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