Query 000829
Match_columns 1265
No_of_seqs 256 out of 1991
Neff 6.6
Searched_HMMs 29240
Date Tue Mar 26 16:21:34 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000829.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_600-604//hhsearch_pdb/000829hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_A DNA-directed RNA polyme 1.0 1 1 2608.5 49.9 1177 12-1250 134-1454(1752)
2 1twf_A B220, DNA-directed RNA 1.0 1 1 2518.5 73.8 1177 12-1251 132-1449(1733)
3 1hqm_D DNA-directed RNA polyme 1.0 1 1 1764.0 2.5 887 87-1243 225-1220(1265)
4 2a6h_D DNA-directed RNA polyme 1.0 1 1 1736.7 23.0 913 86-1246 484-1482(1524)
5 4ayb_A DNA-directed RNA polyme 1.0 1 1 1703.7 53.2 743 11-801 129-876 (880)
6 3lu0_D DNA-directed RNA polyme 1.0 1 1 1569.4 24.0 961 110-1244 232-1365(1407)
7 4ayb_C DNA-directed RNA polyme 1.0 1 1 661.1 15.8 355 876-1251 38-394 (395)
8 3qqc_A DNA-directed RNA polyme 1.0 1 1 406.1 12.2 218 4-259 184-406 (436)
9 3qqc_A DNA-directed RNA polyme 1.0 1 1 51.0 0.6 68 1168-1236 360-431 (436)
10 2j7n_A RNA-dependent RNA polym 1.0 1 1 29.1 4.0 31 405-435 314-347 (1022)
No 1
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=1.00 E-value=1 Score=2608.48 Aligned_cols=1177 Identities=36% Similarity=0.575 Sum_probs=1015.4
Q ss_pred HHHHHHHHHHHHHCCCCCCC----------------------CCCCCCCCCCEEECCEEEEEEEECCCCHHHHHHHHHHH
Q ss_conf 99999999992303799776----------------------98989989717832302218983245214578776631
Q 000829 12 TDLMKSIVKKCSTMASKAVK----------------------CPRCGYINGMVKKAVAVLGIIHDRSKVTESLQEFASAI 69 (1265)
Q Consensus 12 ~~~~k~i~~~c~~~~k~~k~----------------------C~~Cg~~~p~IkK~~~~~ki~~~~~~~~~~~~~~~~~~ 69 (1265)
+.+++++|+.| ++++. |++||+.||.|||++ ++++++ ++ ...
T Consensus 134 k~r~~~V~~~c----k~k~~Ce~~~~~~~~~~~~~~~~~~~~~~gCG~~qP~IRKeg--lkl~~~-~k---------~~k 197 (1752)
T 3h0g_A 134 KNRLNAVWNVC----KTKMVCDTGLSAGSDNFDLSNPSANMGHGGCGAAQPTIRKDG--LRLWGS-WK---------RGK 197 (1752)
T ss_dssp TTTHHHHHHHH----HHCCCCCSSTTCCSSCCCSSCCCCCCSSCSSCCCCCCCEEET--TEEECC-BC---------CSS
T ss_pred HHHHHHHHHHH----CCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCEEEEC--CEEEEE-EC---------CCC
T ss_conf 99999999981----435446787754421000012223456898688587278636--589999-72---------555
Q ss_pred HCCHHHHHHHHCCCCCCCHHHHHHHHHHCCHHHHHHHCCC---CCCCEEEEEEEEECCCCCCCCEECCCCCCCCCHHHHH
Q ss_conf 0021245542001434699999999972382248762599---9955078863120899999924218987677325899
Q 000829 70 THTKESKAAVNVATYILNPVNVLFLFKRMTDTDCEVLYLS---ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITER 146 (1265)
Q Consensus 70 ~~~~e~~~~~~~~~~~L~P~~v~~il~~i~~~d~~~l~~~---~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~ 146 (1265)
.+.++ ...++|+|.+|+++|++||++|+++||++ .+||||||++|||||+++||++.++++.++|||||.+
T Consensus 198 ~~~~~------~~k~~LtP~eVl~ifk~IsdeD~~lLGl~~~~~rPewmiL~vLPVpPp~vRPsv~ldg~~~~edDLt~~ 271 (1752)
T 3h0g_A 198 DESDL------PEKRLLSPLEVHTIFTHISSEDLAHLGLNEQYARPDWMIITVLPVPPPSVRPSISVDGTSRGEDDLTHK 271 (1752)
T ss_dssp SSCBC------SSCCCCCHHHHHHHHHHSCHHHHHHSSCCSSSCCGGGSSBSSCEECCGGGSCCCCCSSSCCCCCTTTTH
T ss_pred CCCCC------CCCEECCHHHHHHHHHHCCHHHHHHHCCCCCCCCHHHEEEECCCCCCCCCCCCEECCCCCCCCCHHHHH
T ss_conf 65544------466322899999999962988999848986679845567320245998766716748976677828999
Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CCCCHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 9999999899999999700001256779879999987743689999765567-887201343205765411245568778
Q 000829 147 LKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQV-ARPLSGFVQRLKGKQGRFRGNLSGKRV 225 (1265)
Q Consensus 147 l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~~~~~~~~~~-~~~~~~i~qrl~gK~G~fR~nl~GKRv 225 (1265)
|++||+.|++|++.+..|++...+.+.|++||++|+.|+||+.+|.+.+.++ ++|++||+||||||+||||+|||||||
T Consensus 272 l~~II~~N~~Lk~~~~~gap~~~~~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~rp~k~~~~~lkgK~GrfR~nl~GKRV 351 (1752)
T 3h0g_A 272 LSDIIKANANVRRCEQEGAPAHIVSEYEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRV 351 (1752)
T ss_dssp HHHHHHHHHHHHGGGGCCSSSTTHHHHHHHHHHHHHHTTCTTCSSCCCCCSSSSCCCCCHHHHHTCSSSSSTTTTSSCCC
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCC
T ss_conf 99999987999999873050678999999999999986067787886322467888751676640201101344445556
Q ss_pred CCCCCEEECCCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEE-CCCCCHHHH
Q ss_conf 9866227808999877755563888864594403364779999999992999998850777799983786-242303454
Q 000829 226 EYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-YGKFRNQLA 304 (1265)
Q Consensus 226 d~s~RsVI~pDp~l~~~evgiP~~~A~~Lt~Pe~Vt~~Ni~~lr~lv~nG~~~~pGa~~i~~~~g~~~~l-~~~~r~~~~ 304 (1265)
||||||||+|||+|++||||||..||++|||||+||+||+++|+++|.|||+.||||+||++.+|.+++| +.+ ...+
T Consensus 352 d~s~RsVI~~dP~l~~~evGvP~~~A~~Lt~Pe~vt~~ni~~l~~lv~nG~~~~pga~~v~~~~~~~~~l~~~~--~~~~ 429 (1752)
T 3h0g_A 352 DFSARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYIIRDTGERIDLRYHK--RAGD 429 (1752)
T ss_dssp SSEEEEEEEEETTSCTTBCBCCHHHHTSCCCCCBCCTTTHHHHHHHHHHCTTSSSCEEEEECTTCCBCCTTTTC--SCCC
T ss_pred CCCCCEEECCCCCCCCCEEECHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEECHHHC--HHHH
T ss_conf 87663134489976555213709999865887655679999999999739865667302663788476412101--1445
Q ss_pred HCCCCCCEEECCCCCCCEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 12653131101013698699815887664643448999826981342024689888997645323456882889999998
Q 000829 305 VELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALL 384 (1265)
Q Consensus 305 ~~L~~g~iV~Rhl~~gd~vl~NRqPsLHk~si~~~~~~v~~~~t~r~~~~~c~~yNADFDGDeMn~h~Pqs~~araEa~~ 384 (1265)
.+|++||+|+|||+|||+|||||||||||+|||||++||+||+||||||+||+||||||||||||+|||||++|||||++
T Consensus 430 ~~l~~g~~v~r~l~~gd~Vl~NRqPtLHr~sima~~~~v~~gktirlh~~vC~~yNADFDGDeMnvHvPqs~eAraEa~~ 509 (1752)
T 3h0g_A 430 IPLRYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSEETRAEIQE 509 (1752)
T ss_dssp CCCCSSCEEEECCCSCCEEEEECSSCCSGGGEEEEECCCCSSSSEEEEGGGSGGGTCCSSSCEEEEECCCSTTHHHHHHH
T ss_pred HHCCCCCEEEEEECCCCEEEEECCCCCCHHHCCCCCCEEECCCEEEECHHHCCCCCCCCCCCEEEEECCCCHHHHHHHHH
T ss_conf 41576737874423697689816862031012144635606863660652278766761000246631688889999999
Q ss_pred HCCCCCCCCCCCCCCCCEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHCCCCCEEECCCCCEECCCCCCCCCEEEEEE
Q ss_conf 72888621159999951720134000336650257667999999999983389840324788300763233664015544
Q 000829 385 LMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILKPVELWTGKQLFSVL 464 (1265)
Q Consensus 385 Lm~~~~~~~sp~~G~pi~gliQD~i~g~~llT~~d~f~~~~~~~~l~~~~~~~~~~~~l~~Pailkp~~lwTGKQi~s~i 464 (1265)
||++++||++|++|+|++|++||+|+|+|+||.+|+|+++++++++++|+..+. ..+|+|||+||+++||||||||++
T Consensus 510 Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~lT~~~~f~~~~e~~~l~~~~~~~~--~~~~~pai~kp~~~wtGkqifs~i 587 (1752)
T 3h0g_A 510 ITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVPDWD--GILPPPVILKPKVLWTGKQILSLI 587 (1752)
T ss_dssp TCCTTTTSEETTTTEESCCCCTHHHHHHHHHHSTTCEEETHHHHGGGGCSSSCC--SSCCCCSBCSSSCEEETTHHHHTT
T ss_pred HHCCCCCEECCCCCCCEEEECCHHHHHEEEECCCCCCCCHHHHHHHHHHHCCCC--CCCCCCCEECCCCCCCHHHHHHHH
T ss_conf 853713261489998026641103321122004655589999999998502237--845766154576787466677666
Q ss_pred ECCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEECCCCCCCCCCCCCCCHHHHHHHHHCH
Q ss_conf 05888862479776313011355444568732323456889980388368420013455433688743289999997193
Q 000829 465 IRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGA 544 (1265)
Q Consensus 465 l~~~~~~~~~in~~~~~k~~~~~~~~~~g~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~li~~i~~~yG~ 544 (1265)
||+. +|+..+.+. . .+++.+|+.|+|+||||++|++||+++|+ +.++|||.++++||+
T Consensus 588 lp~~------~~~~~~~~~---------~------~~~~~~d~~v~i~~gell~g~l~K~~lg~-~~~~li~~i~~~~G~ 645 (1752)
T 3h0g_A 588 IPKG------INLIRDDDK---------Q------SLSNPTDSGMLIENGEIIYGVVDKKTVGA-SQGGLVHTIWKEKGP 645 (1752)
T ss_dssp SCSS------BCEECCCSS---------C------CSSCTTTCSEEECBSCEEEECCSHHHHSS-CTTCHHHHSSSSSCT
T ss_pred CCCC------CCCEECCCC---------C------CCCCCCCCEEEEECCEEEECCCCHHHHCC-CCCCHHHHHHHHHCH
T ss_conf 7687------773004655---------5------67687767378876707753102677345-754299999999799
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 26889985999999999984064121256899920048999999999999999999987299866989997899999999
Q 000829 545 HATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVIT 624 (1265)
Q Consensus 545 ~~a~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~~i~ 624 (1265)
++|+.|||.+++|+++||+.+|||||++|++++++..+++.+.|+++++++.+++.+|..|.++..+|++.++++|..++
T Consensus 646 ~~~~~~ld~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~g~l~~~~g~~~~e~~e~~v~ 725 (1752)
T 3h0g_A 646 EICKGFFNGIQRVVNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMTLRESFEAKVS 725 (1752)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHCCCCCGGGGSCCSHHHHHHHHHHHTTTHHHHHHHTTTTTTCCCCCSSCCTTHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
T ss_conf 99999999999999999986680430633265889999999999999999999999987098755889868999999999
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCCHHCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf 99999999999988627999994222312478889132757761356553589778999877656799999989776530
Q 000829 625 DILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGF 704 (1265)
Q Consensus 625 ~~l~~~~~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~i~G~Rip~g~~~rtLP~f~~~~~~~~a~Gf 704 (1265)
++|+++++++++.+.+.+.++|++++|+.||||||++|++||+||||||+++|+|||+||.+|+||||.++|.+|+|+||
T Consensus 726 ~~l~~~~~~~~~~~~~~l~~~N~~~~M~~SGakGs~~ni~Q~~~~~Gqq~~~GkrIp~g~~~rtLP~f~k~d~~~~a~Gf 805 (1752)
T 3h0g_A 726 RILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPHFPKDDDSPESRGF 805 (1752)
T ss_dssp HHHHHHHHHHHHHHHTTSCSSCTTTHHHHHCSSCCHHHHHHHHTCCCCCCSTTSSSCCCSTTSSSTTSCSSCCSTTTSSC
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 99999999999999986488886999866256647888999985538882578668788888668888888998433761
Q ss_pred ECCCCCCCCCHHHHHHHHCCCCCCCHHCCCCCCCCCHHHHHHHHHHHHEEEEECCEEECCCCCEEEEEECCCCCCCCCCC
Q ss_conf 14456348991234665024653000001004767714799999743137521281775898199997068886444336
Q 000829 705 VANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANME 784 (1265)
Q Consensus 705 I~~sF~~GL~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLik~lEdl~v~YD~TVR~s~g~IiQF~YGeDGld~~~~e 784 (1265)
|.|||++||+|+|||||||||||||+|||||||+||||||||||+||||+|+||+||||++|+||||.|||||+||+++|
T Consensus 806 V~~sF~~GL~p~EfFfhtmggReGLiDTAvKTA~SGYLqRRLVk~leDv~V~YDgTVRns~g~ivQF~YGeDGlD~~~~e 885 (1752)
T 3h0g_A 806 IENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVE 885 (1752)
T ss_dssp CSSCTTTCCCHHHHHHHHHHHTTTTTHHHHTTTHHHHHHHHHHHHHTTCEEETTTEEECTTSCEEESSSSSSCBCGGGEE
T ss_pred HHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHEEEEECCEEECCCCCEEEEECCCCCCCHHHHH
T ss_conf 01013479988999997441032246765402767501799999875248850780686899489874677776867741
Q ss_pred CCCC-----CCCHHHHHHHHHHHCC------------CCCCCCCCCHHHHHHHHHHH--HHH------------------
Q ss_conf 8889-----9832699999988319------------99999778977799999999--853------------------
Q 000829 785 GKSG-----EPLNFDRLLMKVKATC------------PPAGQRYLSPQQVSEIVEKQ--LAA------------------ 827 (1265)
Q Consensus 785 ~~~~-----~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~--l~~------------------ 827 (1265)
++.. .+.+|++.|....... .+......+..|+..+.+.- +..
T Consensus 886 ~q~~~~~~~s~~~f~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~E~~~l~~dr~~lr~~i~~~~~~~~~lP~N~~R 965 (1752)
T 3h0g_A 886 YQVFDSLRLSTKQFEKKYRIDLMEDRSLSLYMENSIENDSSVQDLLDEEYTQLVADRELLCKFIFPKGDARWPLPVNVQR 965 (1752)
T ss_dssp EEECTTTSCCHHHHTTTSCCCTTTTCCGGGTSCSCCTTSCSSTHHHHHHHHHHHHHHTTSSSSSSSCSCCEEEEESCHHH
T ss_pred CCCCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHH
T ss_conf 35554024787999988421225543246778887505788999999999999999999888751043101368714999
Q ss_pred ------CCC--------CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC--------------CCCHHHHHHHHHCC
Q ss_conf ------087--------76219999999999998643221241011335888--------------53202445642035
Q 000829 828 ------YGK--------ESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWD--------------DKSQILEEVTHKTS 879 (1265)
Q Consensus 828 ------~~~--------~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~--------------~~~~~~~~~~~~~~ 879 (1265)
..| +..+..+.+.+++++. ++. .++....+. .++.++.+.+...+
T Consensus 966 ~i~~~~~~f~~~~~~~s~l~p~~~~~~v~~~~~----~l~---~~~g~d~l~~~~~~na~~l~~~~lr~~l~~k~~~~~~ 1038 (1752)
T 3h0g_A 966 IIQNALQIFHLEAKKPTDLLPSDIINGLNELIA----KLT---IFRGSDRITRDVQNNATLLFQILLRSKFAVKRVIMEY 1038 (1752)
T ss_dssp HTTTTTTTSCCCTTSCCCCCHHHHHHHHHHHHT----TCC---CSCCCSTTTTHHHHTSSHHHHHHHTTSSSHHHHHHSS
T ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHH----HHH---CCCCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 999999862778676577988999999999998----654---0258740205656352878889887665444434216
Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCHHHHHHHCCCCCCCCE
Q ss_conf 87999999999999985201458869601000002469843214013444465211210103301574432255445454
Q 000829 880 GITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTPI 959 (1265)
Q Consensus 880 ~l~~~~~~~~~~~~~~~y~~~~~~pGEaVGiIAAQSIGEPsTQMTLnTFH~AGv~~~nVTlGiPRLkEIinask~ikTP~ 959 (1265)
+++.++++||+++|..+|.+++++||||||+|||||||||+|||||||||||||++||||||||||||||||||+||||+
T Consensus 1039 ~l~~~~~~~~~~~~~~~y~~a~v~pGe~VG~iaAQSIgEp~TQMTLnTFHfAGvas~NVTlGVPRLkEIInask~ikTP~ 1118 (1752)
T 3h0g_A 1039 RLNKVAFEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKNIKTPS 1118 (1752)
T ss_dssp CCCHHHHHHHHHHHHHHHHTTBCCSSCCHHHHHHHHHHHHHHHHHHHTTSSCCCCCSSCCCSGGGHHHHHTTCSCCSCCC
T ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCCCE
T ss_conf 76899999999999999987345766511034540268812346577664404435565557500999986632799972
Q ss_pred EEEECCCC--CCHHHHHHHHCCEEEEECCCCCEEEEEEEECCCCEEEEEECHHHHHHHH---------------------
Q ss_conf 99872687--7387999975013587424542128999907961999994836687724---------------------
Q 000829 960 ITAELECN--DNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAH--------------------- 1016 (1265)
Q Consensus 960 i~~~l~~~--~~~~~a~~i~~~le~~~L~di~~~i~~~~~~~~~~~~i~ld~~~i~~~~--------------------- 1016 (1265)
|+++|.++ .+.+.|+.++++||+++|+||+++++++|+|+..+..++.|.++++.|.
