Query 000882
Match_columns 1238
No_of_seqs 346 out of 2105
Neff 6.1
Searched_HMMs 29240
Date Tue Mar 26 16:26:44 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000882.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_652-656//hhsearch_pdb/000882hhsearch_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 2186.6 43.0 1044 5-1087 7-1457(1752)
2 1twf_A B220, DNA-directed RNA 1.0 1 1 2099.4 66.3 1055 1-1091 1-1455(1733)
3 4ayb_A DNA-directed RNA polyme 1.0 1 1 1593.7 46.3 739 9-765 1-866 (880)
4 1hqm_D DNA-directed RNA polyme 1.0 1 1 1565.5 14.6 899 12-1075 3-1219(1265)
5 2a6h_D DNA-directed RNA polyme 1.0 1 1 1452.1 18.6 782 137-1079 506-1481(1524)
6 3lu0_D DNA-directed RNA polyme 1.0 1 1 1422.1 28.9 984 9-1075 12-1363(1407)
7 3qqc_A DNA-directed RNA polyme 1.0 1 1 470.9 17.2 268 10-307 65-414 (436)
8 4ayb_C DNA-directed RNA polyme 1.0 1 1 405.1 7.9 334 715-1084 23-393 (395)
9 3qqc_A DNA-directed RNA polyme 1.0 1 1 50.2 1.7 48 1016-1069 384-431 (436)
10 2j7n_A RNA-dependent RNA polym 1.0 1 1 23.8 2.8 21 436-456 325-346 (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=2186.65 Aligned_cols=1044 Identities=25% Similarity=0.380 Sum_probs=907.8
Q ss_pred CCCCCCCCCCCEEEEECCCHHHHHHCCCCCCCCCC------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 78864454300589834996999860545521257------------888889988999999888998999999788853
Q 000882 5 TSSTILEGQIVGIRFGLATQKEICTASISDCSISH------------ASQLANPFLGLPLEFGKCESCGTSEPGKCEGHF 72 (1238)
Q Consensus 5 ~~~~~~~~~I~~I~F~l~S~eeI~~~Sv~~~~i~~------------~~gl~DprlG~~~~~~~C~TCg~~~~~~CpGHF 72 (1238)
.++.++.++|++|+||++|++||+++||++ |++ ++||+|||||+++++..|+|||++. .+|||||
T Consensus 7 ~~s~~~~~~i~~i~Fg~~S~eeI~~~Sv~~--I~~~~~~d~~~~~P~~~Gl~D~rlG~~~~~~~C~TCg~~~-~~CpGHF 83 (1752)
T 3h0g_A 7 SPSSVPLRRVEEVQFGILSPEEIRSMSVAK--IEFPETMDESGQRPRVGGLLDPRLGTIDRQFKCQTCGETM-ADCPGHF 83 (1752)
T ss_dssp CCCSSCCCCCCCBEECCCCHHHHHHHCCCC--CCCTTCTTCSSSSSCCSSSSSSSCCCSSSSCCCTTSCCSS-SSCCCCC
T ss_pred CCCCCCCEEEEEEEEECCCHHHHHHHCEEE--EECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCC
T ss_conf 877676116526899459989999727468--8560002455687778997571236889999789999987-8378851
Q ss_pred EEEECCCCCCCCCCHHHHHHHHHHHCCCCC-----CC--------------HHHHHHHHHH-------------------
Q ss_conf 258757611245473889999975301346-----70--------------1799999768-------------------
Q 000882 73 GYIELPIPIYHPSHISELKLTMYAFQLQIK-----ND--------------GVAQRLLSSC------------------- 114 (1238)
Q Consensus 73 GhIeL~~PVfHp~f~~~i~~IL~~iCl~i~-----~~--------------g~~~~i~~~C------------------- 114 (1238)
|||||++|||||+||+.|++||+|+|..|. .. ...+++++.|
T Consensus 84 GHIELa~PVfHpgF~~~I~kILr~vC~~C~klll~~~~~~f~~~lrlrd~k~r~~~V~~~ck~k~~Ce~~~~~~~~~~~~ 163 (1752)
T 3h0g_A 84 GHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFNDTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDNFDL 163 (1752)
T ss_dssp EECCCCSCBCCHHHHHHHHHHSSSSCTTTCCCSCCSCSHHHHHHHHSSCTTTTHHHHHHHHHHCCCCCSSTTCCSSCCCS
T ss_pred EEEECCCCEEEEHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHC
T ss_conf 46641533584006689999999999875420466336999999975589999999999814354467877544210000
Q ss_pred -----------H------------------------------------HHHHHHCCCCHHHHHHHCCC-CCCCCCCEEEE
Q ss_conf -----------6------------------------------------99999716994589871259-99999856898
Q 000882 115 -----------C------------------------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILE 146 (1238)
Q Consensus 115 -----------C------------------------------------ev~~IlkkIpded~~~L~~~-g~~ppe~lIL~ 146 (1238)
| +|+++|++|+++|+++|+.. .+.+||||||+
T Consensus 164 ~~~~~~~~~~gCG~~qP~IRKeglkl~~~~k~~k~~~~~~~k~~LtP~eVl~ifk~IsdeD~~lLGl~~~~~rPewmiL~ 243 (1752)
T 3h0g_A 164 SNPSANMGHGGCGAAQPTIRKDGLRLWGSWKRGKDESDLPEKRLLSPLEVHTIFTHISSEDLAHLGLNEQYARPDWMIIT 243 (1752)
T ss_dssp SCCCCCCSSCSSCCCCCCCEEETTEEECCBCCSSSSCBCSSCCCCCHHHHHHHHHHSCHHHHHHSSCCSSSCCGGGSSBS
T ss_pred CCCCCCCCCCCCCCCCCCEEEECCEEEEEECCCCCCCCCCCCEECCHHHHHHHHHHCCHHHHHHHCCCCCCCCHHHEEEE
T ss_conf 12223456898688587278636589999725556554446632289999999996298899984898667984556732
Q ss_pred EECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHHHHHHHHCC--CCCCCC
Q ss_conf 4126999888863138975445202699999999999999950-0699996313444657999999997302--976667
Q 000882 147 YLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVR--GTAKSS 223 (1238)
Q Consensus 147 ~lpVPP~~iRp~~~~~g~~~~~~Dlt~~~l~~Ii~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~--~~~k~~ 223 (1238)
+|||||+|+||++.++|..+.++|+|. +|++||++|+.|++. ..|+|..+. .++|++||.+|++|+|+. +.+.+.
T Consensus 244 vLPVpPp~vRPsv~ldg~~~~edDLt~-~l~~II~~N~~Lk~~~~~gap~~~~-~~~~~~LQ~~v~~~~dn~~~~~~~~~ 321 (1752)
T 3h0g_A 244 VLPVPPPSVRPSISVDGTSRGEDDLTH-KLSDIIKANANVRRCEQEGAPAHIV-SEYEQLLQFHVATYMDNEIAGQPQAL 321 (1752)
T ss_dssp SCEECCGGGSCCCCCSSSCCCCCTTTT-HHHHHHHHHHHHHGGGGCCSSSTTH-HHHHHHHHHHHHHTTCTTCSSCCCCC
T ss_pred CCCCCCCCCCCCEECCCCCCCCCHHHH-HHHHHHHHHHHHHHHHHHCCHHHHH-HHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 024599876671674897667782899-9999999879999998730506789-99999999999986067787886322
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 77556778889999301455532100113468797765167289996533344626621114434432244399999999
Q 000882 224 RDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELV 303 (1238)
Q Consensus 224 ~~~~~~~~~~k~~~~~~k~~~~~~r~~l~gKRvdfs~RsVI~pDP~l~i~evgiP~~~A~~Lt~pe~Vt~~Ni~~l~~lv 303 (1238)
.. ..| ..|.+.+++|||+||||+|||||||||||||||+|||||++||||||..||++|||||+||+|||++|+++|
T Consensus 322 ~~-~~r--p~k~~~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~evGvP~~~A~~Lt~Pe~vt~~ni~~l~~lv 398 (1752)
T 3h0g_A 322 QK-SGR--PLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELV 398 (1752)
T ss_dssp SS-SSC--CCCCHHHHHTCSSSSSTTTTSSCCCSSEEEEEEEEETTSCTTBCBCCHHHHTSCCCCCBCCTTTHHHHHHHH
T ss_pred CC-CCC--CCCCHHHHHHCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCEEECHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf 46-788--875167664020110134444555687663134489976555213709999865887655679999999999
Q ss_pred HCCCCCCCC-------CCCCEEEECCCCC-CCCCCCCCCEEEEEEECCCEEEEECCCCCCCCCCCCEEEEECCCCEEEEC
Q ss_conf 817864147-------9995288136998-86445686444200321573866179987746532017996579814422
Q 000882 304 DNKLCLTYS-------DGSSSYSLREGSK-GHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKIN 375 (1238)
Q Consensus 304 ~ng~~~~~~-------~~~~~~~l~~~~~-~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~i~~~~tirln 375 (1238)
.||+. +|+ +.+.++.|++.++ ....|++||+|+|||+|||+|||||||||||||||||+|+|++++|||||
T Consensus 399 ~nG~~-~~pga~~v~~~~~~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~Vl~NRqPtLHr~sima~~~~v~~gktirlh 477 (1752)
T 3h0g_A 399 RNGPD-EHPGAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLN 477 (1752)
T ss_dssp HHCTT-SSSCEEEEECTTCCBCCTTTTCSCCCCCCCSSCEEEECCCSCCEEEEECSSCCSGGGEEEEECCCCSSSSEEEE
T ss_pred HCCCC-CCCCCEEEECCCCCEEECHHHCHHHHHHCCCCCEEEEEECCCCEEEEECCCCCCHHHCCCCCCEEECCCEEEEC
T ss_conf 73986-56673026637884764121011445415767378744236976898168620310121446356068636606
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEECHHHHHHHHHHH-CCCCCCHHHHHHHHC
Q ss_conf 5677989886674600035678798899999971353322447999944751113455787630-356679999998710
Q 000882 376 PLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAM 454 (1238)
Q Consensus 376 ~~vC~pyNADFDGDeMniH~PQs~eAraEa~~Lm~~~~~ilsP~~G~PiigliQD~llg~~llt-kd~fl~~~~~~ql~~ 454 (1238)
|+||+||||||||||||+|+|||++|||||++||++++||++|++|+|+++++||+|+|+|+|| +|+|++++++++++|
T Consensus 478 ~~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~lT~~~~f~~~~e~~~l~~ 557 (1752)
T 3h0g_A 478 LSVTSPYNADFDGDEMNMHVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIML 557 (1752)
T ss_dssp GGGSGGGTCCSSSCEEEEECCCSTTHHHHHHHTCCTTTTSEETTTTEESCCCCTHHHHHHHHHHSTTCEEETHHHHGGGG
T ss_pred HHHCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHCCCCCEECCCCCCCEEEECCHHHHHEEEECCCCCCCCHHHHHHHHH
T ss_conf 52278766761000246631688889999999853713261489998026641103321122004655589999999998
Q ss_pred CCC---CCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCC------------CCEEEEECCCCCCCCCCCCCCCCHHHHH
Q ss_conf 235---5656323203324554310000234579985346------------8679996342365555567753238779
Q 000882 455 FAL---SPLPRPALSKARCSARWTALQILQSVLPPGFDSC------------GDRYLIKKSEVLKGDFDRDTIPSVINEI 519 (1238)
Q Consensus 455 ~~~---~~lp~PaIlKp~~~~lWTGKQi~S~~lP~~~~~~------------~~~viI~~Gell~g~ldK~~lg~s~~~L 519 (1238)
++. ..+|+|||+||+ ++||||||||++||.++++. ++.|+|++|||++|++||+++|++.++|
T Consensus 558 ~~~~~~~~~~~pai~kp~--~~wtGkqifs~ilp~~~~~~~~~~~~~~~~~~d~~v~i~~gell~g~l~K~~lg~~~~~l 635 (1752)
T 3h0g_A 558 WVPDWDGILPPPVILKPK--VLWTGKQILSLIIPKGINLIRDDDKQSLSNPTDSGMLIENGEIIYGVVDKKTVGASQGGL 635 (1752)
T ss_dssp CSSSCCSSCCCCSBCSSS--CEEETTHHHHTTSCSSBCEECCCSSCCSSCTTTCSEEECBSCEEEECCSHHHHSSCTTCH
T ss_pred HHCCCCCCCCCCCEECCC--CCCCHHHHHHHHCCCCCCCEECCCCCCCCCCCCCEEEEECCEEEECCCCHHHHCCCCCCH
T ss_conf 502237845766154576--787466677666768777300465556768776737887670775310267734575429
Q ss_pred HHHHHHHHCHHHHHHCHHHHHHHHHHHHHHCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH-------------H
Q ss_conf 999998529789995163349999999982483321076545989999999999999999986664-------------3
Q 000882 520 VTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS-------------T 586 (1238)
Q Consensus 520 i~~i~~~~G~~~a~~~L~~lq~L~~~~L~~~GFSigi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~-------------~ 586 (1238)
||.++++||+++|++|||.+|+|+++||+++|||||++|+++++++.+.+++.+++++..+.++.. .
T Consensus 636 i~~i~~~~G~~~~~~~ld~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~g~l~~~~g~~ 715 (1752)
T 3h0g_A 636 VHTIWKEKGPEICKGFFNGIQRVVNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMT 715 (1752)
T ss_dssp HHHSSSSSCTTTHHHHHHHHHHHHHHHHHHHCCCCCGGGGSCCSHHHHHHHHHHHTTTHHHHHHHTTTTTTCCCCCSSCC
T ss_pred HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 99999997999999999999999999998668043063326588999999999999999999999998709875588986
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH----CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 48899999999999999999999871----29743120321002356687897410352146985444454211122233
Q 000882 587 QNELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFE 662 (1238)
Q Consensus 587 ~~~~le~~~~~~l~~~~~~i~~~~~~----~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~g~r~~~r~l~~~~~~~f~ 662 (1238)
..+.+|..+.++|+++++.+++.+.+ .|++.+|+.||||||++|++||+||||||.++|+| +++++..+.+|||.
T Consensus 716 ~~e~~e~~v~~~l~~~~~~~~~~~~~~l~~~N~~~~M~~SGakGs~~ni~Q~~~~~Gqq~~~Gkr-Ip~g~~~rtLP~f~ 794 (1752)
T 3h0g_A 716 LRESFEAKVSRILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKR-IPFGFKYRTLPHFP 794 (1752)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHHHHTTSCSSCTTTHHHHHCSSCCHHHHHHHHTCCCCCCSTTSS-SCCCSTTSSSTTSC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCC-CCCCCCCCCCCCCC
T ss_conf 89999999999999999999999998648888699986625664788899998553888257866-87888886688888
Q ss_pred CCCCCCCCCCCCCCCEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCCHHHHHHHHHHEEEEEECCEEECCCCCC
Q ss_conf 44889989998776400143233589663078623542101112344479884027899987406897410474357885
Q 000882 663 RIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNS 742 (1238)
Q Consensus 663 ~~~p~~~d~~~~a~GfV~~sF~~GL~P~EfFfH~magREGLiDtAvkTa~sGyL~R~L~~~l~d~~v~yd~Tvr~~~~~~ 742 (1238)
+ +|+.|+++|||.|||++||+|+|||||||||||||+|||||||+||||||||||+|||++|+||||||++ +|.
T Consensus 795 k-----~d~~~~a~GfV~~sF~~GL~p~EfFfhtmggReGLiDTAvKTA~SGYLqRRLVk~leDv~V~YDgTVRns-~g~ 868 (1752)
T 3h0g_A 795 K-----DDDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNA-MGD 868 (1752)
T ss_dssp S-----SCCSTTTSSCCSSCTTTCCCHHHHHHHHHHHTTTTTHHHHTTTHHHHHHHHHHHHHTTCEEETTTEEECT-TSC
T ss_pred C-----CCCCCCCCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHEEEEECCEEECC-CCC
T ss_conf 8-----8998433761010134799889999974410322467654027675017999998752488507806868-994
Q ss_pred EEEEEEECCCCCC-------------------------------------------------------------------
Q ss_conf 0223610144544-------------------------------------------------------------------
Q 000882 743 IIQFDYAVNARKS------------------------------------------------------------------- 755 (1238)
Q Consensus 743 IiQf~yg~~g~~~------------------------------------------------------------------- 755 (1238)
||||+||+||+|.
