Query 046825
Match_columns 1208
No_of_seqs 234 out of 1866
Neff 6.3
Searched_HMMs 29240
Date Mon Mar 25 07:58:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046825.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/046825hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_A DNA-directed RNA polyme 100.0 2E-238 7E-243 2308.8 50.0 968 1-1206 69-1126(1752)
2 1twf_A B220, DNA-directed RNA 100.0 4E-230 1E-234 2233.1 59.1 963 1-1206 67-1123(1733)
3 4ayb_A DNA-directed RNA polyme 100.0 8E-200 3E-204 1875.6 55.6 795 1-1048 58-864 (880)
4 1hqm_D DNA-directed RNA polyme 100.0 4E-178 1E-182 1690.1 12.2 740 243-1206 225-1021(1265)
5 2a6h_D DNA-directed RNA polyme 100.0 1E-165 4E-170 1568.2 20.8 724 275-1200 505-1275(1524)
6 3lu0_D DNA-directed RNA polyme 100.0 5E-160 2E-164 1494.4 15.8 670 274-1173 229-942 (1407)
7 3qqc_A DNA-directed RNA polyme 100.0 3.1E-63 1.1E-67 581.3 22.1 274 1-419 121-404 (436)
8 4ayb_C DNA-directed RNA polyme 100.0 1.4E-30 4.7E-35 306.0 4.0 87 1119-1206 43-129 (395)
9 2a6h_D DNA-directed RNA polyme 94.5 0.0066 2.3E-07 79.8 -0.1 49 1-49 73-135 (1524)
10 2j7n_A RNA-dependent RNA polym 33.9 14 0.00048 47.8 1.9 54 497-552 572-636 (1022)
11 1twf_J DNA-directed RNA polyme 23.9 32 0.0011 30.1 1.8 33 40-77 6-38 (70)
No 1
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=1.9e-238 Score=2308.78 Aligned_cols=968 Identities=32% Similarity=0.493 Sum_probs=805.5
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
|+|||++..+|||||||||||+|||||+||+.+++||||+|++||||++++.+. .|.+++++ +. .+++++.+|+
T Consensus 69 C~TCg~~~~~CpGHFGHIELa~PVfHpgF~~~I~kILr~vC~~C~klll~~~~~-~f~~~lrl-rd----~k~r~~~V~~ 142 (1752)
T 3h0g_A 69 CQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNP-KFNDTQRY-RD----PKNRLNAVWN 142 (1752)
T ss_dssp CTTSCCSSSSCCCCCEECCCCSCBCCHHHHHHHHHHSSSSCTTTCCCSCCSCSH-HHHHHHHS-SC----TTTTHHHHHH
T ss_pred CCCCCCCCCcCCCcceeeecccceEeehhhHHHHHHHHHHHHHhcccccccccH-HHHHHHHc-cC----HHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999998876 58887774 22 3456666665
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhcccCCCCCCCCCCceecccceEEEE
Q 046825 81 SESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHM 160 (1208)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~~~kC~~Cg~~~p~Irk~g~~ki~~ 160 (1208)
.|++ ...|+..... +. ...... . + ...++|+|||+.||.|||+++.++..
T Consensus 143 ~ck~--------k~~Ce~~~~~----~~--~~~~~~--~-----------~---~~~~~~~gCG~~qP~IRKeglkl~~~ 192 (1752)
T 3h0g_A 143 VCKT--------KMVCDTGLSA----GS--DNFDLS--N-----------P---SANMGHGGCGAAQPTIRKDGLRLWGS 192 (1752)
T ss_dssp HHHH--------CCCCCSSTTC----CS--SCCCSS--C-----------C---CCCCSSCSSCCCCCCCEEETTEEECC
T ss_pred Hhcc--------ccccCCCCcc----cc--cchhcc--c-----------c---cccccCCCcCCcCCcEEeeccEEEEE
Confidence 5421 1122110000 00 000000 0 0 01357999999999999999865544
Q ss_pred ecCCchhhhhhhhccCCcCCCcCCCccccccCCCCCCCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCccccccccCC
Q 046825 161 NGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLFSG 240 (1208)
Q Consensus 161 ~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (1208)
++..+ +++++ ..++
T Consensus 193 ~k~~k----------------------------------~~~~~----------------------~~k~---------- 206 (1752)
T 3h0g_A 193 WKRGK----------------------------------DESDL----------------------PEKR---------- 206 (1752)
T ss_dssp BCCSS----------------------------------SSCBC----------------------SSCC----------
T ss_pred Ecccc----------------------------------ccccc----------------------ccce----------
Confidence 31100 00000 0123
Q ss_pred CCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHH
Q 046825 241 PLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQA 319 (1208)
Q Consensus 241 ~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~ 319 (1208)
+|+|.+|+++|++||++|+++|++.. ...+||||||++|||||+++||++.+++ .+.|||||++|++||+.