T Consensus 1119 mtv~L~~~~~~d~e~A~~v~~~ie~t~L~~v~~~~~i~~~p~~~~~~i~~d~~~v~~~~~~~~~~~~~~~~~~~~~~~rl 1198 (1752)
T 3h0g_A 1119 LTIYLMPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRL 1198 (1752)
T ss_dssp CEECCCSSSCSSSTTTHHHHTTSSCCSSCSCCSCEEEECCCSTTCCCCSSSCSHHHHHHHTTCSSTTCSSCSCCCCEEEE
T ss_pred EEEEECCCCCCCHHHHHHHHHHHCCEEHHHHEEEEEEEEECCCCCEEEEECHHHHHHHHCCCHHHHHCCCCCCCCEEEEE
T ss_conf 89995675555899999999761407898711078999946865168862589999986242333100100146525899
Q ss_pred ---------CCCCHHHHHHHHHCCCCCCCCCCCEEEE------CCCEEEEECCCC-----C--C---CCEEEHHHHH-HH
Q ss_conf ---------1459999999986086442345752660------563489928999-----9--8---5144257786-10
Q 000829 1017 ---------LCINADIVKESIVQTPKIKLKQQHIKVL------DFRKLEIFPPVD-----K--S---KIHFELYSLK-NV 1070 (1265)
Q Consensus 1017 ---------~~i~~~~i~~~i~~~~~~k~~~~~v~~~------~~~~i~i~~~~~-----~--~---~~~~~l~~l~-~~ 1070 (1265)
.++++++|..+|.+.++ .++.+. ++..+++++... + . +....|+.++ ..
T Consensus 1199 ~l~~~~~~~~~l~~~~I~~~i~~~~~-----~~~~v~~~d~~~~~~~i~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~ 1273 (1752)
T 3h0g_A 1199 ELDRAKMLDKKLSMSDVAGKIAESFE-----RDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHM 1273 (1752)
T ss_dssp ECCTTSSTTTTCCHHHHTTSGGGSST-----TSCCEECCCTTCSSCEEEECCCCCSCCCCCSSCCCSCSCHHHHHHHHHH
T ss_pred EECHHHHHHCCCCHHHHHHHHHHHCC-----CCEEEEECCCCCCCEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 85499998749999999999986436-----8735851577766306999851554444322233321899999999963
Q ss_pred CCCCEEECCCCCEEEEEECCCCCCCHHHCCC---CCCCEEEEEECCCHHHHHCCCCCCCCCCCCCCHHHHHHHHCHHHHH
Q ss_conf 5772871413711799941231100000248---7642899990766777631477446645567799999984799999
Q 000829 1071 LPMVIVKGIKTVERVVIAEKEKEKRKVKENG---EKKKYRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAAR 1147 (1265)
Q Consensus 1071 l~~~~i~Gi~~I~r~~i~~~~~~~~~~~~~~---~~~~~~l~teG~nl~~i~~~~~VD~~r~~sNdI~~v~~~lGIEAAR 1147 (1265)
|++++|+|+++|+||++.+.+. ..+.+.+ .+++|.|+|||+||+++|.+++||++||+||||+||+++|||||||
T Consensus 1274 l~~~~i~Gi~~I~rv~i~~~~~--~~~~~~g~~~~~~~~~l~teG~nL~~v~~~~gVD~~rt~sNdI~ei~~vlGIEAAR 1351 (1752)
T 3h0g_A 1274 LESISLRGVPNITRVYMMEHKI--VRQIEDGTFERADEWVLETDGINLTEAMTVEGVDATRTYSNSFVEILQILGIEATR 1351 (1752)
T ss_dssp TTCCCSSCCTTCCCCCEEEEEE--EEECSSSCEEEEEEEEEECCSCCCSTTTSSSSCCTTTCCCSCHHHHHHHSCHHHHH
T ss_pred CCCEEEECCCCCCEEEEECCCC--EEECCCCCCCCCCEEEEEECCCCHHHHHCCCCCCCCCCEECCHHHHHHHHHHHHHH
T ss_conf 1125884689964799863660--33268875124641799921468999967698846408547899999987599999
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCEEEEECCCCCCCCCCCHHHHHCCHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 99999998986026665572001000000110127974201223456870755701068899999944229865555533
Q 000829 1148 ICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVS 1227 (1265)
Q Consensus 1148 ~~Ii~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~itR~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS 1227 (1265)
++|++||+.||+.||++||+|||+||||+||++|++++||||||+++++|||++||||+|+++|++||++|+.|+|+|||
T Consensus 1352 ~~Ii~Ei~~v~~~~G~~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~s~l~~aSFE~T~~~L~~Aa~~g~~D~l~gvs 1431 (1752)
T 3h0g_A 1352 SALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFEETVEILMDAAASGEKDDCKGIS 1431 (1752)
T ss_dssp HHHHHHHHTTSCSSSCCCCHHHHHHHHHHHTSSSSCCCCCTTSCSCCCSHHHHHHHHSCCTHHHHHHGGGTCCBCCCCST
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf 99999999999843887789999997887613876886123443057988899864897999999999726866664805
Q ss_pred CCEECCCCCCCCCCCEEEEECCC
Q ss_conf 33110577777865337521389
Q 000829 1228 ECIIMGIPMPLGTGILKIRQRDA 1250 (1265)
Q Consensus 1228 ~~Ii~Gk~~~~GTG~fdll~~~~ 1250 (1265)
||||+||++++|||+|||+++..
T Consensus 1432 e~Ii~G~~~~~GTG~fdll~~~~ 1454 (1752)
T 3h0g_A 1432 ENIMLGQLAPMGTGAFDIYLDQD 1454 (1752)
T ss_dssp TGGGTCSCCCSBTTSCEECCCHH
T ss_pred HHHHCCCCCCCCCCEEEEEECHH
T ss_conf 77653887677663278985788
No 2
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Probab=1.00 E-value=1 Score=2518.53 Aligned_cols=1177 Identities=35% Similarity=0.552 Sum_probs=1000.4
Q ss_pred HHHHHHHHHHHHHCCCCCCCC----------------CCCCCCCCCEEECCEEEEEEEECCCCHHHHHHHHHHHHCCHHH
Q ss_conf 999999999923037997769----------------8989989717832302218983245214578776631002124
Q 000829 12 TDLMKSIVKKCSTMASKAVKC----------------PRCGYINGMVKKAVAVLGIIHDRSKVTESLQEFASAITHTKES 75 (1265)
Q Consensus 12 ~~~~k~i~~~c~~~~k~~k~C----------------~~Cg~~~p~IkK~~~~~ki~~~~~~~~~~~~~~~~~~~~~~e~ 75 (1265)
+++++++++.| ++.+.| .+||+.+|.|||.+ ++++++ ++ ..... .+.
T Consensus 132 k~r~~~v~e~c----k~k~~Ce~~~~~~~e~~~~~~~~gCGa~qp~irk~g--l~l~~e-~k---------~~~~~-~e~ 194 (1733)
T 1twf_A 132 KKRFAAIWTLC----KTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDG--LKLVGS-WK---------KDRAT-GDA 194 (1733)
T ss_dssp HHHHHHHHHHH----TTCCBCCSEECCSSCTTSCEECCSCCCBCCCCEECS--SCEEEE-EC---------SSSSC-TTS
T ss_pred HHHHHHHHHHH----CCCCCCCCCCCCHHCCCCCCCCCCCCCCCHHHHHCC--CCEEEE-EC---------CCCCC-CCC
T ss_conf 88999999984----435414654200000234444578787658777457--754776-51---------00343-222
Q ss_pred HHHHHCCCCCCCHHHHHHHHHHCCHHHHHHHCCC---CCCCEEEEEEEEECCCCCCCCEECCCCCCCCCHHHHHHHHHHH
Q ss_conf 5542001434699999999972382248762599---9955078863120899999924218987677325899999999
Q 000829 76 KAAVNVATYILNPVNVLFLFKRMTDTDCEVLYLS---ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQ 152 (1265)
Q Consensus 76 ~~~~~~~~~~L~P~~v~~il~~i~~~d~~~l~~~---~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~ 152 (1265)
.++..+.|+|.+|+++|++||++|+++||++ .+||||||++|||||+++||++.++++.++|||||.+|++||+
T Consensus 195 ---~~~~k~~Ltp~eV~eifk~I~deD~~lLgl~p~~~rPewmiLtvLPVpPp~vRPsv~ldg~~~~edDLT~~l~~II~ 271 (1733)
T 1twf_A 195 ---DEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILK 271 (1733)
T ss_dssp ---CSCEEEEECHHHHHHHHTTSCHHHHHHTTCBTTTBCGGGGEEEEECCCCTTTSCCCCCSSSCCCCCHHHHHHHHHHH
T ss_pred ---CHHHHCCCCHHHHHHHHHHCCHHHHHHHCCCCCCCCHHEEEEEEECCCCCCCCCCEECCCCCCCCCHHHHHHHHHHH
T ss_conf ---10220147999999998738999999847876689802055654226998766756658986057778999999999
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf 9899999999700001256779879999987743689999765567-887201343205765411245568778986622
Q 000829 153 TNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQV-ARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRT 231 (1265)
Q Consensus 153 ~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~~~~~~~~~~-~~~~~~i~qrl~gK~G~fR~nl~GKRvd~s~Rs 231 (1265)
.|++|++....|++...+.+.|.+||.+|+.|+||+.++.+.+.++ ++|++||+||||||+||||+|||||||||||||
T Consensus 272 ~N~~Lk~~~~~gap~~ii~e~~~~LQ~~v~~~~dn~~~~~~~~~~~~~rp~k~i~~~lkgK~GrfR~nl~GKRVd~s~Rs 351 (1733)
T 1twf_A 272 ANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSART 351 (1733)
T ss_dssp HHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHHHCCCSSCCCCCSSCTTCCCCCSTTSCTTTTTTSSGGGTTCSCCSEEEE
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCHHHHCCCCCCCCCCCCE
T ss_conf 99999999974745878889999999999998546766887434578865056787750333112221366556765304
Q ss_pred EECCCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEE-CCCCCHHHHHCCCCC
Q ss_conf 7808999877755563888864594403364779999999992999998850777799983786-242303454126531
Q 000829 232 VISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-YGKFRNQLAVELKSG 310 (1265)
Q Consensus 232 VI~pDp~l~~~evgiP~~~A~~Lt~Pe~Vt~~Ni~~lr~lv~nG~~~~pGa~~i~~~~g~~~~l-~~~~r~~~~~~L~~g 310 (1265)
||+|||+|++||||||..||++|||||+||+||+++|+++|.|||+.||||+++++.+|.+++| +. +......|++|
T Consensus 352 VI~~dP~L~~~evGvP~~~A~~Lt~Pe~vt~~ni~~l~~lv~~g~~~~~ga~~~~~~~g~~~~l~~~--~~~~~~~l~~g 429 (1733)
T 1twf_A 352 VISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYS--KRAGDIQLQYG 429 (1733)
T ss_dssp EEEECTTSCTTEEEEEHHHHTTCEEEEECCTTTHHHHHHHHHHTTTSSSCEEEEECTTCCEEETTSC--TTTTCCCCCTT
T ss_pred EEECCCCCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEECCCC--CHHHHHHCCCC
T ss_conf 7748987626623584999985788841348999999999974986677740378278957853223--22554404657
Q ss_pred CEEECCCCCCCEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf 31101013698699815887664643448999826981342024689888997645323456882889999998728886
Q 000829 311 CIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQN 390 (1265)
Q Consensus 311 ~iV~Rhl~~gd~vl~NRqPsLHk~si~~~~~~v~~~~t~r~~~~~c~~yNADFDGDeMn~h~Pqs~~araEa~~Lm~~~~ 390 (1265)
|+|+|||+|||+|||||||||||+|||||+++|++|+||||||+||+||||||||||||+|||||++|||||++||++.+
T Consensus 430 ~~v~r~l~~gd~VllNRqPTLHr~si~a~~~~v~~~~tirlnp~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~ 509 (1733)
T 1twf_A 430 WKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPL 509 (1733)
T ss_dssp CEEEEECCTTCEEEEECSSCCSGGGEEEEEEEEESSSSEEECGGGHHHHTCCSSSCEEEEECCCSHHHHHHHHHHTBGGG
T ss_pred CEEEEEECCCCEEEEECCCCCCCCCCEEEEEEECCCCEEEECHHHCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCC
T ss_conf 78976512697789807986461342267899706974774765558877661124565105788999999999853734
Q ss_pred CCCCCCCCCCCEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHCCCCCEEECCCCCEECCCCCCCCCEEEEEEECCCCC
Q ss_conf 21159999951720134000336650257667999999999983389840324788300763233664015544058888
Q 000829 391 NLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILKPVELWTGKQLFSVLIRPHAN 470 (1265)
Q Consensus 391 ~~~sp~~G~pi~gliQD~i~g~~llT~~d~f~~~~~~~~l~~~~~~~~~~~~l~~Pailkp~~lwTGKQi~s~il~~~~~ 470 (1265)
||++|++|+|++|++||+|+|+|+||.+|+|+++++++++++++.... ..+|+|||+||+++||||||||++||+.
