHHHHCCC----C----CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH
Q ss_conf 7899988752235----6----7778875443679999887438545731201028989999999997228704614205
Q gi|254780289|r 454 RLVISVAKKYTNR----G----LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525 (682)
Q Consensus 454 r~v~~~~~~~~~~----~----~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~ 525 (682)
T Consensus 502 r~vlki~~epiSle~pig~~~ds~lgdfied~~~~~---------------------p~~~~~~~~l~~~~~-------- 552 (620)
T PRK05658 502 RKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAEL---------------------PIDAATQESLREQTT-------- 552 (620)
T ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------------------HHHHHHHHHHHHHHH--------
T ss_conf 999986489802438878888764001016899998---------------------799999999999999--------
Q ss_pred HHHHHHH-HHHHHHHHHH----CCCCCCHHHHHHHCCCCHHHHHHH----HHHHCCCC
Q ss_conf 8898999-9999998776----088999789998709998999999----98608987
Q gi|254780289|r 526 RDKIHKV-VRTARRMSNK----IKREPTPEEIAKKLAMPVEGVRKV----LKITKEPI 574 (682)
Q Consensus 526 ~~~~~~~-~~~~~~~~~~----~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~ 574 (682)
T Consensus 553 -~vl~~Lt~rE~~vl~~RfGi~~~~~~TLeevg~~f~vtRERiRQIEakalrklrhp~ 609 (620)
T PRK05658 553 -DVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 609 (620)
T ss_pred -HHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
T ss_conf -998479999999999957999999678999998829768989999999999856872