T Consensus 207 ~LtP~eVl~ifk~IsdeD~~lLGl~~--------~~~rPewmiL~vLPVpPp~vRPsv~ldg~~~~edDLt~~l~~II~~ 278 (1752)
T 3h0g_A 207 LLSPLEVHTIFTHISSEDLAHLGLNE--------QYARPDWMIITVLPVPPPSVRPSISVDGTSRGEDDLTHKLSDIIKA 278 (1752)
T ss_dssp CCCHHHHHHHHHHSCHHHHHHSSCCS--------SSCCGGGSSBSSCEECCGGGSCCCCCSSSCCCCCTTTTHHHHHHHH
T ss_pred ecCHHHHHHHHHhcCHHHHHHhCCCc--------cCCChhheEeeccccCCCCccCceEcCCCccCCChHHHHHHHHHHH
Confidence 89999999999999999999999753 4679999999999999999999999987 58999999999999999
Q ss_pred HHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCC--c----CCCChhhHHHHhhcccccccccccCccCCcccee
Q 046825 320 NIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAA--G----QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRS 393 (1208)
Q Consensus 320 n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~--~----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRs 393 (1208)
|++|++.+..+ ++...+.+.|..||.+|++||||+... . .++|++||+||||||+||||+|||||||||||||
T Consensus 279 N~~Lk~~~~~g-ap~~~~~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~rp~k~~~~~lkgK~GrfR~nl~GKRVd~s~Rs 357 (1752)
T 3h0g_A 279 NANVRRCEQEG-APAHIVSEYEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDFSART 357 (1752)
T ss_dssp HHHHHGGGGCC-SSSTTHHHHHHHHHHHHHHTTCTTCSSCCCCCSSSSCCCCCHHHHHTCSSSSSTTTTSSCCCSSEEEE
T ss_pred HHHHHHHHHhc-chhHHHHHHHHHHHHHHHHhhcCCCCCCccccccCCCCCcchHhhhhcccccccccccccccCCccce
Confidence 99999988775 566667788999999999999998762 1 2789999999999999999999999999999999
Q ss_pred eecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhhc
Q 046825 394 VISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTS 473 (1208)
Q Consensus 394 VIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a 473 (1208)
||+|||+|++||||||..||++|||||+||+|||++|+++|.|||+.||||++|++++| .+++|++. +|. .+
T Consensus 358 VI~~dP~l~~~evGvP~~~A~~Lt~Pe~vt~~ni~~l~~lv~nG~~~~pga~~v~~~~~-~~~~l~~~------~~~-~~ 429 (1752)
T 3h0g_A 358 VITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYIIRDTG-ERIDLRYH------KRA-GD 429 (1752)
T ss_dssp EEEEETTSCTTBCBCCHHHHTSCCCCCBCCTTTHHHHHHHHHHCTTSSSCEEEEECTTC-CBCCTTTT------CSC-CC
T ss_pred eecCCCCcccceeeChHHHHHhcCCCccccHHHHHHHHHHHHcCCccccCceeeecCCC-cEeechhh------chh-hh
Confidence 99999999999999999999999999999999999999999999999999999999999 78888764 111 11
Q ss_pred ccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceeccc
Q 046825 474 RGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHF 553 (1208)
Q Consensus 474 ~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~ 553 (1208)
..| .+||+|+|||+|||+|||||||||||+|||||+|||+++ +||||||+||+||||||||||||+||
T Consensus 430 ~~l-----------~~g~~v~r~l~~gd~Vl~NRqPtLHr~sima~~~~v~~g-ktirlh~~vC~~yNADFDGDeMnvHv 497 (1752)
T 3h0g_A 430 IPL-----------RYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPY-STFRLNLSVTSPYNADFDGDEMNMHV 497 (1752)
T ss_dssp CCC-----------CSSCEEEECCCSCCEEEEECSSCCSGGGEEEEECCCCSS-SSEEEEGGGSGGGTCCSSSCEEEEEC
T ss_pred hhc-----------CcCcEEEeeeccCCeEEEecCcccchhhcccccceeecC-ceeeechhhCCCccCccccceeeeec
Confidence 122 579999999999999999999999999999999999998 99999999999999999999999999
Q ss_pred CCCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccCCCCCCCCCCCCcee
Q 046825 554 PQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRV 633 (1208)
Q Consensus 554 pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 633 (1208)
|||++|||||++||++++||++|++|+||+|++||+|+|+|+||++|+|++++++++++++.. .++|
T Consensus 498 Pqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~lT~~~~f~~~~e~~~l~~~~~-------~~~~------ 564 (1752)
T 3h0g_A 498 PQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVP-------DWDG------ 564 (1752)
T ss_dssp CCSTTHHHHHHHTCCTTTTSEETTTTEESCCCCTHHHHHHHHHHSTTCEEETHHHHGGGGCSS-------SCCS------
T ss_pred cCCHHHHHHHHHHhcCccceecCCCCCceeeecchhhhheeeeccccccCCHHHHHHHHHhhc-------ccCC------
Confidence 999999999999999999999999999999999999999999999999999999999998421 2333
Q ss_pred eeecccceeeccCCCccCCCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCcccccc
Q 046825 634 LISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTN 713 (1208)
Q Consensus 634 ~~~~~~~~~~~~~PaIlkp~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~ 713 (1208)
.+|+|||+||+++||||||||++||. ++|+..+.+..
T Consensus 565 ---------~~~~pai~kp~~~wtGkqifs~ilp~------~~~~~~~~~~~---------------------------- 601 (1752)
T 3h0g_A 565 ---------ILPPPVILKPKVLWTGKQILSLIIPK------GINLIRDDDKQ---------------------------- 601 (1752)
T ss_dssp ---------SCCCCSBCSSSCEEETTHHHHTTSCS------SBCEECCCSSC----------------------------
T ss_pred ---------ccCccceecCcCCCchhhHHhhhCcC------CCCceeccccc----------------------------
Confidence 58999999999999999999999984 46665432210
Q ss_pred ccccccCCCccccccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccC--CccHHHHHHHHhCHHHHHHHH
Q 046825 714 KMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFA--DYGLVHTVQELYGSNTAGTLL 791 (1208)
Q Consensus 714 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG--~~~Lih~i~~~yG~~~a~~~l 791 (1208)
.+.+.+|+.|+|+||||++|+|||+++| .++|||.||++||+++|++||
T Consensus 602 -----------------------------~~~~~~d~~v~i~~gell~g~l~K~~lg~~~~~li~~i~~~~G~~~~~~~l 652 (1752)
T 3h0g_A 602 -----------------------------SLSNPTDSGMLIENGEIIYGVVDKKTVGASQGGLVHTIWKEKGPEICKGFF 652 (1752)
T ss_dssp -----------------------------CSSCTTTCSEEECBSCEEEECCSHHHHSSCTTCHHHHSSSSSCTTTHHHHH
T ss_pred -----------------------------cCcCCCcCeEEEEcCeEEecccchHHhccCcccHHHHHHHHHCHHHHHHHH
Confidence 0123678999999999999999999999 789999999999999999999
Q ss_pred HHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcchh
Q 046825 792 SALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAA 871 (1208)
Q Consensus 792 ~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 871 (1208)
|.+++|+++||+++||||||+|+++++++.++++++|++|++++.+++++|.. + .+ ...++...