T Consensus 510 nilsP~~G~Pi~~~~QD~v~g~y~lT~~~~f~~~~e~~~~~~~~~~~~--~~~~~pai~kp~~~wtGkqifs~ilp~~-- 585 (1733)
T 1twf_A 510 QIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWD--GVIPTPAIIKPKPLWSGKQILSVAIPNG-- 585 (1733)
T ss_dssp GSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHSTTCC--SCCCCCSBCSSSCEEEHHHHHHHHSCTT--
T ss_pred CEEECCCCCEEEEEECCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCHHHHHHHHCCCC--
T ss_conf 588657998137651222100034104755699999999998323315--8537743107615752887888767899--
Q ss_pred CCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEECCCCCCCCCCCCCCCHHHHHHHHHCHHHHHHH
Q ss_conf 62479776313011355444568732323456889980388368420013455433688743289999997193268899
Q 000829 471 MRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGC 550 (1265)
Q Consensus 471 ~~~~in~~~~~k~~~~~~~~~~g~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~li~~i~~~yG~~~a~~~ 550 (1265)
+|+..+++. . .+.+.+|+.|+|+||||++|++||+++|+ +.++|||.++++||+++|+.|
T Consensus 586 ----~~~~~~~~~---------~------~~~~~~d~~v~i~~gel~~g~ldKk~lg~-~~~~li~~i~~~~G~~~a~~~ 645 (1733)
T 1twf_A 586 ----IHLQRFDEG---------T------TLLSPKDNGMLIIDGQIIFGVVEKKTVGS-SNGGLIHVVTREKGPQVCAKL 645 (1733)
T ss_dssp ----CCEEECCTT---------C------CTTCTTCCSEEEETTEEEESCCCHHHHSS-CTTSHHHHHHHHHCHHHHHHH
T ss_pred ----CCEEECCCC---------C------CCCCCCCCEEEEECCCEEEEECCHHHHCC-CHHHHHHHHHHHHCHHHHHHH
T ss_conf ----741336877---------6------55786656489867828983016678545-701899999998699999999
Q ss_pred HHHHHHHHHHHHHHCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 85999999999984064121256899920048999999999999999999987299866989997899999999999999
Q 000829 551 MNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRI 630 (1265)
Q Consensus 551 l~~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~~i~~~l~~~ 630 (1265)
||.+++|+++|++.+|||||++|++++++..+++.++++++++++.+++++|..|.++..+|++.++++|++++.+|+++
T Consensus 646 ld~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~i~~~i~~a~~~v~~~~~~~~~g~l~~~pg~~~~e~~e~~v~~il~~~ 725 (1733)
T 1twf_A 646 FGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEA 725 (1733)
T ss_dssp HHHHHHHHHHHHHTTCBCCCGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCEEEEHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 99999999999987666985565375989999999999999999999999998099765889877999999999999999
Q ss_pred HHHHHHHHHCCCCCCCCCEEEECCCCCCCHHCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCC
Q ss_conf 99999988627999994222312478889132757761356553589778999877656799999989776530144563
Q 000829 631 REDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFY 710 (1265)
Q Consensus 631 ~~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~i~G~Rip~g~~~rtLP~f~~~~~~~~a~GfI~~sF~ 710 (1265)
++++++.+.+.+.++|++++|+.||||||++|++||+||||||+++|+|||+||++||||||.++|.+|+|+|||.|||+
T Consensus 726 ~d~~~~~~~~~l~~~N~i~~Ma~SGAKGs~~Ni~Q~~~~~Gqq~~~Gkrip~g~~~RtLPhf~k~d~~p~s~GfI~ssF~ 805 (1733)
T 1twf_A 726 RDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYL 805 (1733)
T ss_dssp HHHHHHHHHHHSCTTCHHHHHHHHTSSCCHHHHHHHHSCCEECCBTTBSCCCCBTTBSSTTSCTTCCSTTTTTEECSCTT
T ss_pred HHHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf 99999999986265887178850467654776999971767754688637778888778887778898001661331000
Q ss_pred CCCCHHHHHHHHCCCCCCCHHCCCCCCCCCHHHHHHHHHHHHEEEEECCEEECCCCCEEEEEECCCCCCCCCCCCCCCC-
Q ss_conf 4899123466502465300000100476771479999974313752128177589819999706888644433688899-
Q 000829 711 SGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGE- 789 (1265)
Q Consensus 711 ~GL~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLik~lEdl~v~YD~TVR~s~g~IiQF~YGeDGld~~~~e~~~~~- 789 (1265)
+||+|+|||||||||||||||||||||+||||||||||+||||+|+|||||||++|.||||.|||||+|+++++++...
T Consensus 806 ~GLtp~EyFfh~mggReGLiDTAvKTA~SGYLqRRLVk~ledv~V~yDgTVR~s~g~IvQF~YGeDGlD~~~~e~~~~~~ 885 (1733)
T 1twf_A 806 RGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDT 885 (1733)
T ss_dssp TCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCEECTTSCEECTTCCEEESSGGGTTBCGGGEEEEECGG
T ss_pred CCCCHHHHHHHHHCCCCCHHHHCEECCCCCCCEEEHHHHHCCEEEEECCCEECCCCCEEEEEECCCCCCCCEEECCCCCC
T ss_conf 24654877655431442012200020568851000333325059970586765899789987136667742100465650
Q ss_pred ----CCHHHHHHHHHHHCC-CCCCCCCCC-------HHHHHHHH----H----H--HHHH----CC--------------
Q ss_conf ----832699999988319-999997789-------77799999----9----9--9853----08--------------
Q 000829 790 ----PLNFDRLLMKVKATC-PPAGQRYLS-------PQQVSEIV----E----K--QLAA----YG-------------- 829 (1265)
Q Consensus 790 ----~~~~~~~~~~~~~~~-~~~~~~~~~-------~~~~~~~~----~----~--~l~~----~~-------------- 829 (1265)
...|++.|....... +-....... ..+....+ + . .+.. ..
T Consensus 886 ~~~~~~~f~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~e~~~l~~~r~~lr~i~~~~~~~~~~P~ni~r~i~ 965 (1733)
T 1twf_A 886 IGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQ 965 (1733)
T ss_dssp GSSCHHHHHHHHCCCTTCTTTSCCTTTBTTHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCEEEEESCHHHHHH
T ss_pred CCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHH
T ss_conf 01579999998534445632247888887787740368889999999999998899998763056634468714999999
Q ss_pred -----C--------CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC--------------CCCHHHHHHHHHCCCCC
Q ss_conf -----7--------76219999999999998643221241011335888--------------53202445642035879
Q 000829 830 -----K--------ESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWD--------------DKSQILEEVTHKTSGIT 882 (1265)
Q Consensus 830 -----~--------~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~--------------~~~~~~~~~~~~~~~l~ 882 (1265)
+ +..+....+.+++.+. +.+.++....+. .++.++.+.+...++++
T Consensus 966 ~~~~~f~~~~~~~s~l~p~~~~~~v~~~~~-------~~~~~~g~d~l~~~~~~n~~~l~~~~~rs~L~~k~~~~~~~l~ 1038 (1733)
T 1twf_A 966 NAQQTFHIDHTKPSDLTIKDIVLGVKDLQE-------NLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLT 1038 (1733)
T ss_dssp HHHHHTTCCTTSCBCCCHHHHHHHHHHHHT-------TCCSCCCCSHHHHHHHHHTTHHHHHHHHHHSCHHHHHHTSCCC
T ss_pred HHHHHHCCCCCCCCCCCHHHHHHHHHHHHH-------HHHCCCCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 888773135554345788999999999998-------6430158762005555252778888766545455566661778
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCHHHHHHHCCCCCCCCEEEE
Q ss_conf 99999999999985201458869601000002469843214013444465211210103301574432255445454998
Q 000829 883 EKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTPIITA 962 (1265)
Q Consensus 883 ~~~~~~~~~~~~~~y~~~~~~pGEaVGiIAAQSIGEPsTQMTLnTFH~AGv~~~nVTlGiPRLkEIinask~ikTP~i~~ 962 (1265)
.+++++++.+|..+|.+++++||||||+|||||||||+|||||||||||||++||||||||||+|||||||+||||+|++
T Consensus 1039 ~~~~~~~l~~i~~ky~~a~v~pGe~VG~iaAQSigEp~TQMTLnTFHfAGva~~NVTLGVPRLkEIinask~ikTP~mtv 1118 (1733)
T 1twf_A 1039 KQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTV 1118 (1733)
T ss_dssp HHHHHHHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC----------CCSCCHHHHHHHHTTTCSSCSSCEEEE
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCEEEE
T ss_conf 99998888999999986557898601567653168853123555444156125574367588999997513789973899
Q ss_pred ECCCC--CCHHHHHHHHCCEEEEECCCCCEEEEEEEECCC--------------------------------CEEEEEEC
Q ss_conf 72687--738799997501358742454212899990796--------------------------------19999948
Q 000829 963 ELECN--DNENAARVVKGRIEKTLLGQVAKSIKIVMTSRL--------------------------------ASIVIALD 1008 (1265)
Q Consensus 963 ~l~~~--~~~~~a~~i~~~le~~~L~di~~~i~~~~~~~~--------------------------------~~~~i~ld 1008 (1265)
+|.++ .+.+.|+.++.+||+++|+||+..++++|+|+. +.+++++|
T Consensus 1119 ~L~~~~~~~~e~A~~v~~~ie~ttL~dv~~~i~i~~dp~~~~tvi~ed~~~~~~y~~i~~~d~~~~~~~~~~~~lrl~l~ 1198 (1733)
T 1twf_A 1119 YLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELD 1198 (1733)
T ss_dssp EBCSSSSSCHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHHTSSCC----------CCCSEEEEEEEC
T ss_pred EECCCCCCCHHHHHHHHHHHCEEEHHHHHHEEEEEECCCCCCEEEECCHHHHHHHHCCCHHHHCCHHHHCCCCEEEEEEC
T ss_conf 95775432599999998763114899820167999736766403313223434332256776210032103400589966
Q ss_pred HHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCEEE-ECC-----CEEEEECCCCC--------CCCEEEHHHH-HHHCCC
Q ss_conf 36687724145999999998608644234575266-056-----34899289999--------8514425778-610577
Q 000829 1009 METIQDAHLCINADIVKESIVQTPKIKLKQQHIKV-LDF-----RKLEIFPPVDK--------SKIHFELYSL-KNVLPM 1073 (1265)
Q Consensus 1009 ~~~i~~~~~~i~~~~i~~~i~~~~~~k~~~~~v~~-~~~-----~~i~i~~~~~~--------~~~~~~l~~l-~~~l~~ 1073 (1265)
...+... ++++++|..+|.+..+ .++.+ .++ ..++++....+ .+..+ ++.+ +..+.+
T Consensus 1199 ~~~~~~~--~l~~~~I~~~i~~~~~-----~~~~~~~~d~~~~~~~~~i~~~~~~~~~~~~~~~~~~~-l~~l~~~~l~~ 1270 (1733)
T 1twf_A 1199 RAAMNDK--DLTMGQVGERIKQTFK-----NDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHM-LKKIENTMLEN 1270 (1733)
T ss_dssp HHHHHHT--TCCHHHHHHHHHHHHG-----GGEEEEECCTTSSSCEEEEEEC----------CCTTHH-HHHHHHHHHHH
T ss_pred HHHHHHC--CCCHHHHHHHHHHHHC-----CCCCEECCCCCCCHHHEEEEECCCCCCCCCCCCHHHHH-HHHHHHHHHHH
T ss_conf 9889763--7999999999987517-----77512047764000111332026752223332014799-99999976300
Q ss_pred CEEECCCCCEEEEEECCCCCCCHHHCC---CCCCCEEEEEECCCHHHHHCCCCCCCCCCCCCCHHHHHHHHCHHHHHHHH
Q ss_conf 287141371179994123110000024---87642899990766777631477446645567799999984799999999
Q 000829 1074 VIVKGIKTVERVVIAEKEKEKRKVKEN---GEKKKYRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICI 1150 (1265)
Q Consensus 1074 ~~i~Gi~~I~r~~i~~~~~~~~~~~~~---~~~~~~~l~teG~nl~~i~~~~~VD~~r~~sNdI~~v~~~lGIEAAR~~I 1150 (1265)
++|+|+++|+||++.+.. .....+. ..+++|.|+|||+||.++|.+++||++||+||||++|+++|||||||++|
T Consensus 1271 ~~v~Gi~~I~r~~i~~~~--~~~~~~~g~~~~~~~~~L~teG~nL~~vl~~~~VD~~rt~SNdI~eI~~vlGIEAAR~~I 1348 (1733)
T 1twf_A 1271 ITLRGVENIERVVMMKYD--RKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAAL 1348 (1733)
T ss_dssp CEEESCTTCCCEEEEEEE--EEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCTTTCBCSCHHHHHHHHCHHHHHHHH
T ss_pred EEEECCCCCCEEEEECCC--CEEECCCCCCCCCCCEEEEEECCCHHHHHCCCCCCCCCCEECCHHHHHHHHHHHHHHHHH
T ss_conf 477157885479995355--312357775245762389960514999960477254110434599999875699999999
Q ss_pred HHHHHHHHHCCCCCCCCCCCEEEECCCCCCCEEEEECCCCCCCCCCCHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCE
Q ss_conf 99998986026665572001000000110127974201223456870755701068899999944229865555533331
Q 000829 1151 IDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECI 1230 (1265)
Q Consensus 1151 i~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~itR~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~I 1230 (1265)
++|++.||+.||++||+|||+||||+||++|.++|||||||+++++|||++||||+|+++|++||++|+.|.|+||||||
T Consensus 1349 i~Ei~~V~~~~Gi~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~S~L~~aSFE~T~~~L~~Aa~~g~~D~l~gvsenI 1428 (1733)
T 1twf_A 1349 YKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENV 1428 (1733)
T ss_dssp HHHHHHHHHTTTCCCCHHHHHHHHHHTTTBSSCCCSSSCSSSCSSCCTTSSCCSSCSHHHHHHHHHHTCEECCCSHHHHH
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCEECCCCHHHHCCCCCCCHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf 99999998605863462334323555600763203331322266887221032254389999987514767355510001
Q ss_pred ECCCCCCCCCCCEEEEECCCC
Q ss_conf 105777778653375213899
Q 000829 1231 IMGIPMPLGTGILKIRQRDAV 1251 (1265)
Q Consensus 1231 i~Gk~~~~GTG~fdll~~~~~ 1251 (1265)
|+|+++|+|||+|||+++.+.