T Consensus 869 ivQF~YGeDGlD~~~~e~q~~~~~~~s~~~f~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~E~~~l~~dr~~lr~~ 948 (1752)
T 3h0g_A 869 IIQFAYGEDGLDATLVEYQVFDSLRLSTKQFEKKYRIDLMEDRSLSLYMENSIENDSSVQDLLDEEYTQLVADRELLCKF 948 (1752)
T ss_dssp EEESSSSSSCBCGGGEEEEECTTTSCCHHHHTTTSCCCTTTTCCGGGTSCSCCTTSCSSTHHHHHHHHHHHHHHTTSSSS
T ss_pred EEEEECCCCCCCHHHHHCCCCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 89874677776867741355540247879999884212255432467788875057889999999999999999998887
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q 000882 756 -------------------------------------------------------------------------------- 755 (1238)
Q Consensus 756 -------------------------------------------------------------------------------- 755 (1238)
T Consensus 949 i~~~~~~~~~lP~N~~R~i~~~~~~f~~~~~~~s~l~p~~~~~~v~~~~~~l~~~~g~d~l~~~~~~na~~l~~~~lr~~ 1028 (1752)
T 3h0g_A 949 IFPKGDARWPLPVNVQRIIQNALQIFHLEAKKPTDLLPSDIINGLNELIAKLTIFRGSDRITRDVQNNATLLFQILLRSK 1028 (1752)
T ss_dssp SSSCSCCEEEEESCHHHHTTTTTTTSCCCTTSCCCCCHHHHHHHHHHHHTTCCCSCCCSTTTTHHHHTSSHHHHHHHTTS
T ss_pred HHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCHHHHHHHHHHHH
T ss_conf 51043101368714999999999862778676577988999999999998654025874020565635287888988766
Q ss_pred -----------------------------CCCCCCCCEEEEECCCCCCCHHHHHHHCCCC-------CCCCCHHHHHHHH
Q ss_conf -----------------------------6767899706652112379067886316699-------9888067899998
Q 000882 756 -----------------------------HSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEIL 799 (1238)
Q Consensus 756 -----------------------------~~l~~~Ge~VG~laaqsigepa~q~~L~t~~-------~~~~g~~rlkEil 799 (1238)
+++++|||+||++||||||||+|||||+||+ |+|+|+||||||+
T Consensus 1029 l~~k~~~~~~~l~~~~~~~~~~~~~~~y~~a~v~pGe~VG~iaAQSIgEp~TQMTLnTFHfAGvas~NVTlGVPRLkEII 1108 (1752)
T 3h0g_A 1029 FAVKRVIMEYRLNKVAFEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIL 1108 (1752)
T ss_dssp SSHHHHHHSSCCCHHHHHHHHHHHHHHHHTTBCCSSCCHHHHHHHHHHHHHHHHHHHTTSSCCCCCSSCCCSGGGHHHHH
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHH
T ss_conf 54444342167689999999999999998734576651103454026881234657766440443556555750099998
Q ss_pred HHHCCCCCCCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCEECHHHHHHEEEEEECCCCCCC----------------
Q ss_conf 7311379999884189972788878764327999999862201026444311368842886445----------------
Q 000882 800 LCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS---------------- 863 (1238)
Q Consensus 800 ~~~~~~k~~~~~~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~v~l~~i~~~i~i~y~~~~~~~---------------- 863 (1238)
+++++ +++|.|++||.+.+.. ++++|++|+++||+++|++|+..+.|.|+++...+
T Consensus 1109 nask~----ikTP~mtv~L~~~~~~----d~e~A~~v~~~ie~t~L~~v~~~~~i~~~p~~~~~~i~~d~~~v~~~~~~~ 1180 (1752)
T 3h0g_A 1109 NVAKN----IKTPSLTIYLMPWIAA----NMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFAIP 1180 (1752)
T ss_dssp TTCSC----CSCCCCEECCCSSSCS----SSTTTHHHHTTSSCCSSCSCCSCEEEECCCSTTCCCCSSSCSHHHHHHHTT
T ss_pred HHHCC----CCCCEEEEEECCCCCC----CHHHHHHHHHHHCCEEHHHHEEEEEEEEECCCCCEEEEECHHHHHHHHCCC
T ss_conf 66327----9997289995675555----899999999761407898711078999946865168862589999986242
Q ss_pred ---------CCCCEEEEEEECHHHHHHCCCCHHHHHHHHHHHHHH-----H------------H-HH------H------
Q ss_conf ---------799608999913888863199975479999985443-----4------------3-10------1------
Q 000882 864 ---------DDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKS-----F------------C-KK------K------ 904 (1238)
Q Consensus 864 ---------~~~~~v~~i~Ld~~~L~~~~lt~~~I~~~l~~~~~~-----~------------~-~~------~------ 904 (1238)
..++|+++++||+++|.+++|++++|++++.+.++. + + .. .
T Consensus 1181 ~~~~~~~~~~~~~~~~rl~l~~~~~~~~~l~~~~I~~~i~~~~~~~~~v~~~d~~~~~~~i~i~~~~~~~~~~~~~~~~~ 1260 (1752)
T 3h0g_A 1181 DEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVAGKIAESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDNMI 1260 (1752)
T ss_dssp CSSTTCSSCSCCCCEEEEECCTTSSTTTTCCHHHHTTSGGGSSTTSCCEECCCTTCSSCEEEECCCCCSCCCCCSSCCCS
T ss_pred HHHHHCCCCCCCCEEEEEEECHHHHHHCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCEEEEEEECCCCCCCCCCCCCCC
T ss_conf 33310010014652589985499998749999999999986436873585157776630699985155444432223332
Q ss_pred -H---HHHHH-HHHCCCEEECCCCCCCCCCCCCCCC-------------CCCEEEEEEEECC-----CCCCCCCHHHCCC
Q ss_conf -2---38998-7620331201442333452114589-------------9456999982047-----7654320000023
Q 000882 905 -K---MKKVV-QFFKNTSLSISECCSFQQSCADKRS-------------NMPCLMFVLRGAS-----DSYLDKLSGVLAN 961 (1238)
Q Consensus 905 -~---~~~~~-~~~~~~~i~~~g~~~~~~~~~~~~~-------------~~~~l~~~~~~~~-----~~~~vd~~~t~sn 961 (1238)
. ...+. ..++++.+ +|+..++++++++++ ++|.+ .++|++ .+++||..||++|
T Consensus 1261 ~~~~~l~~l~~~~l~~~~i--~Gi~~I~rv~i~~~~~~~~~~~g~~~~~~~~~l--~teG~nL~~v~~~~gVD~~rt~sN 1336 (1752)
T 3h0g_A 1261 EEDVFLKTIEGHMLESISL--RGVPNITRVYMMEHKIVRQIEDGTFERADEWVL--ETDGINLTEAMTVEGVDATRTYSN 1336 (1752)
T ss_dssp CSCHHHHHHHHHHTTCCCS--SCCTTCCCCCEEEEEEEEECSSSCEEEEEEEEE--ECCSCCCSTTTSSSSCCTTTCCCS
T ss_pred CHHHHHHHHHHHHCCCEEE--ECCCCCCEEEEECCCCEEECCCCCCCCCCEEEE--EECCCCHHHHHCCCCCCCCCCEEC
T ss_conf 1899999999963112588--468996479986366033268875124641799--921468999967698846408547
Q ss_pred CHHHHHHHHHHCHHHHHHHHHHHHHHHHH----CCCCCCCEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHCC
Q ss_conf 11468787454011899999999996661----25541100122155101330765324321233446332345102101
Q 000882 962 MIYPVLLETIIKENWWVRQRLSASVTMVA----KGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATL 1037 (1238)
Q Consensus 962 ~I~ei~r~tiIkGiew~R~~l~~~~~~~~----~~v~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~~~ 1037 (1238)
+|+||+ .+.||||+|+.|.+++..|. ++||+|||+||||.||++|++++||||||++++.|+|++||||+
T Consensus 1337 dI~ei~---~vlGIEAAR~~Ii~Ei~~v~~~~G~~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~s~l~~aSFE~--- 1410 (1752)
T 3h0g_A 1337 SFVEIL---QILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFEE--- 1410 (1752)
T ss_dssp CHHHHH---HHSCHHHHHHHHHHHHHTTSCSSSCCCCHHHHHHHHHHHTSSSSCCCCCTTSCSCCCSHHHHHHHHSC---
T ss_pred CHHHHH---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCEEEEECHHHHCCCCCCHHHHHHHHH---
T ss_conf 899999---98759999999999999999843887789999997887613876886123443057988899864897---
Q ss_pred CCHHHHHHHHHHHCCCCCCCCCCCHHCCCCCCCCCCCCEEEEEECCCCCC
Q ss_conf 48089999997213987788520110048756654565079984177754
Q 000882 1038 FMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTENEE 1087 (1238)
Q Consensus 1038 ~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~~~~~~~ 1087 (1238)
|+ ++|++||.+|++|+|+||+|||||||++++|||. |||+++.++++
T Consensus 1411 -T~-~~L~~Aa~~g~~D~l~gvse~Ii~G~~~~~GTG~-fdll~~~~~l~ 1457 (1752)
T 3h0g_A 1411 -TV-EILMDAAASGEKDDCKGISENIMLGQLAPMGTGA-FDIYLDQDMLM 1457 (1752)
T ss_dssp -CT-HHHHHHGGGTCCBCCCCSTTGGGTCSCCCSBTTS-CEECCCHHHHH
T ss_pred -HH-HHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCCE-EEEEECHHHHC
T ss_conf -99-9999999726866664805776538876776632-78985788836
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=2099.43 Aligned_cols=1055 Identities=23% Similarity=0.347 Sum_probs=908.6
Q ss_pred CCCCCCCCCCCCCCCEEEEECCCHHHHHHCCCCCCCC----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 9987788644543005898349969998605455212----------578888899889999998889989999997888
Q 000882 1 MEENTSSTILEGQIVGIRFGLATQKEICTASISDCSI----------SHASQLANPFLGLPLEFGKCESCGTSEPGKCEG 70 (1238)
Q Consensus 1 ~~~~~~~~~~~~~I~~I~F~l~S~eeI~~~Sv~~~~i----------~~~~gl~DprlG~~~~~~~C~TCg~~~~~~CpG 70 (1238)
|....++.++.++|++|+|+++|||||+++|+.++.- ...+||+|||||+++++..|+|||.+. .+|||
T Consensus 1 ~~~~~~~~~~~~~i~~I~f~l~SpeeIr~~Sv~eI~~pet~~~~~~~P~~~GL~d~rlG~~~~~~~C~tCg~~~-~~C~G 79 (1733)
T 1twf_A 1 MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGM-NECPG 79 (1733)
T ss_dssp -CCCSCCCSCBCCCCEEECCBCCHHHHHHTCCCCCCCSCCSCTTSCCSCCSSSSCSSSCCCTTCCCSSSCCCCT-TSCCC
T ss_pred CCCCCCCCCCCCCCCEEEEEECCHHHHHHHCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCC-CCCCC
T ss_conf 98888776774512549998389899997281687142211466677776887474437646788708889988-70798
Q ss_pred CCEEEECCCCCCCCCCHHHHHHHHHHHCCCCC-----C-C-------------HHHHHHHHH------------------
Q ss_conf 53258757611245473889999975301346-----7-0-------------179999976------------------
Q 000882 71 HFGYIELPIPIYHPSHISELKLTMYAFQLQIK-----N-D-------------GVAQRLLSS------------------ 113 (1238)
Q Consensus 71 HFGhIeL~~PVfHp~f~~~i~~IL~~iCl~i~-----~-~-------------g~~~~i~~~------------------ 113 (1238)
|||||||++|||||+||+.++++|+|||..|. . + ...+++++.
T Consensus 80 HfGHIELa~PV~HigF~k~i~kiLe~VC~~Cskllld~~~~~~~~~L~~~~pk~r~~~v~e~ck~k~~Ce~~~~~~~e~~ 159 (1733)
T 1twf_A 80 HFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPT 159 (1733)
T ss_dssp CCCCEEEEEEEECGGGHHHHHHHHHHBCTTTCCBSCCTTSHHHHHHHTCCSHHHHHHHHHHHHTTCCBCCSEECCSSCTT
T ss_pred CCCEEECCCCCCCHHHHHHHHHHHHHHHHHCCEEEECCCHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCHHCCC
T ss_conf 46034344451159887558999987767516013142258999999710778899999998443541465420000023
Q ss_pred ----H--H--------------------------------------HHHHHHCCCCHHHHHHHCCC-CCCCCCCEEEEEE
Q ss_conf ----8--6--------------------------------------99999716994589871259-9999985689841
Q 000882 114 ----C--C--------------------------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYL 148 (1238)
Q Consensus 114 ----C--C--------------------------------------ev~~IlkkIpded~~~L~~~-g~~ppe~lIL~~l 148 (1238)
| | +|+++|++|+++|+.+|+.. .+.+||||||++|
T Consensus 160 ~~~~~~gCGa~qp~irk~gl~l~~e~k~~~~~~e~~~~~k~~Ltp~eV~eifk~I~deD~~lLgl~p~~~rPewmiLtvL 239 (1733)
T 1twf_A 160 QLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCL 239 (1733)
T ss_dssp SCEECCSCCCBCCCCEECSSCEEEEECSSSSCTTSCSCEEEEECHHHHHHHHTTSCHHHHHHTTCBTTTBCGGGGEEEEE
T ss_pred CCCCCCCCCCCCHHHHHCCCCEEEEECCCCCCCCCCHHHHCCCCHHHHHHHHHHCCHHHHHHHCCCCCCCCHHEEEEEEE
T ss_conf 44445787876587774577547765100343222102201479999999987389999998478766898020556542
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHHHHHHHHCC--CCCCCCCC
Q ss_conf 26999888863138975445202699999999999999950-0699996313444657999999997302--97666777
Q 000882 149 PVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVR--GTAKSSRD 225 (1238)
Q Consensus 149 pVPP~~iRp~~~~~g~~~~~~Dlt~~~l~~Ii~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~--~~~k~~~~ 225 (1238)
||||+|+||++.++|..+.++|+|. +|++||++|+.|++. ..|+|..+. .+.|.+||.+|++|+|+. +.+.+...
T Consensus 240 PVpPp~vRPsv~ldg~~~~edDLT~-~l~~II~~N~~Lk~~~~~gap~~ii-~e~~~~LQ~~v~~~~dn~~~~~~~~~~~ 317 (1733)
T 1twf_A 240 PVPPPPVRPSISFNESQRGEDDLTF-KLADILKANISLETLEHNGAPHHAI-EEAESLLQFHVATYMDNDIAGQPQALQK 317 (1733)
T ss_dssp CCCCTTTSCCCCCSSSCCCCCHHHH-HHHHHHHHHHHHHHHHSSCCCHHHH-HHHHHHHHHHHHHHHCCCSSCCCCCSSC
T ss_pred CCCCCCCCCCEECCCCCCCCCHHHH-HHHHHHHHHHHHHHHHHCCCHHHHH-HHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 2699876675665898605777899-9999999999999999747458788-8999999999999854676688743457
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHCCCCCCCCCCHHHHHHHHHHHHC
Q ss_conf 55677888999930145553210011346879776516728999653334462662111443443224439999999981
Q 000882 226 VDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDN 305 (1238)
Q Consensus 226 ~~~~~~~~k~~~~~~k~~~~~~r~~l~gKRvdfs~RsVI~pDP~l~i~evgiP~~~A~~Lt~pe~Vt~~Ni~~l~~lv~n 305 (1238)
..| ..|.+.+++|||.||||+|||||||||||||||+|||+|++||||||..||++|||||+||+|||++|+++|.|
T Consensus 318 -~~r--p~k~i~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~L~~~evGvP~~~A~~Lt~Pe~vt~~ni~~l~~lv~~ 394 (1733)
T 1twf_A 318 -SGR--PVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRN 394 (1733)
T ss_dssp -TTC--CCCCSTTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEHHHHTTCEEEEECCTTTHHHHHHHHHH
T ss_pred -CCC--CCHHHHHHHCCCCCHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHC
T ss_conf -886--50567877503331122213665567653047748987626623584999985788841348999999999974
Q ss_pred CCCC------CCCCCCCEEEECCCCC-CCCCCCCCCEEEEEEECCCEEEEECCCCCCCCCCCCEEEEECCCCEEEECCCC
Q ss_conf 7864------1479995288136998-86445686444200321573866179987746532017996579814422567
Q 000882 306 KLCL------TYSDGSSSYSLREGSK-GHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLI 378 (1238)
Q Consensus 306 g~~~------~~~~~~~~~~l~~~~~-~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~i~~~~tirln~~v 378 (1238)
|+.. ..++.+..+.|++.++ ....|++||+|+|||+|||+|||||||||||||||||+|+|++++||||||+|
T Consensus 395 g~~~~~ga~~~~~~~g~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~VllNRqPTLHr~si~a~~~~v~~~~tirlnp~v 474 (1733)
T 1twf_A 395 GPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSV 474 (1733)
T ss_dssp TTTSSSCEEEEECTTCCEEETTSCTTTTCCCCCTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEEESSSSEEECGGG
T ss_pred CCCCCCCCEEEECCCCCEEECCCCCHHHHHHCCCCCEEEEEECCCCEEEEECCCCCCCCCCEEEEEEECCCCEEEECHHH
T ss_conf 98667774037827895785322322554404657789765126977898079864613422678997069747747655
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEECHHHHHHHHHHH-CCCCCCHHHHHHHHCCCC
Q ss_conf 7989886674600035678798899999971353322447999944751113455787630-356679999998710235
Q 000882 379 CGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFAL 457 (1238)
Q Consensus 379 C~pyNADFDGDeMniH~PQs~eAraEa~~Lm~~~~~ilsP~~G~PiigliQD~llg~~llt-kd~fl~~~~~~ql~~~~~ 457 (1238)
|+||||||||||||+|+|||++|||||++||++++||++|++|+|+++++||+|+|+|+|| +++|+++++++++++++.
T Consensus 475 C~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~v~g~y~lT~~~~f~~~~e~~~~~~~~~ 554 (1733)
T 1twf_A 475 TSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVP 554 (1733)
T ss_dssp HHHHTCCSSSCEEEEECCCSHHHHHHHHHHTBGGGGSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHST
T ss_pred CCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCCEEECCCCCEEEEEECCCCCCCEEEECCCCCCCHHHHHHHHHHHH
T ss_conf 58877661124565105788999999999853734588657998137651222100034104755699999999998323
Q ss_pred C---CCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCC------------CCEEEEECCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 5---656323203324554310000234579985346------------8679996342365555567753238779999
Q 000882 458 S---PLPRPALSKARCSARWTALQILQSVLPPGFDSC------------GDRYLIKKSEVLKGDFDRDTIPSVINEIVTS 522 (1238)
Q Consensus 458 ~---~lp~PaIlKp~~~~lWTGKQi~S~~lP~~~~~~------------~~~viI~~Gell~g~ldK~~lg~s~~~Li~~ 522 (1238)
. .+|+|||+||. ++||||||||++||.++++. ++.|+|+||||++|++||+++|++.++|||.