T Consensus 653 d~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~---g------~l-------~~~~g~~~ 716 (1752)
T 3h0g_A 653 NGIQRVVNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQH---N------RL-------KPEPGMTL 716 (1752)
T ss_dssp HHHHHHHHHHHHHHCCCCCGGGGSCCSHHHHHHHHHHHTTTHHHHHHHTTTTT---T------CC-------CCCSSCCT
T ss_pred HHHHHHHHHHHHhcCceechhhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHc---C------CC-------ccCCCCcH
Confidence 99999999999999999999999999999999999999999888776665532 1 00 01123333
Q ss_pred hHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCcccc
Q 046825 872 VAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLP 951 (1208)
Q Consensus 872 ~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~grtLP 951 (1208)
.++++..+.++|++++++ +.+.++ ..+ .++|++++|+.||||||.+|++||+||||||+++|+|||+||+|||||
T Consensus 717 ~e~~e~~v~~~l~~~~~~-~~~~~~-~~l---~~~N~~~~M~~SGakGs~~ni~Q~~~~~Gqq~~~GkrIp~g~~~rtLP 791 (1752)
T 3h0g_A 717 RESFEAKVSRILNQARDN-AGRSAE-HSL---KDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLP 791 (1752)
T ss_dssp THHHHHHHHHHHHHHHHH-HHHHHH-TTS---CSSCTTTHHHHHCSSCCHHHHHHHHTCCCCCCSTTSSSCCCSTTSSST
T ss_pred HHHHHHHHHHHHHHHHHH-HHHHHH-Hhc---CCCCcHHHHhhhccccCHHHHHHHHhccCCCccCCccCCCCCCCccCC
Confidence 477888899999999998 888776 333 478999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEEE
Q 046825 952 SFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQ 1031 (1208)
Q Consensus 952 ~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQ 1031 (1208)
||.++|.+|+|+|||.|||++||+|+|||||||||||||||||||||+||||||||||+||||+|+||+||||++|+|||
T Consensus 792 ~f~k~d~~~~a~GfV~~sF~~GL~p~EfFfhtmggReGLiDTAvKTA~SGYLqRRLVk~leDv~V~YDgTVRns~g~ivQ 871 (1752)
T 3h0g_A 792 HFPKDDDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQ 871 (1752)
T ss_dssp TSCSSCCSTTTSSCCSSCTTTCCCHHHHHHHHHHHTTTTTHHHHTTTHHHHHHHHHHHHHTTCEEETTTEEECTTSCEEE
T ss_pred CCCCCCCCcccCcchhhcccCCCCHHHHHHHhhhhhhhhhHhhhhcCcCchhHHHHHHHHhheEEeeCCeeEcCCCcEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCCcceecccccc-------------ccchhhhhhh-----------------------------cccccccccccc
Q 046825 1032 FCYGEDGVDVHQTSFI-------------SKFDALAARE-----------------------------RGRGRGRNKFCD 1069 (1208)
Q Consensus 1032 F~YGedGld~~k~~~~-------------~~~~~~~~~~-----------------------------~~~~~~~~~~~~ 1069 (1208)
|.|||||+||++.+.- ..|.+...+. ..|..++..+..
T Consensus 872 F~YGeDGlD~~~~e~q~~~~~~~s~~~f~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~E~~~l~~dr~~lr~~i~~ 951 (1752)
T 3h0g_A 872 FAYGEDGLDATLVEYQVFDSLRLSTKQFEKKYRIDLMEDRSLSLYMENSIENDSSVQDLLDEEYTQLVADRELLCKFIFP 951 (1752)
T ss_dssp SSSSSSCBCGGGEEEEECTTTSCCHHHHTTTSCCCTTTTCCGGGTSCSCCTTSCSSTHHHHHHHHHHHHHHTTSSSSSSS
T ss_pred EecCCCCcChHHhhccccccccCCHHHHHHHhcccccccccccHHHHHHhccCHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 9999999999864311 1122111110 011111222223
Q ss_pred CCCceeeechhHHHHHhhhcchh--h-------hHHHHHHhHHHH----------------HHHhHHHHHHh----h---
Q 046825 1070 KGSHTFVMGRNQEMIYKKCSGQL--D-------ASNAYIMELPDA----------------LKDNAEKFADK----F--- 1117 (1208)
Q Consensus 1070 ~~~~~~~~~~n~~~~~~~~~~~~--~-------~~~~~~~~~~~~----------------~~~~~~~~~~~----~--- 1117 (1208)
.....+.++.|+.+++.+..... + .-.+.+..++++ .+.++..+++. .
T Consensus 952 ~~~~~~~lP~N~~R~i~~~~~~f~~~~~~~s~l~p~~~~~~v~~~~~~l~~~~g~d~l~~~~~~na~~l~~~~lr~~l~~ 1031 (1752)
T 3h0g_A 952 KGDARWPLPVNVQRIIQNALQIFHLEAKKPTDLLPSDIINGLNELIAKLTIFRGSDRITRDVQNNATLLFQILLRSKFAV 1031 (1752)
T ss_dssp CSCCEEEEESCHHHHTTTTTTTSCCCTTSCCCCCHHHHHHHHHHHHTTCCCSCCCSTTTTHHHHTSSHHHHHHHTTSSSH
T ss_pred cccccccCCccHHHHHHHHHHhcCCCcCccCCCCHHHHHHHHHHHHHhhhcccCCcchhhhhhhchHHHHHHHHHhhhhh
Confidence 44556778899998876543210 0 001222223333 33344433321 1
Q ss_pred ----hcchhHHHHHHHHH---HHHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHh
Q 046825 1118 ----LSNEMAKQDFLKLV---KHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIA 1190 (1208)
Q Consensus 1118 ----~~~~l~~~~f~~l~---~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~a 1190 (1208)
..++++.++|.+++ +.+|.+++|+||||||+|||||||||+|||||||||||||++||||||||||||||| |
T Consensus 1032 k~~~~~~~l~~~~~~~~~~~~~~~y~~a~v~pGe~VG~iaAQSIgEp~TQMTLnTFHfAGvas~NVTlGVPRLkEIIn-a 1110 (1752)
T 3h0g_A 1032 KRVIMEYRLNKVAFEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILN-V 1110 (1752)
T ss_dssp HHHHHSSCCCHHHHHHHHHHHHHHHHTTBCCSSCCHHHHHHHHHHHHHHHHHHHTTSSCCCCCSSCCCSGGGHHHHHT-T
T ss_pred hhhhhhcCcCHHHHHHHHHHHHHHHHHhccCcccchhhhhhcccCCchhhhhHHhhhhccccccccccCcccHHHHHh-h
Confidence 14677888887776 799999999999999999999999999999999999999999999999999999995 8
Q ss_pred hcCCCCCeEEEecCCC
Q 046825 1191 SKDIKTPVITCPLLVG 1206 (1208)