T Consensus 1429 I~G~~~~~GTG~FdLl~~~~~ 1449 (1733)
T 1twf_A 1429 ILGQMAPIGTGAFDVMIDEES 1449 (1733)
T ss_dssp HTTCCCSSGGGSSEEEECSCC
T ss_pred CCCCCCCCCCCCEEEEECHHH
T ss_conf 047777787740799971033
No 3
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D
Probab=1.00 E-value=1 Score=1764.02 Aligned_cols=887 Identities=26% Similarity=0.368 Sum_probs=700.1
Q ss_pred CHHHHHHHHHHCCHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999999972382248762599995507886312089999992421898767732589999999998999999997000
Q 000829 87 NPVNVLFLFKRMTDTDCEVLYLSERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANS 166 (1265)
Q Consensus 87 ~P~~v~~il~~i~~~d~~~l~~~~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~ 166 (1265)
++.....+|+++...++..-.. .+||||||++||||||++||++.++++..++||||.+|++||+.|++|++.+..|+|
T Consensus 225 ~~~~~~~~~krl~~~~~f~~~~-~~Pewmil~~lPVpPp~~RP~v~l~gg~~~~~Dln~~~~~Ii~~N~~L~~~~~~~ap 303 (1265)
T 1hqm_D 225 SRARRAKARKRLEVVRAFLDSG-NRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAP 303 (1265)
T ss_dssp SHHHHHHHHHHHHHHHHHHSSS-CSSCCSCSSCCCCCSCC------------CCCGGGTHHHHTHHHHHHHHTSSSSCCC
T ss_pred CHHHHHHHHHHHHHHHHHCCCC-CCCCEEEEECCCCCCCCCCCCEECCCCCEECCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 5777788761111666530258-981047631257899867664553897154670689999999999999999974994
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC-CHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCC
Q ss_conf 01256779879999987743689999765567887-20134320576541124556877898662278089998777555
Q 000829 167 AFKSLAGWETLQVEVAQYINSDVRGVPFSMQVARP-LSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVA 245 (1265)
Q Consensus 167 ~~~~~~~~~~lq~~v~~~~~~~~~~~~~~~~~~~~-~~~i~qrl~gK~G~fR~nl~GKRvd~s~RsVI~pDp~l~~~evg 245 (1265)
...+.+.|.+||.+|+.|+||+.+|.|.....++| ++||+||||||+||||+|||||||||||||||||||+|++||||
T Consensus 304 ~~ii~~~~~~LQ~~V~~l~Dn~~~g~~~~~~~~rp~lksl~~~LkGK~GrfR~NLmGKRVdfSaRSVI~pdP~L~i~evG 383 (1265)
T 1hqm_D 304 EIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCG 383 (1265)
T ss_dssp STTTSTTTTTTGGGTTTTSSCCSSCCCSSCSSCCCCCCCSTTTSSSTTCTTTTTTSCCEETTCCCCBEEECCSSSSSBCC
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCC
T ss_conf 56788889999999999967787798765878886664254402461134554202100276663167169876655036
Q ss_pred CCHHHHHHCCCCEEECHHHHHHHHHHHHCCC-CCCCCCEEEECCCCCEEEECCCCCHHHHHCCCCCCEEECCCCCCCEEE
Q ss_conf 6388886459440336477999999999299-999885077779998378624230345412653131101013698699
Q 000829 246 IPIRMARILTYPERVSDHNIEKLRQCIQNGP-DKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVL 324 (1265)
Q Consensus 246 iP~~~A~~Lt~Pe~Vt~~Ni~~lr~lv~nG~-~~~pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~~gd~vl 324 (1265)
||..||++||+|+ | +++||.||+ ..+++|+++... +. ...+. ++.|+||+.|||+||
T Consensus 384 vP~~~A~~L~~P~-----~---~~~lv~~g~~~~i~~ak~~i~~-------~~------~~~~~-~~~v~~~v~~gd~VL 441 (1265)
T 1hqm_D 384 LPKRMALELFKPF-----L---LKKMEEKAFAPNVKAARRMLER-------QR------DIKDE-VWDALEEVIHGKVVL 441 (1265)
T ss_dssp CBHHHHHHHHHHH-----H---HHHHHHTTCSSCSHHHHHHHCS-------SS------CCCHH-HHTTTTTTTTTCCEE
T ss_pred CHHHHHHHHCCHH-----H---HHHHHHCCCCCHHHHHHHHHHH-------CC------CCCCC-CCEEEEEECCCCEEE
T ss_conf 7599998837589-----9---9999983983204666665440-------12------34776-422578730496789
Q ss_pred EECCCCCCCCCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE
Q ss_conf 81588766464344899982698134202468988899764532345688288999999872888621159999951720
Q 000829 325 FNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVAS 404 (1265)
Q Consensus 325 ~NRqPsLHk~si~~~~~~v~~~~t~r~~~~~c~~yNADFDGDeMn~h~Pqs~~araEa~~Lm~~~~~~~sp~~G~pi~gl 404 (1265)
|||||||||+|||||++++++++||||||+||+||||||||||||+|+|||++|||||++||++++|++||++|+|++++
T Consensus 442 lNRqPTLHr~sIma~~~~l~~~ktirlhp~vC~~yNADFDGDeMnvHvPqs~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~ 521 (1265)
T 1hqm_D 442 LNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKP 521 (1265)
T ss_dssp CCCSSCCSGGGSCEEBCCCBSSSSEEECGGGHHHHCCCSSSCBCCCCCCCSTHHHHTTSSSSBSSSSSSSCSSSSCSSCC
T ss_pred EECCCCCCCCCCCCEEEEECCCCEEEECHHHCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHCCCCCEECCCCCCEEEEE
T ss_conf 81686423145421168965897487364326876777543057896479889999999983751048438899814764
Q ss_pred CCCCEEEEEEEECCC--------CCCCHHHHHHHHHHHCCCCCEEECCCCCEE---------------------------
Q ss_conf 134000336650257--------667999999999983389840324788300---------------------------
Q 000829 405 TQDFLTSSFLITRKD--------TFYDRAAFSLMCCYMGDGMDRVDLPTPAIL--------------------------- 449 (1265)
Q Consensus 405 iQD~i~g~~llT~~d--------~f~~~~~~~~l~~~~~~~~~~~~l~~Pail--------------------------- 449 (1265)
+||+|+|+|+||.+| +|+++++++++++.. .+.+|.|..+
T Consensus 522 ~QD~vlg~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~-----~i~l~a~i~~~~~~~~~g~~k~~~t~P~k~I~~~~~g 596 (1265)
T 1hqm_D 522 SRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERG-----EVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHG 596 (1265)
T ss_dssp CTTHHHHHHHTTCCCCCCCCCCCCSSCCTHHHHHTTSS-----CCSSCCCSSSCCSTTSSCCCCCTTTCSHHHHHHHHTT
T ss_pred ECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHCC-----CCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 01233205883121677667775018899999999779-----9898983597066434443444456522212323467
Q ss_pred ------------CC--CCCCCCCEEEEEEECCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf ------------76--3233664015544058888624797763130113554445687323234568899803883684
Q 000829 450 ------------KP--VELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFVYFRNSE 515 (1265)
Q Consensus 450 ------------kp--~~lwTGKQi~s~il~~~~~~~~~in~~~~~k~~~~~~~~~~g~~~~~~~~~~~~d~~v~i~~ge 515 (1265)
|| ..+|||||+||+++|+... + + ..+++ +.+
T Consensus 597 ~~~~q~~~~~~~k~~~~~t~~Gr~if~~~lp~~~~---------~---~-----------------~~p~~--~~~---- 641 (1265)
T 1hqm_D 597 LLDLQDTVTTRYLGRRLETNPGRILFARIVGEAVG---------D---E-----------------KVAQE--LIQ---- 641 (1265)
T ss_dssp SSCSSSCCCCEESSSEECCCHHHHHHHHHHHHHTT---------C---T-----------------TTTTT--SSC----
T ss_pred CCCCCCCCCEECCCCCEECCCCCEEEEEECCCCCC---------C---C-----------------CCCCC--CCE----
T ss_conf 61333232010244533406885677620354323---------4---5-----------------79887--866----
Q ss_pred CEECCCCCCCCCCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCC-CEEEECCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 200134554336887432899999971932688998599999999998406-4121256899920048999999999999
Q 000829 516 LISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHG-FSIGIDDVQPKKELSDKKGKLISENYEV 594 (1265)
Q Consensus 516 ll~G~ldK~~lG~~~~~~li~~i~~~yG~~~a~~~l~~~~~l~~~~l~~~G-fSigi~D~~~~~~~~~~~~~~i~~~~~~ 594 (1265)
+.|++||+++| +|||.+|++||++.|+.|||.+++|+++|++.+| ||||++|++++++ +.+++++++++
T Consensus 642 -~ngvldKk~lG-----~LI~~i~~~~G~~~a~~~ld~l~~l~~~~lt~~G~fSigi~D~~~~~~----k~~~i~~a~~~ 711 (1265)
T 1hqm_D 642 -MDVPQEKNSLK-----DLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGIITIGIDDAVIPEE----KQRYLEEADRK 711 (1265)
T ss_dssp -CSSCCCSSHHH-----HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHTTCCCCSSSSCCCCST----TTTHHHHHHHH
T ss_pred -EEEEECHHHHH-----HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCHH----HHHHHHHHHHH
T ss_conf -83054289999-----999999999799999999999999999999857882585310347878----99999999999
Q ss_pred HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---CCCCCEEEECCCCCCCHHCHHHHHHCCC
Q ss_conf 9999999872998669899978999999999999999999998862799---9994222312478889132757761356
Q 000829 595 CNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLP---WRNSPLIMSQCGSKGSPINISQMVACVG 671 (1265)
Q Consensus 595 ~~~~~~~~~~~~~~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l~---~~N~~~~M~~sGsKGS~~Ni~Qi~~~lG 671 (1265)
+.+++.+|..|.++ .+..++++..+|+++++++++.+++.+. ++|++++|+.||||||++|++||+||+|
T Consensus 712 v~~i~~~y~~g~lt-------~~e~~~~v~~~~~~~~d~~~~~~~~~l~~~~~~N~i~~Ma~SGAKGS~~ni~Ql~g~~G 784 (1265)
T 1hqm_D 712 LRQIEQAYEMGFLT-------DRERYDQVIQLWTETTEKVTQAVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRG 784 (1265)
T ss_dssp HHHHHTTTTSSSSC-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCSSSCTTTTTTTSSSCCHHHHHHHSSCCC
T ss_pred HHHHHHHHHCCCCC-------HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHCC
T ss_conf 99999999829986-------78999999999999999999999987441589886999977167768989999986046
Q ss_pred CCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHCCCCCCCHHCCCCCCCCCHHHHHHHHHH
Q ss_conf 553-5897789998776567999999897765301445634899123466502465300000100476771479999974
Q 000829 672 QQS-VGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKAL 750 (1265)
Q Consensus 672 QQ~-i~G~Rip~g~~~rtLP~f~~~~~~~~a~GfI~~sF~~GL~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLik~l 750 (1265)
||. .+|+++ | ++|.|||++||+|+|||||||||||||+|||||||+||||||||||++
T Consensus 785 ~ma~~~G~~i---------~------------~pI~ssF~eGLtp~EyFfhtmggReGLiDTAvKTA~SGYLqRRLVkv~ 843 (1265)
T 1hqm_D 785 LMQKPSGETF---------E------------VPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVA 843 (1265)
T ss_dssp CCCCTTSCCC---------S------------CCCCCCBTTBCTTCTHHHHHHHHTTHHHHHTHHHHTSSSTHHHHHHHS
T ss_pred CCCCCCCCCC---------C------------CCCCCCCCCCCCHHHHHEECCCCCCCCHHHHHHCCCCCCCEEEEEEEC
T ss_conf 4026899746---------8------------621252335898578530131123650332200166885113445340
Q ss_pred HHEEEEECCEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCHH----------HHHHHHHHHCCCCCCCCCCCHHHHHHH
Q ss_conf 3137521281775898199997068886444336888998326----------999999883199999977897779999
Q 000829 751 EDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNF----------DRLLMKVKATCPPAGQRYLSPQQVSEI 820 (1265)
Q Consensus 751 Edl~v~YD~TVR~s~g~IiQF~YGeDGld~~~~e~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~ 820 (1265)
||++|+||+| ||+||+|+..++. . .++.. +|++.++.+.. .....+.|.
T Consensus 844 qDv~V~~ddc------------~t~dGi~v~~~~~-~-~~i~~~~~~~~~~L~~ri~gr~~~~~--i~~~~~~p~----- 902 (1265)
T 1hqm_D 844 HEIVVREADC------------GTTKYISVPLFQM-D-EVTRTLRLRKRSDIESGLYGRVLARE--VEALGRRLE----- 902 (1265)
T ss_dssp CSCCCCSCCC------------CCCCCEECCSEEC-C-STTCCCEECCTTTTHHHHTTCEESSC--EEETTEEEC-----
T ss_pred CEEEEEECCC------------CCCCCEEEEEEEC-C-CEEECHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCC-----
T ss_conf 5179997898------------9979989898516-8-34400332013689999976652203--310146988-----
Q ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHH--H
Q ss_conf 99998530877621999999999999864322124101133588853202445642035879999999999999852--0
Q 000829 821 VEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSGITEKQLEVFIQTCFSRY--R 898 (1265)
Q Consensus 821 ~~~~l~~~~~~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~y--~ 898 (1265)
..+.-.... +++ .++++.+. ++. ....++.++|+....+|..|+.++ .
T Consensus 903 ------~~~~i~~~~-------~~i--~~~~i~~~-------gi~--------~v~iRs~ltc~s~~gvc~~CYgr~La~ 952 (1265)
T 1hqm_D 903 ------EGRYLSLED-------VHF--LIKAAEAG-------EVR--------EVPVRSPLTCQTRYGVCQKCYGYDLSM 952 (1265)
T ss_dssp ------SSCBCCTTH-------HHH--HHHHHHTT-------SCS--------SCEEECGGGCSCTTSCCSSSSCSCSSS
T ss_pred ------CCCEEECCC-------CHH--HHHHHHHC-------CCC--------EEEEECCCCHHHHHHHHHHHHHHHHCC
T ss_conf ------765785685-------040--69999975-------998--------787636767877999999985412105
Q ss_pred CCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCC-CCCEECCCCHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf 145886960100000246984321401344446521-1210103301574432255445454998726877387999975
Q 000829 899 VKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVA-SMNITQGVPRIKEIINGAKRISTPIITAELECNDNENAARVVK 977 (1265)
Q Consensus 899 ~~~~~pGEaVGiIAAQSIGEPsTQMTLnTFH~AGv~-~~nVTlGiPRLkEIinask~ikTP~i~~~l~~~~~~~~a~~i~ 977 (1265)
+++++||||||+|||||||||+|||||||||+||++ ++|||+|+||++||++|++ +|||.|..++.....
T Consensus 953 ~~lV~~GEaVGiIAAQSIGEPGTQlTLrTFH~gGvas~~dIT~GLPRv~El~eArk-pk~p~i~a~~~g~v~-------- 1023 (1265)
T 1hqm_D 953 ARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELFEARR-PKAKAVISEIDGVVR-------- 1023 (1265)
T ss_dssp SSCCCTTCCHHHHHHHHHHGGGTTSCCCC--------CCTTSSHHHHHHHHHHCCC-CSSCBCCCSSSCBCC--------
T ss_pred CCEECCCCEEEEEECCCCCCCCCEEEEEEEEECCEECCCCCCCCCHHHHHHHHHCC-CCCCEEEEECCCEEE--------
T ss_conf 98701686145540112278874256677888544000233457432898875107-898627984165499--------
Q ss_pred CCEEEEECCCCCEEEEEEEECCCCEEEEEECHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCEEEECCCEEEEECCCCC
Q ss_conf 01358742454212899990796199999483668772414599999999860864423457526605634899289999
Q 000829 978 GRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEIFPPVDK 1057 (1265)
Q Consensus 978 ~~le~~~L~di~~~i~~~~~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~~~k~~~~~v~~~~~~~i~i~~~~~~ 1057 (1265)
+.+ +.... .+. +... + .
T Consensus 1024 -------~~~---------~~~~~----------------~i~---------------i~~~-----g-----------~ 1040 (1265)
T 1hqm_D 1024 -------IEE---------GEDRL----------------SVF---------------VESE-----G-----------F 1040 (1265)
T ss_dssp -------CCC---------CSSCC----------------CCC---------------CBCS-----S-----------C
T ss_pred -------EEE---------CCCCC----------------EEE---------------EEEC-----C-----------C
T ss_conf -------830---------48851----------------799---------------9878-----9-----------2
Q ss_pred CCCEEEHHHHHHHCCCCEEECCCCCEEEEEECCCCCCCHHHCCCCCCCEEEEEECCCHHHHHCCCCCCCCCCCCCCHHHH
Q ss_conf 85144257786105772871413711799941231100000248764289999076677763147744664556779999
Q 000829 1058 SKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEV 1137 (1265)
Q Consensus 1058 ~~~~~~l~~l~~~l~~~~i~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~nl~~i~~~~~VD~~r~~sNdI~~v 1137 (1265)
.+.+ -++...++.+...+ .-......+|| ++|+++|
T Consensus 1041 ~~~~----------------~ip~~~~l~v~~g~----------~v~~g~~lteG------------------~~~~~ei 1076 (1265)
T 1hqm_D 1041 SKEY----------------KLPKDARLLVKDGD----------YVEAGQPLTRG------------------AIDPHQL 1076 (1265)
T ss_dssp CCCC----------------CCSSCCCCCCCSCC----------SSTTCSCCCCS------------------BSHHHHH
T ss_pred EEEE----------------ECCCCEEEEEECCC----------EEECCCEEECC------------------CCCHHHH
T ss_conf 7799----------------74785289984697----------77068035226------------------7519999
Q ss_pred HHHHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCC--------------------------------------
Q ss_conf 998479999999999998986026665572001000000110--------------------------------------
Q 000829 1138 QQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTF-------------------------------------- 1179 (1265)
Q Consensus 1138 ~~~lGIEAAR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~-------------------------------------- 1179 (1265)
++++||||+|.+|++|++.||..||++||+|||+||+|.||.
T Consensus 1077 l~v~Giea~~~~lv~EIq~vyr~QGv~I~dkHievivrqM~~kv~i~~~g~t~~l~Ge~v~~~~~~~~n~~~~~~g~~~~ 1156 (1265)
T 1hqm_D 1077 LEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSPLLEGQVLEKWDVEALNERLIAEGKVPV 1156 (1265)
T ss_dssp HHTTHHHHHHHHHHHHHHHHHHTTSCCCCSSTHHHHHHHHTTEECBSSCCSSCCSCCCEEGGGTTTTTTTTTTC---CCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCEEEECCCCCCCCCCCEECHHHHHHHHHHHHHCCCCCC
T ss_conf 99863999999999999999897486203789999999874253771488867889866509999999999996689852
Q ss_pred --CCEEEEECCCCCCCCCCCHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCEECCCCCCCCCCCE
Q ss_conf --1279742012234568707557010688999999442298655555333311057777786533
Q 000829 1180 --RGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGIL 1243 (1265)
Q Consensus 1180 --~G~~~~itR~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~f 1243 (1265)
++.++||||++++ .+|+|++||||+|+++|++||+.|++|.|.|++||||+|+++|+|||+.