T Consensus 555 ~~~~~~~~pai~kp~--~~wtGkqifs~ilp~~~~~~~~~~~~~~~~~~d~~v~i~~gel~~g~ldKk~lg~~~~~li~~ 632 (1733)
T 1twf_A 555 DWDGVIPTPAIIKPK--PLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHV 632 (1733)
T ss_dssp TCCSCCCCCSBCSSS--CEEEHHHHHHHHSCTTCCEEECCTTCCTTCTTCCSEEEETTEEEESCCCHHHHSSCTTSHHHH
T ss_pred HHCCCCCCCCCCCCC--CCCCHHHHHHHHCCCCCCEEECCCCCCCCCCCCCEEEEECCCEEEEECCHHHHCCCHHHHHHH
T ss_conf 315853774310761--575288788876789974133687765578665648986782898301667854570189999
Q ss_pred HHHHHCHHHHHHCHHHHHHHHHHHHHHCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH-------------HHHH
Q ss_conf 998529789995163349999999982483321076545989999999999999999986664-------------3488
Q 000882 523 IFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS-------------TQNE 589 (1238)
Q Consensus 523 i~~~~G~~~a~~~L~~lq~L~~~~L~~~GFSigi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~-------------~~~~ 589 (1238)
++++||+++|++|||.+|+|+++||+++|||||++|+++++++.+.+++.+++++..+.++.. +.++
T Consensus 633 i~~~~G~~~a~~~ld~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~i~~~i~~a~~~v~~~~~~~~~g~l~~~pg~~~~e 712 (1733)
T 1twf_A 633 VTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRE 712 (1733)
T ss_dssp HHHHHCHHHHHHHHHHHHHHHHHHHHTTCBCCCGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCTTCCHHH
T ss_pred HHHHHCHHHHHHHHHHHHHHHHHHHHHCCEEEEHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHH
T ss_conf 99986999999999999999999998766698556537598999999999999999999999999809976588987799
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH----CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99999999999999999999871----29743120321002356687897410352146985444454211122233448
Q 000882 590 LVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIY 665 (1238)
Q Consensus 590 ~le~~~~~~l~~~~~~i~~~~~~----~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~g~r~~~r~l~~~~~~~f~~~~ 665 (1238)
.+|.++..+|+++++.+++.+.+ .|++.+|+.||||||++|++||+||||||.++|+ ++++++..|++|||.+
T Consensus 713 ~~e~~v~~il~~~~d~~~~~~~~~l~~~N~i~~Ma~SGAKGs~~Ni~Q~~~~~Gqq~~~Gk-rip~g~~~RtLPhf~k-- 789 (1733)
T 1twf_A 713 SFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGK-RIAFGFVDRTLPHFSK-- 789 (1733)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHTSSCCHHHHHHHHSCCEECCBTTB-SCCCCBTTBSSTTSCT--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHCCCCCCCCCC-CCCCCCCCCCCCCCCC--
T ss_conf 9999999999999999999999862658871788504676547769999717677546886-3777888877888777--
Q ss_pred CCCCCCCCCCCCEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCCHHHHHHHHHHEEEEEECCEEECCCCCCEEE
Q ss_conf 89989998776400143233589663078623542101112344479884027899987406897410474357885022
Q 000882 666 PMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQ 745 (1238)
Q Consensus 666 p~~~d~~~~a~GfV~~sF~~GL~P~EfFfH~magREGLiDtAvkTa~sGyL~R~L~~~l~d~~v~yd~Tvr~~~~~~IiQ 745 (1238)
+|++|+|+|||.|||++||+|+|||||||||||||||||||||+|||||||||++|||++|+||||||++ ++.|||
T Consensus 790 ---~d~~p~s~GfI~ssF~~GLtp~EyFfh~mggReGLiDTAvKTA~SGYLqRRLVk~ledv~V~yDgTVR~s-~g~IvQ 865 (1733)
T 1twf_A 790 ---DDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNS-LGNVIQ 865 (1733)
T ss_dssp ---TCCSTTTTTEECSCTTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCEECTTSCEECT-TCCEEE
T ss_pred ---CCCCCCCCCHHHHHHHCCCCHHHHHHHHHCCCCCHHHHCEECCCCCCCEEEHHHHHCCEEEEECCCEECC-CCCEEE
T ss_conf ---8898001661331000246548776554314420122000205688510003333250599705867658-997899
Q ss_pred EEEECCCCCCC---------------------------------------------------------------------
Q ss_conf 36101445446---------------------------------------------------------------------
Q 000882 746 FDYAVNARKSH--------------------------------------------------------------------- 756 (1238)
Q Consensus 746 f~yg~~g~~~~--------------------------------------------------------------------- 756 (1238)
|+||+||+|..
T Consensus 866 F~YGeDGlD~~~~e~~~~~~~~~~~~~f~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~e~~~l~~~r~~lr~ 945 (1733)
T 1twf_A 866 FIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLRE 945 (1733)
T ss_dssp SSGGGTTBCGGGEEEEECGGGSSCHHHHHHHHCCCTTCTTTSCCTTTBTTHHHHTTCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEECCCCCCCCEEECCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 87136667742100465650015799999985344456322478888877877403688899999999999988999987
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q 000882 757 -------------------------------------------------------------------------------- 756 (1238)
Q Consensus 757 -------------------------------------------------------------------------------- 756 (1238)
T Consensus 946 i~~~~~~~~~~P~ni~r~i~~~~~~f~~~~~~~s~l~p~~~~~~v~~~~~~~~~~~g~d~l~~~~~~n~~~l~~~~~rs~ 1025 (1733)
T 1twf_A 946 VFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSR 1025 (1733)
T ss_dssp HTTTCCCEEEEESCHHHHHHHHHHHTTCCTTSCBCCCHHHHHHHHHHHHTTCCSCCCCSHHHHHHHHHTTHHHHHHHHHH
T ss_pred HHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCHHHHHHHHHHHH
T ss_conf 63056634468714999999888773135554345788999999999998643015876200555525277888876654
Q ss_pred ------------------------------CCCCCCCEEEEECCCCCCCHHHHHHHCCCC-------CCCCCHHHHHHHH
Q ss_conf ------------------------------767899706652112379067886316699-------9888067899998
Q 000882 757 ------------------------------SLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEIL 799 (1238)
Q Consensus 757 ------------------------------~l~~~Ge~VG~laaqsigepa~q~~L~t~~-------~~~~g~~rlkEil 799 (1238)
++++|||+||++||||||||+|||||+||+ |+|+|+|||+||+
T Consensus 1026 L~~k~~~~~~~l~~~~~~~~l~~i~~ky~~a~v~pGe~VG~iaAQSigEp~TQMTLnTFHfAGva~~NVTLGVPRLkEIi 1105 (1733)
T 1twf_A 1026 LATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEIL 1105 (1733)
T ss_dssp SCHHHHHHTSCCCHHHHHHHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC----------CCSCCHHHHHHHHT
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf 54555666617789999888899999998655789860156765316885312355544415612557436758899999
Q ss_pred HHHCCCCCCCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCEECHHHHHHEEEEEECCCCCCC----------------
Q ss_conf 7311379999884189972788878764327999999862201026444311368842886445----------------
Q 000882 800 LCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS---------------- 863 (1238)
Q Consensus 800 ~~~~~~k~~~~~~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~v~l~~i~~~i~i~y~~~~~~~---------------- 863 (1238)
+++++ +++|.|+++|.++.. .++++|+.|+.+||+|+|++++..+.|.|+++...+
T Consensus 1106 nask~----ikTP~mtv~L~~~~~----~~~e~A~~v~~~ie~ttL~dv~~~i~i~~dp~~~~tvi~ed~~~~~~y~~i~ 1177 (1733)
T 1twf_A 1106 NVAKN----MKTPSLTVYLEPGHA----ADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLL 1177 (1733)
T ss_dssp TTCSS----CSSCEEEEEBCSSSS----SCHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHHTSSCC-
T ss_pred HHCCC----CCCCEEEEEECCCCC----CCHHHHHHHHHHHCEEEHHHHHHEEEEEECCCCCCEEEECCHHHHHHHHCCC
T ss_conf 75137----899738999577543----2599999998763114899820167999736766403313223434332256
Q ss_pred ---------CCCCEEEEEEECHHHHHHCCCCHHHHHHHHHHHHHHHH-----H-------------H-H---------H-
Q ss_conf ---------79960899991388886319997547999998544343-----1-------------0-1---------2-
Q 000882 864 ---------DDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFC-----K-------------K-K---------K- 905 (1238)
Q Consensus 864 ---------~~~~~v~~i~Ld~~~L~~~~lt~~~I~~~l~~~~~~~~-----~-------------~-~---------~- 905 (1238)
..++|+++++||++.+.+++|++++|.+++.+.++.-. . . . .
T Consensus 1178 ~~d~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~I~~~i~~~~~~~~~~~~~d~~~~~~~~~i~~~~~~~~~~~~~~~~~ 1257 (1733)
T 1twf_A 1178 DEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEED 1257 (1733)
T ss_dssp ---------CCCSEEEEEEECHHHHHHTTCCHHHHHHHHHHHHGGGEEEEECCTTSSSCEEEEEEC----------CCTT
T ss_pred HHHHCCHHHHCCCCEEEEEECHHHHHHCCCCHHHHHHHHHHHHCCCCCEECCCCCCCHHHEEEEECCCCCCCCCCCCHHH
T ss_conf 77621003210340058996698897637999999999987517775120477640001113320267522233320147
Q ss_pred --HHHH-HHHHCCCEEECCCCCCCCCCCCCC--------C-----CCCCEEEEEEEECC-----CCCCCCCHHHCCCCHH
Q ss_conf --3899-876203312014423334521145--------8-----99456999982047-----7654320000023114
Q 000882 906 --MKKV-VQFFKNTSLSISECCSFQQSCADK--------R-----SNMPCLMFVLRGAS-----DSYLDKLSGVLANMIY 964 (1238)
Q Consensus 906 --~~~~-~~~~~~~~i~~~g~~~~~~~~~~~--------~-----~~~~~l~~~~~~~~-----~~~~vd~~~t~sn~I~ 964 (1238)
..++ .+.+.++.+ +|+..+.++.+++ + .++|+ +.++|.+ ..++||..||++|+|+
T Consensus 1258 ~~l~~l~~~~l~~~~v--~Gi~~I~r~~i~~~~~~~~~~~g~~~~~~~~~--L~teG~nL~~vl~~~~VD~~rt~SNdI~ 1333 (1733)
T 1twf_A 1258 HMLKKIENTMLENITL--RGVENIERVVMMKYDRKVPSPTGEYVKEPEWV--LETDGVNLSEVMTVPGIDPTRIYTNSFI 1333 (1733)
T ss_dssp HHHHHHHHHHHHHCEE--ESCTTCCCEEEEEEEEEEECTTSSEEEEEEEE--EEEESCCHHHHTTSTTBCTTTCBCSCHH
T ss_pred HHHHHHHHHHHHHEEE--ECCCCCCEEEEECCCCEEECCCCCCCCCCCEE--EEEECCCHHHHHCCCCCCCCCCEECCHH
T ss_conf 9999999976300477--15788547999535531235777524576238--9960514999960477254110434599
Q ss_pred HHHHHHHHCHHHHHHHHH----HHHHHHHHCCCCCCCEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHCCCCH
Q ss_conf 687874540118999999----9999666125541100122155101330765324321233446332345102101480
Q 000882 965 PVLLETIIKENWWVRQRL----SASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMP 1040 (1238)
Q Consensus 965 ei~r~tiIkGiew~R~~l----~~~~~~~~~~v~~rHl~Llad~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~~~~t~ 1040 (1238)
+|+ -+.||||+|+.| ..+++.+|.+||+|||+||||.||++|+++|||||||++++.|+|++||||+ |.
T Consensus 1334 eI~---~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~S~L~~aSFE~----T~ 1406 (1733)
T 1twf_A 1334 DIM---EVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEE----TV 1406 (1733)
T ss_dssp HHH---HHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTTBSSCCCSSSCSSSCSSCCTTSSCCSSC----SH
T ss_pred HHH---HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCEECCCCHHHHCCCCCCCHHHCCHHH----HH
T ss_conf 999---87569999999999999998605863462334323555600763203331322266887221032254----38
Q ss_pred HHHHHHHHHHCCCCCCCCCCCHHCCCCCCCCCCCCEEEEEECCCCCCCCCC
Q ss_conf 899999972139877885201100487566545650799841777545678
Q 000882 1041 RKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTENEEFNQD 1091 (1238)
Q Consensus 1041 ~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f~l~~~~~~~~~~~~ 1091 (1238)
++|.+||.+|+.|.|+||+||||+||++|+|||+ |||+++.+.++...+
T Consensus 1407 -~~L~~Aa~~g~~D~l~gvsenII~G~~~~~GTG~-FdLl~~~~~~~~~~~ 1455 (1733)
T 1twf_A 1407 -EILFEAGASAELDDCRGVSENVILGQMAPIGTGA-FDVMIDEESLVKYMP 1455 (1733)
T ss_dssp -HHHHHHHHHTCEECCCSHHHHHHTTCCCSSGGGS-SEEEECSCCC-----
T ss_pred -HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC-EEEEECHHHCCCCCC
T ss_conf -9999987514767355510001047777787740-799971033120002
No 3
>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=1593.74 Aligned_cols=739 Identities=28% Similarity=0.386 Sum_probs=639.1
Q ss_pred CCCCCCCEEEEECCCHHHHHHCCCCCCCCCCC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEC
Q ss_conf 44543005898349969998605455212578-----------8888998899999988899899999978885325875
Q 000882 9 ILEGQIVGIRFGLATQKEICTASISDCSISHA-----------SQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIEL 77 (1238)
Q Consensus 9 ~~~~~I~~I~F~l~S~eeI~~~Sv~~~~i~~~-----------~gl~DprlG~~~~~~~C~TCg~~~~~~CpGHFGhIeL 77 (1238)
+..++|++|+||++||+||+++|+.+ |++| +|++|||||+.+++..|+|||.+. .+||||||||||
T Consensus 1 m~~k~i~~I~f~l~SpeeIr~~S~~e--V~~p~t~n~~g~p~~ggl~D~~lG~~~~~~~C~tCg~~~-~~c~ghfGhIeL 77 (880)
T 4ayb_A 1 MSEKNIKGIKFGILSPDEIRKMSVTA--IITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTL-GNCPGHFGHIEL 77 (880)
T ss_dssp --CEEEEEEEEECCCHHHHHHHTCSC--BCCSCCCBSSSSSBCSSSSCGGGCCCSSSCCCTTTCCCG-GGCCCCCEEEEE
T ss_pred CCCCEECEEEEEECCHHHHHHHCCEE--EECCCEECCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCC-CCCCCCCEEECC
T ss_conf 99746355999807999999861649--967110999989268997793349899978789989977-899998863465
Q ss_pred CCCCCCCCCHHHHHHHHHHHCCCCC-----CCH-----------------HHHHH----HH------HH--H--------
Q ss_conf 7611245473889999975301346-----701-----------------79999----97------68--6--------
Q 000882 78 PIPIYHPSHISELKLTMYAFQLQIK-----NDG-----------------VAQRL----LS------SC--C-------- 115 (1238)
Q Consensus 78 ~~PVfHp~f~~~i~~IL~~iCl~i~-----~~g-----------------~~~~i----~~------~C--C-------- 115 (1238)
|.|||||+|++.+.++|+++|..|. .+. ..+++ .+ .| |
T Consensus 78 a~PV~h~~f~~~i~~lL~~~c~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~cg~~~~~i~ 157 (880)
T 4ayb_A 78 VRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRWPSAARRLTEYVKKTAMKAQVCPHCGEKQFKIK 157 (880)
T ss_dssp EEEEECGGGTTHHHHHHHTSCTTSSCCCSSCCHHHHHHHHHHHHGGGCHHHHHHHHHHHHHHHTTCSSCTTTTCCCCCCE
T ss_pred CCCCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCHHCCCHHHHHH
T ss_conf 45023564898999998282361048827889999999998875312707999999999987415400122063246655
Q ss_pred ---------------------HHHHHHCCCCHHHHHHHCCC-CCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf ---------------------99999716994589871259-99999856898412699988886313897544520269
Q 000882 116 ---------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSI 173 (1238)
Q Consensus 116 ---------------------ev~~IlkkIpded~~~L~~~-g~~ppe~lIL~~lpVPP~~iRp~~~~~g~~~~~~Dlt~ 173 (1238)
+++++|++|+++++.+++.. ...+||||||++||||||++||++..++..+.++|+|.
T Consensus 158 ~~~~~~~~~~~~~~~~~l~~~~~~~~l~~i~~~~~~~l~~~~~~~~Pewmil~~lPV~Pp~~RP~v~l~~g~~~~~dl~~ 237 (880)
T 4ayb_A 158 LEKPYNFYEERKEGVAKLTPSDIRERLEKVPESDVEILGYDPTTSRPEWMILTVLPVPPITIRPSIMIESGIRAEDDLTH 237 (880)
T ss_dssp EEETTEEEEEETTEEEECCHHHHHHHHTTCCHHHHHHTTCCTTTCCSGGGEEEEEEECCSSSSCC-----CCCCCCSSHH
T ss_pred HCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHEEEEEEECCCCCCCCHHHCCCCCCCCCHHHH
T ss_conf 23757789999999975389999999998689899995888767982344876665799988835440786413540888
Q ss_pred HHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHHHHHHHHCC--CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCC
Q ss_conf 9999999999999950-0699996313444657999999997302--976667775567788899993014555321001
Q 000882 174 AMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVR--GTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTL 250 (1238)
Q Consensus 174 ~~l~~Ii~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~--~~~k~~~~~~~~~~~~k~~~~~~k~~~~~~r~~ 250 (1238)
+|++|+++|++++.. ..++|..+. .++|.+||.+|++|+|+. +.+... .... ...|.+.+++|||.||||+|
T Consensus 238 -~~~~ii~~N~~lk~~~~~~ap~~i~-~~~~~~LQ~~V~~l~dn~~~g~~~~~-~~~~--rp~ksl~~~lkgK~GrfR~n 312 (880)
T 4ayb_A 238 -KLVDIVRINERLKESIDAGAPQLII-EDLWDLLQYHVATYFDNEIPGLPPSK-HRSG--RPLRTLAQRLKGKEGRFRGN 312 (880)
T ss_dssp -HHHHHHHHHHHHHHHHTSCCCHHHH-HHHHHHHHHHHHHHHCSCCSSSCCCC-CTTS--CCCCCHHHHHHSSSSTHHHH
T ss_pred -HHHHHHHHHHHHHHHHHCCCCHHHH-HHHHHHHHHHHHHHHHCCCCCCCCCC-CCCC--CCCCCHHHHHCCCCHHHHHC
T ss_conf -9999987666655433038826689-99999999999998704677888667-8887--76632666603664233304
Q ss_pred CCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCC------CCCCCCCEEEECCCC
Q ss_conf 13468797765167289996533344626621114434432244399999999817864------147999528813699
Q 000882 251 FIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCL------TYSDGSSSYSLREGS 324 (1238)
Q Consensus 251 l~gKRvdfs~RsVI~pDP~l~i~evgiP~~~A~~Lt~pe~Vt~~Ni~~l~~lv~ng~~~------~~~~~~~~~~l~~~~ 324 (1238)
+|||||||||||||+|||+|++||||||..||++|||||+||+||+++|+++|.|||.. +.+..+..+.++...