Q Consensus 1191 sk~ikTP~~~~~l~~~ 1206 (1208)
||+||||+|||+|.++
T Consensus 1111 sk~ikTP~mtv~L~~~ 1126 (1752)
T 3h0g_A 1111 AKNIKTPSLTIYLMPW 1126 (1752)
T ss_dssp CSCCSCCCCEECCCSS
T ss_pred hcCCCCCeEEEEecCc
Confidence 9999999999999765
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=100.00 E-value=4.2e-230 Score=2233.10 Aligned_cols=963 Identities=31% Similarity=0.468 Sum_probs=785.1
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
|.|||++..+|||||||||||+|||||+||+.++++|+|+|++||+|++++.+. .|.++|++.+ +.+++..+++
T Consensus 67 C~tCg~~~~~C~GHfGHIELa~PV~HigF~k~i~kiLe~VC~~Cskllld~~~~-~~~~~L~~~~-----pk~r~~~v~e 140 (1733)
T 1twf_A 67 CQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNE-LMRQALAIKD-----SKKRFAAIWT 140 (1733)
T ss_dssp SSSCCCCTTSCCCCCCCEEEEEEEECGGGHHHHHHHHHHBCTTTCCBSCCTTSH-HHHHHHTCCS-----HHHHHHHHHH
T ss_pred eCCCCCCCCcCCCccceeecccccccHHHHhhHHHHHHHHhHhcceeeeccchH-HHHHHHHhcC-----HHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999998776 4666655321 2444554444
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhcccCCCCCCCCCCceecccceEEEE
Q 046825 81 SESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIETTKCGNCKAKNPRISKPTFGWIHM 160 (1208)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~~~kC~~Cg~~~p~Irk~g~~ki~~ 160 (1208)
.++. ...|+..... . +++ ...++|.+||+.+|.||++++.++++
T Consensus 141 ~ck~--------k~~Ce~~~~~--------~------------------~e~--~~~~~~~gCGa~qp~irk~gl~l~~e 184 (1733)
T 1twf_A 141 LCKT--------KMVCETDVPS--------E------------------DDP--TQLVSRGGCGNTQPTIRKDGLKLVGS 184 (1733)
T ss_dssp HHTT--------CCBCCSEECC--------S------------------SCT--TSCEECCSCCCBCCCCEECSSCEEEE
T ss_pred Hhcc--------cccccccccc--------h------------------hcc--ccccccCCCCCccHHHHhcCCceEEe
Confidence 3321 1112111000 0 001 01346999999999999999887775
Q ss_pred ecCCchhhhhhhhccCCcCCCcCCCccccccCCCCCCCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCccccccccCC
Q 046825 161 NGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLFSG 240 (1208)
Q Consensus 161 ~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (1208)
+...+ +++++. + ..++
T Consensus 185 ~k~~~----------------------------------~~~e~~-------~-------------~~k~---------- 200 (1733)
T 1twf_A 185 WKKDR----------------------------------ATGDAD-------E-------------PELR---------- 200 (1733)
T ss_dssp ECSSS----------------------------------SCTTSC-------S-------------CEEE----------
T ss_pred ecccc----------------------------------cccccc-------h-------------hhhc----------
Confidence 41000 000000 0 0123
Q ss_pred CCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHH
Q 046825 241 PLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQA 319 (1208)
Q Consensus 241 ~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~ 319 (1208)
.|+|.+|+++|++||++|+++|++. +...+||||||++|||||+++||++.+++ .+.|||||++|++||+.
T Consensus 201 ~Ltp~eV~eifk~I~deD~~lLgl~--------p~~~rPewmiLtvLPVpPp~vRPsv~ldg~~~~edDLT~~l~~II~~ 272 (1733)
T 1twf_A 201 VLSTEEILNIFKHISVKDFTSLGFN--------EVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKA 272 (1733)
T ss_dssp EECHHHHHHHHTTSCHHHHHHTTCB--------TTTBCGGGGEEEEECCCCTTTSCCCCCSSSCCCCCHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHhCCHHHHHHhCCC--------ccCCChheeeeeeeccCCCCccCceecCCCcccCCHHHHHHHHHHHH
Confidence 8999999999999999999999985 24689999999999999999999999876 68999999999999999
Q ss_pred HHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCCc------CCCChhhHHHHhhcccccccccccCccCCcccee
Q 046825 320 NIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAAG------QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRS 393 (1208)
Q Consensus 320 n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~~------~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRs 393 (1208)
|++|++....+ ++...+.+.|..||.+|++||||+.... .++|++||+||||||+||||+|||||||||||||
T Consensus 273 N~~Lk~~~~~g-ap~~ii~e~~~~LQ~~v~~~~dn~~~~~~~~~~~~~rp~k~i~~~lkgK~GrfR~nl~GKRVd~s~Rs 351 (1733)
T 1twf_A 273 NISLETLEHNG-APHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSART 351 (1733)
T ss_dssp HHHHHHHHSSC-CCHHHHHHHHHHHHHHHHHHHCCCSSCCCCCSSCTTCCCCCSTTSCTTTTTTSSGGGTTCSCCSEEEE
T ss_pred HHHHHHHHHcC-chHHHHHHHHHHHHHHHHHHhccCccCCCccccCCCccchhHHHHhccccchhhhcccccccCcccce
Confidence 99999988775 6777677899999999999999987621 2789999999999999999999999999999999
Q ss_pred eecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhhc
Q 046825 394 VISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTS 473 (1208)
Q Consensus 394 VIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a 473 (1208)
||+|||+|++||||||..||++|||||+||+|||++|+++|.|||+.||||+++++++| .+++|++. +|. ..
