HHsearch alignment for GI: 254780163 and conserved domain: COG3829

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms].
Probab=97.24  E-value=0.0013  Score=45.03  Aligned_cols=175  Identities=23%  Similarity=0.394  Sum_probs=92.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHC--CCCCCEEEECCCCCHHHHHHHHHHHHHHCCC--------------CCHHHHEEEEEE
Q ss_conf             611222178999999998622--6778748966764116689999999985489--------------883452014455
Q gi|254780163|r  202 KVDILVGRHEEINRTIQILCR--RSKNNPLYVGDPGVGKTAIAEGFAKQIVDGM--------------VPDILLGARIFS  265 (798)
Q Consensus       202 KLDPVIGRd~EI~riiqIL~R--R~KNn~~lvG~~gvGktaive~la~~i~~~~--------------vp~~l~~~~i~~  265 (798)
T Consensus       243 ~f~~Iig~S~~m~~~~~~akr~A~tdstVLi~GESGTGKEl----fA~~IH~~S~R~~~PFIaiNCaAiPe~LlESELFG  318 (560)
T COG3829         243 TFDDIIGESPAMLRVLELAKRIAKTDSTVLILGESGTGKEL----FARAIHNLSPRANGPFIAINCAAIPETLLESELFG  318 (560)
T ss_pred             CHHHHCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHH----HHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHC
T ss_conf             61002058999999999998633899828995378866899----99998744843479807876433888888888727


Q ss_pred             EEHHHHHCCCCC---CCHHHHHHHHHHHHHCCCCCEEEEECCHHHHHCCCCCCCCCCCH---HHHHHHHHCCC-------
Q ss_conf             404675306343---12378999999987203898399973616630155444344777---88887663026-------
Q gi|254780163|r  266 LDMGNLIAGTRY---RGDFEERIKKIVKEIESYANAILYIDEIHTLVGAGSASGISVDA---SNLLKPALSSG-------  332 (798)
Q Consensus       266 ld~~~l~ag~~~---rg~fe~r~~~~~~~~~~~~~~ilfideih~ligag~~~g~~~d~---an~lkP~L~rg-------  332 (798)
T Consensus       319 ye~GAF-TGA~~~GK~GlfE~----------A~gG-TLFLDEIgem-----------pl~LQaKLLR-VLQEkei~rvG~  374 (560)
T COG3829         319 YEKGAF-TGASKGGKPGLFEL----------ANGG-TLFLDEIGEM-----------PLPLQAKLLR-VLQEKEIERVGG  374 (560)
T ss_pred             CCCCCC-CCCCCCCCCCCEEE----------CCCC-EEEEHHHCCC-----------CHHHHHHHHH-HHHHCEEEECCC
T ss_conf             677642-46445799760544----------1698-3771232039-----------9899999999-875353785378


Q ss_pred             ------CEEEEEECCHHHHHHHHHCCHHHHHHC---EEEEECCCCHHHHHHHHHHHHHHHHHHCCCEECCHHHHHHHHHH
Q ss_conf             ------603887304899999852011143200---14430687868999999861276654103512111789999986
Q gi|254780163|r  333 ------AVRCIGSTTYSEYRQFFEKDKALVRRF---QKIDVSEPSIEDAIEIVKGIKPYFEEHHQLRYSKEAIRAAVQLS  403 (798)
Q Consensus       333 ------~~~~IgatT~~ey~~~~e~d~al~rrF---~~i~v~ep~~~~~~~iL~~~~~~ye~~h~v~~~~~al~~av~ls  403 (798)
T Consensus       375 t~~~~vDVRIIAATN~-nL~~~i~~G~FReDLYYRLNV~~i~iPPLReR~eDI~~L~~---------------~Fl~k~s  438 (560)
T COG3829         375 TKPIPVDVRIIAATNR-NLEKMIAEGTFREDLYYRLNVIPITIPPLRERKEDIPLLAE---------------YFLDKFS  438 (560)
T ss_pred             CCCEEEEEEEEECCCC-CHHHHHHCCCCHHHHEEEECEEEECCCCCCCCCCHHHHHHH---------------HHHHHHH
T ss_conf             8753567899942575-89999863961655300304011147772338201899999---------------9999999


Q ss_pred             HHHCCCCC-CHHHHHHHH
Q ss_conf             54201555-646798899
Q gi|254780163|r  404 VRHFTSRK-LPDKAIDVI  420 (798)
Q Consensus       404 ~ryi~~r~-lPdkAidll  420 (798)
T Consensus       439 ~~~~~~v~~ls~~a~~~L  456 (560)
T COG3829         439 RRYGRNVKGLSPDALALL  456 (560)
T ss_pred             HHCCCCCCCCCHHHHHHH
T ss_conf             872887666899999999