T Consensus 313 l~GKRVd~s~RsVI~~dP~l~~~e~GvP~~~A~~Lt~Pe~vt~~N~~~l~~~v~ng~~~~pga~~~i~~~~~~~~l~~~~ 392 (880)
T 4ayb_A 313 LSGKRVDFSSRTVISPDPNISIDEVGVPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRPDGRRIDLRYVK 392 (880)
T ss_dssp TSSEECSSEEEEEEEECTTSCSSEEEECHHHHTTSEEEEECCTTTHHHHHHHHHHTTSSSSCEEEEECSSCCEEEGGGCS
T ss_pred CCCEEECCCCCEEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHHHHHCCCCCCCCHHHHHHCCCEEEEEECCH
T ss_conf 11025435574255079986126158829999767878588687999999999749744553366542046278730120
Q ss_pred -CC--CCCCCCCCEEEEEEECCCEEEEECCCCCCCCCCCCEEEEECCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf -88--644568644420032157386617998774653201799657981442256779898866746000356787988
Q 000882 325 -KG--HTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAA 401 (1238)
Q Consensus 325 -~~--~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~i~~~~tirln~~vC~pyNADFDGDeMniH~PQs~eA 401 (1238)
+. ...|++||+|+||++|||+|||||||||||||||||+|+|++++||||||+||+||||||||||||+|+|||++|
T Consensus 393 ~~~~~~~~l~~g~~V~rhl~dgd~VLlNRqPTLHr~si~a~~~~l~~gktirlhp~vC~~yNADFDGDeMnvHvPqS~eA 472 (880)
T 4ayb_A 393 DRKELASTLAPGYVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 472 (880)
T ss_dssp SCTTHHHHCCTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEECSSSSEEECGGGHHHHTCCSSSCEEEEECCCSHHH
T ss_pred HHHHHHHHCCCCCEEEEEEECCCEEEECCCCCCCCCCEEEEEEECCCCCEEEECCCCCCCCCCCCCCCEEEEECCCCHHH
T ss_conf 14678876065646755521685899637876565451322344056753650620035434676666147751688899
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCEEEECHHHHHHHHHHH-CCCCCCHHHHHHHHCCCCC--CCCCCCCCCCCCCCCCCHHH
Q ss_conf 99999971353322447999944751113455787630-3566799999987102355--65632320332455431000
Q 000882 402 KAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFALS--PLPRPALSKARCSARWTALQ 478 (1238)
Q Consensus 402 raEa~~Lm~~~~~ilsP~~G~PiigliQD~llg~~llt-kd~fl~~~~~~ql~~~~~~--~lp~PaIlKp~~~~lWTGKQ 478 (1238)
||||++||++++||+||++|+|+++++||+|+|+|+|| +++|+++++++++++.... .+|+|||+||. ++|||||
T Consensus 473 ~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~lT~~~~~~~~~~~~~~~~~~~~~~~~~~p~i~~~~--~~~tgkq 550 (880)
T 4ayb_A 473 IAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQILGVADVKIDLGEPAILAPR--EYYTGKQ 550 (880)
T ss_dssp HHHHHHHSBSGGGCBCSSSSSBCSCCCSHHHHHHHHHTSSSCEECHHHHHHHHTTSCCCCCCCSCSEESSS--EEEEHHH
T ss_pred HHHHHHHHHCHHCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCEECCCCCCCEECCE--EEECCCE
T ss_conf 99999998472016437789830111410787768761575557889986550543210235855022553--5761656
Q ss_pred HCCCCCCCCCCC-------------------CCCEEEEECCCCCCCCCCCCCCCCH-HHHHHHHHHHHHCHHHHHHCHHH
Q ss_conf 023457998534-------------------6867999634236555556775323-87799999985297899951633
Q 000882 479 ILQSVLPPGFDS-------------------CGDRYLIKKSEVLKGDFDRDTIPSV-INEIVTSIFFEKGPEEVLEFFDS 538 (1238)
Q Consensus 479 i~S~~lP~~~~~-------------------~~~~viI~~Gell~g~ldK~~lg~s-~~~Li~~i~~~~G~~~a~~~L~~ 538 (1238)
+||+++|.++++ .+..++|++|+++.|.+||+.+|+. .++|||.++++||+.++..|||.
T Consensus 551 i~s~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~~g~l~~g~ldk~~lg~~~~~~li~~i~~~~G~~~t~~~ld~ 630 (880)
T 4ayb_A 551 VVSAFLPKDFNFHGQANVSSGPRLCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDN 630 (880)
T ss_dssp HHHTTSCTTCCEEEECTTCSGGGCCSSSCCTTSCEEEEETTEEEECCCSTTTSSTTCTTSHHHHHHHTSCHHHHHHHHHH
T ss_pred EEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCEEEEECCEEEEEEECCHHHCCCCCCEEEEHHHHHCCCHHHHHHHHH
T ss_conf 78887236543222257623773335766787656998576565400200121444442032316665030899999999
Q ss_pred HHHHHHHHHHHCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHH
Q ss_conf 49999999982483321076545989999999999999999986664-------------34889999999999999999
Q 000882 539 LQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS-------------TQNELVDLQIENHIRHVKML 605 (1238)
Q Consensus 539 lq~L~~~~L~~~GFSigi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~-------------~~~~~le~~~~~~l~~~~~~ 605 (1238)
+++++++|++++|||||++|+.+++++.+.+.+.++++...+.+... ..++.++.++...|+++++.
T Consensus 631 l~~lg~~~lt~~GfSigi~Di~i~~~~~~~i~~~i~~a~~~v~~i~~~~~~g~l~~~~g~~~~e~~e~~v~~~l~~~~~~ 710 (880)
T 4ayb_A 631 LFRVFIRFVELQGFTMRLEDVSLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDKLRST 710 (880)
T ss_dssp HHHHHHHHHHHHCCCCCGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCSSSCHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999985487501142346505689999999999998899999997088754666509999999999999999999
Q ss_pred HHHHHHH----CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECC
Q ss_conf 9999871----297431203210023566878974103521469854444542111222334488998999877640014
Q 000882 606 VAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKG 681 (1238)
Q Consensus 606 i~~~~~~----~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~~ 681 (1238)
+++.+.+ .|++++|++||||||+.|++||+||||||+++|+| ++|++..+.+|||.. .|.+|+++|||.+
T Consensus 711 ~~~~~~~~l~~~N~i~mMa~SGARGS~~ni~Qlagm~Gqq~~~G~R-Iprg~~~rtLP~f~~-----~d~~p~a~GfI~s 784 (880)
T 4ayb_A 711 AGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQSVRGER-IKRGYMTRTLPHFKP-----YDISPEARGFIYS 784 (880)
T ss_dssp HHHHHHHTSCTTSHHHHHHHHTSSCCSTTHHHHHTCCEECBSSSSB-SCCSBTTBSSTTSCT-----TCCSTTTTSEECS
T ss_pred HHHHHHHHCCCCCCHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCC-CCCCCCCCCCCCCCC-----CCCCCCCCCEEHH
T ss_conf 8799985089998799995437267799999999450451057865-767876677898887-----8998255970720
Q ss_pred CCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCCHHHHHHHHHHEEEEEECCEEECCCCCCEEEEEEECCCCCCCCCCCC
Q ss_conf 32335896630786235421011123444798840278999874068974104743578850223610144544676789
Q 000882 682 CFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPA 761 (1238)
Q Consensus 682 sF~~GL~P~EfFfH~magREGLiDtAvkTa~sGyL~R~L~~~l~d~~v~yd~Tvr~~~~~~IiQf~yg~~g~~~~~l~~~ 761 (1238)
||++||+|+|||||||||||||+|||+|||+|||||||||+++||++|+||||||++ .+.||||.||+||+|+... ..
T Consensus 785 sF~eGLtp~EyF~ht~ggRkGL~DTAlKTA~SGYLtRRLVdv~qDv~V~yDgTVR~~-~g~ivqf~YGeDgldp~~~-~~ 862 (880)
T 4ayb_A 785 SFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRAEYDGTVRSL-YGEVIQVAYGDDGVFPMYS-AH 862 (880)
T ss_dssp CTTTCCCHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTTEEECTTSCEEET-TTEEEESSTTTTCBCTTTS-BT
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHCCHHHCHHHHHHHHHHHHHCCEEEECCCCCCCC-CCCEEEEECCCCCCCEEEC-CC
T ss_conf 023799879999962654121876123212003999999999738799569982389-9958998527763103122-45
Q ss_pred CCEE
Q ss_conf 9706
Q 000882 762 GEPV 765 (1238)
Q Consensus 762 Ge~V 765 (1238)
+.+|
T Consensus 863 ~~~~ 866 (880)
T 4ayb_A 863 GKTV 866 (880)
T ss_dssp TBSC
T ss_pred CCCC
T ss_conf 8853
No 4
>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=1565.53 Aligned_cols=899 Identities=18% Similarity=0.217 Sum_probs=680.9
Q ss_pred CCCCEEEEECCCHHHHHHCCCCCCCCCC------------CCCCCCCCCCCCC---------------CCCCCCCCCCCC
Q ss_conf 4300589834996999860545521257------------8888899889999---------------998889989999
Q 000882 12 GQIVGIRFGLATQKEICTASISDCSISH------------ASQLANPFLGLPL---------------EFGKCESCGTSE 64 (1238)
Q Consensus 12 ~~I~~I~F~l~S~eeI~~~Sv~~~~i~~------------~~gl~DprlG~~~---------------~~~~C~TCg~~~ 64 (1238)
.+|++|+||++||++|++||+.+ |++ .+||+|+|+|+|. ++..|+|||...
T Consensus 3 ~~~~~i~~gl~Spe~Ir~~S~ge--V~~pet~ny~t~kP~~~GLfd~rifGp~k~~~C~Cgkyk~~~~~~~~C~~Cg~~~ 80 (1265)
T 1hqm_D 3 KEVRKVRIALASPEKIRSWSYGE--VEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEV 80 (1265)
T ss_dssp CCBCCCCCCCCCTTTHHHHTTTC--CCCCCC-------------------------------------CCSCSSSSSSSS
T ss_pred CCCCEEEEECCCHHHHHHHHEEE--ECCHHHEECCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf 63135999658989998753799--8152203267896167898675236877563464888544477998879989843
Q ss_pred CCCC---CCCCEEEECCCCCCCCCCHHHHHHHH----HHHC--C----------CCCC---------CHHHHHH------
Q ss_conf 9978---88532587576112454738899999----7530--1----------3467---------0179999------
Q 000882 65 PGKC---EGHFGYIELPIPIYHPSHISELKLTM----YAFQ--L----------QIKN---------DGVAQRL------ 110 (1238)
Q Consensus 65 ~~~C---pGHFGhIeL~~PVfHp~f~~~i~~IL----~~iC--l----------~i~~---------~g~~~~i------ 110 (1238)
.+| |||||||+|+.||||++|++.+..+| +++| + .++. +...+..
T Consensus 81 -~~~~vrrg~~GhIeLa~PV~Hi~y~k~~~s~l~~lL~~~~k~le~v~y~~s~v~~~~~~~l~~~l~~~~~~~~~~~~~~ 159 (1265)
T 1hqm_D 81 -TRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLFATELEQVLYFNKYIVLDPKGAVLDGVPVEKRQLLTDXXXX 159 (1265)
T ss_dssp -CCSSSCCCSCCCCCCCSCCCSTTSTTHHHHTTTCTTTHHHHTTSSSCCCCSCCCCSSSCCCTTCCCCTTHHHHTCCCCC
T ss_pred -CCCCCCCCCCCEEEECCCEEEEEECCCCHHHHHHHHCCCHHHHCCEEEECCEEEECCCCHHHHHCCHHHHHHHHHHCCC
T ss_conf -4266546766137734743565203565679999866787764307513026863688557664279999998652011
Q ss_pred -------------------------HH--------HH-H-----------------HHHHHHCCCCHHHHHHHC------
Q ss_conf -------------------------97--------68-6-----------------999997169945898712------
Q 000882 111 -------------------------LS--------SC-C-----------------EVKEMLKRIPEETRKKLA------ 133 (1238)
Q Consensus 111 -------------------------~~--------~C-C-----------------ev~~IlkkIpded~~~L~------ 133 (1238)
.. .+ | +..+.+++.+++....+.
T Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~krl~~~ 239 (1265)
T 1hqm_D 160 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIDARMGAEAIQELLKELDLEKLERELLEEMKHPSRARRAKARKRLEVV 239 (1265)
T ss_dssp CCCCCCCSSCCCCCCCCTTSCCCCCCCCCCCCCCCCCSHHHHHHHHTHHHHCHHHHHHHTTTCCSSHHHHHHHHHHHHHH
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH
T ss_conf 01111111111111111111111112210232104667256888987337798999999998643577778876111166
Q ss_pred ---CCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHH
Q ss_conf ---59999998568984126999888863138975445202699999999999999950-06999963134446579999
Q 000882 134 ---GKGYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLA 209 (1238)
Q Consensus 134 ---~~g~~ppe~lIL~~lpVPP~~iRp~~~~~g~~~~~~Dlt~~~l~~Ii~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~ 209 (1238)
.....+||||||++||||||++||++.++|..+.++|+|. +|++|+++|++|++. ..++|..+. .++|.+||.+
T Consensus 240 ~~f~~~~~~Pewmil~~lPVpPp~~RP~v~l~gg~~~~~Dln~-~~~~Ii~~N~~L~~~~~~~ap~~ii-~~~~~~LQ~~ 317 (1265)
T 1hqm_D 240 RAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLND-LYRRLINRNNRLKKLLAQGAPEIII-RNEKRMLQEA 317 (1265)
T ss_dssp HHHHSSSCSSCCSCSSCCCCCSCC------------CCCGGGT-HHHHTHHHHHHHHTSSSSCCCSTTT-STTTTTTGGG
T ss_pred HHHCCCCCCCCEEEEECCCCCCCCCCCCEECCCCCEECCHHHH-HHHHHHHHHHHHHHHHHCCCCHHHH-HHHHHHHHHH
T ss_conf 6530258981047631257899867664553897154670689-9999999999999999749945678-8889999999
Q ss_pred HHHHHHCCCCCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHCCCCCC
Q ss_conf 99997302976667775567788-89999301455532100113468797765167289996533344626621114434
Q 000882 210 VGQYLEVRGTAKSSRDVDARFGV-SQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFE 288 (1238)
Q Consensus 210 v~~~~~~~~~~k~~~~~~~~~~~-~k~~~~~~k~~~~~~r~~l~gKRvdfs~RsVI~pDP~l~i~evgiP~~~A~~Lt~p 288 (1238)
|++|+|+....++......| . .|.+.+++|||.||||+|||||||||||||||||||||++||||||..||++||+|
T Consensus 318 V~~l~Dn~~~g~~~~~~~~r--p~lksl~~~LkGK~GrfR~NLmGKRVdfSaRSVI~pdP~L~i~evGvP~~~A~~L~~P 395 (1265)
T 1hqm_D 318 VDAVIDNGRRGSPVTNPGSE--RPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKP 395 (1265)
T ss_dssp TTTTSSCCSSCCCSSCSSCC--CCCCCSTTTSSSTTCTTTTTTSCCEETTCCCCBEEECCSSSSSBCCCBHHHHHHHHHH
T ss_pred HHHHHCCCCCCCCCCCCCCC--CCCCCHHHHCCCCHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCHHHHHHHHCCH
T ss_conf 99996778779876587888--6664254402461134554202100276663167169876655036759999883758
Q ss_pred CCCCHHHHHHHHHHHHCCCCCCCCCCCCEEEE-CCCCCCCCCCCCCCEEEEEEECCCEEEEECCCCCCCCCCCCEEEEEC
Q ss_conf 43224439999999981786414799952881-36998864456864442003215738661799877465320179965
