HHsearch alignment for GI: 254780627 and conserved domain: COG3829
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms].
Probab=97.81 E-value=0.00024 Score=50.97 Aligned_cols=204 Identities=20% Similarity=0.336 Sum_probs=119.4
Q ss_pred CCCHHHHHHHCCCCCHHH--HHHHHHHHHHCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEH-
Q ss_conf 764478876328861478--99999999824100136555554898627888857999999999986306881686469-
Q gi|254780627|r 158 LDSRFVFSTFIEGSSNRV--ALTAAQSIAEVDSHGYTTVRLNPLFIHASVGLGKTHLLQAIANASIKRQPNLRVVYLTA- 234 (502)
Q Consensus 158 LNpryTFDnFVVG~sN~l--A~aAAkaVAe~pg~~~~~~~~NPLfi~G~~GlGKTHLl~ai~~~~~~~~~~~~v~y~~~- 234 (502)
T Consensus 238 ~~a~y~f~~Ii-g~S~~m~~~~~~akr~A~td---------stVLi~GESGTGKElfA~~IH~~S~R~--~~PFIaiNCa 305 (560)
T COG3829 238 LKAKYTFDDII-GESPAMLRVLELAKRIAKTD---------STVLILGESGTGKELFARAIHNLSPRA--NGPFIAINCA 305 (560)
T ss_pred CCCCCCHHHHC-CCCHHHHHHHHHHHHHCCCC---------CCEEEECCCCCCHHHHHHHHHHCCCCC--CCCEEEEECC
T ss_conf 44536610020-58999999999998633899---------828995378866899999987448434--7980787643
Q ss_pred ---------HHHHHH---HHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHH--H--------HHCCC
Q ss_conf ---------888999---9999861988999999740310205444453175069999999999--8--------85698
Q gi|254780627|r 235 ---------EYFMWR---FASAIRDNCALNLKDSLRNIDLLLIDDMQFLQGKLIQHEFCHLLNS--L--------LDSAK 292 (502)
Q Consensus 235 ---------e~F~~~---~~~a~~~~~~~~fr~~~r~~DvLliDDiqfl~gk~tqee~f~~~n~--l--------~~~gk 292 (502)
T Consensus 306 AiPe~LlESELFGye~GAFTGA~~~GK~GlfE--~A~gGTLFLDEIgemp-l~LQaKLLRVLQEkei~rvG~t~~~~vDV 382 (560)
T COG3829 306 AIPETLLESELFGYEKGAFTGASKGGKPGLFE--LANGGTLFLDEIGEMP-LPLQAKLLRVLQEKEIERVGGTKPIPVDV 382 (560)
T ss_pred CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEE--ECCCCEEEEHHHCCCC-HHHHHHHHHHHHHCEEEECCCCCCEEEEE
T ss_conf 38888888887276776424644579976054--4169837712320399-89999999987535378537887535678
Q ss_pred EEEEECCCCHHHH---CCCCHHHHHHHHCCEEEEECCC-------CHHHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHH-
Q ss_conf 7999648756761---3630345765302115775158-------889999999999988643116897-898999999-
Q gi|254780627|r 293 QVVAAADRPPSEL---ESLDPRIRSRLQGGVSVPLGLH-------DYEMRFSILKNRLAISQKEDPKLN-INEEVLMHV- 360 (502)
Q Consensus 293 qiv~tsd~~P~~l---~~l~~rL~SR~~~Gl~~~i~~P-------d~e~r~~Il~~k~~~~~~~~~~~~-l~~~v~~~l- 360 (502)
T Consensus 383 RIIAATN~nL~~~i~~G~FReDLYYRLN---V~~i~iPPLReR~eDI~~L~~~Fl~k~s~--~~~~~v~~ls~~a~~~L~ 457 (560)
T COG3829 383 RIIAATNRNLEKMIAEGTFREDLYYRLN---VIPITIPPLRERKEDIPLLAEYFLDKFSR--RYGRNVKGLSPDALALLL 457 (560)
T ss_pred EEEECCCCCHHHHHHCCCCHHHHEEEEC---EEEECCCCCCCCCCHHHHHHHHHHHHHHH--HCCCCCCCCCHHHHHHHH
T ss_conf 9994257589999863961655300304---01114777233820189999999999998--728876668999999998
Q ss_pred HHHCCCCHHHHHHHHHHHHHH
Q ss_conf 850278889999999999998
Q gi|254780627|r 361 ARTVTTSGRELDGAFNQLVFR 381 (502)
Q Consensus 361 a~~~~~~vR~Legal~~l~~~ 381 (502)
T Consensus 458 ~y~WPGNVRELeNviER~v~~ 478 (560)
T COG3829 458 RYDWPGNVRELENVIERAVNL 478 (560)
T ss_pred HCCCCCHHHHHHHHHHHHHHC
T ss_conf 689996099999999999810