HHsearch alignment for GI: 254780270 and conserved domain: COG3829
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms].
Probab=98.51 E-value=3.4e-06 Score=65.77 Aligned_cols=199 Identities=22% Similarity=0.348 Sum_probs=129.6
Q ss_pred HHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCC---CEEEEECCCCCC---HHHHCCCCC-CCCCCCC----HHHHHH
Q ss_conf 98424446735998605656502799999977088---249986188888---888356320-0145671----289999
Q gi|254780270|r 358 QMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGR---QYVRMSLGGVYD---EADIRGHRR-TYIGSMP----GRIIQS 426 (820)
Q Consensus 358 ~~~~~~~~g~il~l~gppgvGKts~~~sia~al~r---~f~~islgg~~d---~~~i~gh~~-ty~ga~p----g~ii~~ 426 (820)
T Consensus 261 akr~A~tdstVL-i~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe~LlESELFGye~GAFTGA~~~GK~GlfE~A 339 (560)
T COG3829 261 AKRIAKTDSTVL-ILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPETLLESELFGYEKGAFTGASKGGKPGLFELA 339 (560)
T ss_pred HHHHCCCCCCEE-EECCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEC
T ss_conf 986338998289-9537886689999998744843479807876433888888888727677642464457997605441
Q ss_pred HHHCCCCCEEEEEECHHHHHHHCCCCHHHHHHHHCCCCCCCCEEEEE--CCCCCCCCCEEEEEECCC-------------
Q ss_conf 98327887399993315542311771155665540600168133201--035236442799993486-------------
Q gi|254780270|r 427 LKRAKRSNPLLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHY--LEVEYDLSDVMFIMTANT------------- 491 (820)
Q Consensus 427 l~~~~~~npv~~ldeidk~~~~~~gdp~~allevldp~qn~~f~d~y--~~~~~dls~v~fi~tan~------------- 491 (820)
T Consensus 340 ------~gGTLFLDEIgempl~LQa----KLLRVL---QEkei~rvG~t~~~~v---DVRIIAATN~nL~~~i~~G~FRe 403 (560)
T COG3829 340 ------NGGTLFLDEIGEMPLPLQA----KLLRVL---QEKEIERVGGTKPIPV---DVRIIAATNRNLEKMIAEGTFRE 403 (560)
T ss_pred ------CCCEEEEHHHCCCCHHHHH----HHHHHH---HHCEEEECCCCCCEEE---EEEEEECCCCCHHHHHHCCCCHH
T ss_conf ------6983771232039989999----999987---5353785378875356---78999425758999986396165
Q ss_pred --------CC-CCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHH
Q ss_conf --------55-441311724799825878689998999860898998625781313228999999973177410234788
Q gi|254780270|r 492 --------LN-IPLPLMDRMEIIRIAGYTEEEKLQIAKNHLVKKVLTEHALKQEECCISDGVLLDIIRLFTHEAGVRSFE 562 (820)
Q Consensus 492 --------~~-i~~~l~drme~i~~~~y~~~ek~~i~~~~l~p~~~~~~~~~~~~~~~~~~~i~~ii~~Yt~EaGvR~l~ 562 (820)
T Consensus 404 DLYYRLNV~~i~iPPLReR~-----------eDI~~L~~~Fl~k~s~~~~~--~v~~ls~~a~~~-L~~y~WPGNVRELe 469 (560)
T COG3829 404 DLYYRLNVIPITIPPLRERK-----------EDIPLLAEYFLDKFSRRYGR--NVKGLSPDALAL-LLRYDWPGNVRELE 469 (560)
T ss_pred HHEEEECEEEECCCCCCCCC-----------CHHHHHHHHHHHHHHHHCCC--CCCCCCHHHHHH-HHHCCCCCHHHHHH
T ss_conf 53003040111477723382-----------01899999999999987288--766689999999-98689996099999
Q ss_pred HHHHHHHHHHHHHHHCCCCCEECCCHHHHH-HHH
Q ss_conf 879999898765421178520127967867-530
Q gi|254780270|r 563 RALMKIARKAVTKIVKNSDTTVSINENNLQ-DYL 595 (820)
Q Consensus 563 r~i~~i~r~~~~~~~~~~~~~~~i~~~~l~-~~l 595 (820)
T Consensus 470 NviER~-----v~~~~~~~~---I~~~~lp~~~l 495 (560)
T COG3829 470 NVIERA-----VNLVESDGL---IDADDLPAFAL 495 (560)
T ss_pred HHHHHH-----HHCCCCCCE---EEHHHCCHHHH
T ss_conf 999999-----810688662---22522620231