Query 000291
Match_columns 1714
No_of_seqs 483 out of 2129
Neff 6.0
Searched_HMMs 29240
Date Tue Mar 26 16:38:35 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000291.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_70-74//hhsearch_pdb/000291hhsearch_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 2189.6 35.2 1044 5-1087 7-1457(1752)
2 1twf_A B220, DNA-directed RNA 1.0 1 1 2104.1 60.0 1054 1-1090 1-1454(1733)
3 4ayb_A DNA-directed RNA polyme 1.0 1 1 1600.4 43.9 739 9-765 1-866 (880)
4 1hqm_D DNA-directed RNA polyme 1.0 1 1 1573.3 12.9 899 12-1075 3-1219(1265)
5 2a6h_D DNA-directed RNA polyme 1.0 1 1 1465.9 17.2 782 137-1079 506-1481(1524)
6 3lu0_D DNA-directed RNA polyme 1.0 1 1 1441.2 21.6 980 9-1075 12-1363(1407)
7 3qqc_A DNA-directed RNA polyme 1.0 1 1 474.7 16.3 258 10-289 65-405 (436)
8 4ayb_C DNA-directed RNA polyme 1.0 1 1 401.4 2.3 331 715-1084 23-393 (395)
9 2k0m_A Uncharacterized protein 1.0 1 1 202.7 2.9 89 1579-1672 11-99 (104)
10 3qqc_A DNA-directed RNA polyme 1.0 1 1 49.9 1.2 47 1017-1069 385-431 (436)
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=2189.59 Aligned_cols=1044 Identities=25% Similarity=0.374 Sum_probs=906.1
Q ss_pred CCCCCCCCCEEEEEEECCCHHHHHHHCCCCCCCCCC------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 778645531106898249979998705565201468------------88889988999999888898999999798855
Q 000291 5 TSSTILEGQIVGIRFGLATQKEICTASISDCSISHA------------SQLANPFLGLPLEFGKCESCGTSEPGKCEGHF 72 (1714)
Q Consensus 5 ~~~~~~~~~I~~I~F~l~S~eEI~~~Sv~~~~I~~~------------~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHF 72 (1714)
+-..++.++|++|+|+++|++||+++||++ |+++ +||+|||||++++...|+|||++. .+|||||
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 EEEECCCCCCCCCCHHHHHHHHHHHHHHHC-----C-C-------------HHHHHHHHHH-------------------
Q ss_conf 268867522344455889999999976422-----6-1-------------2899999879-------------------
Q 000291 73 GYIELPIPIYHPSHISELKLTMYAFQLQIK-----N-D-------------GVAQRLLSSC------------------- 114 (1714)
Q Consensus 73 GhIeL~~PVfHp~fik~I~~IL~~iC~ri~-----~-~-------------g~~k~i~~~C------------------- 114 (1714)
|||||++|||||+||+.|++||+|||+.|- . . ..++++++.|
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------------------------------------HHHHHHHCCCHHHHHHHCCC-CCCCCCCEEEE
Q ss_conf -----------9------------------------------------99999805995789841148-99998738996
Q 000291 115 -----------C------------------------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILE 146 (1714)
Q Consensus 115 -----------C------------------------------------eV~~IlkkI~~ed~~~L~~~-g~~~pe~lil~ 146 (1714)
| +|++||++|+++|+++|+.. .+.+||||||+
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 ECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCHHHHHHHHHHHHHHHHHHC--CCCCCC
Q ss_conf 3068998887872028986445224799999999999999862-0699973201324437999999998611--877678
Q 000291 147 YLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVR--GTAKSS 223 (1714)
Q Consensus 147 ~lPVPP~~iRp~~~~~g~~~~~~Dlt~~~l~~Ii~~n~~l~~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~--~~~k~~ 223 (1714)
+|||||+|+||++.+++..+.++|+|+ +|++||++|++|++. ..|+|..+. .++|++||.+|++|+|+. +.+.+.
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 CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 88777778778998302456733210002458797663168289997633233112300124324312223199999999
Q 000291 224 RDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELV 303 (1714)
Q Consensus 224 ~~~~~r~~~~k~~~~~~k~k~~~~R~~l~gKRvdfsaRsVI~pDP~l~~~evgiP~~~A~~Lt~pe~vt~~Ni~~l~~lv 303 (1714)
.. ..| ..|.+.+++|||+||||+|||||||||||||||+|||+|++||||||..||++|||||+||+|||++|++||
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 HCCCCCCCCCCCCEEEE---------CCCCC-CCCCCCCCCEEEHEEECCCEEEEECCCCCCCCCCCCEEEEECCCCEEE
Q ss_conf 81676535799952881---------36998-864567853322201126648770888665355321366734888288
Q 000291 304 DNKLCLTYSDGSSSYSL---------REGSK-GHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVK 373 (1714)
Q Consensus 304 ~~g~~~~~~~~~~~~~l---------~~~~~-~~~~l~~G~~V~R~l~dgd~Vl~NRqPsLHr~Sima~~~~i~~~~t~r 373 (1714)
.||+. +|+ ++++++ ++.++ ....|++||+|+|||+|||+|||||||||||+|||||+|+|++++|||
T Consensus 399 ~nG~~-~~p--ga~~v~~~~~~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~Vl~NRqPtLHr~sima~~~~v~~gktir 475 (1752)
T 3h0g_A 399 RNGPD-EHP--GAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFR 475 (1752)
T ss_dssp HHCTT-SSS--CEEEEECTTCCBCCTTTTCSCCCCCCCSSCEEEECCCSCCEEEEECSSCCSGGGEEEEECCCCSSSSEE
T ss_pred HCCCC-CCC--CCEEEECCCCCEEECHHHCHHHHHHCCCCCEEEEEECCCCEEEEECCCCCCHHHCCCCCCEEECCCEEE
T ss_conf 73986-566--730266378847641210114454157673787442369768981686203101214463560686366
Q ss_pred ECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEECHHHHHHHHHHH-CCCCCCHHHHHHH
Q ss_conf 445566878886654520246778799999998850663312347999953751035676888652-1366799999986
Q 000291 374 INPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQL 452 (1714)
Q Consensus 374 ln~~~C~~yNADFDGDeMNihvPQs~eAraEa~~Lm~v~~qilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l 452 (1714)
|||+||+||||||||||||+|||||++|||||++||++++|||+|++|+||++++||+|+|+|+|| +++||+++++++|
T Consensus 476 lh~~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~lT~~~~f~~~~e~~~l 555 (1752)
T 3h0g_A 476 LNLSVTSPYNADFDGDEMNMHVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNI 555 (1752)
T ss_dssp EEGGGSGGGTCCSSSCEEEEECCCSTTHHHHHHHTCCTTTTSEETTTTEESCCCCTHHHHHHHHHHSTTCEEETHHHHGG
T ss_pred ECHHHCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHCCCCCEECCCCCCCEEEECCHHHHHEEEECCCCCCCCHHHHHHH
T ss_conf 06522787667610002466316888899999998537132614899980266411033211220046555899999999
Q ss_pred HCCCC---CCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCC------------CCEEEEECCEECCCCCCCCCCCCHHH
Q ss_conf 10134---5655222202323455401210124489983225------------97799976521333355676423378
Q 000291 453 AMFAL---SPLPRPALSKARCSARWTALQILQSVLPPGFDSC------------GDRYLIKKSEVLKGDFDRDTIPSVIN 517 (1714)
Q Consensus 453 ~~~~~---~~lp~PaI~Kp~~~~lWTGKQi~s~~LP~~~~~~------------~~~viI~~Gell~g~ldK~~lg~s~~ 517 (1714)
+|++. ..+|+|||+||. ++||||||||++||.++++. ++.|+|++||||+|.+||+++|++.+
T Consensus 556 ~~~~~~~~~~~~~pai~kp~--~~wtGkqifs~ilp~~~~~~~~~~~~~~~~~~d~~v~i~~gell~g~l~K~~lg~~~~ 633 (1752)
T 3h0g_A 556 MLWVPDWDGILPPPVILKPK--VLWTGKQILSLIIPKGINLIRDDDKQSLSNPTDSGMLIENGEIIYGVVDKKTVGASQG 633 (1752)
T ss_dssp GGCSSSCCSSCCCCSBCSSS--CEEETTHHHHTTSCSSBCEECCCSSCCSSCTTTCSEEECBSCEEEECCSHHHHSSCTT
T ss_pred HHHHCCCCCCCCCCCEECCC--CCCCHHHHHHHHCCCCCCCEECCCCCCCCCCCCCEEEEECCEEEECCCCHHHHCCCCC
T ss_conf 98502237845766154576--7874666776667687773004655567687767378876707753102677345754
Q ss_pred HHHHHHHHHHCHHHHHHCHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHH------------
Q ss_conf 89999998429799996042229999999984074331077545999999999999999999987554------------
Q 000291 518 EIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS------------ 585 (1714)
Q Consensus 518 ~Li~~i~~~~G~~~a~~fLd~lq~L~~~~L~~~GFSiGl~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~------------ 585 (1714)
+|||.++++||+++|+.|||.+|+|+++||+++||||||+|+++++++.+.+++.|++++..+.++..
T Consensus 634 ~li~~i~~~~G~~~~~~~ld~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~g~l~~~~g 713 (1752)
T 3h0g_A 634 GLVHTIWKEKGPEICKGFFNGIQRVVNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPG 713 (1752)
T ss_dssp CHHHHSSSSSCTTTHHHHHHHHHHHHHHHHHHHCCCCCGGGGSCCSHHHHHHHHHHHTTTHHHHHHHTTTTTTCCCCCSS
T ss_pred CHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 29999999979999999999999999999986680430633265889999999999999999999999987098755889
Q ss_pred -HHHHHHHHHHHHHHHHHHHHHHHHHHH----CCCCCCCCCCCCCHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCC
Q ss_conf -457899999999999999999999971----398421202111013556777867114614079951234552011122
Q 000291 586 -TQNELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASH 660 (1714)
Q Consensus 586 -~~~~~le~~~~~~l~~~~~~i~~~~~~----~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~ 660 (1714)
..++.+|..+..+|+++++.+++.+.+ .|++++|+.||||||++|++||+||||||.++|+| +++++..|.+||
T Consensus 714 ~~~~e~~e~~v~~~l~~~~~~~~~~~~~~l~~~N~~~~M~~SGakGs~~ni~Q~~~~~Gqq~~~Gkr-Ip~g~~~rtLP~ 792 (1752)
T 3h0g_A 714 MTLRESFEAKVSRILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKR-IPFGFKYRTLPH 792 (1752)
T ss_dssp CCTTHHHHHHHHHHHHHHHHHHHHHHHTTSCSSCTTTHHHHHCSSCCHHHHHHHHTCCCCCCSTTSS-SCCCSTTSSSTT
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCC-CCCCCCCCCCCC
T ss_conf 8689999999999999999999999998648888699986625664788899998553888257866-878888866888
Q ss_pred CCCCCCCCCCCCCCCCCEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCCHHHHHHHHHHCEEEEECCCCCCCCC
Q ss_conf 23349899899988652002744446896530786225431023224444798832478999874138972351113468
Q 000291 661 FERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCS 740 (1714)
Q Consensus 661 f~~~~p~~~d~~~ea~GfI~nSF~~GL~P~EfFfHsmagREGLiDTAvkTA~sGYL~RrLv~~led~~v~YD~Tvr~~~~ 740 (1714)
|.+ +|+.|+++|||+|||++||+|+|||||||||||||||||||||+|||||||||++|||++|+||+|||++ .
T Consensus 793 f~k-----~d~~~~a~GfV~~sF~~GL~p~EfFfhtmggReGLiDTAvKTA~SGYLqRRLVk~leDv~V~YDgTVRns-~ 866 (1752)
T 3h0g_A 793 FPK-----DDDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNA-M 866 (1752)
T ss_dssp SCS-----SCCSTTTSSCCSSCTTTCCCHHHHHHHHHHHTTTTTHHHHTTTHHHHHHHHHHHHHTTCEEETTTEEECT-T
T ss_pred CCC-----CCCCCCCCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHEEEEECCEEECC-C
T ss_conf 888-----8998433761010134799889999974410322467654027675017999998752488507806868-9
Q ss_pred CCEEEEEECCCCCCC-----------------------------------------------------------------
Q ss_conf 961388812344544-----------------------------------------------------------------
Q 000291 741 NSIIQFDYAVNARKS----------------------------------------------------------------- 755 (1714)
Q Consensus 741 ~~IiQf~yg~~g~~~----------------------------------------------------------------- 755 (1714)
|+||||+||+||+|.