T Consensus 352 VI~~dP~L~~~evGvP~~~A~~Lt~Pe~vt~~ni~~l~~lv~~g~~~~~ga~~~~~~~g-~~~~l~~~------~~~-~~ 423 (1733)
T 1twf_A 352 VISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSG-DRIDLRYS------KRA-GD 423 (1733)
T ss_dssp EEEECTTSCTTEEEEEHHHHTTCEEEEECCTTTHHHHHHHHHHTTTSSSCEEEEECTTC-CEEETTSC------TTT-TC
T ss_pred EEeCCCCcccccccCcHHHHHhCCCCccccHHHHHHHHHHHHcCCccCCCceeEEcCCC-cEEecccc------chh-hh
Confidence 99999999999999999999999999999999999999999999999999999999999 78888764 111 11
Q ss_pred ccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceeccc
Q 046825 474 RGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHF 553 (1208)
Q Consensus 474 ~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~ 553 (1208)
.. ++.||+|+|||+|||+|||||||||||+|||||+|+|+++ +||||||+||+||||||||||||+||
T Consensus 424 ~~-----------l~~g~~v~r~l~~gd~VllNRqPTLHr~si~a~~~~v~~~-~tirlnp~vC~~yNADFDGDeMnvHv 491 (1733)
T 1twf_A 424 IQ-----------LQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPY-STFRLNLSVTSPYNADFDGDEMNLHV 491 (1733)
T ss_dssp CC-----------CCTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEEESS-SSEEECGGGHHHHTCCSSSCEEEEEC
T ss_pred hh-----------cccCCEEEeeeccCCEEEEeCCCccccccceeEEEEEccC-CeEEeChhhcCCCCccchhhhhhhhc
Confidence 11 2579999999999999999999999999999999999998 89999999999999999999999999
Q ss_pred CCCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccCCCCCCCCCCCCcee
Q 046825 554 PQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRV 633 (1208)
Q Consensus 554 pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 633 (1208)
|||++|||||++||++++||++|++|+||+|++||+|+|+|+||++|+|+++++++++++... .++|
T Consensus 492 Pqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~v~g~y~lT~~~~f~~~~e~~~~~~~~~-------~~~~------ 558 (1733)
T 1twf_A 492 PQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVP-------DWDG------ 558 (1733)
T ss_dssp CCSHHHHHHHHHHTBGGGGSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHST-------TCCS------
T ss_pred CCCHHHHHHHHHHhcCcccEEecCCCCeeEeeeccccccceeeecCcccCCHHHHHHHHHhhh-------hhcC------
Confidence 999999999999999999999999999999999999999999999999999999999998542 2322
Q ss_pred eeecccceeeccCCCccCCCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCcccccc
Q 046825 634 LISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTN 713 (1208)
Q Consensus 634 ~~~~~~~~~~~~~PaIlkp~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~ 713 (1208)
.+|+|||+||+++||||||||++||. ++|+..++ +...|
T Consensus 559 ---------~~~~pai~kp~~~wtGkqifs~ilp~------~~~~~~~~--~~~~~------------------------ 597 (1733)
T 1twf_A 559 ---------VIPTPAIIKPKPLWSGKQILSVAIPN------GIHLQRFD--EGTTL------------------------ 597 (1733)
T ss_dssp ---------CCCCCSBCSSSCEEEHHHHHHHHSCT------TCCEEECC--TTCCT------------------------
T ss_pred ---------ccCCccccCcccCccHHHHHHHhCCC------CCceeecC--CCccc------------------------
Confidence 57999999999999999999999984 46665432 11112
Q ss_pred ccccccCCCccccccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccC--CccHHHHHHHHhCHHHHHHHH
Q 046825 714 KMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFA--DYGLVHTVQELYGSNTAGTLL 791 (1208)
Q Consensus 714 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG--~~~Lih~i~~~yG~~~a~~~l 791 (1208)
.+..|+.|+|+||+|++|+|||+++| .++|||.||++||+++|++||
T Consensus 598 -------------------------------~~~~d~~v~i~~gel~~g~ldKk~lg~~~~~li~~i~~~~G~~~a~~~l 646 (1733)
T 1twf_A 598 -------------------------------LSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLF 646 (1733)
T ss_dssp -------------------------------TCTTCCSEEEETTEEEESCCCHHHHSSCTTSHHHHHHHHHCHHHHHHHH
T ss_pred -------------------------------CCcccceEEEeCCcEEEeecchHHhccChhHHHHHHHHHhCHHHHHHHH
Confidence 22568899999999999999999999 779999999999999999999
Q ss_pred HHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcchh
Q 046825 792 SALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAA 871 (1208)
Q Consensus 792 ~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 871 (1208)
|++++|+++||+++||||||+|+++++++.++++++|++|++++.+++++|..-.- -..++...
T Consensus 647 d~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~i~~~i~~a~~~v~~~~~~~~~g~l----------------~~~pg~~~ 710 (1733)
T 1twf_A 647 GNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLL----------------TAKHGMTL 710 (1733)
T ss_dssp HHHHHHHHHHHHTTCBCCCGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTCC----------------CCCTTCCH
T ss_pred HHHHHHHHHHHHHcceEEehhhcCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC----------------ccCCCCCH
Confidence 99999999999999999999999999999999999999999999988888754110 01122223
Q ss_pred hHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCcccc
Q 046825 872 VAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLP 951 (1208)
Q Consensus 872 ~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~grtLP 951 (1208)
.+.++..+..+|++++++ +.+.++. .+ .++|++++|+.||||||.+|++||+||||||+++|+|||+||+|||||
T Consensus 711 ~e~~e~~v~~il~~~~d~-~~~~~~~-~l---~~~N~i~~Ma~SGAKGs~~Ni~Q~~~~~Gqq~~~Gkrip~g~~~RtLP 785 (1733)
T 1twf_A 711 RESFEDNVVRFLNEARDK-AGRLAEV-NL---KDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLP 785 (1733)
T ss_dssp HHHHHHHHHHHHHHHHHH-HHHHHHH-HS---CTTCHHHHHHHHTSSCCHHHHHHHHSCCEECCBTTBSCCCCBTTBSST
T ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHH-hc---ccCCCeEEEeeccCcccHHhHHHHHhCcCCcccCCccCCCCCCCCCCC