T Consensus 1157 ~~~~~llGITkasl~--t~SflsaASFqeTt~vL~~AAi~gk~D~L~GlkEnVIiG~lipaGTG~~ 1220 (1265)
T 1hqm_D 1157 AWKPLLMGVTKSALS--TKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSD 1220 (1265)
T ss_dssp CBCCCCCCTHHHHTS--CSCHHHHTTSTTHHHHHHHHHHSCCCCTTCSSHHHHHHTCCCSSGGGCT
T ss_pred EEEEEEECCEECCCC--CCCHHHCCCHHHHHHHHHHHHHCCCCCCCCCCHHHEEECCCCCCCCCCH
T ss_conf 554556520522334--6774430556888999999997289876899277633178656875814
No 4
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Probab=1.00 E-value=1 Score=1736.68 Aligned_cols=913 Identities=25% Similarity=0.362 Sum_probs=699.5
Q ss_pred CCHHHHHHHHHHCCHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 69999999997238224876259999550788631208999999242189876773258999999999899999999700
Q 000829 86 LNPVNVLFLFKRMTDTDCEVLYLSERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEAN 165 (1265)
Q Consensus 86 L~P~~v~~il~~i~~~d~~~l~~~~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~ 165 (1265)
.+......+++++..-+...-.. .+||||||++||||||++||++.++++..++||||.+|++||+.|++|+..+..|+
T Consensus 484 ~~~~~~~~~~krl~~~~~F~~~~-~rPewmil~vlPVpPp~lRP~v~ldgg~~~~sDLn~ly~~II~~Nn~Lk~~~~~ga 562 (1524)
T 2a6h_D 484 PSRARRAKARKRLEVVRAFLDSG-NRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGA 562 (1524)
T ss_dssp SCHHHHHHHHHHHHHHHHHHHSS-CCTTTTEEEEEEECCSTTSCEEECSTTCEEECTHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHCHHHHHHHHHHCC-CCCCEEEEECCCCCCCCCCCCEECCCCCEECCHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 03666777545489999986448-87537888326689997788666189826666278999999999899999987325
Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC-CHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCC
Q ss_conf 001256779879999987743689999765567887-2013432057654112455687789866227808999877755
Q 000829 166 SAFKSLAGWETLQVEVAQYINSDVRGVPFSMQVARP-LSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEV 244 (1265)
Q Consensus 166 ~~~~~~~~~~~lq~~v~~~~~~~~~~~~~~~~~~~~-~~~i~qrl~gK~G~fR~nl~GKRvd~s~RsVI~pDp~l~~~ev 244 (1265)
|...+.+.|.+||.+|+.|+||+.+|.|.....++| ++||+|+||||+||||+|||||||||||||||||||+|++|||
T Consensus 563 p~~ii~~e~~~LQ~~V~~liDN~~~g~p~~~~~~Rp~lKslsq~LkGKeGRFRqNLlGKRVDySgRSVI~pdP~L~l~ev 642 (1524)
T 2a6h_D 563 PEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQC 642 (1524)
T ss_dssp CHHHHHHHHHHHHHHHHHHHCSSSSSCCBCSSSCCCBCCCHHHHHSTTTCHHHHHHHCEEESSEEEEEEEECTTSCTTEE
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCC
T ss_conf 07789999999999999996578878876688888767644443035454100044431136667524726987505513
Q ss_pred CCCHHHHHHCCCCEEECHHHHHHHHHHHHCCCCCC-CCCEEEECCCCCEEEECCCCCHHHHHCCCCCCEEECCCCCCCEE
Q ss_conf 56388886459440336477999999999299999-88507777999837862423034541265313110101369869
Q 000829 245 AIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKY-PGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVV 323 (1265)
Q Consensus 245 giP~~~A~~Lt~Pe~Vt~~Ni~~lr~lv~nG~~~~-pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~~gd~v 323 (1265)
|||..||++||+|+ .|++||.||+..+ ++|++++.. +. ...+. ++.|+||+.|||+|
T Consensus 643 GvP~~mA~eLt~Pf--------~~r~Lv~nG~a~nik~AK~li~~-------~~------~~~~~-v~dVlr~vidgd~V 700 (1524)
T 2a6h_D 643 GLPKRMALELFKPF--------LLKKMEEKGIAPNVKAARRMLER-------QR------DIKDE-VWDALEEVIHGKVV 700 (1524)
T ss_dssp EEEHHHHHHHTHHH--------HHHHHHHSTTCSSHHHHHHHHSS-------GG------GCCHH-HHHHHHHHSTTCCE
T ss_pred CCCHHHHHHHCCHH--------HHHHHHHCCCCCCHHHHHHHHHH-------HC------CCCCC-CHHHHEEECCCCEE
T ss_conf 78099999856599--------99999983983422666678764-------11------34653-01220100059667
Q ss_pred EEECCCCCCCCCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEE
Q ss_conf 98158876646434489998269813420246898889976453234568828899999987288862115999995172
Q 000829 324 LFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVA 403 (1265)
Q Consensus 324 l~NRqPsLHk~si~~~~~~v~~~~t~r~~~~~c~~yNADFDGDeMn~h~Pqs~~araEa~~Lm~~~~~~~sp~~G~pi~g 403 (1265)
||||||||||+|||||++++++++||||||+||+||||||||||||+|+|||++|||||++||++++|++||++|+|+++
T Consensus 701 LlNRqPTLHRlSIqAf~~kl~~gkTiRLhplVC~pyNADFDGDEMnvHvPqS~eAraEA~~LM~~~~nilsP~~G~Pi~~ 780 (1524)
T 2a6h_D 701 LLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAK 780 (1524)
T ss_dssp EEECSSCCSGGGEEEEEEEEESSSCEEECSGGGTTTTCCTTTCEEEEECCCSHHHHHHHHHHSBTTTCCBCSSSSSBSSC
T ss_pred EECCCCCCCCCCCCEEEEEECCCCCCEECHHHCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHCCCCCEECCCCCCEEEE
T ss_conf 87058743425640268897578510147232577667756533567627878899999998477144613899981462
Q ss_pred ECCCCEEEEEEEECCC--------CCCCHHHHHHHHHHH-CCCCCE--------------EECCCC--CEECCCCCCCCC
Q ss_conf 0134000336650257--------667999999999983-389840--------------324788--300763233664
Q 000829 404 STQDFLTSSFLITRKD--------TFYDRAAFSLMCCYM-GDGMDR--------------VDLPTP--AILKPVELWTGK 458 (1265)
Q Consensus 404 liQD~i~g~~llT~~d--------~f~~~~~~~~l~~~~-~~~~~~--------------~~l~~P--ailkp~~lwTGK 458 (1265)
++||+|+|+|+||.++ +|+++++++++++.. ..-... ..+|+| +|+|| ||||
T Consensus 781 ~~QD~vlG~y~LT~~~~~~~~~g~~F~~~~e~~~ay~~~~~~l~~~i~v~~~~~~~~~~~~~~p~P~~aIlKp---wtGK 857 (1524)
T 2a6h_D 781 PSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAV---AHGI 857 (1524)
T ss_dssp CCHHHHHHHHHHHCCCCCCCCSCCCTTSCHHHHHHHHHHHHTTSSCSSCCCSSCCHHHHHCEESSHHHHHHHH---HTTS
T ss_pred ECCCCHHHHEECCCCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHCCC---CCCC
T ss_conf 1330023203341246566677865588999999986588676872598424344433234467855641589---8874
Q ss_pred EEEEEE----ECCCCCCCEEEEEEECCCC-CCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEECCCCCCCCCCCCCCC
Q ss_conf 015544----0588886247977631301-13554445687323234568899803883684200134554336887432
Q 000829 459 QLFSVL----IRPHANMRVYVNLTVKEKT-YSNKLIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDG 533 (1265)
Q Consensus 459 Qi~s~i----l~~~~~~~~~in~~~~~k~-~~~~~~~~~g~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~ 533 (1265)
|+++.+ ++.+ ......++. +......... ....+++. ..+.|++||+++| +
T Consensus 858 Qi~~~~~~~~I~~~------~~~tt~Gr~ifn~~lp~~l~------~~~~P~d~-------~~inGvLdKk~LG-----~ 913 (1524)
T 2a6h_D 858 VDLQDVVTVRYMGK------RLETSPGRILFARIVAEAVE------DEKVAWEL-------IQLDVPQEKNSLK-----D 913 (1524)
T ss_dssp SCTTSCCEEECSSC------EECCCHHHHHHHHHHHHHSS------CHHHHHHT-------CCTTSCCCHHHHH-----H
T ss_pred CCCCCCCCCCEECC------EEECCCCHHHHHHHHHHHCC------CCCCCCCC-------CCEECEECHHHHH-----H
T ss_conf 14654321110001------02216654319988566504------56689866-------6220336389999-----9
Q ss_pred HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 89999997193268899859999999999840641212568999200489999999999999999999872998669899
Q 000829 534 LYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGC 613 (1265)
Q Consensus 534 li~~i~~~yG~~~a~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 613 (1265)
|||.+|++||++.|+.|||++++|+++|++.+|||||++|++++++ +.++++++++++.+++.+|..|.++
T Consensus 914 LI~~i~~~yG~~~t~~fLD~lk~Lg~~~lt~~GfSIGI~Dlii~~~----K~eiI~eA~~~v~~i~~~y~~G~lt----- 984 (1524)
T 2a6h_D 914 LVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEE----KKQYLEEADRKLLQIEQAYEMGFLT----- 984 (1524)
T ss_dssp HHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHTCCCCSTTSCCCTT----HHHHHHHHHHHHHHHHHHHHTTCSC-----
T ss_pred HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCEEEHHHCCCCHH----HHHHHHHHHHHHHHHHHHHHCCCCC-----
T ss_conf 9999999859999999999999999999986681420533257777----9999999999999999999839997-----
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---CCCCCEEEECCCCCCCHHCHHHHHHCCCCCC-CCCCCCCCCCCCCCC
Q ss_conf 978999999999999999999998862799---9994222312478889132757761356553-589778999877656
Q 000829 614 DAAQTLEAVITDILNRIREDAGKACMGSLP---WRNSPLIMSQCGSKGSPINISQMVACVGQQS-VGGRRAPNGFIDRSL 689 (1265)
Q Consensus 614 ~~~~~le~~i~~~l~~~~~~~~~~~~~~l~---~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~-i~G~Rip~g~~~rtL 689 (1265)
..+ .+.++..+|+++++++++.|++++. ++|++++|+.||||||++|++||+||+|||. .+|+++| +
T Consensus 985 -~~E-r~~~Vi~iw~~a~d~v~~~~~~~L~~~~~~N~i~~Ma~SGAKGS~~NI~Ql~gmrGqma~p~GkiIp-------~ 1055 (1524)
T 2a6h_D 985 -DRE-RYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFE-------V 1055 (1524)
T ss_dssp -HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHSSSSCCHHHHHHHTSCCCCCBCSSSCBCS-------S
T ss_pred -HHH-HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCC-------C
T ss_conf -799-9999999999999999999997404158988799998716775798999998603660468997722-------5
Q ss_pred CCCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHCCCCCCCHHCCCCCCCCCHHHHHHHHHHHHEEEEECCEEECCCCCEE
Q ss_conf 79999998977653014456348991234665024653000001004767714799999743137521281775898199
Q 000829 690 PHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIV 769 (1265)
Q Consensus 690 P~f~~~~~~~~a~GfI~~sF~~GL~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLik~lEdl~v~YD~TVR~s~g~Ii 769 (1265)
| |.|||++||+|+|||||||||||||+|||||||+||||||||||++||++|.||+|
T Consensus 1056 P--------------I~ssF~eGLtp~EyFfhtmGgReGLvDTAvKTAdSGYLqRRLVkv~qDviVr~dDc--------- 1112 (1524)
T 2a6h_D 1056 P--------------VRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADC--------- 1112 (1524)
T ss_dssp C--------------CCCCSSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCSCC---------
T ss_pred C--------------CCCCCCCCCCHHHHHEECCCCCCCCCCCCEEECCCCCCEEEEEEECCEEEEEECCC---------
T ss_conf 1--------------13432469974774201222357753320110568840342211006069996788---------
Q ss_pred EEEECCCCCCCCCC-CCCCCCCCHH---HHHHHHHHHCCCCCCCCC---CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q ss_conf 99706888644433-6888998326---999999883199999977---8977799999999853087762199999999
Q 000829 770 QFLYGDDGMDPANM-EGKSGEPLNF---DRLLMKVKATCPPAGQRY---LSPQQVSEIVEKQLAAYGKESCSEAFLNSLR 842 (1265)
Q Consensus 770 QF~YGeDGld~~~~-e~~~~~~~~~---~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~ 842 (1265)
+|+||+|+..+ +++...++++ ..+......- ....+.. ..|.. ..++ .. ....+ .+.
T Consensus 1113 ---gt~dGi~v~~~~~g~~~~~~~~~~i~~l~~ri~gR-~~~~di~~~~~~p~~-----~e~i----~~-~~~~I--~~~ 1176 (1524)
T 2a6h_D 1113 ---GTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGR-VLAREVEVLGVRLEE-----GRYL----SM-DDVHL--LIK 1176 (1524)
T ss_dssp ---CCCCCEEEESBCSCSSSSCCCBCCHHHHHHHHTTC-BBSSCEECSSCEECT-----TCBC----CT-TTTTH--HHH
T ss_pred ---CCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHCC-CCHHHHHHHCCCCCC-----CCEE----EC-CCCEE--HHH
T ss_conf ---99798688886307866652068889899877433-113445541258876-----7678----67-99865--189
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHH--HCCCCCCCCCCEEECCCCCCCCC
Q ss_conf 9999864322124101133588853202445642035879999999999999852--01458869601000002469843
Q 000829 843 KFFEGQQDKLDKKIKFVEDIGWDDKSQILEEVTHKTSGITEKQLEVFIQTCFSRY--RVKRVEAGTAIGAIGAQSIGEPG 920 (1265)
Q Consensus 843 ~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~y--~~~~~~pGEaVGiIAAQSIGEPs 920 (1265)
.+... .+. .+..++.++|+....+|..|+.++ ..++++||||||+|||||||||+
T Consensus 1177 ~i~~~---gi~--------------------~v~iRS~ltC~s~~gvc~~CYgr~La~~~~v~~GeaVGiiaAQSIGEPg 1233 (1524)
T 2a6h_D 1177 AAEAG---EIQ--------------------EVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPG 1233 (1524)
T ss_dssp HHHHT---SCS--------------------EEEECCGGGCCCSSCBCHHHHCSCSSSSSSCCTTCCHHHHHHHHHHSGG
T ss_pred HHHHC---CCC--------------------CCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEHHHHCCCCCC
T ss_conf 99971---998--------------------3244365558889999999845331039740344101021332037875
Q ss_pred CCCCCCCCCCCCCC-CCCEECCCCHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHCCEEEEECCCCCEEEEEEEECC
Q ss_conf 21401344446521-12101033015744322554454549987268773879999750135874245421289999079
Q 000829 921 TQMTLKTFHFAGVA-SMNITQGVPRIKEIINGAKRISTPIITAELECNDNENAARVVKGRIEKTLLGQVAKSIKIVMTSR 999 (1265)
Q Consensus 921 TQMTLnTFH~AGv~-~~nVTlGiPRLkEIinask~ikTP~i~~~l~~~~~~~~a~~i~~~le~~~L~di~~~i~~~~~~~ 999 (1265)
|||||||||+||++ ++|||+|+||++||++|++...+++++- +.+.+ ++..+..
T Consensus 1234 TQlTlrTFH~gGv~~~~dIt~GlPRv~El~eARkpk~~aiI~e-------------i~G~V------------~i~~~~~ 1288 (1524)
T 2a6h_D 1234 TQLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAVISE-------------IDGVV------------RIEETEE 1288 (1524)
T ss_dssp GTCCCC-----------CCCCSHHHHHHHHTTCCCSSBCCBCS-------------SCEEE------------EECCCSS
T ss_pred CCCCCEEEEECCCCCCCCCCCCCCCHHHHEECCCCCCCCEEEE-------------ECEEE------------EEEECCC
T ss_conf 4321000453352343332346722455400124788626998-------------31089------------9953178
Q ss_pred CCEEEEEECHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCEEEECCCEEEEECCCCCCCCEEEHHHHHHHCCCCEEECC
Q ss_conf 61999994836687724145999999998608644234575266056348992899998514425778610577287141
Q 000829 1000 LASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGI 1079 (1265)
Q Consensus 1000 ~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~~~k~~~~~v~~~~~~~i~i~~~~~~~~~~~~l~~l~~~l~~~~i~Gi 1079 (1265)
...+.+ ..+ + ... ...+
T Consensus 1289 ~r~i~i----------------------------------------------~~~-~-~~~---------------~~~i 1305 (1524)
T 2a6h_D 1289 KLSVFV----------------------------------------------ESE-G-FSK---------------EYKL 1305 (1524)
T ss_dssp CEEEEE----------------------------------------------ECS-S-CEE---------------EEEE
T ss_pred CEEEEE----------------------------------------------ECC-C-CEE---------------EEEC
T ss_conf 328999----------------------------------------------708-8-404---------------7864
Q ss_pred CCCEEEEEECCCCCCCHHHCCCCCCCEEEEEECCCHHHHHCCCCCCCCCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHH
Q ss_conf 37117999412311000002487642899990766777631477446645567799999984799999999999989860
Q 000829 1080 KTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMK 1159 (1265)
Q Consensus 1080 ~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~nl~~i~~~~~VD~~r~~sNdI~~v~~~lGIEAAR~~Ii~Ei~~v~~ 1159 (1265)
|...++.+...+ .-..+...||| +||+++|++++||||||.+|++|++.||.
T Consensus 1306 p~~~~l~V~~gd----------~v~~g~~lteG------------------~~~~~dil~v~Giea~~~~iv~Eiq~Vyr 1357 (1524)
T 2a6h_D 1306 PKEARLLVKDGD----------YVEAGQPLTRG------------------AIDPHQLLEAKGPEAVERYLVEEIQKVYR 1357 (1524)
T ss_dssp CTTCCCCCCTTS----------EECTTCBSSSS------------------BCCHHHHHHHHCHHHHHHHHHHHHHHHHH
T ss_pred CCCEEEEEECCC----------EEECCEEEECC------------------CCCCHHHEEECCHHHHHHHHHHHHHHHHH
T ss_conf 776078983697----------56437277448------------------78742210106999999999999999998
Q ss_pred CCCCCCCCCCCEEEECCCCC----------------------------------------CCEEEEECCCCCCCCCCCHH
Q ss_conf 26665572001000000110----------------------------------------12797420122345687075
Q 000829 1160 AHGMSIDKRHMMLLADLMTF----------------------------------------RGEVLGITRFGIQKMDKSVL 1199 (1265)
Q Consensus 1160 ~~Gi~Vd~RHl~LlAD~MT~----------------------------------------~G~~~~itR~Gi~~~~~Spl 1199 (1265)
.||++||+|||+||+|.||. ++.++||||++++ .+|+|
T Consensus 1358 ~QGv~I~dKHIevIvrqM~~kv~i~~~Gdt~~l~Ge~v~~~~~~~~n~~~~~~g~~~a~~~~~llGITkasL~--t~SfL 1435 (1524)
T 2a6h_D 1358 AQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALS--TKSWL 1435 (1524)
T ss_dssp TTTCCCCHHHHHHHHHHTTSEEEEEECSSSCSSCEEEHHHHHHHHHHHHTTSCSCCCCEEEECCCCHHHHHHS--CSCHH
T ss_pred HCCCCCCHHHHHHHHHHHHCEEEEECCCCCCCCCCCEEEHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCC--CCCHH
T ss_conf 5585513568999999874425882488766789865419999999999997689852210035420531334--68723
Q ss_pred HHHCCHHHHHHHHHHHHCCCCCCCCCCCCCEECCCCCCCCCCCEEEE
Q ss_conf 57010688999999442298655555333311057777786533752
Q 000829 1200 MLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIR 1246 (1265)
Q Consensus 1200 ~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll 1246 (1265)
++||||+|+++|++||+.|++|+|.|++||||+|+++|+|||++++.
