HHsearch alignment for GI: 254780877 and conserved domain: COG3829
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms].
Probab=97.50 E-value=0.0019 Score=46.90 Aligned_cols=206 Identities=25% Similarity=0.369 Sum_probs=115.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHCC--CCCCCEEEECCCCCCHHHHHHHHHHH----------HHCCCCCHHHCCCEEEEEEH
Q ss_conf 9853333357899999996336--77786689528874077799999998----------73489984445743788731
Q gi|254780877|r 175 GKLDPVIGRDDEMRRAIQVLSR--RTKNNPVLIGDPGVGKTAIIEGLASR----------IINGDIPESLKGKRLMALDM 242 (853)
Q Consensus 175 GkLDPVIGRe~EI~~~~~iL~r--~~k~n~~lvGe~GvGKtaive~la~~----------i~~~~vp~~l~~~~i~~ld~ 242 (853)
T Consensus 242 y~f~~Iig~S~~m~~~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe~LlESELFGye~ 321 (560)
T COG3829 242 YTFDDIIGESPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPETLLESELFGYEK 321 (560)
T ss_pred CCHHHHCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHCCCC
T ss_conf 66100205899999999999863389982899537886689999998744843479807876433888888888727677
Q ss_pred HHHHCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHCCCCCCCCCCCHHHHHHHHHC-------------CCCEE
Q ss_conf 35421745420245458999999860799769996362773026665543358888765312-------------46604
Q gi|254780877|r 243 GALIAGAKFRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKTDGAMDASNLLKPSLA-------------RGELH 309 (853)
Q Consensus 243 ~~l~ag~~~rg~~e~r~~~i~~~~~~~~~~~ilfide~h~~~gaG~~~g~~Daan~LKP~La-------------rG~l~ 309 (853)
T Consensus 322 GAF-TGA~~~GK-----~GlfE~---A~gG-TLFLDEIgemp------l~L-QaKLLR-VLQEkei~rvG~t~~~~vDVR 383 (560)
T COG3829 322 GAF-TGASKGGK-----PGLFEL---ANGG-TLFLDEIGEMP------LPL-QAKLLR-VLQEKEIERVGGTKPIPVDVR 383 (560)
T ss_pred CCC-CCCCCCCC-----CCCEEE---CCCC-EEEEHHHCCCC------HHH-HHHHHH-HHHHCEEEECCCCCCEEEEEE
T ss_conf 642-46445799-----760544---1698-37712320399------899-999999-875353785378875356789
Q ss_pred EEEEECHHHHHHHHHCCH---HHHHCCCEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC-
Q ss_conf 899744899999730011---1320231111157776789999999789865414961015899999863332024576-
Q gi|254780877|r 310 CIGATTLDEYRKYIEKDP---ALARRFQSLLVGEPTVTDTISILRGLKERYEQHHKVRISDSALVSAAVLSNRYITDRF- 385 (853)
Q Consensus 310 ~IgaTT~~Eyrk~iEkD~---Al~RRFq~i~V~Eps~~~t~~iL~gl~~~yE~~H~V~i~d~al~~av~ls~rYi~~r~- 385 (853)
T Consensus 384 IIAATN-~nL~~~i~~G~FReDLYYRLNV~~i~iPPLReR~eDI~~L~~~F---------------l~k~s~~~~~~v~~ 447 (560)
T COG3829 384 IIAATN-RNLEKMIAEGTFREDLYYRLNVIPITIPPLRERKEDIPLLAEYF---------------LDKFSRRYGRNVKG 447 (560)
T ss_pred EEECCC-CCHHHHHHCCCCHHHHEEEECEEEECCCCCCCCCCHHHHHHHHH---------------HHHHHHHCCCCCCC
T ss_conf 994257-58999986396165530030401114777233820189999999---------------99999872887666
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 74778999999999875410222145788799999744
Q gi|254780877|r 386 LPDKAIDLMDEASARVRMQIDTKPEVLDELDRRIICLK 423 (853)
Q Consensus 386 lPDKAIDllDeA~A~~~i~~~~~P~~l~~l~r~i~~l~ 423 (853)
T Consensus 448 ls~~a~~~L---------~~y~WPGNVRELeNviER~v 476 (560)
T COG3829 448 LSPDALALL---------LRYDWPGNVRELENVIERAV 476 (560)
T ss_pred CCHHHHHHH---------HHCCCCCHHHHHHHHHHHHH
T ss_conf 899999999---------86899960999999999998