HHsearch alignment for GI: 254780916 and conserved domain: COG4650
>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms].
Probab=100.00 E-value=9.8e-45 Score=335.93 Aligned_cols=317 Identities=22% Similarity=0.310 Sum_probs=268.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCC-CCCEEEEEECCCCCHHHHHHHHHHHCC---CCCCCCCCCCCCCCCCCCCCHHHHHCCC
Q ss_conf 111222222222222222234-432048873277743679999998426---7543321012346554210024331125
Q gi|254780916|r 140 DSLIAVSPAMIQVVDLARKAG-DCAIPIMIQGEFGVGKKRLSRFIHESG---KRAFFPFFIVNCGMIDQDKIEKFLFGDV 215 (482)
Q Consensus 140 ~~LiG~S~~m~~v~~~i~~~a-~~~~~vli~Ge~GtGK~~~A~~iH~~s---~r~~~~fi~v~c~~~~~~~~e~~lFG~~ 215 (482)
T Consensus 184 sgiatrnp~fnrmieqierva~rsr~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghv 263 (531)
T COG4650 184 SGIATRNPHFNRMIEQIERVAIRSRAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHV 263 (531)
T ss_pred HCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCHHHHHHHHHH
T ss_conf 33321585778899999999861469768646887436689999999998887537862788630004752889987640
Q ss_pred C-CCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHH
Q ss_conf 5-553221110012344667147516642001889998888776420011235532123431565214332111111233
Q gi|254780916|r 216 D-LQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF 294 (482)
Q Consensus 216 ~-~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~f 294 (482)
T Consensus 264 kgaftga~~~r~gllrsadggmlfldeigelgadeqamllkaieekrf~pfgsdr~v~sdfqliagtvrdlrq~vaeg~f 343 (531)
T COG4650 264 KGAFTGARESREGLLRSADGGMLFLDEIGELGADEQAMLLKAIEEKRFYPFGSDRQVSSDFQLIAGTVRDLRQLVAEGKF 343 (531)
T ss_pred HCCCCCCHHHHHHHHCCCCCCEEEHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCH
T ss_conf 01314633455442433778657567433247527889999988712677887400031067764118889999863613
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC------CCCCCHHHHHHHHHHH
Q ss_conf 3799988654334467787744222255667776410112233332111110001223------3898689999999999
Q gi|254780916|r 295 RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY------PWIDNVQELKNILLRA 368 (482)
Q Consensus 295 r~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y------~WPGNvREL~n~i~r~ 368 (482)
T Consensus 344 redl~arinlwtf~lpgl~qr~ediepnldyelerha~~~g~~-vrfntearra~l~fa~spqa~w~gnfrelsasvtrm 422 (531)
T COG4650 344 REDLYARINLWTFTLPGLRQRQEDIEPNLDYELERHASLTGDS-VRFNTEARRAWLAFATSPQATWRGNFRELSASVTRM 422 (531)
T ss_pred HHHHHHHHHEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHCCE-EEEEHHHHHHHHHHCCCCHHHHCCCHHHHHHHHHHH
T ss_conf 7878876311354066311570006988347899988861863-552079888899750583011126688876899999
Q ss_pred HHHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 87438981068895454212445432234322222233444321000000001123444543258999999999999999
Q gi|254780916|r 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMK 448 (482)
Q Consensus 369 ~i~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~ 448 (482)
T Consensus 423 atlad~grit~~~ve~ei~rlr~~w~~~~p--------------~~l~~llg---------~~a~aldlfdrmqle~v~~ 479 (531)
T COG4650 423 ATLADSGRITLDVVEDEINRLRYNWQESRP--------------SALTALLG---------AEAEALDLFDRMQLEHVIA 479 (531)
T ss_pred HHHHCCCCEEHHHHHHHHHHHHHHHHHCCC--------------CHHHHCCC---------CCHHHHHHHHHHHHHHHHH
T ss_conf 887127830088789999999987641386--------------02330346---------6527765788888999999
Q ss_pred HHCCCHH--HHH-HHHCCCH---------HHHHHHHHHHCCCCC
Q ss_conf 8287278--999-7848998---------899999998188814
Q gi|254780916|r 449 LYRAQMS--EVA-RRLGIGR---------STLYRKIREYNIEVD 480 (482)
Q Consensus 449 ~~~Gn~~--~aA-~~LGIsR---------~tL~rKlk~~gi~~d 480 (482)
T Consensus 480 vcr~aktls~agr~lf~vsrq~ka~vndadrlrkylarfgl~w~ 523 (531)
T COG4650 480 ICRQAKSLSAAGRQLFDVSRQGKASVNDADRLRKYLARFGLTWE 523 (531)
T ss_pred HHHCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCHH
T ss_conf 98711516577677753333036898708999999998488799