HHsearch alignment for GI: 254780270 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=95.10 E-value=0.1 Score=31.76 Aligned_cols=213 Identities=22% Similarity=0.363 Sum_probs=106.2
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHHH------HHCCCEEEEECCCCCC---HHHHCCCCC-CCCCCCCHHHHHHHHHCCCC
Q ss_conf 4673599860565650279999997------7088249986188888---888356320-01456712899999832788
Q gi|254780270|r 364 NKGLILCFVGPPGVGKTSLAQSIAK------ATGRQYVRMSLGGVYD---EADIRGHRR-TYIGSMPGRIIQSLKRAKRS 433 (820)
Q Consensus 364 ~~g~il~l~gppgvGKts~~~sia~------al~r~f~~islgg~~d---~~~i~gh~~-ty~ga~pg~ii~~l~~~~~~ 433 (820)
T Consensus 207 sr~p~l-l~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghvkgaftga~~~r--~gllrsad- 282 (531)
T COG4650 207 SRAPIL-LNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARESR--EGLLRSAD- 282 (531)
T ss_pred CCCCEE-EECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCHHHHHHHHHHHCCCCCCHHHH--HHHHCCCC-
T ss_conf 469768-64688743668999999999888753786278863000475288998764001314633455--44243377-
Q ss_pred CEEEEEECHHHHHHHCCCCHHHHHHHHCCCCCCCCEE----EEECCCCCCCCCEEEEE-ECCCC-C-C-----CHHHCCC
Q ss_conf 7399993315542311771155665540600168133----20103523644279999-34865-5-4-----4131172
Q gi|254780270|r 434 NPLLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFV----DHYLEVEYDLSDVMFIM-TANTL-N-I-----PLPLMDR 501 (820)
Q Consensus 434 npv~~ldeidk~~~~~~gdp~~allevldp~qn~~f~----d~y~~~~~dls~v~fi~-tan~~-~-i-----~~~l~dr 501 (820)
T Consensus 283 ggmlfldeigelgadeq----amllkaie---ekrf~pfgsdr~v~sdfq-----liagtvrdlrq~vaeg~fredl~ar 350 (531)
T COG4650 283 GGMLFLDEIGELGADEQ----AMLLKAIE---EKRFYPFGSDRQVSSDFQ-----LIAGTVRDLRQLVAEGKFREDLYAR 350 (531)
T ss_pred CCEEEHHHHHHCCCCHH----HHHHHHHH---HHCCCCCCCCCCCCCCHH-----HHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 86575674332475278----89999988---712677887400031067-----7641188899998636137878876
Q ss_pred --EEEEEECCCCH-HHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCC-CCCHHHHHHHHH-HHHHHHHHHHH
Q ss_conf --47998258786-89998999860898998625781313228999999973177-410234788879-99989876542
Q gi|254780270|r 502 --MEIIRIAGYTE-EEKLQIAKNHLVKKVLTEHALKQEECCISDGVLLDIIRLFT-HEAGVRSFERAL-MKIARKAVTKI 576 (820)
Q Consensus 502 --me~i~~~~y~~-~ek~~i~~~~l~p~~~~~~~~~~~~~~~~~~~i~~ii~~Yt-~EaGvR~l~r~i-~~i~r~~~~~~ 576 (820)
T Consensus 351 inlwtf~lpgl~qr~ediepnldyelerha~~~---g~~vrfntearra~l~fa~spqa~w~gnfrelsasvtrmatl-- 425 (531)
T COG4650 351 INLWTFTLPGLRQRQEDIEPNLDYELERHASLT---GDSVRFNTEARRAWLAFATSPQATWRGNFRELSASVTRMATL-- 425 (531)
T ss_pred HHEEEEECCCCCCCCCCCCCCCCHHHHHHHHHH---CCEEEEEHHHHHHHHHHCCCCHHHHCCCHHHHHHHHHHHHHH--
T ss_conf 311354066311570006988347899988861---863552079888899750583011126688876899999887--
Q ss_pred HCCCCCEECCCHHHHHHHHCCCCCC
Q ss_conf 1178520127967867530520003
Q gi|254780270|r 577 VKNSDTTVSINENNLQDYLGVPRYK 601 (820)
Q Consensus 577 ~~~~~~~~~i~~~~l~~~lg~~~~~ 601 (820)
T Consensus 426 a----d~grit~~~ve~ei~rlr~~ 446 (531)
T COG4650 426 A----DSGRITLDVVEDEINRLRYN 446 (531)
T ss_pred H----CCCCEEHHHHHHHHHHHHHH
T ss_conf 1----27830088789999999987