Q 000882 289 ERVNVHNINYLQELVDNKLCLTYSDGSSSYSL-REGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVH 367 (1238)
Q Consensus 289 e~Vt~~Ni~~l~~lv~ng~~~~~~~~~~~~~l-~~~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~i~ 367 (1238)
|| +++||.||+...++. +++.+ ++.. .. ..+|.|+||++|||+|||||||||||||||||+|+++
T Consensus 396 -----~~---~~~lv~~g~~~~i~~--ak~~i~~~~~---~~-~~~~~v~~~v~~gd~VLlNRqPTLHr~sIma~~~~l~ 461 (1265)
T 1hqm_D 396 -----FL---LKKMEEKAFAPNVKA--ARRMLERQRD---IK-DEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLV 461 (1265)
T ss_dssp -----HH---HHHHHHTTCSSCSHH--HHHHHCSSSC---CC-HHHHTTTTTTTTTCCEECCCSSCCSGGGSCEEBCCCB
T ss_pred -----HH---HHHHHHCCCCCHHHH--HHHHHHHCCC---CC-CCCCEEEEEECCCCEEEEECCCCCCCCCCCCEEEEEC
T ss_conf -----99---999998398320466--6665440123---47-7642257873049678981686423145421168965
Q ss_pred CCCEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEECHHHHHHHHHHH-CC-----
Q ss_conf 798144225677989886674600035678798899999971353322447999944751113455787630-35-----
Q 000882 368 DDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KK----- 441 (1238)
Q Consensus 368 ~~~tirln~~vC~pyNADFDGDeMniH~PQs~eAraEa~~Lm~~~~~ilsP~~G~PiigliQD~llg~~llt-kd----- 441 (1238)
+++||||||+||+||||||||||||+|+|||++|||||++||++++||+||++|+|+++++||+|+|+|+|| ++
T Consensus 462 ~~ktirlhp~vC~~yNADFDGDeMnvHvPqs~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~LT~~~~~~~~ 541 (1265)
T 1hqm_D 462 EGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKG 541 (1265)
T ss_dssp SSSSEEECGGGHHHHCCCSSSCBCCCCCCCSTHHHHTTSSSSBSSSSSSSCSSSSCSSCCCTTHHHHHHHTTCCCCCCCC
T ss_pred CCCEEEECHHHCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHCCCCCEECCCCCCEEEEEECCCCCEEEEECCCCCCCCC
T ss_conf 89748736432687677754305789647988999999998375104843889981476401233205883121677667
Q ss_pred ---CCCCHHHHHHHHCCCCCCCCCCCCCCCC---------------------------------------CCCCCCHHHH
Q ss_conf ---6679999998710235565632320332---------------------------------------4554310000
Q 000882 442 ---YFLDKAFTQQLAMFALSPLPRPALSKAR---------------------------------------CSARWTALQI 479 (1238)
Q Consensus 442 ---~fl~~~~~~ql~~~~~~~lp~PaIlKp~---------------------------------------~~~lWTGKQi 479 (1238)
+|+++++++++.+.....+|.|..++|+ ...+|||||+
T Consensus 542 ~~~~F~~~~e~~~~~~~~~i~l~a~i~~~~~~~~~g~~k~~~t~P~k~I~~~~~g~~~~q~~~~~~~k~~~~~t~~Gr~i 621 (1265)
T 1hqm_D 542 AGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQDTVTTRYLGRRLETNPGRIL 621 (1265)
T ss_dssp CCCCSSCCTHHHHHTTSSCCSSCCCSSSCCSTTSSCCCCCTTTCSHHHHHHHHTTSSCSSSCCCCEESSSEECCCHHHHH
T ss_pred CCCCCCCHHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEECCCCCEE
T ss_conf 77501889999999977998989835970664344434444565222123234676133323201024453340688567
Q ss_pred CCCCCCCCCCCC--CCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCHHHHHHHHHHHHHHCC-CEEEC
Q ss_conf 234579985346--867999634236555556775323877999999852978999516334999999998248-33210
Q 000882 480 LQSVLPPGFDSC--GDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADG-FSVSL 556 (1238)
Q Consensus 480 ~S~~lP~~~~~~--~~~viI~~Gell~g~ldK~~lg~s~~~Li~~i~~~~G~~~a~~~L~~lq~L~~~~L~~~G-FSigi 556 (1238)
|+.++|..++.. .+.+. .+.|++||+++| +|||.++++||+++|+.|||.+++|+++|++++| ||||+
T Consensus 622 f~~~lp~~~~~~~~p~~~~-----~~ngvldKk~lG----~LI~~i~~~~G~~~a~~~ld~l~~l~~~~lt~~G~fSigi 692 (1265)
T 1hqm_D 622 FARIVGEAVGDEKVAQELI-----QMDVPQEKNSLK----DLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGIITIGI 692 (1265)
T ss_dssp HHHHHHHHTTCTTTTTTSS-----CCSSCCCSSHHH----HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHTTCCCCSS
T ss_pred EEEECCCCCCCCCCCCCCC-----EEEEEECHHHHH----HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf 7620354323457988786-----683054289999----9999999997999999999999999999998578825853
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH-------HCCCCCCCCCCCCHHH
Q ss_conf 76545989999999999999999986664--34889999999999999999999987-------1297431203210023
Q 000882 557 EDFSLSKAALWNIQKEIQALYSLLYHRMS--TQNELVDLQIENHIRHVKMLVAKFIL-------KSSTLGYLIDSKSDSA 627 (1238)
Q Consensus 557 ~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~--~~~~~le~~~~~~l~~~~~~i~~~~~-------~~n~l~~Mi~sGSKGS 627 (1238)
+|+++++++.+.+++..+++..+..++.. ...+..+..+..+|+++++.+++.++ +.|++++|+.||||||
T Consensus 693 ~D~~~~~~k~~~i~~a~~~v~~i~~~y~~g~lt~~e~~~~v~~~~~~~~d~~~~~~~~~l~~~~~~N~i~~Ma~SGAKGS 772 (1265)
T 1hqm_D 693 DDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFNNFEENYPFNPLYVMAQSGARGN 772 (1265)
T ss_dssp SSCCCCSTTTTHHHHHHHHHHHHHTTTTSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCSSSCTTTTTTTSSSCC
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCC
T ss_conf 10347878999999999999999999982998678999999999999999999999987441589886999977167768
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCEEEEECCCCCEEEECC
Q ss_conf 56687897410352146985444454211122233448899899987764001432335896630786235421011123
Q 000882 628 VSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSS 707 (1238)
Q Consensus 628 ~~Ni~Qi~g~lGqQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~~sF~~GL~P~EfFfH~magREGLiDtA 707 (1238)
++|++||+||+|||...+|+++ + ++|.|||++||+|+|||||||||||||+|||
T Consensus 773 ~~ni~Ql~g~~G~ma~~~G~~i--------------------~------~pI~ssF~eGLtp~EyFfhtmggReGLiDTA 826 (1265)
T 1hqm_D 773 PQQIRQLCGMRGLMQKPSGETF--------------------E------VPVRSSFREGLTVLEYFISSHGARKGGADTA 826 (1265)
T ss_dssp HHHHHHHSSCCCCCCCTTSCCC--------------------S------CCCCCCBTTBCTTCTHHHHHHHHTTHHHHHT
T ss_pred HHHHHHHHHHCCCCCCCCCCCC--------------------C------CCCCCCCCCCCCHHHHHEECCCCCCCCHHHH
T ss_conf 9899999860464026899746--------------------8------6212523358985785301311236503322
Q ss_pred CCCCCCCCHHHHHHHHHHEEEEEECCEEE--C-----------------------------------C------------
Q ss_conf 44479884027899987406897410474--3-----------------------------------5------------
Q 000882 708 RGLSEPGTLFKNLMAVLRDVVICYDGTVR--N-----------------------------------V------------ 738 (1238)
Q Consensus 708 vkTa~sGyL~R~L~~~l~d~~v~yd~Tvr--~-----------------------------------~------------ 738 (1238)
||||+|||||||||+++||++|+||++.- + +
T Consensus 827 vKTA~SGYLqRRLVkv~qDv~V~~ddc~t~dGi~v~~~~~~~~i~~~~~~~~~~L~~ri~gr~~~~~i~~~~~~p~~~~~ 906 (1265)
T 1hqm_D 827 LRTADSGYLTRKLVDVAHEIVVREADCGTTKYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREVEALGRRLEEGRY 906 (1265)
T ss_dssp HHHHTSSSTHHHHHHHSCSCCCCSCCCCCCCCEECCSEECCSTTCCCEECCTTTTHHHHTTCEESSCEEETTEEECSSCB
T ss_pred HHCCCCCCCEEEEEEECCEEEEEECCCCCCCCEEEEEEECCCEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCE
T ss_conf 00166885113445340517999789899799898985168344003320136899999766522033101469887657
Q ss_pred ------------------------------CCCCEEEEEEECCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHCCCC--
Q ss_conf ------------------------------788502236101445446767899706652112379067886316699--
Q 000882 739 ------------------------------CSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-- 786 (1238)
Q Consensus 739 ------------------------------~~~~IiQf~yg~~g~~~~~l~~~Ge~VG~laaqsigepa~q~~L~t~~-- 786 (1238)
+...+|+.|||++. ..+.+++|||+||++||||||||+|||||+||+
T Consensus 907 i~~~~~~i~~~~i~~~gi~~v~iRs~ltc~s~~gvc~~CYgr~L-a~~~lV~~GEaVGiIAAQSIGEPGTQlTLrTFH~g 985 (1265)
T 1hqm_D 907 LSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDL-SMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTG 985 (1265)
T ss_dssp CCTTHHHHHHHHHHTTSCSSCEEECGGGCSCTTSCCSSSSCSCS-SSSSCCCTTCCHHHHHHHHHHGGGTTSCCCC----
T ss_pred EECCCCHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHH-CCCCEECCCCEEEEEECCCCCCCCCEEEEEEEEEC
T ss_conf 85685040699999759987876367678779999999854121-05987016861455401122788742566778885
Q ss_pred ------CCCCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCEECHHHHHHEEEEEECCCC
Q ss_conf ------98880678999987311379999884189972788878764327999999862201026444311368842886
Q 000882 787 ------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPE 860 (1238)
Q Consensus 787 ------~~~~g~~rlkEil~~~~~~k~~~~~~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~v~l~~i~~~i~i~y~~~~ 860 (1238)
++|+|+||++|++++++ |++|.|+..++..... .++ ++ ..+ +.|. ...
T Consensus 986 Gvas~~dIT~GLPRv~El~eArk-----pk~p~i~a~~~g~v~~---~~~------~~-~~~---------i~i~--~~g 1039 (1265)
T 1hqm_D 986 GVAVGTDITQGLPRVIELFEARR-----PKAKAVISEIDGVVRI---EEG------ED-RLS---------VFVE--SEG 1039 (1265)
T ss_dssp ----CCTTSSHHHHHHHHHHCCC-----CSSCBCCCSSSCBCCC---CCC------SS-CCC---------CCCB--CSS
T ss_pred CEECCCCCCCCCHHHHHHHHHCC-----CCCCEEEEECCCEEEE---EEC------CC-CCE---------EEEE--ECC
T ss_conf 44000233457432898875107-----8986279841654998---304------88-517---------9998--789
Q ss_pred CCCCCCCEEEEEEECHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCC---CCC
Q ss_conf 44579960899991388886319997547999998544343101238998762033120144233345211458---994
Q 000882 861 IISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKR---SNM 937 (1238)
Q Consensus 861 ~~~~~~~~v~~i~Ld~~~L~~~~lt~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~g~~~~~~~~~~~~---~~~ 937 (1238)
.+| .+. + +...+..++.. ...
T Consensus 1040 -----~~~------------~~~----------------------------------i-----p~~~~l~v~~g~~v~~g 1063 (1265)
T 1hqm_D 1040 -----FSK------------EYK----------------------------------L-----PKDARLLVKDGDYVEAG 1063 (1265)
T ss_dssp -----CCC------------CCC----------------------------------C-----SSCCCCCCCSCCSSTTC
T ss_pred -----CEE------------EEE----------------------------------C-----CCCEEEEEECCCEEECC
T ss_conf -----277------------997----------------------------------4-----78528998469777068
Q ss_pred CEEEEEEEECCCCCCCCCHHHCCCCHHHHHHHHHHCHHHHHHHH----HHHHHHHHHCCCCCCCEEEECCCCCC------
Q ss_conf 56999982047765432000002311468787454011899999----99999666125541100122155101------
Q 000882 938 PCLMFVLRGASDSYLDKLSGVLANMIYPVLLETIIKENWWVRQR----LSASVTMVAKGVLKEHLILLANSMTC------ 1007 (1238)
Q Consensus 938 ~~l~~~~~~~~~~~~vd~~~t~sn~I~ei~r~tiIkGiew~R~~----l~~~~~~~~~~v~~rHl~Llad~MT~------ 1007 (1238)
..+ ++| ++++++|+ -++|++++|+. ++.++..||..|+++|++++++.||.
T Consensus 1064 ~~l---teG-------------~~~~~eil---~v~Giea~~~~lv~EIq~vyr~QGv~I~dkHievivrqM~~kv~i~~ 1124 (1265)
T 1hqm_D 1064 QPL---TRG-------------AIDPHQLL---EAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTD 1124 (1265)
T ss_dssp SCC---CCS-------------BSHHHHHH---HTTHHHHHHHHHHHHHHHHHHTTSCCCCSSTHHHHHHHHTTEECBSS
T ss_pred CEE---ECC-------------CCCHHHHH---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCEEEEC
T ss_conf 035---226-------------75199999---98639999999999999998974862037899999998742537714
Q ss_pred ----------------------------------CCEEEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHCCC
Q ss_conf ----------------------------------3307653243212334463323451021014808999999721398
Q 000882 1008 ----------------------------------AGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHT 1053 (1238)
Q Consensus 1008 ----------------------------------~G~~~~~~r~G~~~~~~s~l~~a~Fe~~~~~t~~~~l~~Aa~~g~~ 1053 (1238)
.+.+.||||.+++ .+|+++.||||| |+ ++|.+||.+|++
T Consensus 1125 ~g~t~~l~Ge~v~~~~~~~~n~~~~~~g~~~~~~~~~llGITkasl~--t~SflsaASFqe----Tt-~vL~~AAi~gk~ 1197 (1265)
T 1hqm_D 1125 PGDSPLLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALS--TKSWLSAASFQN----TT-HVLTEAAIAGKK 1197 (1265)
T ss_dssp CCSSCCSCCCEEGGGTTTTTTTTTTC---CCCCBCCCCCCTHHHHTS--CSCHHHHTTSTT----HH-HHHHHHHHSCCC
T ss_pred CCCCCCCCCCEECHHHHHHHHHHHHHCCCCCCEEEEEEECCEECCCC--CCCHHHCCCHHH----HH-HHHHHHHHCCCC
T ss_conf 88867889866509999999999996689852554556520522334--677443055688----89-999999972898
Q ss_pred CCCCCCCCHHCCCCCCCCCCCC
Q ss_conf 7788520110048756654565
Q 000882 1054 DNLSSVVAACSWGKHVAVGTGS 1075 (1238)
Q Consensus 1054 D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1238)
|.|.|+.||||+|+++|+|||.
