HHsearch alignment for GI: 254780552 and conserved domain: COG3829
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms].
Probab=99.50 E-value=9.3e-13 Score=97.51 Aligned_cols=199 Identities=20% Similarity=0.314 Sum_probs=129.4
Q ss_pred CCHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHC---CCCCCCCCCCCCCCH---HHH--
Q ss_conf 987782397999999999999866146776707997378855778999999861---898531257644334---676--
Q gi|254780552|r 25 RTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL---GVNFRSTSGPVIAKA---GDL-- 96 (334)
Q Consensus 25 ~~l~dviGQ~~~~~~l~~~i~a~~~~~~~~~h~Lf~GPpG~GKTtlA~iiA~~l---~~~~~~~s~~~~~~~---~dl-- 96 (334)
T Consensus 242 y~f~~Iig~S~~m~~~~~~a---kr~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe~LlESELFG 318 (560)
T COG3829 242 YTFDDIIGESPAMLRVLELA---KRIAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPETLLESELFG 318 (560)
T ss_pred CCHHHHCCCCHHHHHHHHHH---HHHCCCCCCEEEECCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHC
T ss_conf 66100205899999999999---863389982899537886689999998744843479807876433888888888727
Q ss_pred --HHHHHHHH-----------CCCHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCCEEECCCCCCEEEECCCCC
Q ss_conf --66666410-----------16378887576169899999999863475100256787652000466740055204554
Q gi|254780552|r 97 --AALLTNLE-----------DRDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRV 163 (334)
Q Consensus 97 --~~~~~~~~-----------~~~vlfiDEihrl~~~~q~~Ll~~mE~~~i~i~~~~~~~a~~~~~~~~~f~lI~ATt~~ 163 (334)
T Consensus 319 ye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgempl~LQaKLLRVLQEkei~r-vG~t---~~~~v---DVRIIAATN~n 391 (560)
T COG3829 319 YEKGAFTGASKGGKPGLFELANGGTLFLDEIGEMPLPLQAKLLRVLQEKEIER-VGGT---KPIPV---DVRIIAATNRN 391 (560)
T ss_pred CCCCCCCCCCCCCCCCCEEECCCCEEEEHHHCCCCHHHHHHHHHHHHHCEEEE-CCCC---CCEEE---EEEEEECCCCC
T ss_conf 67764246445799760544169837712320399899999999875353785-3788---75356---78999425758
Q ss_pred CC---------------------CCHHHHHCCCCEEECCCCCHHHHHH----HHHHHHHHCC--CH-HHHHHHHHHHCCC
Q ss_conf 33---------------------5545442012067326454799999----8777654121--01-1111112332022
Q gi|254780552|r 164 GL---------------------LTNPLQDRFGIPIRLNFYEIEDLKT----IVQRGAKLTG--LA-VTDEAACEIAMRS 215 (334)
Q Consensus 164 ~~---------------------l~~~l~sR~~~~~~~~~~~~~el~~----il~~~~~~~~--i~-~~~~al~~ia~~s 215 (334)
T Consensus 392 L~~~i~~G~FReDLYYRLNV~~i~iPPLReR-----------~eDI~~L~~~Fl~k~s~~~~~~v~~ls~~a~~~L~~y~ 460 (560)
T COG3829 392 LEKMIAEGTFREDLYYRLNVIPITIPPLRER-----------KEDIPLLAEYFLDKFSRRYGRNVKGLSPDALALLLRYD 460 (560)
T ss_pred HHHHHHCCCCHHHHEEEECEEEECCCCCCCC-----------CCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCC
T ss_conf 9999863961655300304011147772338-----------20189999999999998728876668999999998689
Q ss_pred -CCCHHHHHHHHHHHHHHHHHHCCCCCCHHHH
Q ss_conf -1015678877754333455415886427787
Q gi|254780552|r 216 -RGTPRIAGRLLRRVRDFAEVAHAKTITREIA 246 (334)
Q Consensus 216 -~Gd~R~AlnlLe~v~d~a~~~~~~~i~~~~~ 246 (334)
T Consensus 461 WPGNVRELeNviER~v~~~--~~~~~I~~~~l 490 (560)
T COG3829 461 WPGNVRELENVIERAVNLV--ESDGLIDADDL 490 (560)
T ss_pred CCCHHHHHHHHHHHHHHCC--CCCCEEEHHHC
T ss_conf 9960999999999998106--88662225226