T Consensus 867 g~ivQF~YGeDGlD~~~~e~q~~~~~~~s~~~f~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~E~~~l~~dr~~lr 946 (1752)
T 3h0g_A 867 GDIIQFAYGEDGLDATLVEYQVFDSLRLSTKQFEKKYRIDLMEDRSLSLYMENSIENDSSVQDLLDEEYTQLVADRELLC 946 (1752)
T ss_dssp SCEEESSSSSSCBCGGGEEEEECTTTSCCHHHHTTTSCCCTTTTCCGGGTSCSCCTTSCSSTHHHHHHHHHHHHHHTTSS
T ss_pred CCEEEEECCCCCCCHHHHHCCCCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 94898746777768677413555402478799998842122554324677888750578899999999999999999988
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q 000291 756 -------------------------------------------------------------------------------- 755 (1714)
Q Consensus 756 -------------------------------------------------------------------------------- 755 (1714)
T Consensus 947 ~~i~~~~~~~~~lP~N~~R~i~~~~~~f~~~~~~~s~l~p~~~~~~v~~~~~~l~~~~g~d~l~~~~~~na~~l~~~~lr 1026 (1752)
T 3h0g_A 947 KFIFPKGDARWPLPVNVQRIIQNALQIFHLEAKKPTDLLPSDIINGLNELIAKLTIFRGSDRITRDVQNNATLLFQILLR 1026 (1752)
T ss_dssp SSSSSCSCCEEEEESCHHHHTTTTTTTSCCCTTSCCCCCHHHHHHHHHHHHTTCCCSCCCSTTTTHHHHTSSHHHHHHHT
T ss_pred HHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCHHHHHHHHHH
T ss_conf 87510431013687149999999998627786765779889999999999986540258740205656352878889887
Q ss_pred -------------------------------CCCCCCCCEEEEECCCCCCHHHHHHHHCCCC-------CCCCCHHHHHH
Q ss_conf -------------------------------6767899605872123479067887424799-------99986577999
Q 000291 756 -------------------------------HSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKE 797 (1714)
Q Consensus 756 -------------------------------~~l~~~Ge~VG~laaqsigepatq~~L~t~~-------~~~~g~~rlkE 797 (1714)
+++++|||+||+|||||||||+|||||+||| ++|+|+|||||
T Consensus 1027 ~~l~~k~~~~~~~l~~~~~~~~~~~~~~~y~~a~v~pGe~VG~iaAQSIgEp~TQMTLnTFHfAGvas~NVTlGVPRLkE 1106 (1752)
T 3h0g_A 1027 SKFAVKRVIMEYRLNKVAFEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKE 1106 (1752)
T ss_dssp TSSSHHHHHHSSCCCHHHHHHHHHHHHHHHHTTBCCSSCCHHHHHHHHHHHHHHHHHHHTTSSCCCCCSSCCCSGGGHHH
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCHHH
T ss_conf 66544443421676899999999999999987345766511034540268812346577664404435565557500999
Q ss_pred HHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHEEEEEECCCCCCC--------------
Q ss_conf 997311378998874199972788888763228999999863210138654421377753896445--------------
Q 000291 798 ILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS-------------- 863 (1714)
Q Consensus 798 il~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~Le~v~l~dv~~~i~i~y~~~~~~~-------------- 863 (1714)
||+++++ +++|.|++||.+.+.. ++++|++|+++||+++|++|+..+.|.|.++...+
T Consensus 1107 IInask~----ikTP~mtv~L~~~~~~----d~e~A~~v~~~ie~t~L~~v~~~~~i~~~p~~~~~~i~~d~~~v~~~~~ 1178 (1752)
T 3h0g_A 1107 ILNVAKN----IKTPSLTIYLMPWIAA----NMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFA 1178 (1752)
T ss_dssp HHTTCSC----CSCCCCEECCCSSSCS----SSTTTHHHHTTSSCCSSCSCCSCEEEECCCSTTCCCCSSSCSHHHHHHH
T ss_pred HHHHHCC----CCCCEEEEEECCCCCC----CHHHHHHHHHHHCCEEHHHHEEEEEEEEECCCCCEEEEECHHHHHHHHC
T ss_conf 9866327----9997289995675555----8999999997614078987110789999468651688625899999862
Q ss_pred -----------CCCCEEEEEEECHHHHHHHCCCHHHHHHHHHHHHHH-H----------------HH-CC----------
Q ss_conf -----------899618999945988987058954458999985554-5----------------42-00----------
Q 000291 864 -----------DDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKS-F----------------CK-KK---------- 904 (1714)
Q Consensus 864 -----------~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~-~----------------~~-~~---------- 904 (1714)
..++|+++|+||+++|.+++|++++|++++.+.++. + +. ..
T Consensus 1179 ~~~~~~~~~~~~~~~~~~rl~l~~~~~~~~~l~~~~I~~~i~~~~~~~~~v~~~d~~~~~~~i~i~~~~~~~~~~~~~~~ 1258 (1752)
T 3h0g_A 1179 IPDEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVAGKIAESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDN 1258 (1752)
T ss_dssp TTCSSTTCSSCSCCCCEEEEECCTTSSTTTTCCHHHHTTSGGGSSTTSCCEECCCTTCSSCEEEECCCCCSCCCCCSSCC
T ss_pred CCHHHHHCCCCCCCCEEEEEEECHHHHHHCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCEEEEEEECCCCCCCCCCCCC
T ss_conf 42333100100146525899854999987499999999999864368735851577766306999851554444322233
Q ss_pred --HHHHHHHHHH-CCCCCCCCCCC--CCCCCCCCCC-------------CCCEEEEEECCCC-----CCCCCCCEECCCC
Q ss_conf --2368999840-25333322222--2351215589-------------9566999972368-----7544310000125
Q 000291 905 --KMKKVVQFFK-NTSLSISECCS--FQQSCADKRS-------------NMPCLMFVLRGAS-----DSYLDKLSGVLAN 961 (1714)
Q Consensus 905 --~~~~i~~~~~-~~~~~~~~~gi--~~~~~~~~~~-------------~~~~l~~~~~~s~-----~~~~vd~~~~~~n 961 (1714)
....++..+. +++..+.++|+ |.+++++++. ++|+ +.++|++ ..++||..+|++|
T Consensus 1259 ~~~~~~~l~~l~~~~l~~~~i~Gi~~I~rv~i~~~~~~~~~~~g~~~~~~~~~--l~teG~nL~~v~~~~gVD~~rt~sN 1336 (1752)
T 3h0g_A 1259 MIEEDVFLKTIEGHMLESISLRGVPNITRVYMMEHKIVRQIEDGTFERADEWV--LETDGINLTEAMTVEGVDATRTYSN 1336 (1752)
T ss_dssp CSCSCHHHHHHHHHHTTCCCSSCCTTCCCCCEEEEEEEEECSSSCEEEEEEEE--EECCSCCCSTTTSSSSCCTTTCCCS
T ss_pred CCCHHHHHHHHHHHHCCCEEEECCCCCCEEEEECCCCEEECCCCCCCCCCEEE--EEECCCCHHHHHCCCCCCCCCCEEC
T ss_conf 32189999999996311258846899647998636603326887512464179--9921468999967698846408547
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEECCCEEEECEEEEECCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 40379888765555899999899888762----25552202333046032020764255210122347432245211023
Q 000291 962 MIYPVLLETIIKENWWVRQRLSASVTMVA----KGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATL 1037 (1714)
Q Consensus 962 ~I~ei~l~tIIkgi~w~r~~l~~~~~~~~----~~V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~ 1037 (1714)
+|+||+. +.|||++|+.|.+++..|+ ++||+|||+||||+||++|++++||||||+++++|+|++||||+|
T Consensus 1337 dI~ei~~---vlGIEAAR~~Ii~Ei~~v~~~~G~~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~s~l~~aSFE~T-- 1411 (1752)
T 3h0g_A 1337 SFVEILQ---ILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFEET-- 1411 (1752)
T ss_dssp CHHHHHH---HSCHHHHHHHHHHHHHTTSCSSSCCCCHHHHHHHHHHHTSSSSCCCCCTTSCSCCCSHHHHHHHHSCC--
T ss_pred CHHHHHH---HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCEEEEECHHHHCCCCCCHHHHHHHHHH--
T ss_conf 8999999---87599999999999999998438877899999978876138768861234430579888998648979--
Q ss_pred CCCHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCCCEEEEEECCCCCC
Q ss_conf 58177999998321988788224464158755534565289996067743
Q 000291 1038 FMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTENEE 1087 (1714)
Q Consensus 1038 ~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~~~~~~ 1087 (1714)
+++|++||.+|++|+|+||+||||+||++++|||+ |||+++.++++
T Consensus 1412 ---~~~L~~Aa~~g~~D~l~gvse~Ii~G~~~~~GTG~-fdll~~~~~l~ 1457 (1752)
T 3h0g_A 1412 ---VEILMDAAASGEKDDCKGISENIMLGQLAPMGTGA-FDIYLDQDMLM 1457 (1752)
T ss_dssp ---THHHHHHGGGTCCBCCCCSTTGGGTCSCCCSBTTS-CEECCCHHHHH
T ss_pred ---HHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCCE-EEEEECHHHHC
T ss_conf ---99999999726866664805776538876776632-78985788836
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=2104.08 Aligned_cols=1054 Identities=22% Similarity=0.338 Sum_probs=901.7
Q ss_pred CCCCCCCCCCCCCEEEEEEECCCHHHHHHHCCCCCCCCC------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 988777864553110689824997999870556520146------------88888998899999988889899999979
Q 000291 1 MEENTSSTILEGQIVGIRFGLATQKEICTASISDCSISH------------ASQLANPFLGLPLEFGKCESCGTSEPGKC 68 (1714)
Q Consensus 1 ~~~~~~~~~~~~~I~~I~F~l~S~eEI~~~Sv~~~~I~~------------~~gl~DprLG~~~~~~~C~TCg~~~~~~C 68 (1714)
|...+-..++.++|++|+|+++||+||+++||.++ ++ ++||+|||||+++++..|+|||.+. .+|
T Consensus 1 ~~~~~~~~~~~~~i~~I~f~l~SpeeIr~~Sv~eI--~~pet~~~~~~~P~~~GL~d~rlG~~~~~~~C~tCg~~~-~~C 77 (1733)
T 1twf_A 1 MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKI--RFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGM-NEC 77 (1733)
T ss_dssp -CCCSCCCSCBCCCCEEECCBCCHHHHHHTCCCCC--CCSCCSCTTSCCSCCSSSSCSSSCCCTTCCCSSSCCCCT-TSC
T ss_pred CCCCCCCCCCCCCCCEEEEEECCHHHHHHHCEEEE--ECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCC-CCC
T ss_conf 98888776774512549998389899997281687--142211466677776887474437646788708889988-707
Q ss_pred CCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHHC----CC---------------HHHHHHHHH----------------
Q ss_conf 8855268867522344455889999999976422----61---------------289999987----------------
Q 000291 69 EGHFGYIELPIPIYHPSHISELKLTMYAFQLQIK----ND---------------GVAQRLLSS---------------- 113 (1714)
Q Consensus 69 pGHFGhIeL~~PVfHp~fik~I~~IL~~iC~ri~----~~---------------g~~k~i~~~---------------- 113 (1714)
|||||||||++|||||+||+.|++||+|||+.|- .. ...++++..
T Consensus 78 ~GHfGHIELa~PV~HigF~k~i~kiLe~VC~~Cskllld~~~~~~~~~L~~~~pk~r~~~v~e~ck~k~~Ce~~~~~~~e 157 (1733)
T 1twf_A 78 PGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDD 157 (1733)
T ss_dssp CCCCCCEEEEEEEECGGGHHHHHHHHHHBCTTTCCBSCCTTSHHHHHHHTCCSHHHHHHHHHHHHTTCCBCCSEECCSSC
T ss_pred CCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHCCEEEECCCHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCHHC
T ss_conf 98460343444511598875589999877675160131422589999997107788999999984435414654200000
Q ss_pred ------H--H--------------------------------------HHHHHHHCCCHHHHHHHCCC-CCCCCCCEEEE
Q ss_conf ------9--9--------------------------------------99999805995789841148-99998738996
Q 000291 114 ------C--C--------------------------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILE 146 (1714)
Q Consensus 114 ------C--C--------------------------------------eV~~IlkkI~~ed~~~L~~~-g~~~pe~lil~ 146 (1714)
| | +|+++|++|+++|+++|... .+.+||||||+
T Consensus 158 ~~~~~~~~gCGa~qp~irk~gl~l~~e~k~~~~~~e~~~~~k~~Ltp~eV~eifk~I~deD~~lLgl~p~~~rPewmiLt 237 (1733)
T 1twf_A 158 PTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILT 237 (1733)
T ss_dssp TTSCEECCSCCCBCCCCEECSSCEEEEECSSSSCTTSCSCEEEEECHHHHHHHHTTSCHHHHHHTTCBTTTBCGGGGEEE
T ss_pred CCCCCCCCCCCCCCHHHHHCCCCEEEEECCCCCCCCCCHHHHCCCCHHHHHHHHHHCCHHHHHHHCCCCCCCCHHEEEEE
T ss_conf 23444457878765877745775477651003432221022014799999999873899999984787668980205565
Q ss_pred ECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCHHHHHHHHHHHHHHHHHHC--CCCCCC
Q ss_conf 3068998887872028986445224799999999999999862-0699973201324437999999998611--877678
Q 000291 147 YLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVR--GTAKSS 223 (1714)
Q Consensus 147 ~lPVPP~~iRp~~~~~g~~~~~~Dlt~~~l~~Ii~~n~~l~~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~--~~~k~~ 223 (1714)
+|||||+|+||++.+++..+.++|||+ +|++||++|++|++. ..|+|..+. .+.|.+||.+|+.|+|+. +.+.+.