T Consensus 1198 D~L~GlkEnVIiG~lipaGTG~ 1219 (1265)
T 1hqm_D 1198 DELIGLKENVILGRLIPAGTGS 1219 (1265)
T ss_dssp CTTCSSHHHHHHTCCCSSGGGC
T ss_pred CCCCCCHHHEEECCCCCCCCCC
T ss_conf 7689927763317865687581
No 5
>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=1452.06 Aligned_cols=782 Identities=18% Similarity=0.208 Sum_probs=596.4
Q ss_pred CCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99998568984126999888863138975445202699999999999999950-06999963134446579999999973
Q 000882 137 YFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLE 215 (1238)
Q Consensus 137 ~~ppe~lIL~~lpVPP~~iRp~~~~~g~~~~~~Dlt~~~l~~Ii~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~ 215 (1238)
..+|+||||++||||||++||++.++|..+.++|+|. +|++||++|++|++. ..++|..+. .++|.+||.+|++|+|
T Consensus 506 ~~rPewmil~vlPVpPp~lRP~v~ldgg~~~~sDLn~-ly~~II~~Nn~Lk~~~~~gap~~ii-~~e~~~LQ~~V~~liD 583 (1524)
T 2a6h_D 506 GNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLND-LYRRLINRNNRLKKLLAQGAPEIII-RNEKRMLQEAVDALLD 583 (1524)
T ss_dssp SCCTTTTEEEEEEECCSTTSCEEECSTTCEEECTHHH-HHHHHHHHHHHHHHHHHHCCCHHHH-HHHHHHHHHHHHHHHC
T ss_pred CCCCCEEEEECCCCCCCCCCCCEECCCCCEECCHHHH-HHHHHHHHHHHHHHHHHHCCHHHHH-HHHHHHHHHHHHHHHC
T ss_conf 8875378883266899977886661898266662789-9999999989999998732507789-9999999999999965
Q ss_pred CCCCCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHCCCCCCCCCCHH
Q ss_conf 02976667775567788-89999301455532100113468797765167289996533344626621114434432244
Q 000882 216 VRGTAKSSRDVDARFGV-SQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVH 294 (1238)
Q Consensus 216 ~~~~~k~~~~~~~~~~~-~k~~~~~~k~~~~~~r~~l~gKRvdfs~RsVI~pDP~l~i~evgiP~~~A~~Lt~pe~Vt~~ 294 (1238)
+....++......| . .|.+.+.+|||.||||+|||||||||||||||||||+|++||||||..||++||+|+
T Consensus 584 N~~~g~p~~~~~~R--p~lKslsq~LkGKeGRFRqNLlGKRVDySgRSVI~pdP~L~l~evGvP~~mA~eLt~Pf----- 656 (1524)
T 2a6h_D 584 NGRRGAPVTNPGSD--RPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPF----- 656 (1524)
T ss_dssp SSSSSCCBCSSSCC--CBCCCHHHHHSTTTCHHHHHHHCEEESSEEEEEEEECTTSCTTEEEEEHHHHHHHTHHH-----
T ss_pred CCCCCCCCCCCCCC--CCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCHHHHHHHCCHH-----
T ss_conf 78878876688888--76764444303545410004443113666752472698750551378099999856599-----
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCEEEE-CCCCCCCCCCCCCCEEEEEEECCCEEEEECCCCCCCCCCCCEEEEECCCCEEE
Q ss_conf 39999999981786414799952881-36998864456864442003215738661799877465320179965798144
Q 000882 295 NINYLQELVDNKLCLTYSDGSSSYSL-REGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVK 373 (1238)
Q Consensus 295 Ni~~l~~lv~ng~~~~~~~~~~~~~l-~~~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~i~~~~tir 373 (1238)
.|++||.||+...++. +++.+ ++.. ..+ .+|.|+||++|||+|||||||||||||||||+|++++++|||
T Consensus 657 ---~~r~Lv~nG~a~nik~--AK~li~~~~~---~~~-~v~dVlr~vidgd~VLlNRqPTLHRlSIqAf~~kl~~gkTiR 727 (1524)
T 2a6h_D 657 ---LLKKMEEKGIAPNVKA--ARRMLERQRD---IKD-EVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQ 727 (1524)
T ss_dssp ---HHHHHHHSTTCSSHHH--HHHHHSSGGG---CCH-HHHHHHHHHSTTCCEEEECSSCCSGGGEEEEEEEEESSSCEE
T ss_pred ---HHHHHHHCCCCCCHHH--HHHHHHHHCC---CCC-CCHHHHEEECCCCEEEECCCCCCCCCCCCEEEEEECCCCCCE
T ss_conf ---9999998398342266--6678764113---465-301220100059667870587434256402688975785101
Q ss_pred ECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEECHHHHHHHHHHHC---------CCCC
Q ss_conf 2256779898866746000356787988999999713533224479999447511134557876303---------5667
Q 000882 374 INPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMFK---------KYFL 444 (1238)
Q Consensus 374 ln~~vC~pyNADFDGDeMniH~PQs~eAraEa~~Lm~~~~~ilsP~~G~PiigliQD~llg~~lltk---------d~fl 444 (1238)
|||+||+||||||||||||+|+|||++|||||++||++++||+||++|+|+++++||+|+|+|+||+ ++|+
T Consensus 728 LhplVC~pyNADFDGDEMnvHvPqS~eAraEA~~LM~~~~nilsP~~G~Pi~~~~QD~vlG~y~LT~~~~~~~~~g~~F~ 807 (1524)
T 2a6h_D 728 LHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFA 807 (1524)
T ss_dssp ECSGGGTTTTCCTTTCEEEEECCCSHHHHHHHHHHSBTTTCCBCSSSSSBSSCCCHHHHHHHHHHHCCCCCCCCSCCCTT
T ss_pred ECHHHCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHCCCCCEECCCCCCEEEEECCCCHHHHEECCCCCCCCCCCCCEEC
T ss_conf 47232577667756533567627878899999998477144613899981462133002320334124656667786558
Q ss_pred CHHHHHHHHCC------CCCCC--------------CCC--CCCCCCCCCCCCHHHHCCCC----CCC-CCCCCCCEEEE
Q ss_conf 99999987102------35565--------------632--32033245543100002345----799-85346867999
Q 000882 445 DKAFTQQLAMF------ALSPL--------------PRP--ALSKARCSARWTALQILQSV----LPP-GFDSCGDRYLI 497 (1238)
Q Consensus 445 ~~~~~~ql~~~------~~~~l--------------p~P--aIlKp~~~~lWTGKQi~S~~----lP~-~~~~~~~~viI 497 (1238)
++++++.+.+. ....+ |+| ||+|| |||||+++.+ ++. .+.++.|+.++
T Consensus 808 ~~~e~~~ay~~~~~~l~~~i~v~~~~~~~~~~~~~~p~P~~aIlKp-----wtGKQi~~~~~~~~I~~~~~~tt~Gr~if 882 (1524)
T 2a6h_D 808 TPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAV-----AHGIVDLQDVVTVRYMGKRLETSPGRILF 882 (1524)
T ss_dssp SCHHHHHHHHHHHHTTSSCSSCCCSSCCHHHHHCEESSHHHHHHHH-----HTTSSCTTSCCEEECSSCEECCCHHHHHH
T ss_pred CHHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHCCC-----CCCCCCCCCCCCCCEECCEEECCCCHHHH
T ss_conf 8999999986588676872598424344433234467855641589-----88741465432111000102216654319
Q ss_pred E--------------CCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCHHHHHHHHHHHHHHCCCEEECCCCCCCH
Q ss_conf 6--------------34236555556775323877999999852978999516334999999998248332107654598
Q 000882 498 K--------------KSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSK 563 (1238)
Q Consensus 498 ~--------------~Gell~g~ldK~~lg~s~~~Li~~i~~~~G~~~a~~~L~~lq~L~~~~L~~~GFSigi~Dl~~~~ 563 (1238)
. +...+.|++||+++| +|||.++++||++.|+.|||++++|+++|++++|||||++|+++++
T Consensus 883 n~~lp~~l~~~~~P~d~~~inGvLdKk~LG----~LI~~i~~~yG~~~t~~fLD~lk~Lg~~~lt~~GfSIGI~Dlii~~ 958 (1524)
T 2a6h_D 883 ARIVAEAVEDEKVAWELIQLDVPQEKNSLK----DLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPE 958 (1524)
T ss_dssp HHHHHHHSSCHHHHHHTCCTTSCCCHHHHH----HHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHTCCCCSTTSCCCT
T ss_pred HHHHHHHCCCCCCCCCCCCEECEECHHHHH----HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCEEEHHHCCCCH
T ss_conf 988566504566898666220336389999----9999999985999999999999999999998668142053325777
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHH-------HCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 99999999999999999866643--4889999999999999999999987-------12974312032100235668789
Q 000882 564 AALWNIQKEIQALYSLLYHRMST--QNELVDLQIENHIRHVKMLVAKFIL-------KSSTLGYLIDSKSDSAVSKVVQQ 634 (1238)
Q Consensus 564 ~~~~~i~~~i~~~~~~~~~~~~~--~~~~le~~~~~~l~~~~~~i~~~~~-------~~n~l~~Mi~sGSKGS~~Ni~Qi 634 (1238)
++.+.+++..+++..+..++... ..+..+..+..+|+++++.+++.++ +.|++++|+.||||||++|++||
T Consensus 959 ~K~eiI~eA~~~v~~i~~~y~~G~lt~~Er~~~Vi~iw~~a~d~v~~~~~~~L~~~~~~N~i~~Ma~SGAKGS~~NI~Ql 1038 (1524)
T 2a6h_D 959 EKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQL 1038 (1524)
T ss_dssp THHHHHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHSSSSCCHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCHHHHHHH
T ss_conf 79999999999999999999839997799999999999999999999999740415898879999871677579899999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCC
Q ss_conf 74103521469854444542111222334488998999877640014323358966307862354210111234447988
Q 000882 635 AGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPG 714 (1238)
Q Consensus 635 ~g~lGqQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~~sF~~GL~P~EfFfH~magREGLiDtAvkTa~sG 714 (1238)
+||+|||...+|+++ ..| |.|||++||+|+|||||||||||||+|||||||+||
T Consensus 1039 ~gmrGqma~p~GkiI--------------------p~P------I~ssF~eGLtp~EyFfhtmGgReGLvDTAvKTAdSG 1092 (1524)
T 2a6h_D 1039 CGLRGLMQKPSGETF--------------------EVP------VRSSFREGLTVLEYFISSHGARKGGADTALRTADSG 1092 (1524)
T ss_dssp TSCCCCCBCSSSCBC--------------------SSC------CCCCSSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHCCCCCCCCCCCC--------------------CCC------CCCCCCCCCCHHHHHEECCCCCCCCCCCCEEECCCC
T ss_conf 860366046899772--------------------251------134324699747742012223577533201105688
Q ss_pred CHHHHHHHHHHEEEEEECCEE-------EC------------------------------C-------------------
Q ss_conf 402789998740689741047-------43------------------------------5-------------------
Q 000882 715 TLFKNLMAVLRDVVICYDGTV-------RN------------------------------V------------------- 738 (1238)
Q Consensus 715 yL~R~L~~~l~d~~v~yd~Tv-------r~------------------------------~------------------- 738 (1238)
|||||||+++||++|+||.+. .. +
T Consensus 1093 YLqRRLVkv~qDviVr~dDcgt~dGi~v~~~~~g~~~~~~~~~~i~~l~~ri~gR~~~~di~~~~~~p~~~e~i~~~~~~ 1172 (1524)
T 2a6h_D 1093 YLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVH 1172 (1524)
T ss_dssp HHHHHHHHHHTTCCBCCSCCCCCCCEEEESBCSCSSSSCCCBCCHHHHHHHHTTCBBSSCEECSSCEECTTCBCCTTTTT
T ss_pred CCEEEEEEECCEEEEEECCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCEEECCCCE
T ss_conf 40342211006069996788997986888863078666520688898998774331134455412588767678679986
Q ss_pred -----------------------CCCCEEEEEEECCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHCCCC--------C
Q ss_conf -----------------------788502236101445446767899706652112379067886316699--------9
Q 000882 739 -----------------------CSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP--------S 787 (1238)
Q Consensus 739 -----------------------~~~~IiQf~yg~~g~~~~~l~~~Ge~VG~laaqsigepa~q~~L~t~~--------~ 787 (1238)
+...+|+.|||.+. ....++++||+||++||||||||+|||||+||+ +
T Consensus 1173 I~~~~i~~~gi~~v~iRS~ltC~s~~gvc~~CYgr~L-a~~~~v~~GeaVGiiaAQSIGEPgTQlTlrTFH~gGv~~~~d 1251 (1524)
T 2a6h_D 1173 LLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDL-SMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAAD 1251 (1524)
T ss_dssp HHHHHHHHTSCSEEEECCGGGCCCSSCBCHHHHCSCS-SSSSSCCTTCCHHHHHHHHHHSGGGTCCCC-----------C
T ss_pred EHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCC-CCCCCCCCCCCEEEHHHHCCCCCCCCCCCEEEEECCCCCCCC
T ss_conf 5189999719983244365558889999999845331-039740344101021332037875432100045335234333
Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCC-EEEEECCCCCCCCCCCCHHHHHHHHHHHCEECHHHHHHEEEEEECCCCCCCCCC
Q ss_conf 8880678999987311379999884-189972788878764327999999862201026444311368842886445799
Q 000882 788 SNNSWELMKEILLCRVSFNNDPIDR-RVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDE 866 (1238)
Q Consensus 788 ~~~g~~rlkEil~~~~~~k~~~~~~-~~~l~L~~~~~~~~~~~e~~a~~V~~~le~v~l~~i~~~i~i~y~~~~~~~~~~ 866 (1238)
+|+|+||++|++++++...+..... ...+.+.+ .....
T Consensus 1252 It~GlPRv~El~eARkpk~~aiI~ei~G~V~i~~------------------------------------~~~~r----- 1290 (1524)
T 2a6h_D 1252 ITQGLPRVIELFEARRPKAKAVISEIDGVVRIEE------------------------------------TEEKL----- 1290 (1524)
T ss_dssp CCCSHHHHHHHHTTCCCSSBCCBCSSCEEEEECC------------------------------------CSSCE-----
T ss_pred CCCCCCCHHHHEECCCCCCCCEEEEECEEEEEEE------------------------------------CCCCE-----
T ss_conf 2346722455400124788626998310899953------------------------------------17832-----
Q ss_pred CEEEEEEECHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCCEEEEEEEE
Q ss_conf 60899991388886319997547999998544343101238998762033120144233345211458994569999820
Q 000882 867 GLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMFVLRG 946 (1238)
Q Consensus 867 ~~v~~i~Ld~~~L~~~~lt~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~g~~~~~~~~~~~~~~~~~l~~~~~~ 946 (1238)
.+.|.-+. .. ..+ .++...+..++. ++ .+ ..|
T Consensus 1291 --~i~i~~~~---~~----------------~~~---------------------~ip~~~~l~V~~-gd--~v---~~g 1322 (1524)
T 2a6h_D 1291 --SVFVESEG---FS----------------KEY---------------------KLPKEARLLVKD-GD--YV---EAG 1322 (1524)
T ss_dssp --EEEEECSS---CE----------------EEE---------------------EECTTCCCCCCT-TS--EE---CTT
T ss_pred --EEEEECCC---CE----------------EEE---------------------ECCCCEEEEEEC-CC--EE---ECC
T ss_conf --89997088---40----------------478---------------------647760789836-97--56---437
Q ss_pred CCCCCCCCCHHHCCCCHHHHHHHHHHCHHHHHHHH----HHHHHHHHHCCCCCCCEEEECCCCCC---------------
Q ss_conf 47765432000002311468787454011899999----99999666125541100122155101---------------
Q 000882 947 ASDSYLDKLSGVLANMIYPVLLETIIKENWWVRQR----LSASVTMVAKGVLKEHLILLANSMTC--------------- 1007 (1238)
Q Consensus 947 ~~~~~~vd~~~t~sn~I~ei~r~tiIkGiew~R~~----l~~~~~~~~~~v~~rHl~Llad~MT~--------------- 1007 (1238)
..-++| ++++++|+ -|+|++++|+. ++.++..||..|+++|+++++|.||.
T Consensus 1323 ~~lteG-------~~~~~dil---~v~Giea~~~~iv~Eiq~Vyr~QGv~I~dKHIevIvrqM~~kv~i~~~Gdt~~l~G 1392 (1524)
T 2a6h_D 1323 QPLTRG-------AIDPHQLL---EAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEG 1392 (1524)
T ss_dssp CBSSSS-------BCCHHHHH---HHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTSEEEEEECSSSCSSCE
T ss_pred EEEECC-------CCCCHHHE---EECCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCEEEEECCCCCCCCCC
T ss_conf 277448-------78742210---10699999999999999999855855135689999998744258824887667898
Q ss_pred -------------------------CCEEEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHCCCCCCCCCCCH
Q ss_conf -------------------------3307653243212334463323451021014808999999721398778852011
Q 000882 1008 -------------------------AGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAA 1062 (1238)
Q Consensus 1008 -------------------------~G~~~~~~r~G~~~~~~s~l~~a~Fe~~~~~t~~~~l~~Aa~~g~~D~l~gv~~~ 1062 (1238)
.+.+.||||++++ ..|+++.||||+ |+ ++|.+||.+|++|.|.|+.||
T Consensus 1393 e~v~~~~~~~~n~~~~~~g~~~a~~~~~llGITkasL~--t~SfLsaASFqe----Tt-rvLt~AAi~Gk~D~L~GlkEN 1465 (1524)
T 2a6h_D 1393 QVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALS--TKSWLSAASFQN----TT-HVLTEAAIAGKKDELIGLKEN 1465 (1524)
T ss_dssp EEHHHHHHHHHHHHTTSCSCCCCEEEECCCCHHHHHHS--CSCHHHHHHSSC----HH-HHHHHHHHTTEEEECCSHHHH
T ss_pred CEEEHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCC--CCCHHHHCCHHH----HH-HHHHHHHHCCCCCCCCCCHHH
T ss_conf 65419999999999997689852210035420531334--687233157488----89-999999863898778982787
Q ss_pred HCCCCCCCCCCCCEEEE
Q ss_conf 00487566545650799
Q 000882 1063 CSWGKHVAVGTGSRFDL 1079 (1238)
Q Consensus 1063 ii~Gk~~~~GTG~~f~l 1079 (1238)
||+|+++|+|||. +++
T Consensus 1466 VIiG~lIPaGTG~-~~~ 1481 (1524)
T 2a6h_D 1466 VILGRLIPAGTGS-DFV 1481 (1524)
T ss_dssp HHTTCCCSSSTTC-TTT
T ss_pred EEECCCCCCCCCC-HHH
T ss_conf 1116875678686-101
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=1422.15 Aligned_cols=984 Identities=19% Similarity=0.235 Sum_probs=668.2
Q ss_pred CCCCCCCEEEEECCCHHHHHHCCCCCCCCCCC------------CCCCCCCC-CCCC--------------CCCCCCCCC
Q ss_conf 44543005898349969998605455212578------------88889988-9999--------------998889989
Q 000882 9 ILEGQIVGIRFGLATQKEICTASISDCSISHA------------SQLANPFL-GLPL--------------EFGKCESCG 61 (1238)
Q Consensus 9 ~~~~~I~~I~F~l~S~eeI~~~Sv~~~~i~~~------------~gl~Dprl-G~~~--------------~~~~C~TCg 61 (1238)
.....+..|++++.||++|++||+.+ |++| +||+|+|. |+.. ++..|++||
T Consensus 12 ~~~~~~~~i~i~laSpe~I~~ws~GE--V~kpetinyrt~kPe~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~C~~Cg 89 (1407)
T 3lu0_D 12 TKTEEFDAIKIALASPDMIRSWSFGE--VKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCG 89 (1407)
T ss_dssp --CCCCCCEEECCCCHHHHHHHBCSC--CCSCCCCCSSCCSCCSSSSSCTTTTCCSSSSCCSSCSCCSTTCSSSCCSSSC
T ss_pred CCCCCCCEEEEEECCHHHHHHHCCEE--ECCCCCCCCCCCCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCCCCCCCC
T ss_conf 66676563999967989998536827--8780200267788778971242323877684796753135166887778878
Q ss_pred CCCCCCCC---CCCEEEECCCCCCCCCCHHHH----HHHHHHHCCCC------C-----CC-------------------
Q ss_conf 99999788---853258757611245473889----99997530134------6-----70-------------------
Q 000882 62 TSEPGKCE---GHFGYIELPIPIYHPSHISEL----KLTMYAFQLQI------K-----ND------------------- 104 (1238)
Q Consensus 62 ~~~~~~Cp---GHFGhIeL~~PVfHp~f~~~i----~~IL~~iCl~i------~-----~~------------------- 104 (1238)
... .+|. .|||||+|+.||.|++||+.+ ..+|.+.|..| . ..
T Consensus 90 vev-t~~~vRr~rmGhI~La~PV~Hiwy~k~~ps~i~~lL~~~~k~le~viy~~~~iv~~~~~~~l~~~~~~~~~~~~~~ 168 (1407)
T 3lu0_D 90 VEV-TQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDA 168 (1407)
T ss_dssp CCC-CCTTHHHHCBCEEEEEEEECCTHHHHSSSCTTTTTTTSCSSTTHHHHSSSCCCEECCSSSCSCSSCCCCSTTCCCC
T ss_pred CCC-CCCCCHHHHCCEEEECCCEEEEEECCCCCHHHHHHHCCCHHHHHHHEECCEEEEECCCCCCCCHHCCCCHHHHHHH
T ss_conf 765-6572113204434104861676313688369999839988886450021105865688775203034689999999
Q ss_pred ------------H--HHHHHHHHH-----H-HHHHHHCCC-CHHHHHHHC---------CCCCCCCCCEEEEEECCCCCC
Q ss_conf ------------1--799999768-----6-999997169-945898712---------599999985689841269998
Q 000882 105 ------------G--VAQRLLSSC-----C-EVKEMLKRI-PEETRKKLA---------GKGYFPQDGYILEYLPVPPNC 154 (1238)
Q Consensus 105 ------------g--~~~~i~~~C-----C-ev~~IlkkI-pded~~~L~---------~~g~~ppe~lIL~~lpVPP~~ 154 (1238)
| ..+++++.. + +..+.++.. +.....++. .....+||||||++||||||+
T Consensus 169 ~~~~~~~~~~~~Gaeai~~lL~~~dl~~~~~~l~~~~~~~~~~~k~~~~~krl~~v~~F~~s~~rPewmil~~lPVpPp~ 248 (1407)
T 3lu0_D 169 LEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPD 248 (1407)
T ss_dssp CSSSCCCCCEECSSHHHHHHHHTCCHHHHHHTHHHHHHHCCCTTTTTTTTTSSTTHHHHHSSSCCGGGSSEEEEECCCST
T ss_pred HHHHCHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHEEECCCCC
T ss_conf 87613233024258999999985677999999999998661078899998899999999856998898664256259987
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 88863138975445202699999999999999950-06999963134446579999999973029766677755677888
Q 000882 155 LSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVS 233 (1238)
Q Consensus 155 iRp~~~~~g~~~~~~Dlt~~~l~~Ii~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~~~~k~~~~~~~~~~~~ 233 (1238)
+||++..++..+.++|+|. +|++||++|++|++. ..++|..+. .++|.+||.+|++|+|+....++...... ...
