HHsearch alignment for GI: 254780163 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=97.22 E-value=0.0072 Score=39.75 Aligned_cols=212 Identities=17% Similarity=0.262 Sum_probs=113.2
Q ss_pred HHHHHHHCHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCHHHHHHHHHHH------HHCCCCEEEEEHHHHHCCC
Q ss_conf 0246653458999999999877520445657874068861432003889999987------3047733772068861246
Q gi|254780163|r 474 NLGTVVYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLA------FALGVQLLRFDMSEYMERH 547 (798)
Q Consensus 474 ~l~~~v~GQ~~ai~~v~~~i~~~~~gl~~~~rP~g~flf~GptGvGKTelak~la------~~~~~~lir~dmsey~e~~ 547 (798)
T Consensus 181 ~lksgiatrnp~fnrmieqierva--~r-sr~p---~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~ 254 (531)
T COG4650 181 FLKSGIATRNPHFNRMIEQIERVA--IR-SRAP---ILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDT 254 (531)
T ss_pred HHHHCCCCCCHHHHHHHHHHHHHH--HH-CCCC---EEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCH
T ss_conf 997333215857788999999998--61-4697---68646887436689999999998887537862788630004752
Q ss_pred CCCHHCCCCCH-HCCCCC--CCCCCHHHHHCCCEEEEECCHHHCCHHHHHHHHHHHHHHHCC-CCCCCEECCCCEEEEEE
Q ss_conf 53011047800-025644--431003555158517774044550289999999987775021-77997761254299994
Q gi|254780163|r 548 AVSRLIGAPPG-YVGFGQ--GGILADSVDQNPYSVVLLDEIEKSHPDVLNILLQIMDYGILT-DQSGKKISFRNVILIMT 623 (798)
Q Consensus 548 ~vs~LiGappG-YvG~~e--gg~Lte~vr~~P~sVvl~DEiEKAh~~v~~~llqild~G~lt-d~~Gr~vdf~n~iii~T 623 (798)
T Consensus 255 amsalfghvkgaftga~~~r~gll----rsadggmlfldeigelgadeqamllkaieekrf~pfgsdr~v~sdfqlia-- 328 (531)
T COG4650 255 AMSALFGHVKGAFTGARESREGLL----RSADGGMLFLDEIGELGADEQAMLLKAIEEKRFYPFGSDRQVSSDFQLIA-- 328 (531)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHH----CCCCCCEEEHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHH--
T ss_conf 889987640013146334554424----33778657567433247527889999988712677887400031067764--
Q ss_pred CCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHCCHHHHCCCCEEEECCCCC----HHHHHHHHHHHHHHHHHHHHHCCCEE
Q ss_conf 24214553303689882111488999998728878817768289628899----99999999999999999998669889
Q gi|254780163|r 624 TNAGALEMSKARIGFGSSRNDDADKEALRNFLSPEFLNRLDSIIPFFPLS----SDIIRQVVHKFIMKLELQLQEKGISF 699 (798)
Q Consensus 624 sN~G~~~~~~~~~g~~~~~~~~~~~~~l~~~f~peflnRid~ii~F~~l~----~~~~~~i~~~~l~~l~~~l~~~~i~l 699 (798)
T Consensus 329 ---g--------------tvrdlrq~vaeg~fredl~arin-lwtf~lpgl~qr~ediepnldyel---erha~~~g~~v 387 (531)
T COG4650 329 ---G--------------TVRDLRQLVAEGKFREDLYARIN-LWTFTLPGLRQRQEDIEPNLDYEL---ERHASLTGDSV 387 (531)
T ss_pred ---H--------------HHHHHHHHHHCCCHHHHHHHHHH-EEEEECCCCCCCCCCCCCCCCHHH---HHHHHHHCCEE
T ss_conf ---1--------------18889999863613787887631-135406631157000698834789---99888618635
Q ss_pred EECHHHHHHHHHCCCCCCC
Q ss_conf 9988999999971898101
Q gi|254780163|r 700 HFSEEVINWLVSHGYDVKM 718 (798)
Q Consensus 700 ~~~~~~~~~l~~~~~~~~~ 718 (798)
T Consensus 388 rfntearra~l~fa~spqa 406 (531)
T COG4650 388 RFNTEARRAWLAFATSPQA 406 (531)
T ss_pred EEEHHHHHHHHHHCCCCHH
T ss_conf 5207988889975058301