HHsearch alignment for GI: 254780413 and conserved domain: COG3829

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms].
Probab=98.61  E-value=3e-06  Score=63.77  Aligned_cols=229  Identities=15%  Similarity=0.111  Sum_probs=124.2

Q ss_pred             HHHHHHCCCCEEE-EECCEEEEECHHHHHHHCCCCHHHHCCCCCCHHHHCCCCCCHHHHHHHHHHHHHCCCEEEEEEEEE
Q ss_conf             9999634997899-709958872068898837984477224676112202455451356789998750586655999999
Q gi|254780413|r  323 PETVDKCPIPFFV-YSHGNLFYANPSFLLLTKYKSVDDIEIAGGLSTLLDAPKLSDNNAIKPVMLYRSDRTCIAASARLH  401 (820)
Q Consensus       323 ~~ild~lp~gv~i-~~~gri~~~N~a~~~l~G~~~~e~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  401 (820)
T Consensus         4 ~~~l~~~~~~~~vi~~~~~~~~~~~~a~~~~~~~~~~~i~~--~~~~i~~~~~~~------~v~----~~~~~~~~~~~~   71 (560)
T COG3829           4 EGILKSILDGPVVIDKNTGIDVANALALAKRQKNAEAVIGR--PLREILETLGME------RVE----QSRDKELTERLK   71 (560)
T ss_pred             HHHHHHCCCCEEEEECCCCEEEECHHHHHHHHCCEEEEECC--CHHHHHCCCCCC------EEE----CCCCCCEEEEEE
T ss_conf             44566504640899717754760337776510544787423--411111125862------341----067652013554


Q ss_pred             EEEECCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCHHEEECCCCEEEEEHHH
Q ss_conf             997389449999996324333200233344567888899999999-9999999999997422043078599838721568
Q gi|254780413|r  402 TIQWNRENSLAMTFIPFEKANQFPENMPQNGIEPEDVDTRINKRK-MEIEVMQLCSILEATSDGIAIINREGIILSTNRA  480 (820)
Q Consensus       402 ~i~~~g~~~~~l~~~~~~~~d~~~~~~~~~~~~~dit~~~~~~~~-L~~~~~~L~~ile~~~~gI~~~D~~G~i~~~N~a  480 (820)
T Consensus        72 --~~-~---~~~~~~~~~~~~~~~~~~g~~~~~~~~~e~~~~~~~~l~~~~~~l~~il~~~~~~l~vvD~~G~~i~~N~~  145 (560)
T COG3829          72 --LK-V---KRIVVVGKTPVDEQGRVVGVLEVFLDISEALELIEENLRQLRQRLEAILDSIDDGLLVVDEDGIIIYYNKA  145 (560)
T ss_pred             --CC-C---EEEEECCCCEEECCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCEEEECHH
T ss_conf             --06-4---04898178524127744455125451498999999999999999999986256745998699968998477


Q ss_pred             HHHHHCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCEEEEEEEEEECC---CCCEEEEE
Q ss_conf             998848960320786443345645627789999988606984022348887638972899999988717---88739999
Q gi|254780413|r  481 VSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLP---FSSCYSLT  557 (820)
Q Consensus       481 ~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~v  557 (820)
T Consensus       146 ~~~~~gl~~e~~~gk~~~~v~~~~~~s~~----l~vl~~~kp~~~~~~~~---~~~~~-i--~~~~pv~~~g~l~G~v~~  215 (560)
T COG3829         146 YAKLLGLSPEEVLGKHLLDVVSAGEDSTL----LEVLRTGKPIRDVVQTY---NGNKI-I--VNVAPVYADGQLIGVVGI  215 (560)
T ss_pred             HHHHHCCCHHHHCCCCHHHHHHCCCCCEE----HHHHHCCCCCEEEEEEE---CCCCE-E--EEECCEECCCCEEEEEEE
T ss_conf             89883999899819718988723677410----11341588512035530---48734-6--764447317827889975


Q ss_pred             EEEHHHHHHHHHHHHHHHHHHH
Q ss_conf             8651444434576544668878
Q gi|254780413|r  558 MHDISEWKQEKNKLSHAKKIAE  579 (820)
Q Consensus       558 ~~Dite~k~~e~el~~~~~~~e  579 (820)
T Consensus       216 ~~~~~~l~~l~~~~~~~~~~~~  237 (560)
T COG3829         216 SKDVSELERLTRELEESEGLLR  237 (560)
T ss_pred             ECCHHHHHHHHHHHHHHHHHHC
T ss_conf             2024888999999998753220