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