T Consensus 1436 saASFqeTtrvLt~AAi~Gk~D~L~GlkENVIiG~lIPaGTG~~~~~ 1482 (1524)
T 2a6h_D 1436 SAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVR 1482 (1524)
T ss_dssp HHHHSSCHHHHHHHHHHTTEEEECCSHHHHHHTTCCCSSSTTCTTTS
T ss_pred HHCCHHHHHHHHHHHHHCCCCCCCCCCHHHEEECCCCCCCCCCHHHC
T ss_conf 31574888999999986389877898278711168756786861011
No 5
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Probab=1.00 E-value=1 Score=1703.69 Aligned_cols=743 Identities=40% Similarity=0.673 Sum_probs=687.0
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEECCEEEEEEEECCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCCHHH
Q ss_conf 99999999999230379977698989989717832302218983245214578776631002124554200143469999
Q 000829 11 KTDLMKSIVKKCSTMASKAVKCPRCGYINGMVKKAVAVLGIIHDRSKVTESLQEFASAITHTKESKAAVNVATYILNPVN 90 (1265)
Q Consensus 11 r~~~~k~i~~~c~~~~k~~k~C~~Cg~~~p~IkK~~~~~ki~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~L~P~~ 90 (1265)
.+.+.+.+.+.+ .+.+.|++||+.++.+++... ..+..+. + .....|+|.+
T Consensus 129 ~~~~~~~~~~~~----~~~~~c~~cg~~~~~i~~~~~-~~~~~~~-----------------~-------~~~~~l~~~~ 179 (880)
T 4ayb_A 129 ARRLTEYVKKTA----MKAQVCPHCGEKQFKIKLEKP-YNFYEER-----------------K-------EGVAKLTPSD 179 (880)
T ss_dssp HHHHHHHHHHHH----TTCSSCTTTTCCCCCCEEEET-TEEEEEE-----------------T-------TEEEECCHHH
T ss_pred HHHHHHHHHHHH----CCCCCCHHCCCHHHHHHHCCC-CCHHHHH-----------------H-------HHHHHCCHHH
T ss_conf 999999999874----154001220632466552375-7789999-----------------9-------9997538999
Q ss_pred HHHHHHHCCHHHHHHHCCC---CCCCEEEEEEEEECCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9999972382248762599---9955078863120899999924218987677325899999999989999999970000
Q 000829 91 VLFLFKRMTDTDCEVLYLS---ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSA 167 (1265)
Q Consensus 91 v~~il~~i~~~d~~~l~~~---~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~ 167 (1265)
++++|++|+++|+.++++. .+||||||++||||||++||++.++++..++||||.+|++|++.|++++.....+++.
T Consensus 180 ~~~~l~~i~~~~~~~l~~~~~~~~Pewmil~~lPV~Pp~~RP~v~l~~g~~~~~dl~~~~~~ii~~N~~lk~~~~~~ap~ 259 (880)
T 4ayb_A 180 IRERLEKVPESDVEILGYDPTTSRPEWMILTVLPVPPITIRPSIMIESGIRAEDDLTHKLVDIVRINERLKESIDAGAPQ 259 (880)
T ss_dssp HHHHHTTCCHHHHHHTTCCTTTCCSGGGEEEEEEECCSSSSCC-----CCCCCCSSHHHHHHHHHHHHHHHHHHTSCCCH
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCHHEEEEEEECCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCH
T ss_conf 99999986898999958887679823448766657999888354407864135408889999987666655433038826
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCC
Q ss_conf 1256779879999987743689999765567-887201343205765411245568778986622780899987775556
Q 000829 168 FKSLAGWETLQVEVAQYINSDVRGVPFSMQV-ARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAI 246 (1265)
Q Consensus 168 ~~~~~~~~~lq~~v~~~~~~~~~~~~~~~~~-~~~~~~i~qrl~gK~G~fR~nl~GKRvd~s~RsVI~pDp~l~~~evgi 246 (1265)
..+.+.|.+||++|+.|+||+.+|.+...++ ++|++||+|+|+||+||||+|||||||||||||||+|||+|++|||||
T Consensus 260 ~i~~~~~~~LQ~~V~~l~dn~~~g~~~~~~~~~rp~ksl~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~e~Gv 339 (880)
T 4ayb_A 260 LIIEDLWDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGV 339 (880)
T ss_dssp HHHHHHHHHHHHHHHHHHCSCCSSSCCCCCTTSCCCCCHHHHHHSSSSTHHHHTSSEECSSEEEEEEEECTTSCSSEEEE
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCHHHHHCCCCEEECCCCCEEEECCCCCCCCCCCC
T ss_conf 68999999999999998704677888667888776632666603664233304110254355742550799861261588
Q ss_pred CHHHHHHCCCCEEECHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEE-CCCCCHHHHHCCCCCCEEECCCCCCCEEEE
Q ss_conf 3888864594403364779999999992999998850777799983786-242303454126531311010136986998
Q 000829 247 PIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-YGKFRNQLAVELKSGCIVDRHLEDGDVVLF 325 (1265)
Q Consensus 247 P~~~A~~Lt~Pe~Vt~~Ni~~lr~lv~nG~~~~pGa~~i~~~~g~~~~l-~~~~r~~~~~~L~~g~iV~Rhl~~gd~vl~ 325 (1265)
|..||++||+||+||+||+++|+++|+|||++||||+++++.+|.++.+ +.+.|...+..|++||+|+|||+|||+|||
T Consensus 340 P~~~A~~Lt~Pe~vt~~N~~~l~~~v~ng~~~~pga~~~i~~~~~~~~l~~~~~~~~~~~~l~~g~~V~rhl~dgd~VLl 419 (880)
T 4ayb_A 340 PEIIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVVERHLTDGDVVLF 419 (880)
T ss_dssp CHHHHTTSEEEEECCTTTHHHHHHHHHHTTSSSSCEEEEECSSCCEEEGGGCSSCTTHHHHCCTTCEEEEECCTTCEEEE
T ss_pred CHHHHHHCCCCEEECHHHHHHHHHHHHCCCCCCCCHHHHHHCCCEEEEEECCHHHHHHHHHCCCCCEEEEEEECCCEEEE
T ss_conf 29999767878588687999999999749744553366542046278730120146788760656467555216858996
Q ss_pred ECCCCCCCCCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEC
Q ss_conf 15887664643448999826981342024689888997645323456882889999998728886211599999517201
Q 000829 326 NRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVAST 405 (1265)
Q Consensus 326 NRqPsLHk~si~~~~~~v~~~~t~r~~~~~c~~yNADFDGDeMn~h~Pqs~~araEa~~Lm~~~~~~~sp~~G~pi~gli 405 (1265)
||||||||+|||||+++|+||+||||||+||+||||||||||||+|||||++|||||++||++++||+||++|+|+++++
T Consensus 420 NRqPTLHr~si~a~~~~l~~gktirlhp~vC~~yNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~ 499 (880)
T 4ayb_A 420 NRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAA 499 (880)
T ss_dssp ECSSCCSGGGEEEEEEEECSSSSEEECGGGHHHHTCCSSSCEEEEECCCSHHHHHHHHHHSBSGGGCBCSSSSSBCSCCC
T ss_pred CCCCCCCCCCEEEEEEECCCCCEEEECCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHCHHCCCCCCCCCCCCCCC
T ss_conf 37876565451322344056753650620035434676666147751688899999999984720164377898301114
Q ss_pred CCCEEEEEEEECCCCCCCHHHHHHHHHHHCCCCCEEECCCCCEECCCCCCCCCEEEEEEECCCCCCCEEEEEEECCCCCC
Q ss_conf 34000336650257667999999999983389840324788300763233664015544058888624797763130113
Q 000829 406 QDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDRVDLPTPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYS 485 (1265)
Q Consensus 406 QD~i~g~~llT~~d~f~~~~~~~~l~~~~~~~~~~~~l~~Pailkp~~lwTGKQi~s~il~~~~~~~~~in~~~~~k~~~ 485 (1265)
||+|+|+|+||.+|+|++++++++++++.. ..+.+|+|||+||+++|||||+||+++|.. +|+..+.+...
T Consensus 500 QD~vlg~y~lT~~~~~~~~~~~~~~~~~~~---~~~~~~~p~i~~~~~~~tgkqi~s~~lp~~------~~~~~~~~~~~ 570 (880)
T 4ayb_A 500 QDYISGAYLLTVKTTLLTKEEAQQILGVAD---VKIDLGEPAILAPREYYTGKQVVSAFLPKD------FNFHGQANVSS 570 (880)
T ss_dssp SHHHHHHHHHTSSSCEECHHHHHHHHTTSC---CCCCCCSCSEESSSEEEEHHHHHHTTSCTT------CCEEEECTTCS
T ss_pred CCHHHHHHHHHCCCCCCCHHHHHHHHCCCC---EECCCCCCCEECCEEEECCCEEEEEEECCC------CCCCCEEEEEC
T ss_conf 107877687615755578899865505432---102358550225535761656788872365------43222257623
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEECCCCCCCCCCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 55444568732323456889980388368420013455433688743289999997193268899859999999999840
Q 000829 486 NKLIRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNH 565 (1265)
Q Consensus 486 ~~~~~~~g~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~li~~i~~~yG~~~a~~~l~~~~~l~~~~l~~~ 565 (1265)
.. +. .....++.|+.|+|+||+|++|++||+++|+...++|+|.++++||+..|+.|||.+++|+++|++.+
T Consensus 571 ~~------~~--~~~~~~~~~~~v~i~~g~l~~g~ldk~~lg~~~~~~li~~i~~~~G~~~t~~~ld~l~~lg~~~lt~~ 642 (880)
T 4ayb_A 571 GP------RL--CKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIRFVELQ 642 (880)
T ss_dssp GG------GC--CSSSCCTTSCEEEEETTEEEECCCSTTTSSTTCTTSHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CC------CC--CCCCCCCCCCEEEEECCEEEEEEECCHHHCCCCCCEEEEHHHHHCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 77------33--35766787656998576565400200121444442032316665030899999999999999999854
Q ss_pred CCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 64121256899920048999999999999999999987299866989997899999999999999999999886279999
Q 000829 566 GFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPWR 645 (1265)
Q Consensus 566 GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l~~~ 645 (1265)
|||||++|+.++++..+++.+.+++++.++++++++|..|.++..+|.+.++.+|..+..+|+++++.+++.+.+.++++
T Consensus 643 GfSigi~Di~i~~~~~~~i~~~i~~a~~~v~~i~~~~~~g~l~~~~g~~~~e~~e~~v~~~l~~~~~~~~~~~~~~l~~~ 722 (880)
T 4ayb_A 643 GFTMRLEDVSLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDKLRSTAGDIASKYLDPF 722 (880)
T ss_dssp CCCCCGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTSCTT
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 87501142346505689999999999998899999997088754666509999999999999999999879998508999
Q ss_pred CCCEEEECCCCCCCHHCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHCCC
Q ss_conf 94222312478889132757761356553589778999877656799999989776530144563489912346650246
Q 000829 646 NSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGG 725 (1265)
Q Consensus 646 N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~i~G~Rip~g~~~rtLP~f~~~~~~~~a~GfI~~sF~~GL~p~EfFfH~m~G 725 (1265)
|++++|+.||||||.+|++||+||+|||+++|+|||+|+.+||||||.++|..|+|+|||.+||++||+|+|||||||||
T Consensus 723 N~i~mMa~SGARGS~~ni~Qlagm~Gqq~~~G~RIprg~~~rtLP~f~~~d~~p~a~GfI~ssF~eGLtp~EyF~ht~gg 802 (880)
T 4ayb_A 723 NFAYVMARTGARGSVLNITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGG 802 (880)
T ss_dssp SHHHHHHHHTSSCCSTTHHHHHTCCEECBSSSSBSCCSBTTBSSTTSCTTCCSTTTTSEECSCTTTCCCHHHHHHHHHHH
T ss_pred CCHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHHCCCCCCCHHHHHHHHHHH
T ss_conf 87999954372677999999994504510578657678766778988878998255970720023799879999962654
Q ss_pred CCCCHHCCCCCCCCCHHHHHHHHHHHHEEEEECCEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 5300000100476771479999974313752128177589819999706888644433688899832699999988
Q 000829 726 REGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLMKVK 801 (1265)
Q Consensus 726 ReGLiDTAvKTa~sGYlqRrLik~lEdl~v~YD~TVR~s~g~IiQF~YGeDGld~~~~e~~~~~~~~~~~~~~~~~ 801 (1265)
||||+|||||||+||||||||||+||||+|+||||||+++|+||||.|||||+||.+.+.. .+++|+++++++.
T Consensus 803 RkGL~DTAlKTA~SGYLtRRLVdv~qDv~V~yDgTVR~~~g~ivqf~YGeDgldp~~~~~~--~~~~~~~i~~~v~ 876 (880)
T 4ayb_A 803 REGLVDTAVRTSQSGYMQRRLINALSDLRAEYDGTVRSLYGEVIQVAYGDDGVFPMYSAHG--KTVDVNRIFERVV 876 (880)
T ss_dssp HHHHHHHHHTHHHHHHHHHHHHHHHTTEEECTTSCEEETTTEEEESSTTTTCBCTTTSBTT--BSCCHHHHHHHHT
T ss_pred HHHHHHCCHHHCHHHHHHHHHHHHHCCEEEECCCCCCCCCCCEEEEECCCCCCCEEECCCC--CCCCHHHHHHHHC
T ss_conf 1218761232120039999999997387995699823899958998527763103122458--8537999866412
No 6
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*
Probab=1.00 E-value=1 Score=1569.40 Aligned_cols=961 Identities=27% Similarity=0.403 Sum_probs=660.0
Q ss_pred CCCCEEEEEEEEECCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 99550788631208999999242189876773258999999999899999999700001256779879999987743689
Q 000829 110 ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDV 189 (1265)
Q Consensus 110 ~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~lq~~v~~~~~~~~ 189 (1265)
.+||||||++||||||++||++.++++..++||||.+|++||+.|++|++.+..++|...+.+.|++||++|+.|+||+.