Confidence 366778888889988888 7776653 33 378999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEEE
Q 046825 952 SFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQ 1031 (1208)
Q Consensus 952 ~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQ 1031 (1208)
||.++|++|+|+|||.|||++||+|+|||||||||||||||||||||+||||||||||+||||+|+|||||||++|+|||
T Consensus 786 hf~k~d~~p~s~GfI~ssF~~GLtp~EyFfh~mggReGLiDTAvKTA~SGYLqRRLVk~ledv~V~yDgTVR~s~g~IvQ 865 (1733)
T 1twf_A 786 HFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQ 865 (1733)
T ss_dssp TSCTTCCSTTTTTEECSCTTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCEECTTSCEECTTCCEEE
T ss_pred CCCCCCCCccccchhhhhhhcccchHHHhhhhhccccchhhhceecccCCcceeehhhhhcceEEEecCcEecCCCCEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCCcceecccccc---------ccchhhhh----hh--------c-------------------------ccccccc
Q 046825 1032 FCYGEDGVDVHQTSFI---------SKFDALAA----RE--------R-------------------------GRGRGRN 1065 (1208)
Q Consensus 1032 F~YGedGld~~k~~~~---------~~~~~~~~----~~--------~-------------------------~~~~~~~ 1065 (1208)
|.|||||+||+..+.- ..|...+. +. . .|..++
T Consensus 866 F~YGeDGlD~~~~e~~~~~~~~~~~~~f~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~e~~~l~~~r~~lr- 944 (1733)
T 1twf_A 866 FIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLR- 944 (1733)
T ss_dssp SSGGGTTBCGGGEEEEECGGGSSCHHHHHHHHCCCTTCTTTSCCTTTBTTHHHHTTCHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred EEeccccCCcceeecccccccccCHHHHHHHhccccccccccCCHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHH-
Confidence 9999999999865321 01110000 00 0 000000
Q ss_pred ccccCCCceeeechhHHHHHhhhcchh----------------hhHHHHHHh---------HHHHHHHhHHHHH----Hh
Q 046825 1066 KFCDKGSHTFVMGRNQEMIYKKCSGQL----------------DASNAYIME---------LPDALKDNAEKFA----DK 1116 (1208)
Q Consensus 1066 ~~~~~~~~~~~~~~n~~~~~~~~~~~~----------------~~~~~~~~~---------~~~~~~~~~~~~~----~~ 1116 (1208)
.+.......+.++.|+.+++....... ..+.++.++ +..+.+.++..++ ++
T Consensus 945 ~i~~~~~~~~~~P~ni~r~i~~~~~~f~~~~~~~s~l~p~~~~~~v~~~~~~~~~~~g~d~l~~~~~~n~~~l~~~~~rs 1024 (1733)
T 1twf_A 945 EVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRS 1024 (1733)
T ss_dssp HHTTTCCCEEEEESCHHHHHHHHHHHTTCCTTSCBCCCHHHHHHHHHHHHTTCCSCCCCSHHHHHHHHHTTHHHHHHHHH
T ss_pred HhhccccccccCChhHHHHHHHHHHHhcccccccccCCHHHHHHHHHHHHHhhhcccCCcchhhhhhhchHHHHHHHhhh
Confidence 011123334556777776654322110 111111111 1223333333222 22
Q ss_pred hh-------cchhHHHHHHHHH---HHHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHH
Q 046825 1117 FL-------SNEMAKQDFLKLV---KHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEI 1186 (1208)
Q Consensus 1117 ~~-------~~~l~~~~f~~l~---~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEI 1186 (1208)
.+ ..+++.++|.+++ +.||.+++|+||||||+|||||||||+|||||||||||||++||||||||||+||
T Consensus 1025 ~L~~k~~~~~~~l~~~~~~~~l~~i~~ky~~a~v~pGe~VG~iaAQSigEp~TQMTLnTFHfAGva~~NVTLGVPRLkEI 1104 (1733)
T 1twf_A 1025 RLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEI 1104 (1733)
T ss_dssp HSCHHHHHHTSCCCHHHHHHHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC----------CCSCCHHHHHHHH
T ss_pred hhhhhhhhhhcCCCHHHHHHHHHHHHHHHHhccCCCCchhhhHhhhhcCCccccccccccccccccccCcccCcHHHHHH
Confidence 11 3467788887776 8999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCCCCCeEEEecCCC
Q 046825 1187 LTIASKDIKTPVITCPLLVG 1206 (1208)
Q Consensus 1187 i~~ask~ikTP~~~~~l~~~ 1206 (1208)
|| |||+||||+|||+|.++
T Consensus 1105 in-ask~ikTP~mtv~L~~~ 1123 (1733)
T 1twf_A 1105 LN-VAKNMKTPSLTVYLEPG 1123 (1733)
T ss_dssp TT-TCSSCSSCEEEEEBCSS
T ss_pred HH-hccCCCCCeEEEEeCCc
Confidence 95 68999999999999865
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=100.00 E-value=8e-200 Score=1875.58 Aligned_cols=795 Identities=35% Similarity=0.502 Sum_probs=691.0
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
|+|||....+|||||||||||+|||||+||+.+++||+|+|++|++++++..++..|...+..+..+....++
T Consensus 58 C~tCg~~~~~c~ghfGhIeLa~PV~h~~f~~~i~~lL~~~c~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------- 130 (880)
T 4ayb_A 58 CPTCGNTLGNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRWPSAAR------- 130 (880)
T ss_dssp CTTTCCCGGGCCCCCEEEEEEEEEECGGGTTHHHHHHHTSCTTSSCCCSSCCHHHHHHHHHHHHGGGCHHHHH-------
T ss_pred CCCCCCCCCCCCCCCeeecccccccchhHHHHHHHHHhCccccccCCcCCHHHHHHHHHHHHHhhccChHHHH-------
Confidence 9999999999999999999999999999999999999999999999999998888887766655432221111
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhc--ccCCCCCCCCCCceecccceEE
Q 046825 81 SESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIE--TTKCGNCKAKNPRISKPTFGWI 158 (1208)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~--~~kC~~Cg~~~p~Irk~g~~ki 158 (1208)
.+.+.+.+.+ ...|++||+.+++|++++...+
T Consensus 131 ----------------------------------------------~~~~~~~~~~~~~~~c~~cg~~~~~i~~~~~~~~ 164 (880)
T 4ayb_A 131 ----------------------------------------------RLTEYVKKTAMKAQVCPHCGEKQFKIKLEKPYNF 164 (880)
T ss_dssp ----------------------------------------------HHHHHHHHHHTTCSSCTTTTCCCCCCEEEETTEE
T ss_pred ----------------------------------------------HHHHHHHHHhcccccchhccchhhhhhhcCcCCH
Confidence 1111222222 5689999999999987765444
Q ss_pred EEecCCchhhhhhhhccCCcCCCcCCCccccccCCCCCCCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCcccccccc
Q 046825 159 HMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLF 238 (1208)
Q Consensus 159 ~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (1208)
.+.. .+ ...