T Consensus 238 vLPVpPp~vRPsv~ldg~~~~edDLT~-~l~~II~~N~~Lk~~~~~gap~~ii-~e~~~~LQ~~v~~~~dn~~~~~~~~~ 315 (1733)
T 1twf_A 238 CLPVPPPPVRPSISFNESQRGEDDLTF-KLADILKANISLETLEHNGAPHHAI-EEAESLLQFHVATYMDNDIAGQPQAL 315 (1733)
T ss_dssp EECCCCTTTSCCCCCSSSCCCCCHHHH-HHHHHHHHHHHHHHHHSSCCCHHHH-HHHHHHHHHHHHHHHCCCSSCCCCCS
T ss_pred EECCCCCCCCCCEECCCCCCCCCHHHH-HHHHHHHHHHHHHHHHHCCCHHHHH-HHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 422699876675665898605777899-9999999999999999747458788-89999999999998546766887434
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 88777778778998302456733210002458797663168289997633233112300124324312223199999999
Q 000291 224 RDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELV 303 (1714)
Q Consensus 224 ~~~~~r~~~~k~~~~~~k~k~~~~R~~l~gKRvdfsaRsVI~pDP~l~~~evgiP~~~A~~Lt~pe~vt~~Ni~~l~~lv 303 (1714)
.. ..| ..|.+.+++|||+||||+|||||||||||||||+|||+|++||||||..||++|||||+||+|||++|++||
T Consensus 316 ~~-~~r--p~k~i~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~L~~~evGvP~~~A~~Lt~Pe~vt~~ni~~l~~lv 392 (1733)
T 1twf_A 316 QK-SGR--PVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLV 392 (1733)
T ss_dssp SC-TTC--CCCCSTTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEHHHHTTCEEEEECCTTTHHHHHHHH
T ss_pred CC-CCC--CCHHHHHHHCCCCCHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf 57-886--505678775033311222136655676530477489876266235849999857888413489999999999
Q ss_pred HCCCCC------CCCCCCCEEEECCCCC-CCCCCCCCCEEEHEEECCCEEEEECCCCCCCCCCCCEEEEECCCCEEEECC
Q ss_conf 816765------3579995288136998-864567853322201126648770888665355321366734888288445
Q 000291 304 DNKLCL------TYSDGSSSYSLREGSK-GHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINP 376 (1714)
Q Consensus 304 ~~g~~~------~~~~~~~~~~l~~~~~-~~~~l~~G~~V~R~l~dgd~Vl~NRqPsLHr~Sima~~~~i~~~~t~rln~ 376 (1714)
.||+.. +.++.+.++.|++.++ ....|++||+|+|||+|||+|||||||||||+|||||+|+|++++||||||
T Consensus 393 ~~g~~~~~ga~~~~~~~g~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~VllNRqPTLHr~si~a~~~~v~~~~tirlnp 472 (1733)
T 1twf_A 393 RNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNL 472 (1733)
T ss_dssp HHTTTSSSCEEEEECTTCCEEETTSCTTTTCCCCCTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEEESSSSEEECG
T ss_pred HCCCCCCCCCEEEECCCCCEEECCCCCHHHHHHCCCCCEEEEEECCCCEEEEECCCCCCCCCCEEEEEEECCCCEEEECH
T ss_conf 74986677740378278957853223225544046577897651269778980798646134226789970697477476
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEECHHHHHHHHHHH-CCCCCCHHHHHHHHCC
Q ss_conf 566878886654520246778799999998850663312347999953751035676888652-1366799999986101
Q 000291 377 LICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMF 455 (1714)
Q Consensus 377 ~~C~~yNADFDGDeMNihvPQs~eAraEa~~Lm~v~~qilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~ 455 (1714)
+||+||||||||||||+|||||++|||||++||++++|||+|++|+||++++||+|+|+|+|| +++|++++++++++|+
T Consensus 473 ~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~v~g~y~lT~~~~f~~~~e~~~~~~~ 552 (1733)
T 1twf_A 473 SVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYW 552 (1733)
T ss_dssp GGHHHHTCCSSSCEEEEECCCSHHHHHHHHHHTBGGGGSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHHHH
T ss_pred HHCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCCEEECCCCCEEEEEECCCCCCCEEEECCCCCCCHHHHHHHHHH
T ss_conf 55588776611245651057889999999998537345886579981376512221000341047556999999999983
Q ss_pred CC---CCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCC------------CCEEEEECCEECCCCCCCCCCCCHHHHHH
Q ss_conf 34---5655222202323455401210124489983225------------97799976521333355676423378899
Q 000291 456 AL---SPLPRPALSKARCSARWTALQILQSVLPPGFDSC------------GDRYLIKKSEVLKGDFDRDTIPSVINEIV 520 (1714)
Q Consensus 456 ~~---~~lp~PaI~Kp~~~~lWTGKQi~s~~LP~~~~~~------------~~~viI~~Gell~g~ldK~~lg~s~~~Li 520 (1714)
+. ..+|+|||+||. ++|||||||+++||.++++. ++.|+|++|||++|++||+++|++.++||
T Consensus 553 ~~~~~~~~~~pai~kp~--~~wtGkqifs~ilp~~~~~~~~~~~~~~~~~~d~~v~i~~gel~~g~ldKk~lg~~~~~li 630 (1733)
T 1twf_A 553 VPDWDGVIPTPAIIKPK--PLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLI 630 (1733)
T ss_dssp STTCCSCCCCCSBCSSS--CEEEHHHHHHHHSCTTCCEEECCTTCCTTCTTCCSEEEETTEEEESCCCHHHHSSCTTSHH
T ss_pred HHHHCCCCCCCCCCCCC--CCCCHHHHHHHHCCCCCCEEECCCCCCCCCCCCCEEEEECCCEEEEECCHHHHCCCHHHHH
T ss_conf 23315853774310761--5752887888767899741336877655786656489867828983016678545701899
Q ss_pred HHHHHHHCHHHHHHCHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHH-------------HH
Q ss_conf 99998429799996042229999999984074331077545999999999999999999987554-------------45
Q 000291 521 TSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS-------------TQ 587 (1714)
Q Consensus 521 ~~i~~~~G~~~a~~fLd~lq~L~~~~L~~~GFSiGl~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~-------------~~ 587 (1714)
|.++++||+.+|+.|||.+++|+++||+++||||||+|+++++++.+.+++.|++++..+.++.. ..
T Consensus 631 ~~i~~~~G~~~a~~~ld~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~i~~~i~~a~~~v~~~~~~~~~g~l~~~pg~~~ 710 (1733)
T 1twf_A 631 HVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTL 710 (1733)
T ss_dssp HHHHHHHCHHHHHHHHHHHHHHHHHHHHTTCBCCCGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCTTCCH
T ss_pred HHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCEEEEHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCH
T ss_conf 99999869999999999999999999987666985565375989999999999999999999999998099765889877
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH----CCCCCCCCCCCCCHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCCCCC
Q ss_conf 7899999999999999999999971----398421202111013556777867114614079951234552011122233
Q 000291 588 NELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFER 663 (1714)
Q Consensus 588 ~~~le~~~~~~l~~~~~~i~~~~~~----~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~ 663 (1714)
++.+|.++..+|+++++.+++.+++ .|++++|+.||||||++|++||+||||||.++|+ ++++++..|++|||.+
T Consensus 711 ~e~~e~~v~~il~~~~d~~~~~~~~~l~~~N~i~~Ma~SGAKGs~~Ni~Q~~~~~Gqq~~~Gk-rip~g~~~RtLPhf~k 789 (1733)
T 1twf_A 711 RESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGK-RIAFGFVDRTLPHFSK 789 (1733)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHTSSCCHHHHHHHHSCCEECCBTTB-SCCCCBTTBSSTTSCT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHCCCCCCCCCC-CCCCCCCCCCCCCCCC
T ss_conf 999999999999999999999999862658871788504676547769999717677546886-3777888877888777
Q ss_pred CCCCCCCCCCCCCCEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCCHHHHHHHHHHCEEEEECCCCCCCCCCCE
Q ss_conf 49899899988652002744446896530786225431023224444798832478999874138972351113468961
Q 000291 664 IYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSI 743 (1714)
Q Consensus 664 ~~p~~~d~~~ea~GfI~nSF~~GL~P~EfFfHsmagREGLiDTAvkTA~sGYL~RrLv~~led~~v~YD~Tvr~~~~~~I 743 (1714)
+|++|+++|||++||++||+|+|||||||||||||||||||||+|||||||||++|||++|+||+|||+ +.|.|
T Consensus 790 -----~d~~p~s~GfI~ssF~~GLtp~EyFfh~mggReGLiDTAvKTA~SGYLqRRLVk~ledv~V~yDgTVR~-s~g~I 863 (1733)
T 1twf_A 790 -----DDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRN-SLGNV 863 (1733)
T ss_dssp -----TCCSTTTTTEECSCTTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCEECTTSCEEC-TTCCE
T ss_pred -----CCCCCCCCCHHHHHHHCCCCHHHHHHHHHCCCCCHHHHCEECCCCCCCEEEHHHHHCCEEEEECCCEEC-CCCCE
T ss_conf -----889800166133100024654877655431442012200020568851000333325059970586765-89978
Q ss_pred EEEEECCCCCCCC-------------------------------------------------------------------
Q ss_conf 3888123445446-------------------------------------------------------------------
Q 000291 744 IQFDYAVNARKSH------------------------------------------------------------------- 756 (1714)
Q Consensus 744 iQf~yg~~g~~~~------------------------------------------------------------------- 756 (1714)
|||+||+||+|..
T Consensus 864 vQF~YGeDGlD~~~~e~~~~~~~~~~~~~f~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~e~~~l~~~r~~l 943 (1733)
T 1twf_A 864 IQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFL 943 (1733)
T ss_dssp EESSGGGTTBCGGGEEEEECGGGSSCHHHHHHHHCCCTTCTTTSCCTTTBTTHHHHTTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEEEECCCCCCCCEEECCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99871366677421004656500157999999853444563224788888778774036888999999999999889999
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q 000291 757 -------------------------------------------------------------------------------- 756 (1714)
Q Consensus 757 -------------------------------------------------------------------------------- 756 (1714)
T Consensus 944 r~i~~~~~~~~~~P~ni~r~i~~~~~~f~~~~~~~s~l~p~~~~~~v~~~~~~~~~~~g~d~l~~~~~~n~~~l~~~~~r 1023 (1733)
T 1twf_A 944 REVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLR 1023 (1733)
T ss_dssp HHHTTTCCCEEEEESCHHHHHHHHHHHTTCCTTSCBCCCHHHHHHHHHHHHTTCCSCCCCSHHHHHHHHHTTHHHHHHHH
T ss_pred HHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCHHHHHHHHHH
T ss_conf 87630566344687149999998887731355543457889999999999986430158762005555252778888766
Q ss_pred --------------------------------CCCCCCCEEEEECCCCCCHHHHHHHHCCCC-------CCCCCHHHHHH
Q ss_conf --------------------------------767899605872123479067887424799-------99986577999
Q 000291 757 --------------------------------SLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKE 797 (1714)
Q Consensus 757 --------------------------------~l~~~Ge~VG~laaqsigepatq~~L~t~~-------~~~~g~~rlkE 797 (1714)
++++|||+||+|||||||||+|||||+||| ++|+|+|||+|
T Consensus 1024 s~L~~k~~~~~~~l~~~~~~~~l~~i~~ky~~a~v~pGe~VG~iaAQSigEp~TQMTLnTFHfAGva~~NVTLGVPRLkE 1103 (1733)
T 1twf_A 1024 SRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKE 1103 (1733)
T ss_dssp HHSCHHHHHHTSCCCHHHHHHHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC----------CCSCCHHHHHHH
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
T ss_conf 54545556666177899998888999999986557898601567653168853123555444156125574367588999
Q ss_pred HHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHEEEEEECCCCCCC--------------
Q ss_conf 997311378998874199972788888763228999999863210138654421377753896445--------------
Q 000291 798 ILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS-------------- 863 (1714)
Q Consensus 798 il~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~Le~v~l~dv~~~i~i~y~~~~~~~-------------- 863 (1714)
||+++++ +++|.|+++|.+++.. ++++|+.|+.+||+|+|++|+..+.|.|+++...+
T Consensus 1104 Iinask~----ikTP~mtv~L~~~~~~----~~e~A~~v~~~ie~ttL~dv~~~i~i~~dp~~~~tvi~ed~~~~~~y~~ 1175 (1733)
T 1twf_A 1104 ILNVAKN----MKTPSLTVYLEPGHAA----DQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFS 1175 (1733)
T ss_dssp HTTTCSS----CSSCEEEEEBCSSSSS----CHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHHTSSC
T ss_pred HHHHCCC----CCCCEEEEEECCCCCC----CHHHHHHHHHHHCEEEHHHHHHEEEEEECCCCCCEEEECCHHHHHHHHC
T ss_conf 9975137----8997389995775432----5999999987631148998201679997367664033132234343322
Q ss_pred -----------CCCCEEEEEEECHHHHHHHCCCHHHHHHHHHHHHHHHH-----HC------------C-----------
Q ss_conf -----------89961899994598898705895445899998555454-----20------------0-----------
Q 000291 864 -----------DDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFC-----KK------------K----------- 904 (1714)
Q Consensus 864 -----------~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~~-----~~------------~----------- 904 (1714)
..++|+++|+||+++|.+++|++++|..++.+.++... .. .