T Consensus 232 ~rPewmil~~lPVpPp~lRP~v~l~gg~~~~~DLn~ly~~II~~N~~Lk~~~~~~ap~~ii~~~~~~LQ~~V~~l~Dn~~ 311 (1407)
T 3lu0_D 232 NKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGR 311 (1407)
T ss_dssp CCGGGSSEEEEECCCSTTSCCCBCSTTCBCCCTTTTTHHHHHHTTTTTGGGTSSCCCTTTHHHHHHHHHHHHHHHHCSSS
T ss_pred CCHHHHHHHEEECCCCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 98898664256259987788279689854568567899999998999999987499588999999999998887627787
Q ss_pred CCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHH
Q ss_conf 99976556788720134320576541124556877898662278089998777555638888645944033647799999
Q 000829 190 RGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLR 269 (1265)
Q Consensus 190 ~~~~~~~~~~~~~~~i~qrl~gK~G~fR~nl~GKRvd~s~RsVI~pDp~l~~~evgiP~~~A~~Lt~Pe~Vt~~Ni~~lr 269 (1265)
++.+.....++|++||+||||||+||||+|||||||||||||||||||+|++||||||..||++||+| ||+++|+
T Consensus 312 ~g~~~~~~~~rplksl~qrLkGKeGrfR~NLmGKRVDfSaRSVIspdP~L~i~evGvP~~~A~~L~~P-----f~i~~L~ 386 (1407)
T 3lu0_D 312 RGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKP-----FIYGKLE 386 (1407)
T ss_dssp SCCCCBTTBCCCCCCTTHHHHTSSSTHHHHTTCCCCSSBCEEEEEECSSCCTTEEEEESHHHHHHTCH-----HHHHHHT
T ss_pred CCCCCCCCCCCCCCCHHHHHCCCCCHHHCCCCCCCCCCCCCEEEECCCCCCCEEEECCHHHHHHHCCH-----HHHHHHH
T ss_conf 78765477898564367774444301222446677787671488379986320542789999874526-----7799998
Q ss_pred HHHHCCCCC-CCCCEEEECCCCCEEEECCCCCHHHHHCCCCCCEEECCCCCCCEEEEECCCCCCCCCEEEEEEEEECCCE
Q ss_conf 999929999-9885077779998378624230345412653131101013698699815887664643448999826981
Q 000829 270 QCIQNGPDK-YPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRT 348 (1265)
Q Consensus 270 ~lv~nG~~~-~pGa~~i~~~~g~~~~l~~~~r~~~~~~L~~g~iV~Rhl~~gd~vl~NRqPsLHk~si~~~~~~v~~~~t 348 (1265)
+ +|+.. ++.|+... . + ....+| .|.||+.+||+|||||||||||+|||||++++++++|
T Consensus 387 ~---~g~~~~i~~ak~~v----------~--~----~~~~v~-~vl~~vi~gd~VLlNRqPTLHr~sIma~~~~l~~~kt 446 (1407)
T 3lu0_D 387 L---RGLATTIKAAKKMV----------E--R----EEAVVW-DILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKA 446 (1407)
T ss_dssp T---SSSCSSTTTTTTTT----------T--S----SCSSHH-HHHHTTTTSCCEEEEESSCCSGGGEEEEEEEEESSSS
T ss_pred H---CCCCCCHHHHHHHH----------H--H----CCCCHH-HHHHHHHHCEEEEECCCCCCCCCCCEEEEEEECCCCE
T ss_conf 7---38602378899988----------7--5----188335-6899875342566548863122443244678648965
Q ss_pred EEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEECCCCEEEEEEEECCCC--------
Q ss_conf 342024689888997645323456882889999998728886211599999517201340003366502576--------
Q 000829 349 LRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDT-------- 420 (1265)
Q Consensus 349 ~r~~~~~c~~yNADFDGDeMn~h~Pqs~~araEa~~Lm~~~~~~~sp~~G~pi~gliQD~i~g~~llT~~d~-------- 420 (1265)
|||||+||+||||||||||||+|+|||++|||||++||++++|++||++|+|+++++||+++|+|+||.++.
T Consensus 447 irlnp~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~lT~~~~~~~~~~~~ 526 (1407)
T 3lu0_D 447 IQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMV 526 (1407)
T ss_dssp EEECTGGGGTTTCCSSSCEEEEECCCSSHHHHTTTTSSBTTTCCSCSSSSSCSSCCCSHHHHHHHHHSCCCCCSCCSCCC
T ss_pred EEECHHHCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCHHEEEEEECCCCCCCCCCCE
T ss_conf 88676564434577344235542378999999999997170232348899822500130011157752246566677622
Q ss_pred CCCHHHHHHHHHHHC-CCCCE--EECCC--C-------CEECCCCCCCCCEEEEEEECCCCCCCEEEEEEECCCCCCCCC
Q ss_conf 679999999999833-89840--32478--8-------300763233664015544058888624797763130113554
Q 000829 421 FYDRAAFSLMCCYMG-DGMDR--VDLPT--P-------AILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKL 488 (1265)
Q Consensus 421 f~~~~~~~~l~~~~~-~~~~~--~~l~~--P-------ailkp~~lwTGKQi~s~il~~~~~~~~~in~~~~~k~~~~~~ 488 (1265)
|.+.+++++++.... .-... +.++. | ...++.++|||||+||++||+..
T Consensus 527 F~~~~ev~~al~~g~v~l~a~i~vr~~~~~~~~~g~~~~~~~~~~tt~Gr~ifs~ilP~~~------------------- 587 (1407)
T 3lu0_D 527 LTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGL------------------- 587 (1407)
T ss_dssp CSSCSHHHHHHHHSSSSSSSCSSSSCCCCSCSHHHHHHHTTTSCCSSSHHHHHHHHGGGSS-------------------
T ss_pred ECCHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCCCEEEECCCCCCCHHHHCCCCC-------------------
T ss_conf 3889999999975998889725886576554767752455235655875003775498999-------------------
Q ss_pred CCCCCCCCCCCCCCCCCCCEEEEECCCCEECCCCCCCCCCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCE
Q ss_conf 44568732323456889980388368420013455433688743289999997193268899859999999999840641
Q 000829 489 IRTEGDEEIRIETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFS 568 (1265)
Q Consensus 489 ~~~~g~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~lG~~~~~~li~~i~~~yG~~~a~~~l~~~~~l~~~~l~~~GfS 568 (1265)
. -++++|++||+.+| +|||.+|++||++.|+.|||.+++|+++|++.+|||
T Consensus 588 --------------~----------~~~ing~l~KK~lg-----~LI~~i~~~~G~~~t~~flD~lk~Lgf~~at~~GfS 638 (1407)
T 3lu0_D 588 --------------P----------YSIVNQALGKKAIS-----KMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGAS 638 (1407)
T ss_dssp --------------C----------CTTTTTCCSSSTTT-----THHHHHHHHSCSHHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred --------------C----------CEEEECCCCHHHHH-----HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCEE
T ss_conf --------------8----------05663644511499-----999999998599999999999999999999766847
Q ss_pred EEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC------
Q ss_conf 21256899920048999999999999999999987299866989997899999999999999999999886279------
Q 000829 569 IGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSL------ 642 (1265)
Q Consensus 569 igi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~~i~~~l~~~~~~~~~~~~~~l------ 642 (1265)
||++|+++++ ++.+++++++++|.+++++|..|.++.... ++++..+|+++++++++.+++.+
T Consensus 639 IgI~D~~ip~----~K~~iI~~A~~eV~ei~~~y~~G~lt~~er-------~~kVi~iw~~a~e~v~~~m~~~l~~~~~~ 707 (1407)
T 3lu0_D 639 VGIDDMVIPE----KKHEIISEAEAEVAEIQEQFQSGLVTAGER-------YNKVIDIWAAANDRVSKAMMDNLQTETVI 707 (1407)
T ss_dssp CCSTTSCCCT----THHHHHHHHHTHHHHHHHHHHHTSCCSSTT-------TTTHHHHHHTHHHHHHHHHHTTHHHH---
T ss_pred EEECCCCCCH----HHHHHHHHHHHHHHHHHHHHHCCCCCCCHH-------HHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 7433271586----799999999999999999997599862268-------99999999999999999999860213222
Q ss_pred ---------CCCCCCEEEECCCCCCCHHCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCC
Q ss_conf ---------99994222312478889132757761356553589778999877656799999989776530144563489
Q 000829 643 ---------PWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGL 713 (1265)
Q Consensus 643 ---------~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~i~G~Rip~g~~~rtLP~f~~~~~~~~a~GfI~~sF~~GL 713 (1265)
+++|++++|+.||||||..|++||+||+|||.. |.|.. . ..+|.+||++||
T Consensus 708 d~~G~~~~l~~~N~i~mMa~SGARGS~~qI~QLaGmrGlmak-----pdG~i--------------i-e~PI~ssFreGL 767 (1407)
T 3lu0_D 708 NRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAK-----PDGSI--------------I-ETPITANFREGL 767 (1407)
T ss_dssp ---------CSCCHHHHHHHSSSSCCTTHHHHHSSCCCCCBC-----SSSCB--------------C-SSCCCCCSSSCC
T ss_pred CCCCCCCCCCCCCCHHEEEECCCCCCHHHHHHHHHHCCCCCC-----CCCCC--------------C-CHHHHCCCCCCC
T ss_conf 334642236789886205400146799999999871287338-----99887--------------4-101322520279
Q ss_pred CHHHHHHHHCCCCCCCHHCCCCCCCCCHHHHHHHHHHHHEEEEECCEEECCCCCEEEEEE-CCCCCCCCCCCCCCCCCCH
Q ss_conf 912346650246530000010047677147999997431375212817758981999970-6888644433688899832
Q 000829 714 SATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLY-GDDGMDPANMEGKSGEPLN 792 (1265)
Q Consensus 714 ~p~EfFfH~m~GReGLiDTAvKTa~sGYlqRrLik~lEdl~v~YD~TVR~s~g~IiQF~Y-GeDGld~~~~e~~~~~~~~ 792 (1265)
+|+|||||||||||||+|||||||+||||||||||++||++|.++.|-. ..|-.+.-.. |++-+.+. +
T Consensus 768 tp~EyFfst~GaRKGL~DTALKTAdSGYLTRRLVdv~QDviV~e~DCGT-~~Gi~v~~~~~~~~vi~~L--~-------- 836 (1407)
T 3lu0_D 768 NVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGT-HEGIMMTPVIEGGDVKEPL--R-------- 836 (1407)
T ss_dssp CHHHHHHHHHHHHHHHHHTTTTTTCTTTTTHHHHTTSTTCCBCCCSCCC-CSSCEEEESSCCCSSSSCC--C--------
T ss_pred CHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCEEEEECCCCC-CCCEEEEEEECCCEEEEEH--H--------
T ss_conf 7778521023201123452444243214788998864654997467899-8887999860498687664--3--------
Q ss_pred HHHHHHHHHH--CCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHH
Q ss_conf 6999999883--19999997789777999999998530877621999999999999864322124101133588853202
Q 000829 793 FDRLLMKVKA--TCPPAGQRYLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDKSQI 870 (1265)
Q Consensus 793 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~~~i~~~~~~l~~~~~~~~~~~l~~~~~~ 870 (1265)
+|++..+.+ +........+.+ ..+ . +.+.+ ++++.+. ++
T Consensus 837 -~ri~GRv~a~di~~p~tgevi~~------------~n~------~----I~e~~---a~~i~~~-------gi------ 877 (1407)
T 3lu0_D 837 -DRVLGRVTAEDVLKPGTADILVP------------RNT------L----LHEQW---CDLLEEN-------SV------ 877 (1407)
T ss_dssp -CCCSSCBBSSCBCCSSSCCBCSS------------CBC------C----HHHHH---HHHHTTT-------TC------
T ss_pred -HHEEEEEEHHHEECCCCCCEEEE------------CCC------C----CCHHH---HHHHHHC-------CC------
T ss_conf -40242555867254889938973------------898------3----79999---9999986-------99------
Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHH--HHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCC-CEE-------C
Q ss_conf 44564203587999999999999985--2014588696010000024698432140134444652112-101-------0
Q 000829 871 LEEVTHKTSGITEKQLEVFIQTCFSR--YRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASM-NIT-------Q 940 (1265)
Q Consensus 871 ~~~~~~~~~~l~~~~~~~~~~~~~~~--y~~~~~~pGEaVGiIAAQSIGEPsTQMTLnTFH~AGv~~~-nVT-------l 940 (1265)
+.+..++.+||+.-..+|..||-+ ....+++.|||||+|||||||||+||+||+|||.+|+++. .+. -
T Consensus 878 --~~V~IRS~LTC~s~~GVC~~CYGrdLa~g~~V~iGEAVGiIAAQSIGEPGTQLTMRTFHtGGvas~~~~~~~i~a~~~ 955 (1407)
T 3lu0_D 878 --DAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNK 955 (1407)
T ss_dssp --SEEEECCSSSCSCSSSBCSTTTCSCSSSSSCCCSSCCTTHHHHHHHHSGGGSSCCSCTTCCCCCCCCCCCSCEECCSC
T ss_pred --CEEEECCCEEECCCCCCCHHHHCCCCCCCCCCCCCCEEEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCC
T ss_conf --889971864464898504777690504898831573554663200488754126352330662234321001673347
Q ss_pred CCCHHHHHH---HCCCCC--CCCEEEEECCCCCCHHHH--HHHHCC------------------------------EEEE
Q ss_conf 330157443---225544--545499872687738799--997501------------------------------3587
Q 000829 941 GVPRIKEII---NGAKRI--STPIITAELECNDNENAA--RVVKGR------------------------------IEKT 983 (1265)
Q Consensus 941 GiPRLkEIi---nask~i--kTP~i~~~l~~~~~~~~a--~~i~~~------------------------------le~~ 983 (1265)
|.-++..+- |...+. -+....+.+.+....+.. ....+. --++
T Consensus 956 G~v~~~~~~~v~~~~g~~vv~~r~~~i~i~d~~g~~~~~~~ip~gs~l~v~~g~~V~~g~~ia~wDp~~~piise~~G~v 1035 (1407)
T 3lu0_D 956 GSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFV 1035 (1407)
T ss_dssp EEEECCSCCCEECTTSCEECCCSSEEEEEECSSCCBCCCEEECTTCEESSCSSCEECTTCEEEECCSSCCCEECSSCEEE
T ss_pred CEEEEECCEEEECCCCCEEEEECCEEEEEECCCCCEEEEEECCCCCEEEECCCCEECCCCEEEEEECCCEEEEECCCEEE
T ss_conf 68997166799868898899946718999848996788997588978997088996279889999667605996352589
Q ss_pred ECCCCCEEEEE--EEECCCCE-EEEEECHHHH----HHHHCCCCHHHHHHHHHCCCCCCCCCC------------CEE--
Q ss_conf 42454212899--99079619-9999483668----772414599999999860864423457------------526--
Q 000829 984 LLGQVAKSIKI--VMTSRLAS-IVIALDMETI----QDAHLCINADIVKESIVQTPKIKLKQQ------------HIK-- 1042 (1265)
Q Consensus 984 ~L~di~~~i~~--~~~~~~~~-~~i~ld~~~i----~~~~~~i~~~~i~~~i~~~~~~k~~~~------------~v~-- 1042 (1265)
.+.|+++.++. ..+..... -.+-.+...- .++.-.+...+ .+...+++... .+.
T Consensus 1036 ~f~d~~~g~t~~~~~d~~tg~~~~~v~~~~~~~~~~~~~~p~i~i~~-----~~g~~~~~~~~~~~~~y~lp~~a~~~v~ 1110 (1407)
T 3lu0_D 1036 RFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVD-----AQGNDVLIPGTDMPAQYFLPGKAIVQLE 1110 (1407)
T ss_dssp EEESCCBTTTEEEEECSSSCCEEEEECCSSSSCTTTTSCCCEEEEEC-----SSSCBCBCTTSCCBCEEECCTTCCCCCC
T ss_pred EEEEECCCCEEEEEECCCCCCEEEEEEECCCCCCCCCCCCCEEEEEC-----CCCCEEECCCCCCCEEEECCCCCEEEEC
T ss_conf 97650368336787516779568999730545565556774399976-----9998874247876426745898489954
Q ss_pred ----EECCCEEEEECCC--CCCCCEEEHHHHHHH----CC--CCEEECCCCC----------EEEEEECCCCCCCHHHCC
Q ss_conf ----6056348992899--998514425778610----57--7287141371----------179994123110000024
Q 000829 1043 ----VLDFRKLEIFPPV--DKSKIHFELYSLKNV----LP--MVIVKGIKTV----------ERVVIAEKEKEKRKVKEN 1100 (1265)
Q Consensus 1043 ----~~~~~~i~i~~~~--~~~~~~~~l~~l~~~----l~--~~~i~Gi~~I----------~r~~i~~~~~~~~~~~~~ 1100 (1265)
+...+.+.-.+.. ...+..--|..+... -| ..++..+.|+ .++++...+
T Consensus 1111 ~g~~v~~g~vlakip~~~~k~~DIt~GLprv~eLfEar~pk~~a~i~ei~G~v~~~~~~~~~~~~~i~~~~--------- 1181 (1407)
T 3lu0_D 1111 DGVQISSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVD--------- 1181 (1407)
T ss_dssp SSCEECTTCEEECCCCCCCCSSCCCCSHHHHHHHHTTCCCSSCCCCCSSCSCCEECCCCSSCEEEECCCSS---------
T ss_pred CCCEECCCCEEEECCHHHCCCCCHHCCCHHHHHHHHCCCCCCCEEEECCCEEEEEEECCCCCEEEEEEECC---------
T ss_conf 79885168668863314316430313727899887504898852772340599972116884599997189---------
Q ss_pred C-CCCCEEEEEECCCHHHHHCCCCC---CCCCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEECC
Q ss_conf 8-76428999907667776314774---4664556779999998479999999999998986026665572001000000
Q 000829 1101 G-EKKKYRLLVEGTGLQAVMGAEGI---DGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADL 1176 (1265)
Q Consensus 1101 ~-~~~~~~l~teG~nl~~i~~~~~V---D~~r~~sNdI~~v~~~lGIEAAR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LlAD~ 1176 (1265)
+ ...+| +.-.|..+. +..-+.| |.-.--+.|.++|++++||||+|++|++|++.||..||++||+|||.+|++.