T Consensus 249 lRP~v~l~gg~~~~~DLn~-ly~~II~~N~~Lk~~~~~~ap~~ii-~~~~~~LQ~~V~~l~Dn~~~g~~~~~~~~--rpl 324 (1407)
T 3lu0_D 249 LRPLVPLDGGRFATSDLND-LYRRVINRNNRLKRLLDLAAPDIIV-RNEKRMLQEAVDALLDNGRRGRAITGSNK--RPL 324 (1407)
T ss_dssp TSCCCBCSTTCBCCCTTTT-THHHHHHTTTTTGGGTSSCCCTTTH-HHHHHHHHHHHHHHHCSSSSCCCCBTTBC--CCC
T ss_pred CCCCEEECCCCCCCCCHHH-HHHHHHHHHHHHHHHHHCCCCHHHH-HHHHHHHHHHHHHHCCCCCCCCCCCCCCC--CCC
T ss_conf 7882796898545685678-9999999899999998749958899-99999999988876277877876547789--856
Q ss_pred CCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 99993014555321001134687977651672899965333446266211144344322443999999998178641479
Q 000882 234 QDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSD 313 (1238)
Q Consensus 234 k~~~~~~k~~~~~~r~~l~gKRvdfs~RsVI~pDP~l~i~evgiP~~~A~~Lt~pe~Vt~~Ni~~l~~lv~ng~~~~~~~ 313 (1238)
|.+.+++|||.||||+|||||||||||||||||||+|++||||||..||++||+| ||+++|+ .+|....++.
T Consensus 325 ksl~qrLkGKeGrfR~NLmGKRVDfSaRSVIspdP~L~i~evGvP~~~A~~L~~P-----f~i~~L~---~~g~~~~i~~ 396 (1407)
T 3lu0_D 325 KSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKP-----FIYGKLE---LRGLATTIKA 396 (1407)
T ss_dssp CCTTHHHHTSSSTHHHHTTCCCCSSBCEEEEEECSSCCTTEEEEESHHHHHHTCH-----HHHHHHT---TSSSCSSTTT
T ss_pred CCHHHHHCCCCCHHHCCCCCCCCCCCCCEEEECCCCCCCEEEECCHHHHHHHCCH-----HHHHHHH---HCCCCCCHHH
T ss_conf 4367774444301222446677787671488379986320542789999874526-----7799998---7386023788
Q ss_pred CCCEEEECCCCCCCCCCCCCCEEEEEEECCCEEEEECCCCCCCCCCCCEEEEECCCCEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf 99528813699886445686444200321573866179987746532017996579814422567798988667460003
Q 000882 314 GSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHL 393 (1238)
Q Consensus 314 ~~~~~~l~~~~~~~~~L~~g~iV~Rhl~dgD~VL~NRqPSLHr~Simah~v~i~~~~tirln~~vC~pyNADFDGDeMni 393 (1238)
.. ++ +. ... ...|.|+||++|||+|||||||||||+|||||++++++++||||||+||+||||||||||||+
T Consensus 397 ak-~~-v~-----~~~-~~v~~vl~~vi~gd~VLlNRqPTLHr~sIma~~~~l~~~ktirlnp~vC~~yNADFDGDeMnv 468 (1407)
T 3lu0_D 397 AK-KM-VE-----REE-AVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAV 468 (1407)
T ss_dssp TT-TT-TT-----SSC-SSHHHHHHTTTTSCCEEEEESSCCSGGGEEEEEEEEESSSSEEECTGGGGTTTCCSSSCEEEE
T ss_pred HH-HH-HH-----HCC-CCHHHHHHHHHHCEEEEECCCCCCCCCCCEEEEEEECCCCEEEECHHHCCCCCCCCCCCEEEE
T ss_conf 99-98-87-----518-833568998753425665488631224432446786489658867656443457734423554
Q ss_pred CCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEECHHHHHHHHHHH-CCC--------CCCHHHHHHHHCCCC------C
Q ss_conf 5678798899999971353322447999944751113455787630-356--------679999998710235------5
Q 000882 394 FYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKY--------FLDKAFTQQLAMFAL------S 458 (1238)
Q Consensus 394 H~PQs~eAraEa~~Lm~~~~~ilsP~~G~PiigliQD~llg~~llt-kd~--------fl~~~~~~ql~~~~~------~ 458 (1238)
|+|||++|||||++||++++||+||++|+|+++++||+++|+|+|| ++. |.+.++++++..... +
T Consensus 469 HvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~lT~~~~~~~~~~~~F~~~~ev~~al~~g~v~l~a~i 548 (1407)
T 3lu0_D 469 HVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARV 548 (1407)
T ss_dssp ECCCSSHHHHTTTTSSBTTTCCSCSSSSSCSSCCCSHHHHHHHHHSCCCCCSCCSCCCCSSCSHHHHHHHHSSSSSSSCS
T ss_pred ECCCCHHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCHHEEEEEECCCCCCCCCCCEECCHHHHHHHHHCCCCCCCCEE
T ss_conf 23789999999999971702323488998225001300111577522465666776223889999999975998889725
Q ss_pred CCCCC-----------CCCCCCCCCCCCHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 65632-----------3203324554310000234579985346867999634236555556775323877999999852
Q 000882 459 PLPRP-----------ALSKARCSARWTALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEK 527 (1238)
Q Consensus 459 ~lp~P-----------aIlKp~~~~lWTGKQi~S~~lP~~~~~~~~~viI~~Gell~g~ldK~~lg~s~~~Li~~i~~~~ 527 (1238)
.+..| ...++. +.|||||+||.+||.++++ +++.|.++|+.+| +||+.++++|
T Consensus 549 ~vr~~~~~~~~~g~~~~~~~~~--~tt~Gr~ifs~ilP~~~~~----------~~ing~l~KK~lg----~LI~~i~~~~ 612 (1407)
T 3lu0_D 549 KVRITEYEKDANGELVAKTSLK--DTTVGRAILWMIVPKGLPY----------SIVNQALGKKAIS----KMLNTCYRIL 612 (1407)
T ss_dssp SSSCCCCSCSHHHHHHHTTTSC--CSSSHHHHHHHHGGGSSCC----------TTTTTCCSSSTTT----THHHHHHHHS
T ss_pred EEECCCCCCCCCCCCCCCCEEE--ECCCCCCCHHHHCCCCCCC----------EEEECCCCHHHHH----HHHHHHHHHH
T ss_conf 8865765547677524552356--5587500377549899980----------5663644511499----9999999985
Q ss_pred CHHHHHHCHHHHHHHHHHHHHHCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
Q ss_conf 978999516334999999998248332107654598999999999999999998666-------4348899999999999
Q 000882 528 GPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRM-------STQNELVDLQIENHIR 600 (1238)
Q Consensus 528 G~~~a~~~L~~lq~L~~~~L~~~GFSigi~Dl~~~~~~~~~i~~~i~~~~~~~~~~~-------~~~~~~le~~~~~~l~ 600 (1238)
|+++|..|||++++++++|++.+|||+|++|+.+|+++.+.+++..+++..+..++. +.|++.+ .+|+
T Consensus 613 G~~~t~~flD~lk~Lgf~~at~~GfSIgI~D~~ip~~K~~iI~~A~~eV~ei~~~y~~G~lt~~er~~kVi-----~iw~ 687 (1407)
T 3lu0_D 613 GLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVI-----DIWA 687 (1407)
T ss_dssp CSHHHHHHHHHHHHHHHHHHHHHTCCCCSTTSCCCTTHHHHHHHHHTHHHHHHHHHHHTSCCSSTTTTTHH-----HHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH-----HHHH
T ss_conf 99999999999999999999766847743327158679999999999999999999759986226899999-----9999
Q ss_pred HHHHHHHHHHHH-------------------CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 999999999871-------------------2974312032100235668789741035214698544445421112223
Q 000882 601 HVKMLVAKFILK-------------------SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHF 661 (1238)
Q Consensus 601 ~~~~~i~~~~~~-------------------~n~l~~Mi~sGSKGS~~Ni~Qi~g~lGqQ~~~g~r~~~r~l~~~~~~~f 661 (1238)
++++.+++.+++ .|++++|++||||||++|++||+||+|||....|+.+
T Consensus 688 ~a~e~v~~~m~~~l~~~~~~d~~G~~~~l~~~N~i~mMa~SGARGS~~qI~QLaGmrGlmakpdG~ii------------ 755 (1407)
T 3lu0_D 688 AANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSII------------ 755 (1407)
T ss_dssp THHHHHHHHHHTTHHHH------------CSCCHHHHHHHSSSSCCTTHHHHHSSCCCCCBCSSSCBC------------
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHEEEECCCCCCHHHHHHHHHHCCCCCCCCCCCC------------
T ss_conf 99999999999860213222334642236789886205400146799999999871287338998874------------
Q ss_pred CCCCCCCCCCCCCCCCEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCCHHHHHHHHHHEEEEEEC--CEEEC--
Q ss_conf 34488998999877640014323358966307862354210111234447988402789998740689741--04743--
Q 000882 662 ERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--GTVRN-- 737 (1238)
Q Consensus 662 ~~~~p~~~d~~~~a~GfV~~sF~~GL~P~EfFfH~magREGLiDtAvkTa~sGyL~R~L~~~l~d~~v~yd--~Tvr~-- 737 (1238)
+.| |.+||++||+|+|||||||||||||+|||+|||+|||||||||+++||++|.++ ||.++
T Consensus 756 --------e~P------I~ssFreGLtp~EyFfst~GaRKGL~DTALKTAdSGYLTRRLVdv~QDviV~e~DCGT~~Gi~ 821 (1407)
T 3lu0_D 756 --------ETP------ITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIM 821 (1407)
T ss_dssp --------SSC------CCCCSSSCCCHHHHHHHHHHHHHHHHHTTTTTTCTTTTTHHHHTTSTTCCBCCCSCCCCSSCE
T ss_pred --------CHH------HHCCCCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCEEEEECCCCCCCCEE
T ss_conf --------101------322520279777852102320112345244424321478899886465499746789988879
Q ss_pred ---------------------------------------------------------------C----CCCCEEEEEEEC
Q ss_conf ---------------------------------------------------------------5----788502236101
Q 000882 738 ---------------------------------------------------------------V----CSNSIIQFDYAV 750 (1238)
Q Consensus 738 ---------------------------------------------------------------~----~~~~IiQf~yg~ 750 (1238)
. +...|||.|||+
T Consensus 822 v~~~~~~~~vi~~L~~ri~GRv~a~di~~p~tgevi~~~n~~I~e~~a~~i~~~gi~~V~IRS~LTC~s~~GVC~~CYGr 901 (1407)
T 3lu0_D 822 MTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGR 901 (1407)
T ss_dssp EEESSCCCSSSSCCCCCCSSCBBSSCBCCSSSCCBCSSCBCCHHHHHHHHHTTTTCSEEEECCSSSCSCSSSBCSTTTCS
T ss_pred EEEEECCCEEEEEHHHHEEEEEEHHHEECCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEECCCEEECCCCCCCHHHHCC
T ss_conf 99860498687664340242555867254889938973898379999999998699889971864464898504777690
Q ss_pred CCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHCCCCC--CCC-CH------------HHHHHHHHHHCCCCCC-CCCCEE
Q ss_conf 4454467678997066521123790678863166999--888-06------------7899998731137999-988418
Q 000882 751 NARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSPS--SNN-SW------------ELMKEILLCRVSFNND-PIDRRV 814 (1238)
Q Consensus 751 ~g~~~~~l~~~Ge~VG~laaqsigepa~q~~L~t~~~--~~~-g~------------~rlkEil~~~~~~k~~-~~~~~~ 814 (1238)
|. ....+++.||+||++||||||||+||+||+||+- +.+ +. =++..+...+...... ...+..
T Consensus 902 dL-a~g~~V~iGEAVGiIAAQSIGEPGTQLTMRTFHtGGvas~~~~~~~i~a~~~G~v~~~~~~~v~~~~g~~vv~~r~~ 980 (1407)
T 3lu0_D 902 DL-ARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNT 980 (1407)
T ss_dssp CS-SSSSCCCSSCCTTHHHHHHHHSGGGSSCCSCTTCCCCCCCCCCCSCEECCSCEEEECCSCCCEECTTSCEECCCSSE
T ss_pred CC-CCCCCCCCCCEEEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCEEEEECCEEEECCCCCEEEEECCE
T ss_conf 50-48988315735546632004887541263523306622343210016733476899716679986889889994671
Q ss_pred EEECCCCCCC--CCCCCHHHHH------------------------HHHHHHCEECHHHHHHEEEEE--ECCCCCCC---
Q ss_conf 9972788878--7643279999------------------------998622010264443113688--42886445---
Q 000882 815 ILYLNDCGCG--RKYCQERAAY------------------------MVKNQLKRVSLKDAAVEFLIE--YKKPEIIS--- 863 (1238)
Q Consensus 815 ~l~L~~~~~~--~~~~~e~~a~------------------------~V~~~le~v~l~~i~~~i~i~--y~~~~~~~--- 863 (1238)
.+.+.+.... .+|.-.+.|. .+...--.+.++|+..-+.+. .+..+...
T Consensus 981 ~i~i~d~~g~~~~~~~ip~gs~l~v~~g~~V~~g~~ia~wDp~~~piise~~G~v~f~d~~~g~t~~~~~d~~tg~~~~~ 1060 (1407)
T 3lu0_D 981 ELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLV 1060 (1407)
T ss_dssp EEEEECSSCCBCCCEEECTTCEESSCSSCEECTTCEEEECCSSCCCEECSSCEEEEEESCCBTTTEEEEECSSSCCEEEE
T ss_pred EEEEECCCCCEEEEEECCCCCEEEECCCCEECCCCEEEEEECCCEEEEECCCEEEEEEEECCCCEEEEEECCCCCCEEEE
T ss_conf 89998489967889975889789970889962798899996676059963525899765036833678751677956899
Q ss_pred ------------CCCCEEEEEEECHHHH--------HHCCCCHHHHH--------------HHHHHHHHHHHHHH-HHHH
Q ss_conf ------------7996089999138888--------63199975479--------------99998544343101-2389
Q 000882 864 ------------DDEGLVGHIHLNKILL--------EDLRISMHDIL--------------PKCQETLKSFCKKK-KMKK 908 (1238)
Q Consensus 864 ------------~~~~~v~~i~Ld~~~L--------~~~~lt~~~I~--------------~~l~~~~~~~~~~~-~~~~ 908 (1238)
.-.|-+.-..=+-+.+ ..|.|....++ -++-....+.+.-. ....
T Consensus 1061 v~~~~~~~~~~~~~~p~i~i~~~~g~~~~~~~~~~~~~y~lp~~a~~~v~~g~~v~~g~vlakip~~~~k~~DIt~GLpr 1140 (1407)
T 3lu0_D 1061 VLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPR 1140 (1407)
T ss_dssp ECCSSSSCTTTTSCCCEEEEECSSSCBCBCTTSCCBCEEECCTTCCCCCCSSCEECTTCEEECCCCCCCCSSCCCCSHHH
T ss_pred EEECCCCCCCCCCCCCEEEEECCCCCEEECCCCCCCEEEECCCCCEEEECCCCEECCCCEEEECCHHHCCCCCHHCCCHH
T ss_conf 97305455655567743999769998874247876426745898489954798851686688633143164303137278
Q ss_pred HHHHHCCCE------E-ECCCCCCC-------CCCCCCCC-C--CCCEEEEEEEECC----CCCCC---CCHHHCCCCHH
Q ss_conf 987620331------2-01442333-------45211458-9--9456999982047----76543---20000023114
Q 000882 909 VVQFFKNTS------L-SISECCSF-------QQSCADKR-S--NMPCLMFVLRGAS----DSYLD---KLSGVLANMIY 964 (1238)
Q Consensus 909 ~~~~~~~~~------i-~~~g~~~~-------~~~~~~~~-~--~~~~l~~~~~~~~----~~~~v---d~~~t~sn~I~ 964 (1238)
+.+.|---. + -..|...+ .++++..+ + ...++ + -.+.. +-+-| +.+.-=+.+.+
T Consensus 1141 v~eLfEar~pk~~a~i~ei~G~v~~~~~~~~~~~~~i~~~~g~~~~~y~-i-~~~~~~~v~~gd~v~~G~~l~~G~~~p~ 1218 (1407)
T 3lu0_D 1141 VADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEM-I-PKWRQLNVFEGERVERGDVISDGPEAPH 1218 (1407)
T ss_dssp HHHHHTTCCCSSCCCCCSSCSCCEECCCCSSCEEEECCCSSCCTTCEEE-E-CSSSCCCCCSSSCCCTTCCCSSSCCCHH
T ss_pred HHHHHHCCCCCCCEEEECCCEEEEEEECCCCCEEEEEEECCCCEEEEEE-C-CCCCEEEECCCCEECCCCCCCCCCCCHH
T ss_conf 9988750489885277234059997211688459999718997058997-4-6896355158998747987468999999
Q ss_pred HHHHHHHHCHHHHHHHH----HHHHHHHHHCCCCCCCEEEECCCCCCCCE------------------------------
Q ss_conf 68787454011899999----99999666125541100122155101330------------------------------
Q 000882 965 PVLLETIIKENWWVRQR----LSASVTMVAKGVLKEHLILLANSMTCAGD------------------------------ 1010 (1238)
Q Consensus 965 ei~r~tiIkGiew~R~~----l~~~~~~~~~~v~~rHl~Llad~MT~~G~------------------------------ 1010 (1238)
+|+ -|+|++++++. ++.++..||..|+++|+.++++.||.+.+
T Consensus 1219 dil---~v~Giea~~~ylv~Evq~VYr~QGV~IndKHIEvIvrqM~~kv~I~d~Gdt~fl~Ge~vd~~~~~~~N~~~~~~ 1295 (1407)
T 3lu0_D 1219 DIL---RLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEAN 1295 (1407)
T ss_dssp HHH---HHSCHHHHHHHTTTTTHHHHHHHTCCCCSHHHHTTTGGGTSBCEESSCSSSCSCCCCBSHHHHHHHHHHHTTSS
T ss_pred HHH---HHHCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCEEEEECCCCCCCCCCEECHHHHHHHHHHHHHC
T ss_conf 999---86399999999999999999866943021148899999727469941787666775422099999999999976
Q ss_pred ----------EEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHCCCCCCCCCCCHHCCCCCCCCCCCC
Q ss_conf ----------76532432123344633234510210148089999997213987788520110048756654565
Q 000882 1011 ----------LVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1238)
Q Consensus 1011 ----------~~~~~r~G~~~~~~s~l~~a~Fe~~~~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1238)
++|||+.+++ ..|++..||||| |+ ++|.+||.+|++|.|.|+.||||+|+++|+|||.