T Consensus 1176 i~~~d~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~I~~~i~~~~~~~~~~~~~d~~~~~~~~~i~~~~~~~~~~~~~~~ 1255 (1733)
T 1twf_A 1176 LLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAE 1255 (1733)
T ss_dssp C----------CCCSEEEEEEECHHHHHHTTCCHHHHHHHHHHHHGGGEEEEECCTTSSSCEEEEEEC----------CC
T ss_pred CCHHHHCCHHHHCCCCEEEEEECHHHHHHCCCCHHHHHHHHHHHHCCCCCEECCCCCCCHHHEEEEECCCCCCCCCCCCH
T ss_conf 56776210032103400589966988976379999999999875177751204776400011133202675222333201
Q ss_pred HHHHHHHHHHCCCCCCCCCCC--CCCCCCCC--------C-----CCCCEEEEEECCCC-----CCCCCCCEECCCCCCH
Q ss_conf 236899984025333322222--23512155--------8-----99566999972368-----7544310000125403
Q 000291 905 KMKKVVQFFKNTSLSISECCS--FQQSCADK--------R-----SNMPCLMFVLRGAS-----DSYLDKLSGVLANMIY 964 (1714)
Q Consensus 905 ~~~~i~~~~~~~~~~~~~~gi--~~~~~~~~--------~-----~~~~~l~~~~~~s~-----~~~~vd~~~~~~n~I~ 964 (1714)
....+..++.+++..+.++|+ |.++++++ + ..+++ +.++|.+ ..++||..+|++|+|+
T Consensus 1256 ~~~~l~~l~~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~g~~~~~~~~~--L~teG~nL~~vl~~~~VD~~rt~SNdI~ 1333 (1733)
T 1twf_A 1256 EDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWV--LETDGVNLSEVMTVPGIDPTRIYTNSFI 1333 (1733)
T ss_dssp TTHHHHHHHHHHHHHCEEESCTTCCCEEEEEEEEEEECTTSSEEEEEEEE--EEEESCCHHHHTTSTTBCTTTCBCSCHH
T ss_pred HHHHHHHHHHHHHHHEEEECCCCCCEEEEECCCCEEECCCCCCCCCCCEE--EEEECCCHHHHHCCCCCCCCCCEECCHH
T ss_conf 47999999997630047715788547999535531235777524576238--9960514999960477254110434599
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH----HCCCCCCEEEEECCCEEEECEEEEECCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 7988876555589999989988876----225552202333046032020764255210122347432245211023581
Q 000291 965 PVLLETIIKENWWVRQRLSASVTMV----AKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMP 1040 (1714)
Q Consensus 965 ei~l~tIIkgi~w~r~~l~~~~~~~----~~~V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~ 1040 (1714)
+|+. +.|||++|+.|.+++..| |.+||+|||+||||+||++|++++||||||++++.|+|++|+||+|
T Consensus 1334 eI~~---vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~S~L~~aSFE~T----- 1405 (1733)
T 1twf_A 1334 DIME---VLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEET----- 1405 (1733)
T ss_dssp HHHH---HHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTTBSSCCCSSSCSSSCSSCCTTSSCCSSCS-----
T ss_pred HHHH---HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCEECCCCHHHHCCCCCCCHHHCCHHHH-----
T ss_conf 9998---75699999999999999986058634623343235556007632033313222668872210322543-----
Q ss_pred HHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCCCEEEEEECCCCCCCCC
Q ss_conf 77999998321988788224464158755534565289996067743466
Q 000291 1041 RKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTENEEFNQ 1090 (1714)
Q Consensus 1041 ~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~~~~~~~~~ 1090 (1714)
+++|.+||.+|++|.|+||+||||+||++|+|||+ |||+++.+.++...
T Consensus 1406 ~~~L~~Aa~~g~~D~l~gvsenII~G~~~~~GTG~-FdLl~~~~~~~~~~ 1454 (1733)
T 1twf_A 1406 VEILFEAGASAELDDCRGVSENVILGQMAPIGTGA-FDVMIDEESLVKYM 1454 (1733)
T ss_dssp HHHHHHHHHHTCEECCCSHHHHHHTTCCCSSGGGS-SEEEECSCCC----
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC-EEEEECHHHCCCCC
T ss_conf 89999987514767355510001047777787740-79997103312000
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=1600.39 Aligned_cols=739 Identities=28% Similarity=0.385 Sum_probs=639.9
Q ss_pred CCCCCEEEEEEECCCHHHHHHHCCCCCCCCCC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEC
Q ss_conf 45531106898249979998705565201468-----------8888998899999988889899999979885526886
Q 000291 9 ILEGQIVGIRFGLATQKEICTASISDCSISHA-----------SQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIEL 77 (1714)
Q Consensus 9 ~~~~~I~~I~F~l~S~eEI~~~Sv~~~~I~~~-----------~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL 77 (1714)
+..++|++|+|+++||+||+++||.+ |++| +||+|||||+++++..|+|||.+. .+||||||||||
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 CCCCCCCCCHHHHHHHHHHHHHHHC-----CCH-----------------HHHHH----HH------HH--H--------
Q ss_conf 7522344455889999999976422-----612-----------------89999----98------79--9--------
Q 000291 78 PIPIYHPSHISELKLTMYAFQLQIK-----NDG-----------------VAQRL----LS------SC--C-------- 115 (1714)
Q Consensus 78 ~~PVfHp~fik~I~~IL~~iC~ri~-----~~g-----------------~~k~i----~~------~C--C-------- 115 (1714)
|.|||||+||+.|++||+++|..|- ... ..+++ .+ .| |
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 ---------------------HHHHHHHCCCHHHHHHHCC-CCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf ---------------------9999980599578984114-899998738996306899888787202898644522479
Q 000291 116 ---------------------EVKEMLKRIPEETRKKLAG-KGYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSI 173 (1714)
Q Consensus 116 ---------------------eV~~IlkkI~~ed~~~L~~-~g~~~pe~lil~~lPVPP~~iRp~~~~~g~~~~~~Dlt~ 173 (1714)
+++++|++|+++++.++.. ....+||||||++||||||++||++..++..+.++|+|.
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-HCCCCCCCCHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf 9999999999999862-0699973201324437999999998611--877678887777787789983024567332100
Q 000291 174 AMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVR--GTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTL 250 (1714)
Q Consensus 174 ~~l~~Ii~~n~~l~~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~--~~~k~~~~~~~r~~~~k~~~~~~k~k~~~~R~~ 250 (1714)
+|++|+++|++|+.. ..++|..+. .++|.+||.+|++|+|+. +.+... .... ...|.+.+.+|||+||||+|
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 CCCCCCCCCCCEEEECCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCCC------CCCCCCCEEEECCCC
Q ss_conf 02458797663168289997633233112300124324312223199999999816765------357999528813699
Q 000291 251 FIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCL------TYSDGSSSYSLREGS 324 (1714)
Q Consensus 251 l~gKRvdfsaRsVI~pDP~l~~~evgiP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~------~~~~~~~~~~l~~~~ 324 (1714)
||||||||||||||+|||+|+++|||||..||++|||||+||+||+++|+++|.||+.. +.+..+..+.++...
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--CCCCCCCCEEEHEEECCCEEEEECCCCCCCCCCCCEEEEECCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf -88--645678533222011266487708886653553213667348882884455668788866545202467787999
Q 000291 325 -KG--HTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAA 401 (1714)
Q Consensus 325 -~~--~~~l~~G~~V~R~l~dgd~Vl~NRqPsLHr~Sima~~~~i~~~~t~rln~~~C~~yNADFDGDeMNihvPQs~eA 401 (1714)
+. ...|++||+|+|||+|||+|||||||||||+|||||+|+|++++||||||+||+||||||||||||+|||||++|
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 HHHHHHHCCCCCCCCCCCCCCCEEEECHHHHHHHHHHH-CCCCCCHHHHHHHHCCCC--CCCCCCCCCCCCCCCCCCEEE
Q ss_conf 99998850663312347999953751035676888652-136679999998610134--565522220232345540121
Q 000291 402 KAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFAL--SPLPRPALSKARCSARWTALQ 478 (1714)
Q Consensus 402 raEa~~Lm~v~~qilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~--~~lp~PaI~Kp~~~~lWTGKQ 478 (1714)
||||++||++++||++|++|+|+++++||+|+|+|+|| +++|+++++++++++... ..+|+|||+||. ++|||||
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 ECCCCCCCCCCC-------------------CCCEEEEECCEECCCCCCCCCCCCH-HHHHHHHHHHHHCHHHHHHCHHH
Q ss_conf 012448998322-------------------5977999765213333556764233-78899999984297999960422
Q 000291 479 ILQSVLPPGFDS-------------------CGDRYLIKKSEVLKGDFDRDTIPSV-INEIVTSIFFEKGPEEVLEFFDS 538 (1714)
Q Consensus 479 i~s~~LP~~~~~-------------------~~~~viI~~Gell~g~ldK~~lg~s-~~~Li~~i~~~~G~~~a~~fLd~ 538 (1714)
+|++++|.++++ .+..|+|++|+|+.|.+||+.+|+. ..+|||.+++.||+.+|..|||.
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 HHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHH
Q ss_conf 29999999984074331077545999999999999999999987554-------------45789999999999999999
Q 000291 539 LQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS-------------TQNELVDLQIENHIRHVKML 605 (1714)
Q Consensus 539 lq~L~~~~L~~~GFSiGl~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~-------------~~~~~le~~~~~~l~~~~~~ 605 (1714)
+++|+++|++.+|||||++|+++++++.+.+.+.++++...+.++.. ..++.++.++...|+++++.
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----CCCCCCCCCCCCCHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECC
Q ss_conf 9999971----398421202111013556777867114614079951234552011122233498998999886520027
Q 000291 606 VAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKG 681 (1714)
Q Consensus 606 i~~~~~~----~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~d~~~ea~GfI~n 681 (1714)
+++.+.+ .|++++|++||||||+.|++||+||||||+++|+| ++|++..+++|||.. .+.+|+++|||.+
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 CCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCCHHHHHHHHHHCEEEEECCCCCCCCCCCEEEEEECCCCCCCCCCCCC
Q ss_conf 44446896530786225431023224444798832478999874138972351113468961388812344544676789
Q 000291 682 CFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPA 761 (1714)
Q Consensus 682 SF~~GL~P~EfFfHsmagREGLiDTAvkTA~sGYL~RrLv~~led~~v~YD~Tvr~~~~~~IiQf~yg~~g~~~~~l~~~ 761 (1714)
||++||+|+|||||||||||||+|||||||+|||||||||++|||++|+||||||++ .|+||||.||+||+|+... ..
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 9605
Q 000291 762 GEPV 765 (1714)
Q Consensus 762 Ge~V 765 (1714)
+.+|
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=1573.31 Aligned_cols=899 Identities=18% Similarity=0.214 Sum_probs=678.9
Q ss_pred CCEEEEEEECCCHHHHHHHCCCCCCCCCC------------CCCCCCCCCCCC---------------CCCCCCCCCCCC
Q ss_conf 31106898249979998705565201468------------888899889999---------------998888989999
Q 000291 12 GQIVGIRFGLATQKEICTASISDCSISHA------------SQLANPFLGLPL---------------EFGKCESCGTSE 64 (1714)
Q Consensus 12 ~~I~~I~F~l~S~eEI~~~Sv~~~~I~~~------------~gl~DprLG~~~---------------~~~~C~TCg~~~ 64 (1714)
.+|++|+|+++||++|+++|+.+ |++| +||+|+|||+|. ++..|+|||...
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---CCCCEEEECCCCCCCCCCHHHHHHH----HHHHHHHH----------C-CC----------HHHHH-------
Q ss_conf 9979---8855268867522344455889999----99997642----------2-61----------28999-------
Q 000291 65 PGKC---EGHFGYIELPIPIYHPSHISELKLT----MYAFQLQI----------K-ND----------GVAQR------- 109 (1714)
Q Consensus 65 ~~~C---pGHFGhIeL~~PVfHp~fik~I~~I----L~~iC~ri----------~-~~----------g~~k~------- 109 (1714)
.+| |||||||||+.||||++||+.+..+ |+++|..| + .. .....
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 --------------------------------------------HHHHH-----H-HHHHHHHCCCHHHHHHHC------
Q ss_conf --------------------------------------------99879-----9-999998059957898411------
Q 000291 110 --------------------------------------------LLSSC-----C-EVKEMLKRIPEETRKKLA------ 133 (1714)
Q Consensus 110 --------------------------------------------i~~~C-----C-eV~~IlkkI~~ed~~~L~------ 133 (1714)
++... + ++.+.+++++.+...++.