T Consensus 165 ~~~~-------------------------------------~~--------------------------~~~-------- 173 (880)
T 4ayb_A 165 YEER-------------------------------------KE--------------------------GVA-------- 173 (880)
T ss_dssp EEEE-------------------------------------TT--------------------------EEE--------
T ss_pred HHHH-------------------------------------HH--------------------------HHH--------
Confidence 3210 00 012
Q ss_pred CCCCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHH
Q 046825 239 SGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVL 317 (1208)
Q Consensus 239 ~~~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii 317 (1208)
.|+|.+|+++|++||++|..++++. +..++||||||++|||||+++||++.+++ ..++||+|++|++||
T Consensus 174 --~l~~~~~~~~l~~i~~~~~~~l~~~--------~~~~~Pewmil~~lPV~Pp~~RP~v~l~~g~~~~~dl~~~~~~ii 243 (880)
T 4ayb_A 174 --KLTPSDIRERLEKVPESDVEILGYD--------PTTSRPEWMILTVLPVPPITIRPSIMIESGIRAEDDLTHKLVDIV 243 (880)
T ss_dssp --ECCHHHHHHHHTTCCHHHHHHTTCC--------TTTCCSGGGEEEEEEECCSSSSCC-----CCCCCCSSHHHHHHHH
T ss_pred --hcCHHHHHHHHHHhHHHHHHHhCCC--------CcCCCchheEEeeeeCCCCCCCchhhcCCcccccchHHHHHHHHH
Confidence 6899999999999999999999874 34689999999999999999999999876 678999999999999
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCC--c----CCCChhhHHHHhhcccccccccccCccCCccc
Q 046825 318 QANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAA--G----QRDMASGICQLLEKKEGLFRQKLMGKRVNYAC 391 (1208)
Q Consensus 318 ~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~--~----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~sa 391 (1208)
+.|++|++....+ ++...+.+.|..||++|++||||+.+. . .++|++||+|+||||+||||+|||||||||||
T Consensus 244 ~~N~~lk~~~~~~-ap~~i~~~~~~~LQ~~V~~l~dn~~~g~~~~~~~~~rp~ksl~~~lkgK~GrfR~nl~GKRVd~s~ 322 (880)
T 4ayb_A 244 RINERLKESIDAG-APQLIIEDLWDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSS 322 (880)
T ss_dssp HHHHHHHHHHTSC-CCHHHHHHHHHHHHHHHHHHHCSCCSSSCCCCCTTSCCCCCHHHHHHSSSSTHHHHTSSEECSSEE
T ss_pred HhhhhhhhhhhcC-CchhHHHHHHHHHHHHHHHHHhccCCCCCccCCCCCCcccchhhhhcccchhhhhcccceeecccC
Confidence 9999999998875 777778889999999999999998762 1 16899999999999999999999999999999
Q ss_pred eeeecCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhh
Q 046825 392 RSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLD 471 (1208)
Q Consensus 392 RsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~ 471 (1208)
||||||||+|+++|||||..||++||+||+||+||+++|+++|.|||++||||+++++.+| .++++... .+|..
T Consensus 323 RsVI~~dP~l~~~e~GvP~~~A~~Lt~Pe~vt~~N~~~l~~~v~ng~~~~pga~~~i~~~~-~~~~l~~~-----~~~~~ 396 (880)
T 4ayb_A 323 RTVISPDPNISIDEVGVPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRPDG-RRIDLRYV-----KDRKE 396 (880)
T ss_dssp EEEEEECTTSCSSEEEECHHHHTTSEEEEECCTTTHHHHHHHHHHTTSSSSCEEEEECSSC-CEEEGGGC-----SSCTT
T ss_pred ceeeeCCCCccccccCCcHHHHHhCCCCeEEcHHHHHHHHHHHHcCCccccchhhhhhccc-eEEEeecc-----hhhhH
Confidence 9999999999999999999999999999999999999999999999999999999999999 77777543 34566
Q ss_pred hcccccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceec
Q 046825 472 TSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNV 551 (1208)
Q Consensus 472 ~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~ 551 (1208)
+++.| ..||+|+|||+|||+|||||||||||+|||||+|+|+++ +||||||+||+||||||||||||+
T Consensus 397 ~~~~l-----------~~g~~V~rhl~dgd~VLlNRqPTLHr~si~a~~~~l~~g-ktirlhp~vC~~yNADFDGDeMnv 464 (880)
T 4ayb_A 397 LASTL-----------APGYVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKG-LTFRLNLLVCPPYNADFDGDEMNL 464 (880)
T ss_dssp HHHHC-----------CTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEECSS-SSEEECGGGHHHHTCCSSSCEEEE
T ss_pred HHHhc-----------cccceEeeeeecCcEEEecCCCcccccceeeeeeecccC-ceeeeccccccccccCcccceeEE
Confidence 66666 579999999999999999999999999999999999997 999999999999999999999999
Q ss_pred ccCCCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCccccCHHHHHHHHHhcCccCCCCCCCCCCCCc
Q 046825 552 HFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQ 631 (1208)
Q Consensus 552 h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 631 (1208)
|||||++|||||++||++++||+||+||+||++++||+|+|+|+||.+|+|+++++++++++.+.+
T Consensus 465 HvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~lT~~~~~~~~~~~~~~~~~~~~-------------- 530 (880)
T 4ayb_A 465 HVPQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQILGVADV-------------- 530 (880)
T ss_dssp ECCCSHHHHHHHHHHSBSGGGCBCSSSSSBCSCCCSHHHHHHHHHTSSSCEECHHHHHHHHTTSCC--------------
T ss_pred eccCCHHHHHHHHHHHhChhccccCCCCCccccccccHHHHhHHhhcCcccCCHHHHhhhhcccce--------------
Confidence 999999999999999999999999999999999999999999999999999999999999874331
Q ss_pred eeeeecccceeeccCCCccCCCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCcccc
Q 046825 632 RVLISRSEQEVLPLLPAIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSK 711 (1208)
Q Consensus 632 ~~~~~~~~~~~~~~~PaIlkp~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 711 (1208)
.+.+++|||++|+++||||||||+++|. .+++..+.++....+
T Consensus 531 ---------~~~~~~p~i~~~~~~~tgkqi~s~~lp~------~~~~~~~~~~~~~~~---------------------- 573 (880)
T 4ayb_A 531 ---------KIDLGEPAILAPREYYTGKQVVSAFLPK------DFNFHGQANVSSGPR---------------------- 573 (880)
T ss_dssp ---------CCCCCSCSEESSSEEEEHHHHHHTTSCT------TCCEEEECTTCSGGG----------------------
T ss_pred ---------ecccCccceecceeEeccceEEEEEecc------cccccceeEeecCCc----------------------
Confidence 2578999999999999999999999874 355544333321111