T Consensus 1182 g~~~~~y-~i~~~~~~~-v~~gd~v~~G~~l~~G~~~p~dil~v~Giea~~~ylv~Evq~VYr~QGV~IndKHIEvIvrq 1259 (1407)
T 3lu0_D 1182 GSDPYEE-MIPKWRQLN-VFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQ 1259 (1407)
T ss_dssp CCTTCEE-EECSSSCCC-CCSSSCCCTTCCCSSSCCCHHHHHHHSCHHHHHHHTTTTTHHHHHHHTCCCCSHHHHTTTGG
T ss_pred CCEEEEE-ECCCCCEEE-ECCCCEECCCCCCCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 9705899-746896355-15899874798746899999999986399999999999999999866943021148899999
Q ss_pred CCCCC----------------------------------------EEEEECCCCCCCCCCCHHHHHCCHHHHHHHHHHHH
Q ss_conf 11012----------------------------------------79742012234568707557010688999999442
Q 000829 1177 MTFRG----------------------------------------EVLGITRFGIQKMDKSVLMLASFEKTADHLFNASV 1216 (1265)
Q Consensus 1177 MT~~G----------------------------------------~~~~itR~Gi~~~~~Spl~~aSFE~T~~~L~~AA~ 1216 (1265)
||++. .++||||++++ .+|+|++||||+|+++|++||+
T Consensus 1260 M~~kv~I~d~Gdt~fl~Ge~vd~~~~~~~N~~~~~~g~~pa~~~p~llGITkasl~--t~SflSaASFQeTtkvLteAAi 1337 (1407)
T 3lu0_D 1260 MLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLA--TESFISAASFQETTRVLTEAAV 1337 (1407)
T ss_dssp GTSBCEESSCSSSCSCCCCBSHHHHHHHHHHHTTSSSCCCCCEECCCCCTTTTTTS--CSCTTTGGGSSCHHHHHHHHHH
T ss_pred HHCCEEEEECCCCCCCCCCEECHHHHHHHHHHHHHCCCCCCEEEEEEECEEECCCC--CCCCHHHCCHHHHHHHHHHHHH
T ss_conf 72746994178766677542209999999999997699984334445122421235--7885022205668999999886
Q ss_pred CCCCCCCCCCCCCEECCCCCCCCCCCEE
Q ss_conf 2986555553333110577777865337
Q 000829 1217 NGRDDRIEGVSECIIMGIPMPLGTGILK 1244 (1265)
Q Consensus 1217 ~g~~D~l~gvS~~Ii~Gk~~~~GTG~fd 1244 (1265)
.|++|+|.|++||||+|+++|+|||+..
T Consensus 1338 ~Gk~D~L~GlkENVIvG~lIPaGTG~~~ 1365 (1407)
T 3lu0_D 1338 AGKRDELRGLKENVIVGRLIPAGTGYAY 1365 (1407)
T ss_dssp TCCEECCCSSHHHHTTTCCCTTTTTSTT
T ss_pred CCCCCCCCCCCCCEEECCCCCCCCCCHH
T ss_conf 3897757885325275463467768226
No 7
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Probab=1.00 E-value=1 Score=661.11 Aligned_cols=355 Identities=35% Similarity=0.564 Sum_probs=305.9
Q ss_pred HHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCHHHHHHHCCCCC
Q ss_conf 20358799999999999998520145886960100000246984321401344446521121010330157443225544
Q 000829 876 HKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRI 955 (1265)
Q Consensus 876 ~~~~~l~~~~~~~~~~~~~~~y~~~~~~pGEaVGiIAAQSIGEPsTQMTLnTFH~AGv~~~nVTlGiPRLkEIinask~i 955 (1265)
.....++..+++++++.|..+|.+++++||||||+|||||||||+|||||||||+||++++|||+|+||++||++|++++
T Consensus 38 ~~~~~~~~~~~~~~~~~~~~~y~r~lv~pGEAVGiIAAQSIGEPgTQlTLrTFH~gGva~~nvT~GlPRl~Ei~~a~k~~ 117 (395)
T 4ayb_C 38 NKEVLVTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVP 117 (395)
T ss_dssp HSTTCCCHHHHHHHHHHHHHHHHHTBCCTTCCHHHHHHHHHHHHHHTCC-------------CCCSHHHHHHHHTCCSSC
T ss_pred CCEEECCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCHHHHCCCCCEEEEECCEEEECCCCCEEEECCCCCCC
T ss_conf 12251699999999999999998735899735768777650781032202340551232110134754347712465477
Q ss_pred CCCEEEEECCCC--CCHHHHHHHHCCEEEEECCCCCEEEEEEEECCCCEEEEEECHHHHHHHHCCCCHHHHHHHHHCCCC
Q ss_conf 545499872687--738799997501358742454212899990796199999483668772414599999999860864
Q 000829 956 STPIITAELECN--DNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPK 1033 (1265)
Q Consensus 956 kTP~i~~~l~~~--~~~~~a~~i~~~le~~~L~di~~~i~~~~~~~~~~~~i~ld~~~i~~~~~~i~~~~i~~~i~~~~~ 1033 (1265)
+||+|++++.+. .+.+.+..++.+++.+++.+++...++.+. .....+++|.+.+... .++.+++...+....
T Consensus 118 ~tp~~~i~l~~~~~~~~e~~~~~~~~ie~~~~~~~~~~~~i~~~--~~~~~~~~d~~~~~~~--~~~~~~i~~~~~~~~- 192 (395)
T 4ayb_C 118 STPMMTIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDIA--SMSIILQLDNEMLKDK--GVTVDDVKKAINRLK- 192 (395)
T ss_dssp SSCEEEECCTTTGGGCHHHHHHHHHHHHCCCHHHHEEEEEEETT--TTEEEEEECGGGGBTT--BCHHHHHHHHHHHSC-
T ss_pred CCCCEEEEECCCCCCCHHHHHHHCCCEEEEECCCEEEEEEEEEC--CCCEEEEHHHHHHHHC--CCCHHHHHHHHHHHC-
T ss_conf 78723899546544228888763143158872211356677405--6414552002345413--744999998776522-
Q ss_pred CCCCCCCEEEECCCEEEEECCCCCCCCEEEHHHHHHHCCCCEEECCCCCEEEEEECCCCCCCHHHCCCCCCCEEEEEECC
Q ss_conf 42345752660563489928999985144257786105772871413711799941231100000248764289999076
Q 000829 1034 IKLKQQHIKVLDFRKLEIFPPVDKSKIHFELYSLKNVLPMVIVKGIKTVERVVIAEKEKEKRKVKENGEKKKYRLLVEGT 1113 (1265)
Q Consensus 1034 ~k~~~~~v~~~~~~~i~i~~~~~~~~~~~~l~~l~~~l~~~~i~Gi~~I~r~~i~~~~~~~~~~~~~~~~~~~~l~teG~ 1113 (1265)
.....+.......+.+.+. ..+....+..++..+..+.++|++||.|+.+..+ +++|.+.|+|.
T Consensus 193 --~~~~~~~~~~~~~~~~~~~--~~~~v~~l~~~~~~~~~~~i~gi~gi~r~~~~~~------------~~~~~~~t~g~ 256 (395)
T 4ayb_C 193 --LGEFVIDESEGNTLNISFA--NIDSIAALFKLRDKILNTKIKGIKGIKRAIVQKK------------GDEYIILTDGS 256 (395)
T ss_dssp --CSSEEEEECSSEEEEEECC--SSCCCCCTHHHHHHHHHHCCCSSSSCCEEEEEEE------------TTEEEEEEESC
T ss_pred --CCCEEEECCCCCEEEEECC--CCCHHHHHHHHHHHCCCCEEECCCCEEEEEEECC------------CCEEEEEECCC
T ss_conf --6757985266727886237--8716999999875303617734556058777416------------98799872587
Q ss_pred CHHHHHCCCCCCCCCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCEEEEECCCCCCC
Q ss_conf 67776314774466455677999999847999999999999898602666557200100000011012797420122345
Q 000829 1114 GLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQK 1193 (1265)
Q Consensus 1114 nl~~i~~~~~VD~~r~~sNdI~~v~~~lGIEAAR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LlAD~MT~~G~~~~itR~Gi~~ 1193 (1265)
|+.++|..+++|+++++||||++|+++|||||||++|++|++.||..||++||+|||+||||+||++|.+++++|+|++.
T Consensus 257 ~l~~~~~~~~vd~~~~~sn~i~eI~~vlGiEAar~~iv~Ei~~V~~~~Gv~In~rHi~li~d~Mt~~G~~~~igr~g~s~ 336 (395)
T 4ayb_C 257 NLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTG 336 (395)
T ss_dssp CHHHHTTSTTCCTTTCEESCTTHHHHHHCHHHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHGGGSCCCSSSSSHHH
T ss_pred CCEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHHHHHCCCEEECCCCCCCCC
T ss_conf 73156675022132114674054330000888899998767778760685103378655541320136475267525657
Q ss_pred CCCCHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCEECCCCCCCCCCCEEEEECCCC
Q ss_conf 6870755701068899999944229865555533331105777778653375213899
Q 000829 1194 MDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKIRQRDAV 1251 (1265)
Q Consensus 1194 ~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~~~GTG~fdll~~~~~ 1251 (1265)
..+|||++||||+|+++|++||++|+.|+|+|+|||||+|+++|+|||+|||+++..+
T Consensus 337 ~t~S~LsaASFqeTt~vLteAAi~Gk~D~L~GlkENVIvGklipaGTG~f~l~~~p~~ 394 (395)
T 4ayb_C 337 EKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTMRPIL 394 (395)
T ss_dssp HCSCHHHHHHHSCTHHHHHHHHHTTCBCCCCSHHHHHHHTCCCSSGGGTCEEEECSCC
T ss_pred CCCCHHHHHCCHHHHHHHHHHHHCCCCCCCCCHHHHEECCCCCCCCCCCEEEEECCCC
T ss_conf 9989999832763999999998548977787869971018988888676288715666
No 8
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus}
Probab=1.00 E-value=1 Score=406.08 Aligned_cols=218 Identities=33% Similarity=0.506 Sum_probs=191.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEECCEEEEEEEECCCCHHHHHHHHHHHHCCHHHHHHHHCCC
Q ss_conf 84108999999999999923037997769898998971783230221898324521457877663100212455420014
Q 000829 4 PKMEALRKTDLMKSIVKKCSTMASKAVKCPRCGYINGMVKKAVAVLGIIHDRSKVTESLQEFASAITHTKESKAAVNVAT 83 (1265)
Q Consensus 4 ~~~~~~~r~~~~k~i~~~c~~~~k~~k~C~~Cg~~~p~IkK~~~~~ki~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ 83 (1265)
++.....++.+++++++.| ++.+.|++||+.||.||+++. +.+.+..+ +++ + ....
T Consensus 184 ~~~~~~~~k~~~~~i~~~~----k~~~~C~gCG~~qp~Ir~e~~--~~~~~~~~--------------~~~-~---~~~k 239 (436)
T 3qqc_A 184 ARNRRSEFNEIIKEIHKKA----KERMVCPHCGAPQYPIKFEKP--TIYWEIRK--------------DEQ-G---NEYR 239 (436)
T ss_dssp TSSCHHHHHHHHHHHHHHH----HTCCSCC-------CCCBCSS--SCEEEECC--------------C-------CCCE
T ss_pred HHHCCCCHHHHHHHHHHHC----CCCCCCCCCCCCCCEEEEECC--EEEEECCC--------------CCC-C---CCCC
T ss_conf 5430303889999999971----557758663773864898055--12210245--------------544-5---5324
Q ss_pred CCCCHHHHHHHHHHCCHHHHHHHCCC---CCCCEEEEEEEEECCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 34699999999972382248762599---995507886312089999992421898767732589999999998999999
Q 000829 84 YILNPVNVLFLFKRMTDTDCEVLYLS---ERPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQE 160 (1265)
Q Consensus 84 ~~L~P~~v~~il~~i~~~d~~~l~~~---~~p~~~~l~~lpVpP~~~RP~~~~~~~~~~~ddlt~~l~~Ii~~n~~l~~~ 160 (1265)
+.|+|++|+++|++|+++|+++||++ .+||||||++||||||++||++.++++.++|||||++|++||+.|+.|++.
T Consensus 240 ~~LtP~~vl~ifk~IsdeD~~lLGl~~~~~rPewmIlt~LPVpPp~vRPsv~~~~g~~~edDLT~kl~~II~~N~~L~~~ 319 (436)
T 3qqc_A 240 HRLMPTEVRDWLEKIPDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDLTHKLVDIIRINNRLKQN 319 (436)
T ss_dssp EEECHHHHHHHHHHSCTTTGGGSSCCTTTCCGGGGEEEEEEECCGGGSCCBCC---CCBCCHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHCCHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 12199999999986798889885446567984206764022499867662783787577875899999999998999999
Q ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCC-EEECCCCC
Q ss_conf 99700001256779879999987743689999765567-88720134320576541124556877898662-27808999
Q 000829 161 LVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQV-ARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGR-TVISPDPN 238 (1265)
Q Consensus 161 ~~~~~~~~~~~~~~~~lq~~v~~~~~~~~~~~~~~~~~-~~~~~~i~qrl~gK~G~fR~nl~GKRvd~s~R-sVI~pDp~ 238 (1265)
...|+|...+.+.|++||++|++|+||+.+|.|.+.++ ++|++||+||||||+||||+||||||||||+| |||
T Consensus 320 ~~~gap~~~i~~~~~lLQ~~V~~~~dn~~~g~~~~~~~~~rp~ksi~~rLkGKeGRfR~NL~GKRVdy~~~~s~~----- 394 (436)
T 3qqc_A 320 IEAGAPQLIIEDLWDLLQYHVTTYINNEAPGVPPAKHKSGRPLKTLAQRLKGKEGRFRGNLSGGAGSGAGSGSVL----- 394 (436)
T ss_dssp HHSCCCSHHHHHHHHHHHHHHHHHHCTTCTTCCCCBCTTSCBCCCHHHHHCC----------------------------
T ss_pred HHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCEECCCCCCCCCCCCCCHHHH-----
T ss_conf 974996778999999999998752057888887434578987643676624655411475788888866522299-----
Q ss_pred CCCCCCCCCHHHHHHCCCCEE
Q ss_conf 877755563888864594403
Q 000829 239 LKITEVAIPIRMARILTYPER 259 (1265)
Q Consensus 239 l~~~evgiP~~~A~~Lt~Pe~ 259 (1265)
..+|.+||+|..
T Consensus 395 ---------~~~~~e~~~~~~ 406 (436)
T 3qqc_A 395 ---------ARAAFEITVQHL 406 (436)
T ss_dssp -------------CCCCHHHH
T ss_pred ---------HHHHHHHHHHHH
T ss_conf ---------998899879999
No 9
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus}
Probab=1.00 E-value=1 Score=51.02 Aligned_cols=68 Identities=32% Similarity=0.399 Sum_probs=48.6
Q ss_pred CCCEEEECCCC-CCCEEEEE---CCCCCCCCCCCHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCEECCCCC
Q ss_conf 00100000011-01279742---01223456870755701068899999944229865555533331105777
Q 000829 1168 RHMMLLADLMT-FRGEVLGI---TRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPM 1236 (1265)
Q Consensus 1168 RHl~LlAD~MT-~~G~~~~i---tR~Gi~~~~~Spl~~aSFE~T~~~L~~AA~~g~~D~l~gvS~~Ii~Gk~~ 1236 (1265)
|-+.=|.+.+. -.|.+++= -|-.... +.|+|.+|+||.+..||.+|+.+|++|+++||.++|+.|+.-
T Consensus 360 rp~ksi~~rLkGKeGRfR~NL~GKRVdy~~-~~s~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 431 (436)
T 3qqc_A 360 RPLKTLAQRLKGKEGRFRGNLSGGAGSGAG-SGSVLARAAFEITVQHLFEAAEKGEVDNLNGVIENVLIGQKH 431 (436)
T ss_dssp CBCCCHHHHHCC----------------------------CCCCHHHHHHHHHHTCEEECCSSCCTTSCC---
T ss_pred CCCCCHHHHHCCCCCEECCCCCCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCC
T ss_conf 876436766246554114757888888665-222999988998799999999845563056678786304333
No 10
>2j7n_A RNA-dependent RNA polymerase; RNAI response, RNA-directed RNA polymerase, hydrolase; 2.30A {Neurospora crassa} PDB: 2j7o_A
Probab=1.00 E-value=1 Score=29.13 Aligned_cols=31 Identities=13% Similarity=0.149 Sum_probs=15.0
Q ss_pred CCCCEE---EEEEEECCCCCCCHHHHHHHHHHHC
Q ss_conf 134000---3366502576679999999999833
Q 000829 405 TQDFLT---SSFLITRKDTFYDRAAFSLMCCYMG 435 (1265)
Q Consensus 405 iQD~i~---g~~llT~~d~f~~~~~~~~l~~~~~ 435 (1265)
..|... ..|.+|--==.+++.-+..+...+.
T Consensus 314 ~dDI~~~~g~g~vFTDGvG~IS~~lA~~I~~~l~ 347 (1022)
T 2j7n_A 314 KTDLLSPSGTGEVMNDGVGRMSRSVAKRIRDVLG 347 (1022)
T ss_dssp SSCCBCTTSSCCBSSTTEEEECHHHHHHHHHHHT
T ss_pred CCCCCCCCCCCCEECCCCHHHHHHHHHHHHHHCC
T ss_conf 7852067889875157725752999999999829
Done!