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 ---CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCHHHHHHHHHHH
Q ss_conf ---48999987389963068998887872028986445224799999999999999862-06999732013244379999
Q 000291 134 ---GKGYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLA 209 (1714)
Q Consensus 134 ---~~g~~~pe~lil~~lPVPP~~iRp~~~~~g~~~~~~Dlt~~~l~~Ii~~n~~l~~~-~~g~p~~~~~~~~~~~LQ~~ 209 (1714)
.....+||||||++|||||||+||++.+++..+.++|+|. +|++||++|++|+.. ..++|..+. .++|.+||.+
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 HHHHHHHCCCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCHHHCCCCCCCC
Q ss_conf 99998611877678887777787-78998302456733210002458797663168289997633233112300124324
Q 000291 210 VGQYLEVRGTAKSSRDVDARFGV-SQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFE 288 (1714)
Q Consensus 210 v~~~~~~~~~~k~~~~~~~r~~~-~k~~~~~~k~k~~~~R~~l~gKRvdfsaRsVI~pDP~l~~~evgiP~~~A~~Lt~p 288 (1714)
|++|+|+....++......| . .|.+.+++|||+||||+|||||||||||||||+|||+|++||||||..||++||+|
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 CCCCHHHHHHHHHHHHCCCCCCCCCCCCEEEEC-CCCCCCCCCCCCCEEEHEEECCCEEEEECCCCCCCCCCCCEEEEEC
Q ss_conf 312223199999999816765357999528813-6998864567853322201126648770888665355321366734
Q 000291 289 ERVNVHNINYLQELVDNKLCLTYSDGSSSYSLR-EGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVH 367 (1714)
Q Consensus 289 e~vt~~Ni~~l~~lv~~g~~~~~~~~~~~~~l~-~~~~~~~~l~~G~~V~R~l~dgd~Vl~NRqPsLHr~Sima~~~~i~ 367 (1714)
+ | +++||.||+...++. +++.++ +.. ..+ .++.|+||++|||+|||||||||||||||||+|+++
T Consensus 396 ~-----~---~~~lv~~g~~~~i~~--ak~~i~~~~~---~~~-~~~~v~~~v~~gd~VLlNRqPTLHr~sIma~~~~l~ 461 (1265)
T 1hqm_D 396 F-----L---LKKMEEKAFAPNVKA--ARRMLERQRD---IKD-EVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLV 461 (1265)
T ss_dssp H-----H---HHHHHHTTCSSCSHH--HHHHHCSSSC---CCH-HHHTTTTTTTTTCCEECCCSSCCSGGGSCEEBCCCB
T ss_pred H-----H---HHHHHHCCCCCHHHH--HHHHHHHCCC---CCC-CCCEEEEEECCCCEEEEECCCCCCCCCCCCEEEEEC
T ss_conf 9-----9---999998398320466--6665440123---477-642257873049678981686423145421168965
Q ss_pred CCCEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEECHHHHHHHHHHH-CC-----
Q ss_conf 888288445566878886654520246778799999998850663312347999953751035676888652-13-----
Q 000291 368 DDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KK----- 441 (1714)
Q Consensus 368 ~~~t~rln~~~C~~yNADFDGDeMNihvPQs~eAraEa~~Lm~v~~qilsp~~G~Piigl~QD~llg~~llt-kd----- 441 (1714)
+++||||||+||+||||||||||||+|||||++|||||++||++++||+||++|+|+++++||+|+|+|+|| ++
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 ---CCCCHHHHHHHHCCCCCCCCCCCCCCCCC---------------------------------------CCCCCEEEE
Q ss_conf ---66799999986101345655222202323---------------------------------------455401210
Q 000291 442 ---YFLDKAFTQQLAMFALSPLPRPALSKARC---------------------------------------SARWTALQI 479 (1714)
Q Consensus 442 ---~fl~~~~~~~l~~~~~~~lp~PaI~Kp~~---------------------------------------~~lWTGKQi 479 (1714)
+|+++++++++++...+.+|.|..++++. ..+|||||+
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--CCEEEEECCEECCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCHHHHHHHHHHHHHHCC-CEEEE
Q ss_conf 124489983225--977999765213333556764233788999999842979999604222999999998407-43310
Q 000291 480 LQSVLPPGFDSC--GDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADG-FSVSL 556 (1714)
Q Consensus 480 ~s~~LP~~~~~~--~~~viI~~Gell~g~ldK~~lg~s~~~Li~~i~~~~G~~~a~~fLd~lq~L~~~~L~~~G-FSiGl 556 (1714)
|++++|+.++.. .+.+. .+.|.+||+++| +|||.+|++||+++|+.|||.+++|+++||+++| |||||
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-------HCCCCCCCCCCCCCHH
Q ss_conf 77545999999999999999999987554--45789999999999999999999997-------1398421202111013
Q 000291 557 EDFSLSKAALWNIQKEIQALYSLLYHRMS--TQNELVDLQIENHIRHVKMLVAKFIL-------KSSTLGYLIDSKSDSA 627 (1714)
Q Consensus 557 ~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~--~~~~~le~~~~~~l~~~~~~i~~~~~-------~~n~l~~Mi~SGSKGS 627 (1714)
+|+++++++.+.+++..+++..+..++.. ...+..+..+..+|+++++.+++.++ +.|++++|+.||||||
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 HHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCEEEEECCCCCEEEECC
Q ss_conf 55677786711461407995123455201112223349899899988652002744446896530786225431023224
Q 000291 628 VSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSS 707 (1714)
Q Consensus 628 ~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~d~~~ea~GfI~nSF~~GL~P~EfFfHsmagREGLiDTA 707 (1714)
++|++||+||||||..++|+++ + +||.|||++||+|+|||||||||||||+|||
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 CCCCCCCCHHHHHHHHHHCEEEEECCCCC--C-----------------------------------C------------
Q ss_conf 44479883247899987413897235111--3-----------------------------------4------------
Q 000291 708 RGLSEPGTLFKNLMAVLRDVVICYDGTVR--N-----------------------------------V------------ 738 (1714)
Q Consensus 708 vkTA~sGYL~RrLv~~led~~v~YD~Tvr--~-----------------------------------~------------ 738 (1714)
||||+|||||||||+++||++|+||.+.. + +
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 ------------------------------CCCCEEEEEECCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHCCCC--
Q ss_conf ------------------------------689613888123445446767899605872123479067887424799--
Q 000291 739 ------------------------------CSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-- 786 (1714)
Q Consensus 739 ------------------------------~~~~IiQf~yg~~g~~~~~l~~~Ge~VG~laaqsigepatq~~L~t~~-- 786 (1714)
+...||+.|||.+. ..+.++++||+||++||||||||+|||||+|||
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 ------CCCCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHEEEEEECCCC
Q ss_conf ------99986577999997311378998874199972788888763228999999863210138654421377753896
Q 000291 787 ------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPE 860 (1714)
Q Consensus 787 ------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~Le~v~l~dv~~~i~i~y~~~~ 860 (1714)
++|+|+||++|++++++ |+++.|+..+...... ..+ +. .. .+.|
T Consensus 986 Gvas~~dIT~GLPRv~El~eArk-----pk~p~i~a~~~g~v~~---~~~------~~-~~---------~i~i------ 1035 (1265)
T 1hqm_D 986 GVAVGTDITQGLPRVIELFEARR-----PKAKAVISEIDGVVRI---EEG------ED-RL---------SVFV------ 1035 (1265)
T ss_dssp ----CCTTSSHHHHHHHHHHCCC-----CSSCBCCCSSSCBCCC---CCC------SS-CC---------CCCC------
T ss_pred CEECCCCCCCCCHHHHHHHHHCC-----CCCCEEEEECCCEEEE---EEC------CC-CC---------EEEE------
T ss_conf 44000233457432898875107-----8986279841654998---304------88-51---------7999------
Q ss_pred CCCCCCCEEEEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC---CCC
Q ss_conf 44589961899994598898705895445899998555454200236899984025333322222235121558---995
Q 000291 861 IISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKR---SNM 937 (1714)
Q Consensus 861 ~~~~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~gi~~~~~~~~~---~~~ 937 (1714)
..+ + .+ ..+ .++. ..+..++.. ...
T Consensus 1036 ------------~~~-------g----~~--------~~~-----------~ip~----------~~~l~v~~g~~v~~g 1063 (1265)
T 1hqm_D 1036 ------------ESE-------G----FS--------KEY-----------KLPK----------DARLLVKDGDYVEAG 1063 (1265)
T ss_dssp ------------BCS-------S----CC--------CCC-----------CCSS----------CCCCCCCSCCSSTTC
T ss_pred ------------EEC-------C----CE--------EEE-----------ECCC----------CEEEEEECCCEEECC
T ss_conf ------------878-------9----27--------799-----------7478----------528998469777068
Q ss_pred CEEEEEECCCCCCCCCCCEECCCCCCHHHHHHHHHHHHHHHHHH----HHHHHHHHHCCCCCCEEEEECCCE--------
Q ss_conf 66999972368754431000012540379888765555899999----899888762255522023330460--------
Q 000291 938 PCLMFVLRGASDSYLDKLSGVLANMIYPVLLETIIKENWWVRQR----LSASVTMVAKGVLKEHLILLANSM-------- 1005 (1714)
Q Consensus 938 ~~l~~~~~~s~~~~~vd~~~~~~n~I~ei~l~tIIkgi~w~r~~----l~~~~~~~~~~V~~rHl~LlAd~M-------- 1005 (1714)
..+ ++++ +++++|++ +.|++.+|.. ++.+++.+|..|++||+.|+++.|
T Consensus 1064 ~~l---teG~-------------~~~~eil~---v~Giea~~~~lv~EIq~vyr~QGv~I~dkHievivrqM~~kv~i~~ 1124 (1265)
T 1hqm_D 1064 QPL---TRGA-------------IDPHQLLE---AKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTD 1124 (1265)
T ss_dssp SCC---CCSB-------------SHHHHHHH---TTHHHHHHHHHHHHHHHHHHTTSCCCCSSTHHHHHHHHTTEECBSS
T ss_pred CEE---ECCC-------------CCHHHHHH---HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCEEEEC
T ss_conf 035---2267-------------51999999---8639999999999999998974862037899999998742537714
Q ss_pred --------------------------------EEECEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf --------------------------------320207642552101223474322452110235817799999832198
Q 000291 1006 --------------------------------TCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHT 1053 (1714)
Q Consensus 1006 --------------------------------T~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~ 1053 (1714)
|+.+.++||||++++ .+|+|+.||||+| .++|.+||++|++
T Consensus 1125 ~g~t~~l~Ge~v~~~~~~~~n~~~~~~g~~~~~~~~~llGITkasl~--t~SflsaASFqeT-----t~vL~~AAi~gk~ 1197 (1265)
T 1hqm_D 1125 PGDSPLLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALS--TKSWLSAASFQNT-----THVLTEAAIAGKK 1197 (1265)
T ss_dssp CCSSCCSCCCEEGGGTTTTTTTTTTC---CCCCBCCCCCCTHHHHTS--CSCHHHHTTSTTH-----HHHHHHHHHSCCC
T ss_pred CCCCCCCCCCEECHHHHHHHHHHHHHCCCCCCEEEEEEECCEECCCC--CCCHHHCCCHHHH-----HHHHHHHHHCCCC
T ss_conf 88867889866509999999999996689852554556520522334--6774430556888-----9999999972898
Q ss_pred CCCCCHHHHHHCCCCCCCCCCC
Q ss_conf 8788224464158755534565
Q 000291 1054 DNLSSVVAACSWGKHVAVGTGS 1075 (1714)
Q Consensus 1054 D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1714)
|.|.|+.||||+|+++|+|||.
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=1465.92 Aligned_cols=782 Identities=18% Similarity=0.206 Sum_probs=593.4
Q ss_pred CCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99987389963068998887872028986445224799999999999999862-06999732013244379999999986
Q 000291 137 YFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLE 215 (1714)
Q Consensus 137 ~~~pe~lil~~lPVPP~~iRp~~~~~g~~~~~~Dlt~~~l~~Ii~~n~~l~~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~ 215 (1714)
..+|+||||++|||||||+||++.+++..+.++|+|. +|++||++|++|+.. ..++|..+. .+++.+||.+|++|+|
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 HCCCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCHHHCCCCCCCCCCCCHH
Q ss_conf 11877678887777787-78998302456733210002458797663168289997633233112300124324312223
Q 000291 216 VRGTAKSSRDVDARFGV-SQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVH 294 (1714)
Q Consensus 216 ~~~~~k~~~~~~~r~~~-~k~~~~~~k~k~~~~R~~l~gKRvdfsaRsVI~pDP~l~~~evgiP~~~A~~Lt~pe~vt~~ 294 (1714)
+....++.....+| . .|.+.+.+|||+||||+|||||||||||||||+|||+|++||||||..||++||+|+
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 HHHHHHHHHHCCCCCCCCCCCCEEEEC-CCCCCCCCCCCCCEEEHEEECCCEEEEECCCCCCCCCCCCEEEEECCCCEEE
Q ss_conf 199999999816765357999528813-6998864567853322201126648770888665355321366734888288
Q 000291 295 NINYLQELVDNKLCLTYSDGSSSYSLR-EGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVK 373 (1714)
Q Consensus 295 Ni~~l~~lv~~g~~~~~~~~~~~~~l~-~~~~~~~~l~~G~~V~R~l~dgd~Vl~NRqPsLHr~Sima~~~~i~~~~t~r 373 (1714)
.|++||.||+...++. +++.++ +. ...+. ++.|+||++|||+|||||||||||||||||+|++++++|||
T Consensus 657 ---~~r~Lv~nG~a~nik~--AK~li~~~~---~~~~~-v~dVlr~vidgd~VLlNRqPTLHRlSIqAf~~kl~~gkTiR 727 (1524)
T 2a6h_D 657 ---LLKKMEEKGIAPNVKA--ARRMLERQR---DIKDE-VWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQ 727 (1524)
T ss_dssp ---HHHHHHHSTTCSSHHH--HHHHHSSGG---GCCHH-HHHHHHHHSTTCCEEEECSSCCSGGGEEEEEEEEESSSCEE
T ss_pred ---HHHHHHHCCCCCCHHH--HHHHHHHHC---CCCCC-CHHHHEEECCCCEEEECCCCCCCCCCCCEEEEEECCCCCCE
T ss_conf ---9999998398342266--667876411---34653-01220100059667870587434256402688975785101
Q ss_pred ECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHC---------CCCC
Q ss_conf 4455668788866545202467787999999988506633123479999537510356768886521---------3667
Q 000291 374 INPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMFK---------KYFL 444 (1714)
Q Consensus 374 ln~~~C~~yNADFDGDeMNihvPQs~eAraEa~~Lm~v~~qilsp~~G~Piigl~QD~llg~~lltk---------d~fl 444 (1714)
|||+||+||||||||||||+|||||++|||||++||++++||+||++|+|+++++||+|+|+|+||+ ++|+
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--CCCCCCCCCCCCEEEECCCC----CCC-CCCCCCCEEEE
Q ss_conf 99999986101------34565--------------522--22023234554012101244----899-83225977999
Q 000291 445 DKAFTQQLAMF------ALSPL--------------PRP--ALSKARCSARWTALQILQSV----LPP-GFDSCGDRYLI 497 (1714)
Q Consensus 445 ~~~~~~~l~~~------~~~~l--------------p~P--aI~Kp~~~~lWTGKQi~s~~----LP~-~~~~~~~~viI 497 (1714)
++++++.+.+. ..+.+ |+| +|+|| |||||+++.+ ++. .+.++.++.+|
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--------------CCEECCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCHHHHHHHHHHHHHHCCCEEEECCCCCCH
Q ss_conf 7--------------65213333556764233788999999842979999604222999999998407433107754599
Q 000291 498 K--------------KSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSK 563 (1714)
Q Consensus 498 ~--------------~Gell~g~ldK~~lg~s~~~Li~~i~~~~G~~~a~~fLd~lq~L~~~~L~~~GFSiGl~Dl~~~~ 563 (1714)
. +-..+.|++||+++| +|||.+|+.||+.+|+.|||.+++|+++||+++||||||+|+++++
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 HHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH-------HCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 9999999999999999987554--45789999999999999999999997-------13984212021110135567778
Q 000291 564 AALWNIQKEIQALYSLLYHRMS--TQNELVDLQIENHIRHVKMLVAKFIL-------KSSTLGYLIDSKSDSAVSKVVQQ 634 (1714)
Q Consensus 564 ~~~~~i~~~i~~~~~~~~~~~~--~~~~~le~~~~~~l~~~~~~i~~~~~-------~~n~l~~Mi~SGSKGS~~Ni~Qi 634 (1714)
++.+.+.+..+++..+..++.. ...+..+..+..+|+++++.+++.++ +.|++++|+.||||||++|++||
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 HHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCC
Q ss_conf 67114614079951234552011122233498998999886520027444468965307862254310232244447988
Q 000291 635 AGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPG 714 (1714)
Q Consensus 635 ~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~d~~~ea~GfI~nSF~~GL~P~EfFfHsmagREGLiDTAvkTA~sG 714 (1714)
+||||||....|+++ .. +|.|||++||+|+|||||||||||||+|||||||+||
T Consensus 1039 ~gmrGqma~p~GkiI--------------------p~------PI~ssF~eGLtp~EyFfhtmGgReGLvDTAvKTAdSG 1092 (1524)
T 2a6h_D 1039 CGLRGLMQKPSGETF--------------------EV------PVRSSFREGLTVLEYFISSHGARKGGADTALRTADSG 1092 (1524)
T ss_dssp TSCCCCCBCSSSCBC--------------------SS------CCCCCSSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHCCCCCCCCCCCC--------------------CC------CCCCCCCCCCCHHHHHEECCCCCCCCCCCCEEECCCC
T ss_conf 860366046899772--------------------25------1134324699747742012223577533201105688
Q ss_pred CHHHHHHHHHHCEEEEECCCCC--C-----------------------------------C-------------------
Q ss_conf 3247899987413897235111--3-----------------------------------4-------------------
Q 000291 715 TLFKNLMAVLRDVVICYDGTVR--N-----------------------------------V------------------- 738 (1714)
Q Consensus 715 YL~RrLv~~led~~v~YD~Tvr--~-----------------------------------~------------------- 738 (1714)
|||||||+++||++|+||.+.. + +
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 -----------------------CCCCEEEEEECCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHCCCC--------C
Q ss_conf -----------------------689613888123445446767899605872123479067887424799--------9
Q 000291 739 -----------------------CSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP--------S 787 (1714)
Q Consensus 739 -----------------------~~~~IiQf~yg~~g~~~~~l~~~Ge~VG~laaqsigepatq~~L~t~~--------~ 787 (1714)
+...||+.|||.+. ..+.++.+|++||++||||||||+|||||+||| +
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-EEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHEEEEEECCCCCCCCCC
Q ss_conf 9986577999997311378998874-199972788888763228999999863210138654421377753896445899
Q 000291 788 SNNSWELMKEILLCRVSFNNDPIDR-RVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDE 866 (1714)
Q Consensus 788 ~~~g~~rlkEil~~~~~~k~~~~d~-~~~l~L~~~~~~~~~~~e~~a~~V~~~Le~v~l~dv~~~i~i~y~~~~~~~~~~ 866 (1714)
+|+|+||++|+++|++...+.++.. ...+.+.. .....
