HHsearch alignment for GI: 254780567 and conserved domain: COG3829
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms].
Probab=97.13 E-value=0.015 Score=35.51 Aligned_cols=185 Identities=16% Similarity=0.229 Sum_probs=107.5
Q ss_pred CCCCCCCCCEEECCCHHH--HHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCC-----HHHHHH--HHHHHH
Q ss_conf 776688454165361899--99999851016788499987877786889999998627620-----135676--444546
Q gi|254780567|r 34 RCLGISRDDLLVHSAIEQ--AVRLIDSWPSWPSRVVILVGPSGSGKSCLANIWSDKSRSTR-----FSNIAK--SLDSIL 104 (246)
Q Consensus 34 ~~~~~~~dnFiv~~~N~~--A~~~i~~~~~~~~~~l~i~G~~GsGKTHLl~a~~~~~~~~~-----~~~~~~--~~~~~~ 104 (246)
T Consensus 238 ~~a~y~f~~Ii-g~S~~m~~~~~~akr~A~-tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe~LlESE 315 (560)
T COG3829 238 LKAKYTFDDII-GESPAMLRVLELAKRIAK-TDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPETLLESE 315 (560)
T ss_pred CCCCCCHHHHC-CCCHHHHHHHHHHHHHCC-CCCCEEEECCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHH
T ss_conf 44536610020-589999999999986338-9982899537886689999998744843479807876433888888888
Q ss_pred ----------------------HHHHHHHHHHHHHCCCCC-CHHHHHHHHHH----------HCCCCCEEEEECCCCCCH
Q ss_conf ----------------------666665334332100376-10335455543----------112342156403543200
Q gi|254780567|r 105 ----------------------IDTRKPVLLEDIDLLDFN-DTQLFHIINSI----------HQYDSSLLMTARTFPVSW 151 (246)
Q Consensus 105 ----------------------~~~~~~i~iddi~~~~~~-ee~lf~l~n~~----------~~~~~~iilts~~~p~~~ 151 (246)
T Consensus 316 LFGye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgempl~LQaKLLRVLQEkei~rvG~t~~~~vDVRIIAATN~nL~~~ 395 (560)
T COG3829 316 LFGYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEMPLPLQAKLLRVLQEKEIERVGGTKPIPVDVRIIAATNRNLEKM 395 (560)
T ss_pred HHCCCCCCCCCCCCCCCCCCEEECCCCEEEEHHHCCCCHHHHHHHHHHHHHCEEEECCCCCCEEEEEEEEECCCCCHHHH
T ss_conf 72767764246445799760544169837712320399899999999875353785378875356789994257589999
Q ss_pred ---HHHHHHHHHHHHHCCEEEECC----CCH-HHH-HHHHHHHHHHCC--CC-CCHHHHHHHHH-CCCCCHHHHHHHHHH
Q ss_conf ---223456678852122245078----897-899-999999866628--97-98899999994-066798999999999
Q gi|254780567|r 152 ---GVCLPDLCSRLKAATVVKISL----PDD-DFL-EKVIVKMFADRQ--IF-IDKKLAAYIVQ-RMERSLVFAEKLVDK 218 (246)
Q Consensus 152 ---~~~l~DL~SRl~~g~~~~I~~----pdd-e~~-~~il~k~~~~r~--i~-l~~~v~~yl~~-r~~Rs~~~l~~~l~~ 218 (246)
T Consensus 396 i~~G~FReDLYYRLNV~~-i~iPPLReR~eDI~~L~~~Fl~k~s~~~~~~v~~ls~~a~~~L~~y~WPGNVRELeNviER 474 (560)
T COG3829 396 IAEGTFREDLYYRLNVIP-ITIPPLRERKEDIPLLAEYFLDKFSRRYGRNVKGLSPDALALLLRYDWPGNVRELENVIER 474 (560)
T ss_pred HHCCCCHHHHEEEECEEE-ECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 863961655300304011-1477723382018999999999999872887666899999999868999609999999999
Q ss_pred HHH
Q ss_conf 999
Q gi|254780567|r 219 MDN 221 (246)
Q Consensus 219 Ld~ 221 (246)
T Consensus 475 ~v~ 477 (560)
T COG3829 475 AVN 477 (560)
T ss_pred HHH
T ss_conf 981