HHsearch alignment for GI: 254780916 and conserved domain: COG3829
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms].
Probab=100.00 E-value=0 Score=736.89 Aligned_cols=320 Identities=35% Similarity=0.548 Sum_probs=289.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 22111111112222222222222222344320488732777436799999984267543321012346554210024331
Q gi|254780916|r 133 ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF 212 (482)
Q Consensus 133 ~~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF 212 (482)
T Consensus 238 ~~a~y~f~~Iig~S~~m~~~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe~LlESELF 317 (560)
T COG3829 238 LKAKYTFDDIIGESPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPETLLESELF 317 (560)
T ss_pred CCCCCCHHHHCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHH
T ss_conf 44536610020589999999999986338998289953788668999999874484347980787643388888888872
Q ss_pred CCC-CCCCCCCCC-CCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf 125-555322111-001234466714751664200188999888877642001123553212343156521433211111
Q gi|254780916|r 213 GDV-DLQTKNSAQ-FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVK 290 (482)
Q Consensus 213 G~~-~~~~~~~~~-~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~ 290 (482)
T Consensus 318 Gye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgempl~LQaKLLRVLQEkei~rvG~t~~~~vDVRIIAATN~nL~~~i~ 397 (560)
T COG3829 318 GYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEMPLPLQAKLLRVLQEKEIERVGGTKPIPVDVRIIAATNRNLEKMIA 397 (560)
T ss_pred CCCCCCCCCCCCCCCCCCEEECCCCEEEEHHHCCCCHHHHHHHHHHHHHCEEEECCCCCCEEEEEEEEECCCCCHHHHHH
T ss_conf 76776424644579976054416983771232039989999999987535378537887535678999425758999986
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 12333799988654334467787744222255667776410112233332111110001223389868999999999987
Q gi|254780916|r 291 SHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVI 370 (482)
Q Consensus 291 ~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i 370 (482)
T Consensus 398 ~G~FReDLYYRLNV~~i~iPPLReR~eDI~~L~~~Fl~k~s~~~~~~v~~ls~~a~~~L~~y~WPGNVRELeNviER~v~ 477 (560)
T COG3829 398 EGTFREDLYYRLNVIPITIPPLRERKEDIPLLAEYFLDKFSRRYGRNVKGLSPDALALLLRYDWPGNVRELENVIERAVN 477 (560)
T ss_pred CCCCHHHHEEEECEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 39616553003040111477723382018999999999999872887666899999999868999609999999999981
Q ss_pred -HCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf -4389810688954542124454322343222222334443210000000011234445432589999999999999998
Q gi|254780916|r 371 -GLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKL 449 (482)
Q Consensus 371 -~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~ 449 (482)
T Consensus 478 ~~~~~~~I~~~~lp~~~l~~k~~~~~----------------~~----------~~~~~~~l~~~~e~~Ek~~I~~aL~~ 531 (560)
T COG3829 478 LVESDGLIDADDLPAFALEEKEPRPE----------------TT----------KQIEVGSLKEALEEYEKHLIREALER 531 (560)
T ss_pred CCCCCCEEEHHHCCHHHHCCCCCCCC----------------CC----------CCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 06886622252262023113466767----------------66----------67666448889999999999999998
Q ss_pred HCCCHHHHHHHHCCCHHHHHHHHHHHCCC
Q ss_conf 28727899978489988999999981888
Q gi|254780916|r 450 YRAQMSEVARRLGIGRSTLYRKIREYNIE 478 (482)
Q Consensus 450 ~~Gn~~~aA~~LGIsR~tL~rKlk~~gi~ 478 (482)
T Consensus 532 ~~gn~~~aAk~LgIsrttL~rKlkk~~l~ 560 (560)
T COG3829 532 HGGNKSKAAKELGISRTTLYRKLKKYGLR 560 (560)
T ss_pred HCCCHHHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf 27989899999699789999999985689