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 CEEEEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf 61899994598898705895445899998555454200236899984025333322222235121558995669999723
Q 000291 867 GLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMFVLRG 946 (1714)
Q Consensus 867 ~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~l~~~~~~ 946 (1714)
.+.|.-+.+ . ..+. + +. ..+..++. ++ .+ ..+
T Consensus 1291 --~i~i~~~~~--------~--------~~~~-i-------------p~----------~~~l~V~~-gd--~v---~~g 1322 (1524)
T 2a6h_D 1291 --SVFVESEGF--------S--------KEYK-L-------------PK----------EARLLVKD-GD--YV---EAG 1322 (1524)
T ss_dssp --EEEEECSSC--------E--------EEEE-E-------------CT----------TCCCCCCT-TS--EE---CTT
T ss_pred --EEEEECCCC--------E--------EEEE-C-------------CC----------CEEEEEEC-CC--EE---ECC
T ss_conf --899970884--------0--------4786-4-------------77----------60789836-97--56---437
Q ss_pred CCCCCCCCCEECCCCCCHHHHHHHHHHHHHHHHHHH----HHHHHHHHCCCCCCEEEEECCCE-----------------
Q ss_conf 687544310000125403798887655558999998----99888762255522023330460-----------------
Q 000291 947 ASDSYLDKLSGVLANMIYPVLLETIIKENWWVRQRL----SASVTMVAKGVLKEHLILLANSM----------------- 1005 (1714)
Q Consensus 947 s~~~~~vd~~~~~~n~I~ei~l~tIIkgi~w~r~~l----~~~~~~~~~~V~~rHl~LlAd~M----------------- 1005 (1714)
..-++|. +++++|++ |+|++.+|+.| +.+++.+|..|++||++|+++.|
T Consensus 1323 ~~lteG~-------~~~~dil~---v~Giea~~~~iv~Eiq~Vyr~QGv~I~dKHIevIvrqM~~kv~i~~~Gdt~~l~G 1392 (1524)
T 2a6h_D 1323 QPLTRGA-------IDPHQLLE---AKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEG 1392 (1524)
T ss_dssp CBSSSSB-------CCHHHHHH---HHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTSEEEEEECSSSCSSCE
T ss_pred EEEECCC-------CCCHHHEE---ECCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCEEEEECCCCCCCCCC
T ss_conf 2774487-------87422101---0699999999999999999855855135689999998744258824887667898
Q ss_pred -----------------------EEECEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHH
Q ss_conf -----------------------320207642552101223474322452110235817799999832198878822446
Q 000291 1006 -----------------------TCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAA 1062 (1714)
Q Consensus 1006 -----------------------T~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ 1062 (1714)
|+.+.++||||++++ ..|+|+.||||+| .++|.+||++|++|.|.|+.||
T Consensus 1393 e~v~~~~~~~~n~~~~~~g~~~a~~~~~llGITkasL~--t~SfLsaASFqeT-----trvLt~AAi~Gk~D~L~GlkEN 1465 (1524)
T 2a6h_D 1393 QVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALS--TKSWLSAASFQNT-----THVLTEAAIAGKKDELIGLKEN 1465 (1524)
T ss_dssp EEHHHHHHHHHHHHTTSCSCCCCEEEECCCCHHHHHHS--CSCHHHHHHSSCH-----HHHHHHHHHTTEEEECCSHHHH
T ss_pred CEEEHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCC--CCCHHHHCCHHHH-----HHHHHHHHHCCCCCCCCCCHHH
T ss_conf 65419999999999997689852210035420531334--6872331574888-----9999999863898778982787
Q ss_pred HHCCCCCCCCCCCEEEE
Q ss_conf 41587555345652899
Q 000291 1063 CSWGKHVAVGTGSRFDL 1079 (1714)
Q Consensus 1063 ii~Gk~~~~GTG~~~~l 1079 (1714)
||+|+++|+|||+ |++
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=1441.15 Aligned_cols=980 Identities=19% Similarity=0.234 Sum_probs=666.5
Q ss_pred CCCCCEEEEEEECCCHHHHHHHCCCCCCCCCC------------CCCCCCCC-CCCC--------------CCCCCCCCC
Q ss_conf 45531106898249979998705565201468------------88889988-9999--------------998888989
Q 000291 9 ILEGQIVGIRFGLATQKEICTASISDCSISHA------------SQLANPFL-GLPL--------------EFGKCESCG 61 (1714)
Q Consensus 9 ~~~~~I~~I~F~l~S~eEI~~~Sv~~~~I~~~------------~gl~DprL-G~~~--------------~~~~C~TCg 61 (1714)
.....+..|+++|.||++|+.+|+.| |++| .||+++|. |+.. ++..|++||
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----HHHHHHHHH---HHC--------CC-------------------
Q ss_conf 99999798---855268867522344455889----999999976---422--------61-------------------
Q 000291 62 TSEPGKCE---GHFGYIELPIPIYHPSHISEL----KLTMYAFQL---QIK--------ND------------------- 104 (1714)
Q Consensus 62 ~~~~~~Cp---GHFGhIeL~~PVfHp~fik~I----~~IL~~iC~---ri~--------~~------------------- 104 (1714)
... .+|. .|||||+|+.||+|++||+.+ ..+|.+.|. +++ ..
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-HHHHHHHCC-CHHHHHHHC---------CCCCCCCCCEEEEECCCCCCC
Q ss_conf ------------2--899999879-----9-999998059-957898411---------489999873899630689988
Q 000291 105 ------------G--VAQRLLSSC-----C-EVKEMLKRI-PEETRKKLA---------GKGYFPQDGYILEYLPVPPNC 154 (1714)
Q Consensus 105 ------------g--~~k~i~~~C-----C-eV~~IlkkI-~~ed~~~L~---------~~g~~~pe~lil~~lPVPP~~ 154 (1714)
| ..++++... + ++++.++.. ....+.++. .....+|+||||++||||||+
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-HCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf 87872028986445224799999999999999862-06999732013244379999999986118776788877777877
Q 000291 155 LSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVS 233 (1714)
Q Consensus 155 iRp~~~~~g~~~~~~Dlt~~~l~~Ii~~n~~l~~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~~~~k~~~~~~~r~~~~ 233 (1714)
+||++.+++..+.++|+|. +|++||++|++|+.. ..++|..+. .++|.+||.+|++|+|+....++...... ...
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 CCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 89983024567332100024587976631682899976332331123001243243122231999999998167653579
Q 000291 234 QDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSD 313 (1714)
Q Consensus 234 k~~~~~~k~k~~~~R~~l~gKRvdfsaRsVI~pDP~l~~~evgiP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~~~~~ 313 (1714)
|.+.+++|||+||||+|||||||||||||||+|||+|++||||||..||++||+| ||+++|+ .+|....++.
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 CCCEEEECCCCCCCCCCCCCCEEEHEEECCCEEEEECCCCCCCCCCCCEEEEECCCCEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf 99528813699886456785332220112664877088866535532136673488828844556687888665452024
Q 000291 314 GSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHL 393 (1714)
Q Consensus 314 ~~~~~~l~~~~~~~~~l~~G~~V~R~l~dgd~Vl~NRqPsLHr~Sima~~~~i~~~~t~rln~~~C~~yNADFDGDeMNi 393 (1714)
.. ++ +. .... ..+.|+||+++||+|||||||||||+|||||++++++++||||||+||+||||||||||||+
T Consensus 397 ak-~~-v~-----~~~~-~v~~vl~~vi~gd~VLlNRqPTLHr~sIma~~~~l~~~ktirlnp~vC~~yNADFDGDeMnv 468 (1407)
T 3lu0_D 397 AK-KM-VE-----REEA-VVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAV 468 (1407)
T ss_dssp TT-TT-TT-----SSCS-SHHHHHHTTTTSCCEEEEESSCCSGGGEEEEEEEEESSSSEEECTGGGGTTTCCSSSCEEEE
T ss_pred HH-HH-HH-----HCCC-CHHHHHHHHHHCEEEEECCCCCCCCCCCEEEEEEECCCCEEEECHHHCCCCCCCCCCCEEEE
T ss_conf 99-98-87-----5188-33568998753425665488631224432446786489658867656443457734423554
Q ss_pred CCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEECHHHHHHHHHHH-CCC--------CCCHHHHHHHHCCCC------C
Q ss_conf 6778799999998850663312347999953751035676888652-136--------679999998610134------5
Q 000291 394 FYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKY--------FLDKAFTQQLAMFAL------S 458 (1714)
Q Consensus 394 hvPQs~eAraEa~~Lm~v~~qilsp~~G~Piigl~QD~llg~~llt-kd~--------fl~~~~~~~l~~~~~------~ 458 (1714)
|+|||++|||||++||++++||++|++|+|+++++||+|+|+|+|| ++. |++.+++++++.... +
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 CCCCCC-----------CCCCCCCCCCCEEEECCCCCCCCCCCCCCEEEEECCEECCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 655222-----------202323455401210124489983225977999765213333556764233788999999842
Q 000291 459 PLPRPA-----------LSKARCSARWTALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEK 527 (1714)
Q Consensus 459 ~lp~Pa-----------I~Kp~~~~lWTGKQi~s~~LP~~~~~~~~~viI~~Gell~g~ldK~~lg~s~~~Li~~i~~~~ 527 (1714)
.+..|. ..++. ++|+|||||+++||+++.+ +++.+.++|+.++ +||+.+|++|
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 CHHHHHHCHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
Q ss_conf 979999604222999999998407433107754599999999999999999998755-------4457899999999999
Q 000291 528 GPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRM-------STQNELVDLQIENHIR 600 (1714)
Q Consensus 528 G~~~a~~fLd~lq~L~~~~L~~~GFSiGl~Dl~~~~~~~~~i~~~i~~~~~~~~~~~-------~~~~~~le~~~~~~l~ 600 (1714)
|+.+|+.|||++++|+++|++.+|||||++|+++|+++.+.+.+..+++..+..++. +.|++.++ +|+
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 GLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVID-----IWA 687 (1407)
T ss_dssp CSHHHHHHHHHHHHHHHHHHHHHTCCCCSTTSCCCTTHHHHHHHHHTHHHHHHHHHHHTSCCSSTTTTTHHH-----HHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH-----HHH
T ss_conf 999999999999999999997668477433271586799999999999999999997599862268999999-----999
Q ss_pred HHHHHHHHHHHH-------------------CCCCCCCCCCCCCHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCCC
Q ss_conf 999999999971-------------------3984212021110135567778671146140799512345520111222
Q 000291 601 HVKMLVAKFILK-------------------SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHF 661 (1714)
Q Consensus 601 ~~~~~i~~~~~~-------------------~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f 661 (1714)
++++.+.+.+++ .|++++|++||||||+.|++||+||+|||..+.++.+
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 CCCCCCCCCCCCCCCCEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCCHHHHHHHHHHCEEEEEC--CCCCCC-
Q ss_conf 33498998999886520027444468965307862254310232244447988324789998741389723--511134-
Q 000291 662 ERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYD--GTVRNV- 738 (1714)
Q Consensus 662 ~~~~p~~~d~~~ea~GfI~nSF~~GL~P~EfFfHsmagREGLiDTAvkTA~sGYL~RrLv~~led~~v~YD--~Tvr~~- 738 (1714)
+. +|.+||++||+|+|||||||+|||||+|||||||+|||||||||+++||++|.++ ||.+++
T Consensus 756 --------e~------PI~ssFreGLtp~EyFfst~GaRKGL~DTALKTAdSGYLTRRLVdv~QDviV~e~DCGT~~Gi~ 821 (1407)
T 3lu0_D 756 --------ET------PITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIM 821 (1407)
T ss_dssp --------SS------CCCCCSSSCCCHHHHHHHHHHHHHHHHHTTTTTTCTTTTTHHHHTTSTTCCBCCCSCCCCSSCE
T ss_pred --------CH------HHHCCCCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCEEEEECCCCCCCCEE
T ss_conf --------10------1322520279777852102320112345244424321478899886465499746789988879
Q ss_pred --------------------------------------------------------------------CCCCEEEEEECC
Q ss_conf --------------------------------------------------------------------689613888123
Q 000291 739 --------------------------------------------------------------------CSNSIIQFDYAV 750 (1714)
Q Consensus 739 --------------------------------------------------------------------~~~~IiQf~yg~ 750 (1714)
+...||+.|||+
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 CCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHCCCCC--CCC-CH---------------HHHHHHHHHHCCCCCCCCCC
Q ss_conf 4454467678996058721234790678874247999--998-65---------------77999997311378998874
Q 000291 751 NARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSPS--SNN-SW---------------ELMKEILLCRVSFNNDPIDR 812 (1714)
Q Consensus 751 ~g~~~~~l~~~Ge~VG~laaqsigepatq~~L~t~~~--~~~-g~---------------~rlkEil~~~~~~k~~~~d~ 812 (1714)
+. ....++..||+||++||||||||+||+||+|||- +.+ +. ..++-+.+ +.. ..-...+
T Consensus 902 dL-a~g~~V~iGEAVGiIAAQSIGEPGTQLTMRTFHtGGvas~~~~~~~i~a~~~G~v~~~~~~~v~~-~~g-~~vv~~r 978 (1407)
T 3lu0_D 902 DL-ARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVKSVVN-SSG-KLVITSR 978 (1407)
T ss_dssp CS-SSSSCCCSSCCTTHHHHHHHHSGGGSSCCSCTTCCCCCCCCCCCSCEECCSCEEEECCSCCCEEC-TTS-CEECCCS
T ss_pred CC-CCCCCCCCCCEEEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCEEEEECCEEEEC-CCC-CEEEEEC
T ss_conf 50-48988315735546632004887541263523306622343210016733476899716679986-889-8899946
Q ss_pred EEEEECCCCCCC--CCCCCHHHHH-HH-----------------------HHHHCCCCHHHHHHEEEE--EECCCCCCC-
Q ss_conf 199972788888--7632289999-99-----------------------863210138654421377--753896445-
Q 000291 813 RVILYLNDCGCG--RKYCQERAAY-MV-----------------------KNQLKRVSLKDAAVEFLI--EYKKPEIIS- 863 (1714)
Q Consensus 813 ~~~l~L~~~~~~--~~~~~e~~a~-~V-----------------------~~~Le~v~l~dv~~~i~i--~y~~~~~~~- 863 (1714)
...+.+.+.... .+|.-.+.|. .| ...--.+.|+|+..-+.+ +.+..+...