T Consensus 1296 g~~pa~~~p~llGITkasl~--t~SflSaASFQe----Tt-kvLteAAi~Gk~D~L~GlkENVIvG~lIPaGTG~ 1363 (1407)
T 3lu0_D 1296 GKVGATYSRDLLGITKASLA--TESFISAASFQE----TT-RVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGY 1363 (1407)
T ss_dssp SCCCCCEECCCCCTTTTTTS--CSCTTTGGGSSC----HH-HHHHHHHHTCCEECCCSSHHHHTTTCCCTTTTTS
T ss_pred CCCCCEEEEEEECEEECCCC--CCCCHHHCCHHH----HH-HHHHHHHHCCCCCCCCCCCCCEEECCCCCCCCCC
T ss_conf 99984334445122421235--788502220566----89-9999988638977578853252754634677682
No 7
>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=470.92 Aligned_cols=268 Identities=21% Similarity=0.303 Sum_probs=215.3
Q ss_pred CCCCCCEEEEECCCHHHHHHCCCCCCCC---------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCC
Q ss_conf 4543005898349969998605455212---------5788888998899999988899899999978885325875761
Q 000882 10 LEGQIVGIRFGLATQKEICTASISDCSI---------SHASQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELPIP 80 (1238)
Q Consensus 10 ~~~~I~~I~F~l~S~eeI~~~Sv~~~~i---------~~~~gl~DprlG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~P 80 (1238)
.+++|++|+||++||+||+++||+++.. +.++||+|||||++++...|+|||.+. .+||||||||+|++|
T Consensus 65 ~~~~i~~i~F~~~s~eeI~~~Sv~~I~~~~~~d~~~~P~~gGl~D~rlG~~~~~~~C~TCg~~~-~~CpGHfGhIeL~~P 143 (436)
T 3qqc_A 65 GGKVIGSIEFGILSPQEIRKMSAVEVTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGRA-GECPGHFGHIELARP 143 (436)
T ss_dssp --CEEEEEECCBCCHHHHHHTEEEECCBCCCCC----CCCSBSSCSSSCCCSSCCCCSSSCCCS-SSCCCCEEEEEEEEE
T ss_pred CCCEEEEEEECCCCHHHHHHHCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCEEEEECHH
T ss_conf 5535632263139989999848868846621478897367885575446779999889999977-727997436750427
Q ss_pred CCCCCCHHHHHHHHHHHCCCC-----CCC---H-----------------HHHHHHHHH--------H------------
Q ss_conf 124547388999997530134-----670---1-----------------799999768--------6------------
Q 000882 81 IYHPSHISELKLTMYAFQLQI-----KND---G-----------------VAQRLLSSC--------C------------ 115 (1238)
Q Consensus 81 VfHp~f~~~i~~IL~~iCl~i-----~~~---g-----------------~~~~i~~~C--------C------------ 115 (1238)
||||+|++.|++||+|+|..| ... . ..+++++.| |
T Consensus 144 Vfh~gF~~~I~kILr~vC~~C~klll~~~~~~~f~~~lr~~~~~~~~~k~~~~~i~~~~k~~~~C~gCG~~qp~Ir~e~~ 223 (436)
T 3qqc_A 144 VIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNRRSEFNEIIKEIHKKAKERMVCPHCGAPQYPIKFEKP 223 (436)
T ss_dssp EECGGGHHHHHHHHHHSCSTTCCCSSCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHTCCSCC-------CCCBCSS
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECC
T ss_conf 77777999999999877787563246622299999999865430303889999999971557758663773864898055
Q ss_pred ----------------------HHHHHHCCCCHHHHHHHCCC-CCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf ----------------------99999716994589871259-9999985689841269998888631389754452026
Q 000882 116 ----------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLS 172 (1238)
Q Consensus 116 ----------------------ev~~IlkkIpded~~~L~~~-g~~ppe~lIL~~lpVPP~~iRp~~~~~g~~~~~~Dlt 172 (1238)
+|+++|++|+++|+.+|+.. .+.+||||||++||||||++||++.++++.+.+||+|
T Consensus 224 ~~~~~~~~~~~~~~~k~~LtP~~vl~ifk~IsdeD~~lLGl~~~~~rPewmIlt~LPVpPp~vRPsv~~~~g~~~edDLT 303 (436)
T 3qqc_A 224 TIYWEIRKDEQGNEYRHRLMPTEVRDWLEKIPDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDLT 303 (436)
T ss_dssp SCEEEECCC---CCCEEEECHHHHHHHHHHSCTTTGGGSSCCTTTCCGGGGEEEEEEECCGGGSCCBCC---CCBCCHHH
T ss_pred EEEEECCCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCEEECCCCCCCCHHH
T ss_conf 12210245544553241219999999998679888988544656798420676402249986766278378757787589
Q ss_pred HHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHHHHHHHHCC--CCCCCCCCCCCCCC-CCCCCCCCHHHHHHHHH
Q ss_conf 99999999999999950-0699996313444657999999997302--97666777556778-88999930145553210
Q 000882 173 IAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVR--GTAKSSRDVDARFG-VSQDPNSTTKAWLEKMR 248 (1238)
Q Consensus 173 ~~~l~~Ii~~~~~l~~~-~~g~~~~~~~~~~~~~LQ~~v~~~~~~~--~~~k~~~~~~~~~~-~~k~~~~~~k~~~~~~r 248 (1238)
+ +|++||++|+.|++. ..|+|..+. .+.|++||.+|++|+|+. |.+.+. ++.+ ..|.+.+++|||+||||
T Consensus 304 ~-kl~~II~~N~~L~~~~~~gap~~~i-~~~~~lLQ~~V~~~~dn~~~g~~~~~----~~~~rp~ksi~~rLkGKeGRfR 377 (436)
T 3qqc_A 304 H-KLVDIIRINNRLKQNIEAGAPQLII-EDLWDLLQYHVTTYINNEAPGVPPAK----HKSGRPLKTLAQRLKGKEGRFR 377 (436)
T ss_dssp H-HHHHHHHHHHHHHHHHHSCCCSHHH-HHHHHHHHHHHHHHHCTTCTTCCCCB----CTTSCBCCCHHHHHCC------
T ss_pred H-HHHHHHHHHHHHHHHHHCCCCHHHH-HHHHHHHHHHHHHHCCCCCCCCCCCC----CCCCCCCCCHHHHHCCCCCEEC
T ss_conf 9-9999999989999999749967789-99999999998752057888887434----5789876436766246554114
Q ss_pred CCCCCCCCCCCCC-EEEECCCCCCCCCCCCCHHHHCCCCCCCCCCHHHHHHHHHHHHCCC
Q ss_conf 0113468797765-1672899965333446266211144344322443999999998178
Q 000882 249 TLFIRKGSGFSSR-SVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKL 307 (1238)
Q Consensus 249 ~~l~gKRvdfs~R-sVI~pDP~l~i~evgiP~~~A~~Lt~pe~Vt~~Ni~~l~~lv~ng~ 307 (1238)
+||||||||||+| ||| ..+|.+|++| .|...+..|.
T Consensus 378 ~NL~GKRVdy~~~~s~~--------------~~~~~e~~~~---------~~~~~~~~~~ 414 (436)
T 3qqc_A 378 GNLSGGAGSGAGSGSVL--------------ARAAFEITVQ---------HLFEAAEKGE 414 (436)
T ss_dssp -----------------------------------CCCCHH---------HHHHHHHHTC
T ss_pred CCCCCCCCCCCCCHHHH--------------HHHHHHHHHH---------HHHHHHHHCC
T ss_conf 75788888866522299--------------9988998799---------9999998455
No 8
>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=405.06 Aligned_cols=334 Identities=17% Similarity=0.211 Sum_probs=265.7
Q ss_pred CHHHHHHHHHHEEEEEEC--CEEECC-CCCCEEEEEEECCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHCCCC-----
Q ss_conf 402789998740689741--047435-788502236101445446767899706652112379067886316699-----
Q 000882 715 TLFKNLMAVLRDVVICYD--GTVRNV-CSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP----- 786 (1238)
Q Consensus 715 yL~R~L~~~l~d~~v~yd--~Tvr~~-~~~~IiQf~yg~~g~~~~~l~~~Ge~VG~laaqsigepa~q~~L~t~~----- 786 (1238)
.++.++.+.+++..+... .|.... .--.+|..||+. ++++||||||++||||||||+|||||+||+
T Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r------~lv~pGEAVGiIAAQSIGEPgTQlTLrTFH~gGva 96 (395)
T 4ayb_C 23 ILPQKIVEDLKNLISNKEVLVTRDEIDKIFDLAIKEYSE------GLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIR 96 (395)
T ss_dssp TSCSHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHH------TBCCTTCCHHHHHHHHHHHHHHTCC----------
T ss_pred CCCHHHHHHHHHHHCCCEEECCHHHHHHHHHHHHHHHHH------HCCCCCCHHHHHHHHHCCCCHHHHCCCCCEEEEEC
T ss_conf 130999999998740122516999999999999999987------35899735768777650781032202340551232
Q ss_pred --CCCCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCEECHHHHHHEEEEEECCCCCCCC
Q ss_conf --988806789999873113799998841899727888787643279999998622010264443113688428864457
Q 000882 787 --SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISD 864 (1238)
Q Consensus 787 --~~~~g~~rlkEil~~~~~~k~~~~~~~~~l~L~~~~~~~~~~~e~~a~~V~~~le~v~l~~i~~~i~i~y~~~~~~~~ 864 (1238)
++|+|+||++|++++++. +++|.++++|.+... .++++|..++.+++.+++++++....+.+.+.
T Consensus 97 ~~nvT~GlPRl~Ei~~a~k~----~~tp~~~i~l~~~~~----~~~e~~~~~~~~ie~~~~~~~~~~~~i~~~~~----- 163 (395)
T 4ayb_C 97 ELNVTLGLPRLIEIVDAKKV----PSTPMMTIYLTDEYK----HDKEKALEVARKLEYTKIENVVSSTSIDIASM----- 163 (395)
T ss_dssp ---CCCSHHHHHHHHTCCSS----CSSCEEEECCTTTGG----GCHHHHHHHHHHHHCCCHHHHEEEEEEETTTT-----
T ss_pred CEEEECCCCCEEEECCCCCC----CCCCCEEEEECCCCC----CCHHHHHHHCCCEEEEECCCEEEEEEEEECCC-----
T ss_conf 11013475434771246547----778723899546544----22888876314315887221135667740564-----
Q ss_pred CCCEEEEEEECHHHHHHCCCCHHHHHHHHHHHHH-HHH--H-H--------------HHHHHHHHHHCCCEEECCCCCCC
Q ss_conf 9960899991388886319997547999998544-343--1-0--------------12389987620331201442333
Q 000882 865 DEGLVGHIHLNKILLEDLRISMHDILPKCQETLK-SFC--K-K--------------KKMKKVVQFFKNTSLSISECCSF 926 (1238)
Q Consensus 865 ~~~~v~~i~Ld~~~L~~~~lt~~~I~~~l~~~~~-~~~--~-~--------------~~~~~~~~~~~~~~i~~~g~~~~ 926 (1238)
...+++|.+.+.+++++++++..++.+... .+. . . .....+...+.+..+ +|+..+
T Consensus 164 ----~~~~~~d~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~i--~gi~gi 237 (395)
T 4ayb_C 164 ----SIILQLDNEMLKDKGVTVDDVKKAINRLKLGEFVIDESEGNTLNISFANIDSIAALFKLRDKILNTKI--KGIKGI 237 (395)
T ss_dssp ----EEEEEECGGGGBTTBCHHHHHHHHHHHSCCSSEEEEECSSEEEEEECCSSCCCCCTHHHHHHHHHHCC--CSSSSC
T ss_pred ----CEEEEHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEECCCCCEEEEECCCCCHHHHHHHHHHHCCCCEE--ECCCCE
T ss_conf ----14552002345413744999998776522675798526672788623787169999998753036177--345560
Q ss_pred CCCCCCCCCCCCEEEEEEEECC-----CCCCCCCHHHCCCCHHHHHHHHHHCHHHHHHHHH----HHHHHHHHCCCCCCC
Q ss_conf 4521145899456999982047-----7654320000023114687874540118999999----999966612554110
Q 000882 927 QQSCADKRSNMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVRQRL----SASVTMVAKGVLKEH 997 (1238)
Q Consensus 927 ~~~~~~~~~~~~~l~~~~~~~~-----~~~~vd~~~t~sn~I~ei~r~tiIkGiew~R~~l----~~~~~~~~~~v~~rH 997 (1238)
.+..+.++++.+++ .++|++ ..+++|..++.+|+|++|+ -+.|+|++|+.+ ..++..+|.+||+||
T Consensus 238 ~r~~~~~~~~~~~~--~t~g~~l~~~~~~~~vd~~~~~sn~i~eI~---~vlGiEAar~~iv~Ei~~V~~~~Gv~In~rH 312 (395)
T 4ayb_C 238 KRAIVQKKGDEYII--LTDGSNLSGVLSVKGVDIAKVETNNIREIE---EVFGIEAAREIIIREISKVLAEQGLDVDMRH 312 (395)
T ss_dssp CEEEEEEETTEEEE--EEESCCHHHHTTSTTCCTTTCEESCTTHHH---HHHCHHHHHHHHHHHHHHHHHTTSCCCCHHH
T ss_pred EEEEEECCCCEEEE--EECCCCCEEEEEEECCCCCCCCCCCCHHHH---HHHHHHHHHHHHHHHHHHHHHCCCCEECHHH
T ss_conf 58777416987998--725877315667502213211467405433---0000888899998767778760685103378
Q ss_pred EEEECCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHCCCCCCCCCCCHHCCCCCCCCCCCCEE
Q ss_conf 01221551013307653243212334463323451021014808999999721398778852011004875665456507
Q 000882 998 LILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRF 1077 (1238)
Q Consensus 998 l~Llad~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~~~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~f 1077 (1238)
+.|+||.||++|.+.++||+|++.+..|+|++||||+ |+ ++|.+||.+|++|+|.|++||||+||++|+|||+ |
T Consensus 313 i~li~d~Mt~~G~~~~igr~g~s~~t~S~LsaASFqe----Tt-~vLteAAi~Gk~D~L~GlkENVIvGklipaGTG~-f 386 (395)
T 4ayb_C 313 ILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEV----TV-KHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGM-V 386 (395)
T ss_dssp HHHHHHHHHGGGSCCCSSSSSHHHHCSCHHHHHHHSC----TH-HHHHHHHHTTCBCCCCSHHHHHHHTCCCSSGGGT-C
T ss_pred HHHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHCCHH----HH-HHHHHHHHCCCCCCCCCHHHHEECCCCCCCCCCC-E
T ss_conf 6555413201364752675256579989999832763----99-9999998548977787869971018988888676-2
Q ss_pred EEEECCC
Q ss_conf 9984177
Q 000882 1078 DLLWQTE 1084 (1238)
Q Consensus 1078 ~l~~~~~ 1084 (1238)
||++++.
T Consensus 387 ~l~~~p~ 393 (395)
T 4ayb_C 387 ELTMRPI 393 (395)
T ss_dssp EEEECSC
T ss_pred EEEECCC
T ss_conf 8871566
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=50.17 Aligned_cols=48 Identities=29% Similarity=0.293 Sum_probs=41.0
Q ss_pred CCCCCCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHCCCCCCCCCCCHHCCCCCC
Q ss_conf 432123344633234510210148089999997213987788520110048756
Q 000882 1016 SGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHV 1069 (1238)
Q Consensus 1016 r~G~~~~~~s~l~~a~Fe~~~~~t~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~ 1069 (1238)
|-.+ ..+.|++.+++||. +.++|++|+.+|++|+++||.|||++||.-
T Consensus 384 RVdy-~~~~s~~~~~~~e~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 431 (436)
T 3qqc_A 384 AGSG-AGSGSVLARAAFEI-----TVQHLFEAAEKGEVDNLNGVIENVLIGQKH 431 (436)
T ss_dssp ----------------CCC-----CHHHHHHHHHHTCEEECCSSCCTTSCC---
T ss_pred CCCC-CCCHHHHHHHHHHH-----HHHHHHHHHHHCCCCHHHHHHHHHHHCCCC
T ss_conf 8886-65222999988998-----799999999845563056678786304333
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=23.83 Aligned_cols=21 Identities=10% Similarity=0.158 Sum_probs=9.8
Q ss_pred HHHHCCC-CCCHHHHHHHHCCC
Q ss_conf 7630356-67999999871023
Q 000882 436 KVMFKKY-FLDKAFTQQLAMFA 456 (1238)
Q Consensus 436 ~lltkd~-fl~~~~~~ql~~~~ 456 (1238)
|.+|..+ ++++.-+.++...+
T Consensus 325 ~vFTDGvG~IS~~lA~~I~~~l 346 (1022)
T 2j7n_A 325 EVMNDGVGRMSRSVAKRIRDVL 346 (1022)
T ss_dssp CBSSTTEEEECHHHHHHHHHHH
T ss_pred CEECCCCHHHHHHHHHHHHHHC
T ss_conf 7515772575299999999982
Done!