T Consensus 979 ~~~i~i~d~~g~~~~~~~ip~gs~l~v~~g~~V~~g~~ia~wDp~~~piise~~G~v~f~d~~~g~t~~~~~d~~tg~~~ 1058 (1407)
T 3lu0_D 979 NTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSS 1058 (1407)
T ss_dssp SEEEEEECSSCCBCCCEEECTTCEESSCSSCEECTTCEEEECCSSCCCEECSSCEEEEEESCCBTTTEEEEECSSSCCEE
T ss_pred CEEEEEECCCCCEEEEEECCCCCEEEECCCCEECCCCEEEEEECCCEEEEECCCEEEEEEEECCCCEEEEEECCCCCCEE
T ss_conf 71899984899678899758897899708899627988999966760599635258997650368336787516779568
Q ss_pred --------------CCCCEEEEEEECH--HHH--------HHHCCCH--------------HHHHHHHHHHHHHHHHCC-
Q ss_conf --------------8996189999459--889--------8705895--------------445899998555454200-
Q 000291 864 --------------DDEGLVGHIHLNK--ILL--------EDLRISM--------------HDILPKCQETLKSFCKKK- 904 (1714)
Q Consensus 864 --------------~~~~wv~~i~Ld~--e~L--------~~~~lt~--------------~~I~~k~~~~~~~~~~~~- 904 (1714)
.-.|-+ .| +|. +.+ ..|.|.+ .+|+.++-....+.....
T Consensus 1059 ~~v~~~~~~~~~~~~~~p~i-~i-~~~~g~~~~~~~~~~~~~y~lp~~a~~~v~~g~~v~~g~vlakip~~~~k~~DIt~ 1136 (1407)
T 3lu0_D 1059 LVVLDSAERTAGGKDLRPAL-KI-VDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITG 1136 (1407)
T ss_dssp EEECCSSSSCTTTTSCCCEE-EE-ECSSSCBCBCTTSCCBCEEECCTTCCCCCCSSCEECTTCEEECCCCCCCCSSCCCC
T ss_pred EEEEECCCCCCCCCCCCCEE-EE-ECCCCCEEECCCCCCCEEEECCCCCEEEECCCCEECCCCEEEECCHHHCCCCCHHC
T ss_conf 99973054556555677439-99-76999887424787642674589848995479885168668863314316430313
Q ss_pred HHHHHHHHHH-----CCCCCCCCCCCC---------CCCCCCCC-C--CCCEEEEEECCCC----CCCCCCCEECCC---
Q ss_conf 2368999840-----253333222222---------35121558-9--9566999972368----754431000012---
Q 000291 905 KMKKVVQFFK-----NTSLSISECCSF---------QQSCADKR-S--NMPCLMFVLRGAS----DSYLDKLSGVLA--- 960 (1714)
Q Consensus 905 ~~~~i~~~~~-----~~~~~~~~~gi~---------~~~~~~~~-~--~~~~l~~~~~~s~----~~~~vd~~~~~~--- 960 (1714)
....+.+.|- ..-+-+-+.|.+ .+.++..+ + ...++ + -.+.. +-+-|..=..++
T Consensus 1137 GLprv~eLfEar~pk~~a~i~ei~G~v~~~~~~~~~~~~~i~~~~g~~~~~y~-i-~~~~~~~v~~gd~v~~G~~l~~G~ 1214 (1407)
T 3lu0_D 1137 GLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEM-I-PKWRQLNVFEGERVERGDVISDGP 1214 (1407)
T ss_dssp SHHHHHHHHTTCCCSSCCCCCSSCSCCEECCCCSSCEEEECCCSSCCTTCEEE-E-CSSSCCCCCSSSCCCTTCCCSSSC
T ss_pred CCHHHHHHHHCCCCCCCEEEECCCEEEEEEECCCCCEEEEEEECCCCEEEEEE-C-CCCCEEEECCCCEECCCCCCCCCC
T ss_conf 72789988750489885277234059997211688459999718997058997-4-689635515899874798746899
Q ss_pred CCCHHHHHHHHHHHHHHHHHH----HHHHHHHHHCCCCCCEEEEECCCEEEEC---------------------------
Q ss_conf 540379888765555899999----8998887622555220233304603202---------------------------
Q 000291 961 NMIYPVLLETIIKENWWVRQR----LSASVTMVAKGVLKEHLILLANSMTCAG--------------------------- 1009 (1714)
Q Consensus 961 n~I~ei~l~tIIkgi~w~r~~----l~~~~~~~~~~V~~rHl~LlAd~MT~~G--------------------------- 1009 (1714)
.+.++|++ |+|++.+++. ++.+++.+|..|+++|+.++++.||.+.
T Consensus 1215 ~~p~dil~---v~Giea~~~ylv~Evq~VYr~QGV~IndKHIEvIvrqM~~kv~I~d~Gdt~fl~Ge~vd~~~~~~~N~~ 1291 (1407)
T 3lu0_D 1215 EAPHDILR---LRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRE 1291 (1407)
T ss_dssp CCHHHHHH---HSCHHHHHHHTTTTTHHHHHHHTCCCCSHHHHTTTGGGTSBCEESSCSSSCSCCCCBSHHHHHHHHHHH
T ss_pred CCHHHHHH---HHCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCEEEEECCCCCCCCCCEECHHHHHHHHHH
T ss_conf 99999998---639999999999999999986694302114889999972746994178766677542209999999999
Q ss_pred -------------EEEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCCC
Q ss_conf -------------076425521012234743224521102358177999998321988788224464158755534565
Q 000291 1010 -------------DLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075 (1714)
Q Consensus 1010 -------------~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~ 1075 (1714)
.++|||+..+ ..+|+|+.|||++| .++|.+||++|++|.|.|+.||||+|+++|+|||.
T Consensus 1292 ~~~~g~~pa~~~p~llGITkasl--~t~SflSaASFQeT-----tkvLteAAi~Gk~D~L~GlkENVIvG~lIPaGTG~ 1363 (1407)
T 3lu0_D 1292 LEANGKVGATYSRDLLGITKASL--ATESFISAASFQET-----TRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGY 1363 (1407)
T ss_dssp TTSSSCCCCCEECCCCCTTTTTT--SCSCTTTGGGSSCH-----HHHHHHHHHTCCEECCCSSHHHHTTTCCCTTTTTS
T ss_pred HHHCCCCCCEEEEEEECEEECCC--CCCCCHHHCCHHHH-----HHHHHHHHHCCCCCCCCCCCCCEEECCCCCCCCCC
T ss_conf 99769998433444512242123--57885022205668-----99999988638977578853252754634677682
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=474.72 Aligned_cols=258 Identities=21% Similarity=0.300 Sum_probs=211.5
Q ss_pred CCCCEEEEEEECCCHHHHHHHCCCCCCCCC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECC
Q ss_conf 553110689824997999870556520146-----------888889988999999888898999999798855268867
Q 000291 10 LEGQIVGIRFGLATQKEICTASISDCSISH-----------ASQLANPFLGLPLEFGKCESCGTSEPGKCEGHFGYIELP 78 (1714)
Q Consensus 10 ~~~~I~~I~F~l~S~eEI~~~Sv~~~~I~~-----------~~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~ 78 (1714)
..++|++|+|+++||+||+++||++ |++ ++||+|||||++++...|+|||.+. .+||||||||+|+
T Consensus 65 ~~~~i~~i~F~~~s~eeI~~~Sv~~--I~~~~~~d~~~~P~~gGl~D~rlG~~~~~~~C~TCg~~~-~~CpGHfGhIeL~ 141 (436)
T 3qqc_A 65 GGKVIGSIEFGILSPQEIRKMSAVE--VTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGRA-GECPGHFGHIELA 141 (436)
T ss_dssp --CEEEEEECCBCCHHHHHHTEEEE--CCBCCCCC----CCCSBSSCSSSCCCSSCCCCSSSCCCS-SSCCCCEEEEEEE
T ss_pred CCCEEEEEEECCCCHHHHHHHCCEE--EECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCEEEEEC
T ss_conf 5535632263139989999848868--846621478897367885575446779999889999977-7279974367504
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHH---CCC-----H-----------------HHHHHHHHH--------H----------
Q ss_conf 52234445588999999997642---261-----2-----------------899999879--------9----------
Q 000291 79 IPIYHPSHISELKLTMYAFQLQI---KND-----G-----------------VAQRLLSSC--------C---------- 115 (1714)
Q Consensus 79 ~PVfHp~fik~I~~IL~~iC~ri---~~~-----g-----------------~~k~i~~~C--------C---------- 115 (1714)
+|||||+||+.|++||+|+|..| +-+ . ..+++.+.| |
T Consensus 142 ~PVfh~gF~~~I~kILr~vC~~C~klll~~~~~~~f~~~lr~~~~~~~~~k~~~~~i~~~~k~~~~C~gCG~~qp~Ir~e 221 (436)
T 3qqc_A 142 RPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNRRSEFNEIIKEIHKKAKERMVCPHCGAPQYPIKFE 221 (436)
T ss_dssp EEEECGGGHHHHHHHHHHSCSTTCCCSSCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHTCCSCC-------CCCBC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEE
T ss_conf 27777779999999998777875632466222999999998654303038899999999715577586637738648980
Q ss_pred ------------------------HHHHHHHCCCHHHHHHHCC-CCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf ------------------------9999980599578984114-899998738996306899888787202898644522
Q 000291 116 ------------------------EVKEMLKRIPEETRKKLAG-KGYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSD 170 (1714)
Q Consensus 116 ------------------------eV~~IlkkI~~ed~~~L~~-~g~~~pe~lil~~lPVPP~~iRp~~~~~g~~~~~~D 170 (1714)
+|++||++|+++|+++|+. ..+.+||||||++||||||++||++.+++..+.+||
T Consensus 222 ~~~~~~~~~~~~~~~~~k~~LtP~~vl~ifk~IsdeD~~lLGl~~~~~rPewmIlt~LPVpPp~vRPsv~~~~g~~~edD 301 (436)
T 3qqc_A 222 KPTIYWEIRKDEQGNEYRHRLMPTEVRDWLEKIPDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDD 301 (436)
T ss_dssp SSSCEEEECCC---CCCEEEECHHHHHHHHHHSCTTTGGGSSCCTTTCCGGGGEEEEEEECCGGGSCCBCC---CCBCCH
T ss_pred CCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCEEECCCCCCCCH
T ss_conf 55122102455445532412199999999986798889885446567984206764022499867662783787577875
Q ss_pred HHHHHHHHHHHHHHHHHHH-HCCCCCCCCHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 4799999999999999862-0699973201324437999999998611--877678887777787789983024567332
Q 000291 171 LSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVR--GTAKSSRDVDARFGVSQDPNSTTKAWLEKM 247 (1714)
Q Consensus 171 lt~~~l~~Ii~~n~~l~~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~--~~~k~~~~~~~r~~~~k~~~~~~k~k~~~~ 247 (1714)
||+ +|++||++|+.|+.. ..|+|..+. .+.|++||++|++|+|+. +.+.+... .. ...|.+.+++|||+|||
T Consensus 302 LT~-kl~~II~~N~~L~~~~~~gap~~~i-~~~~~lLQ~~V~~~~dn~~~g~~~~~~~-~~--rp~ksi~~rLkGKeGRf 376 (436)
T 3qqc_A 302 LTH-KLVDIIRINNRLKQNIEAGAPQLII-EDLWDLLQYHVTTYINNEAPGVPPAKHK-SG--RPLKTLAQRLKGKEGRF 376 (436)
T ss_dssp HHH-HHHHHHHHHHHHHHHHHSCCCSHHH-HHHHHHHHHHHHHHHCTTCTTCCCCBCT-TS--CBCCCHHHHHCC-----
T ss_pred HHH-HHHHHHHHHHHHHHHHHCCCCHHHH-HHHHHHHHHHHHHHCCCCCCCCCCCCCC-CC--CCCCCHHHHHCCCCCEE
T ss_conf 899-9999999989999999749967789-9999999999875205788888743457-89--87643676624655411
Q ss_pred HHCCCCCCCCCCCC-EEEECCCCCCCCCCCCHHHCCCCCCCCC
Q ss_conf 10002458797663-1682899976332331123001243243
Q 000291 248 RTLFIRKGSGFSSR-SVITGDAYKRVNEIGVPFEIAQRITFEE 289 (1714)
Q Consensus 248 R~~l~gKRvdfsaR-sVI~pDP~l~~~evgiP~~~A~~Lt~pe 289 (1714)
|+||||||||||+| ||| ..+|.+|++|.
T Consensus 377 R~NL~GKRVdy~~~~s~~--------------~~~~~e~~~~~ 405 (436)
T 3qqc_A 377 RGNLSGGAGSGAGSGSVL--------------ARAAFEITVQH 405 (436)
T ss_dssp ------------------------------------CCCCHHH
T ss_pred CCCCCCCCCCCCCCHHHH--------------HHHHHHHHHHH
T ss_conf 475788888866522299--------------99889987999
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=401.43 Aligned_cols=331 Identities=16% Similarity=0.198 Sum_probs=256.3
Q ss_pred CHHHHHHHHHHCEEEEEC--CCCCCCCC--CCEEEEEECCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHCCCC----
Q ss_conf 324789998741389723--51113468--9613888123445446767899605872123479067887424799----
Q 000291 715 TLFKNLMAVLRDVVICYD--GTVRNVCS--NSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSP---- 786 (1714)
Q Consensus 715 YL~RrLv~~led~~v~YD--~Tvr~~~~--~~IiQf~yg~~g~~~~~l~~~Ge~VG~laaqsigepatq~~L~t~~---- 786 (1714)
.|+.++++.+++..+... .|... +. -.+|..||+ +++++|||+||++||||||||+|||||+|||
T Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~y~------r~lv~pGEAVGiIAAQSIGEPgTQlTLrTFH~gGv 95 (395)
T 4ayb_C 23 ILPQKIVEDLKNLISNKEVLVTRDE-IDKIFDLAIKEYS------EGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGI 95 (395)
T ss_dssp TSCSHHHHHHHHHHHHSTTCCCHHH-HHHHHHHHHHHHH------HTBCCTTCCHHHHHHHHHHHHHHTCC---------
T ss_pred CCCHHHHHHHHHHHCCCEEECCHHH-HHHHHHHHHHHHH------HHCCCCCCHHHHHHHHHCCCCHHHHCCCCCEEEEE
T ss_conf 1309999999987401225169999-9999999999998------73589973576877765078103220234055123
Q ss_pred ---CCCCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHEEEEEECCCCCCC
Q ss_conf ---99986577999997311378998874199972788888763228999999863210138654421377753896445
Q 000291 787 ---SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS 863 (1714)
Q Consensus 787 ---~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~Le~v~l~dv~~~i~i~y~~~~~~~ 863 (1714)
++|+|+||++||+++++. +++|.++++|.+.+.. ++++|++++.+++.+++++++..+.+.+.+.
T Consensus 96 a~~nvT~GlPRl~Ei~~a~k~----~~tp~~~i~l~~~~~~----~~e~~~~~~~~ie~~~~~~~~~~~~i~~~~~---- 163 (395)
T 4ayb_C 96 RELNVTLGLPRLIEIVDAKKV----PSTPMMTIYLTDEYKH----DKEKALEVARKLEYTKIENVVSSTSIDIASM---- 163 (395)
T ss_dssp ----CCCSHHHHHHHHTCCSS----CSSCEEEECCTTTGGG----CHHHHHHHHHHHHCCCHHHHEEEEEEETTTT----
T ss_pred CCEEEECCCCCEEEECCCCCC----CCCCCEEEEECCCCCC----CHHHHHHHCCCEEEEECCCEEEEEEEEECCC----
T ss_conf 211013475434771246547----7787238995465442----2888876314315887221135667740564----
Q ss_pred CCCCEEEEEEECHHHHHHHCCCHHHHHHHHHHHHH-HHH---HCC--------------HHHHHHHHHHCCCCCCCCCCC
Q ss_conf 89961899994598898705895445899998555-454---200--------------236899984025333322222
Q 000291 864 DDEGLVGHIHLNKILLEDLRISMHDILPKCQETLK-SFC---KKK--------------KMKKVVQFFKNTSLSISECCS 925 (1714)
Q Consensus 864 ~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~-~~~---~~~--------------~~~~i~~~~~~~~~~~~~~gi 925 (1714)
.+.+++|.+.+.++++++++|..++..... .+. ... ..+.+...+. ...++++
T Consensus 164 -----~~~~~~d~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~----~~~i~gi 234 (395)
T 4ayb_C 164 -----SIILQLDNEMLKDKGVTVDDVKKAINRLKLGEFVIDESEGNTLNISFANIDSIAALFKLRDKIL----NTKIKGI 234 (395)
T ss_dssp -----EEEEEECGGGGBTTBCHHHHHHHHHHHSCCSSEEEEECSSEEEEEECCSSCCCCCTHHHHHHHH----HHCCCSS
T ss_pred -----CEEEEHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEECCCCCEEEEECCCCCHHHHHHHHHHHCC----CCEEECC
T ss_conf -----1455200234541374499999877652267579852667278862378716999999875303----6177345
Q ss_pred --CCCCCCCCCCCCCEEEEEECCCC-----CCCCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHHHH----HHHHHCCCC
Q ss_conf --23512155899566999972368-----7544310000125403798887655558999998998----887622555
Q 000291 926 --FQQSCADKRSNMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETIIKENWWVRQRLSAS----VTMVAKGVL 994 (1714)
Q Consensus 926 --~~~~~~~~~~~~~~l~~~~~~s~-----~~~~vd~~~~~~n~I~ei~l~tIIkgi~w~r~~l~~~----~~~~~~~V~ 994 (1714)
+.++.+.++++.+++ .+++++ ..++++..++.+|+|++|++ +.|++++|+.|..+ +..+|..||
T Consensus 235 ~gi~r~~~~~~~~~~~~--~t~g~~l~~~~~~~~vd~~~~~sn~i~eI~~---vlGiEAar~~iv~Ei~~V~~~~Gv~In 309 (395)
T 4ayb_C 235 KGIKRAIVQKKGDEYII--LTDGSNLSGVLSVKGVDIAKVETNNIREIEE---VFGIEAAREIIIREISKVLAEQGLDVD 309 (395)
T ss_dssp SSCCEEEEEEETTEEEE--EEESCCHHHHTTSTTCCTTTCEESCTTHHHH---HHCHHHHHHHHHHHHHHHHHTTSCCCC
T ss_pred CCEEEEEEECCCCEEEE--EECCCCCEEEEEEECCCCCCCCCCCCHHHHH---HHHHHHHHHHHHHHHHHHHHCCCCEEC
T ss_conf 56058777416987998--7258773156675022132114674054330---000888899998767778760685103
Q ss_pred CCEEEEECCCEEEECEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCC
Q ss_conf 22023330460320207642552101223474322452110235817799999832198878822446415875553456
Q 000291 995 KEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTG 1074 (1714)
Q Consensus 995 ~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG 1074 (1714)
+|||.|+||.||++|.+++++|+|+..+..|+|++||||+| .++|.+||.+|++|+|.|++||||+||++|+|||
T Consensus 310 ~rHi~li~d~Mt~~G~~~~igr~g~s~~t~S~LsaASFqeT-----t~vLteAAi~Gk~D~L~GlkENVIvGklipaGTG 384 (395)
T 4ayb_C 310 MRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVT-----VKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTG 384 (395)
T ss_dssp HHHHHHHHHHHHGGGSCCCSSSSSHHHHCSCHHHHHHHSCT-----HHHHHHHHHTTCBCCCCSHHHHHHHTCCCSSGGG
T ss_pred HHHHHHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHCCHHH-----HHHHHHHHHCCCCCCCCCHHHHEECCCCCCCCCC
T ss_conf 37865554132013647526752565799899998327639-----9999999854897778786997101898888867
Q ss_pred CEEEEEECCC
Q ss_conf 5289996067
Q 000291 1075 SRFDLLWQTE 1084 (1714)
Q Consensus 1075 ~~~~l~~~~~ 1084 (1714)
+ |||++++.
T Consensus 385 ~-f~l~~~p~ 393 (395)
T 4ayb_C 385 M-VELTMRPI 393 (395)
T ss_dssp T-CEEEECSC
T ss_pred C-EEEEECCC
T ss_conf 6-28871566
No 9
>2k0m_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Rhodospirillum rubrum atcc 11170}
Probab=1.00 E-value=1 Score=202.72 Aligned_cols=89 Identities=27% Similarity=0.634 Sum_probs=81.2
Q ss_pred HHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCC
Q ss_conf 66653027899999998612699999966986156499998522997100036983159980279989861799994089
Q 000291 1579 QDILSDVEPIMRSIRRIMHQSGYNDGDRLSADDKSFIFDNVFNYHPDKAMKMGAGIDHFKVDKHGSFQDSRCLFVVSTDG 1658 (1714)
Q Consensus 1579 ~~i~~~~~~~~~~~~~il~~~~y~~g~~l~~~d~~~~l~~ll~~Hp~~~~Kig~gi~~~~v~~~p~~~~srcf~vvr~Dg 1658 (1714)
.+.|.++..++.++|+||| +|++|++|+++|+.+ |+.||.|||++++||||||++|+|+.| .| +||||||||+||
T Consensus 11 ~~~F~s~~~~~~~~k~iL~--~y~~g~~l~~~d~~~-l~~lL~~HP~~~~KiG~Gi~~i~V~~h-~~-~srCFfvvR~DG 85 (104)
T 2k0m_A 11 GHEFARKADALAFMKVMLN--RYRPGDIVSTVDGAF-LVEALKRHPDATSKIGPGVRNFEVRSA-DY-GTQCFWILRTDG 85 (104)
T ss_dssp TEEESSHHHHHHHHHHHHH--HSCTTEECCHHHHHH-HHHHHHTSTTHHHHHTTCEEEEEEEES-SS-SCEEEEEEETTS
T ss_pred CEECCCHHHHHHHHHHHHH--HCCCCCCCCHHHHHH-HHHHHHHCCCHHHHCCCCCCEEEEECC-CC-CCCEEEEEEECC
T ss_conf 9801899999999999998--689989648889999-999998597278862899045998338-99-986799999589
Q ss_pred CCCCCCHHHHHHHH
Q ss_conf 83122089999753
Q 000291 1659 SQQDFSYRKCLESF 1672 (1714)
Q Consensus 1659 ~~~dFSy~kCi~~~ 1672 (1714)
|.+||||+|||++-
T Consensus 86 t~~DFSy~KCv~~~ 99 (104)
T 2k0m_A 86 SEERFSYKKCVLEH 99 (104)
T ss_dssp CEEECCGGGSSCCT
T ss_pred CEEEEEHHHHHHHH
T ss_conf 83203589986523
No 10
>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=49.90 Aligned_cols=47 Identities=30% Similarity=0.294 Sum_probs=40.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHCCCCC
Q ss_conf 21012234743224521102358177999998321988788224464158755
Q 000291 1017 GGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHV 1069 (1714)
Q Consensus 1017 ~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~ 1069 (1714)
-.+ ..+.|++.+++||.+ .++|++|+.+|++|+|+||++||++||.-
T Consensus 385 Vdy-~~~~s~~~~~~~e~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 431 (436)
T 3qqc_A 385 GSG-AGSGSVLARAAFEIT-----VQHLFEAAEKGEVDNLNGVIENVLIGQKH 431 (436)
T ss_dssp ---------------CCCC-----HHHHHHHHHHTCEEECCSSCCTTSCC---
T ss_pred CCC-CCCHHHHHHHHHHHH-----HHHHHHHHHHCCCCHHHHHHHHHHHCCCC
T ss_conf 886-652229999889987-----99999999845563056678786304333
Done!