Q ss_pred ccccccccCCCccccccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccC---CccHHHHHHHHhCHHHHH
Q 046825 712 TNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFA---DYGLVHTVQELYGSNTAG 788 (1208)
Q Consensus 712 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG---~~~Lih~i~~~yG~~~a~ 788 (1208)
....+.++.|..|+|+||+|++|++||+++| .++|+|.+|++||+..|+
T Consensus 574 ----------------------------~~~~~~~~~~~~v~i~~g~l~~g~ldk~~lg~~~~~~li~~i~~~~G~~~t~ 625 (880)
T 4ayb_A 574 ----------------------------LCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGK 625 (880)
T ss_dssp ----------------------------CCSSSCCTTSCEEEEETTEEEECCCSTTTSSTTCTTSHHHHHHHTSCHHHHH
T ss_pred ----------------------------cccCccCCCcceEEEeCceeeeeeecchhhcccccceeeehhhhhcccHHHH
Confidence 0112234678899999999999999999999 368999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCc
Q 046825 789 TLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGG 868 (1208)
Q Consensus 789 ~~l~~l~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~ 868 (1208)
.|||.+++|+++|++.+|||||++|+.+++++.+++.+++++++.++.+++++|....-. ..++
T Consensus 626 ~~ld~l~~lg~~~lt~~GfSigi~Di~i~~~~~~~i~~~i~~a~~~v~~i~~~~~~g~l~----------------~~~g 689 (880)
T 4ayb_A 626 WLMDNLFRVFIRFVELQGFTMRLEDVSLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELE----------------PIPG 689 (880)
T ss_dssp HHHHHHHHHHHHHHHHHCCCCCGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCC----------------CCSS
T ss_pred HHHHHHHHHHHHHHHhcCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHcCCCc----------------cccc
Confidence 999999999999999999999999999999999999999999999998888887541111 0122
Q ss_pred chhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCc
Q 046825 869 DAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGK 948 (1208)
Q Consensus 869 ~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~gr 948 (1208)
...++.++..+...|++++++ +.+.+. . ..+++|++++|+.||||||.+|++||+||||||+++|+|||+|+.+|
T Consensus 690 ~~~~e~~e~~v~~~l~~~~~~-~~~~~~-~---~l~~~N~i~mMa~SGARGS~~ni~Qlagm~Gqq~~~G~RIprg~~~r 764 (880)
T 4ayb_A 690 RTLEESLENYILDTLDKLRST-AGDIAS-K---YLDPFNFAYVMARTGARGSVLNITQMAAMLGQQSVRGERIKRGYMTR 764 (880)
T ss_dssp SCHHHHHHHHHHHHHHHHHHH-HHHHHH-H---TSCTTSHHHHHHHHTSSCCSTTHHHHHTCCEECBSSSSBSCCSBTTB
T ss_pred chHHHHHHHHHHHHHHHHHHH-HHHHHH-h---hCCCCCCHHHHhhcCccCCHHHHHHHHhcccccccCCccCcCCCccC
Confidence 222356677777888888877 666554 2 23589999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCC
Q 046825 949 TLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGS 1028 (1208)
Q Consensus 949 tLP~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~ 1028 (1208)
|||||.++|.+|+|+|||.|||++||+|+|||||||||||||+|||||||+||||||||||+||||+|+||||||+++|+
T Consensus 765 tLP~f~~~d~~p~a~GfI~ssF~eGLtp~EyF~ht~ggRkGL~DTAlKTA~SGYLtRRLVdv~qDv~V~yDgTVR~~~g~ 844 (880)
T 4ayb_A 765 TLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRAEYDGTVRSLYGE 844 (880)
T ss_dssp SSTTSCTTCCSTTTTSEECSCTTTCCCHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTTEEECTTSCEEETTTE
T ss_pred CCCCCCCCCCCcccCCeEhhcccCCCCHHHHHHhhhhhhhhHHhcchhhchhhHHHHHHHHHHcCEEEecCCCccCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeeecCCcceeccccccc
Q 046825 1029 IVQFCYGEDGVDVHQTSFIS 1048 (1208)
Q Consensus 1029 IvQF~YGedGld~~k~~~~~ 1048 (1208)
||||.|||||+||++.+...
T Consensus 845 ivqf~YGeDgldp~~~~~~~ 864 (880)
T 4ayb_A 845 VIQVAYGDDGVFPMYSAHGK 864 (880)
T ss_dssp EEESSTTTTCBCTTTSBTTB
T ss_pred EEEEecCCcccceeecccCC
Confidence 99999999999999876554
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=100.00 E-value=3.8e-178 Score=1690.06 Aligned_cols=740 Identities=22% Similarity=0.275 Sum_probs=550.2
Q ss_pred CHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHH
Q 046825 243 LPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANI 321 (1208)
Q Consensus 243 ~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~ 321 (1208)
++....++|++|..-+. +. ...++||||||++|||||+++||++.+++ .+++||+|.+|++||+.|+
T Consensus 225 ~~~~~~~~~krl~~~~~--f~----------~~~~~Pewmil~~lPVpPp~~RP~v~l~gg~~~~~Dln~~~~~Ii~~N~ 292 (1265)
T 1hqm_D 225 SRARRAKARKRLEVVRA--FL----------DSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNN 292 (1265)
T ss_dssp SHHHHHHHHHHHHHHHH--HH----------SSSCSSCCSCSSCCCCCSCC------------CCCGGGTHHHHTHHHHH
T ss_pred cHHHHHHHhhhhhhhhh--hc----------ccCCCcceEeeeccCCCCCcCccceecCCCceecChhHHHHHHHHHHHH
Confidence 34555667777643222 11 13579999999999999999999999876 6789999999999999999
Q ss_pred HHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCC--c---CCCC-hhhHHHHhhcccccccccccCccCCccceeee
Q 046825 322 YLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAA--G---QRDM-ASGICQLLEKKEGLFRQKLMGKRVNYACRSVI 395 (1208)
Q Consensus 322 ~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~--~---~~~~-~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVI 395 (1208)
+|++++..+ ++...+.+.|.+||.+|++||||+... . .++| ++||+||||||+||||+|||||||||||||||
T Consensus 293 ~L~~~~~~~-ap~~ii~~~~~~LQ~~V~~l~Dn~~~g~~~~~~~~rp~lksl~~~LkGK~GrfR~NLmGKRVdfSaRSVI 371 (1265)
T 1hqm_D 293 RLKKLLAQG-APEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVI 371 (1265)
T ss_dssp HHHTSSSSC-CCSTTTSTTTTTTGGGTTTTSSCCSSCCCSSCSSCCCCCCCSTTTSSSTTCTTTTTTSCCEETTCCCCBE
T ss_pred HHHHHHHcC-CchhHHHHHHHHHHHHHHHHhCCCCCCCCccCCCCCccccchhhhcccchhhhhhhhcccccCcccceeE
Confidence 999987764 555556678999999999999998763 1 2778 99999999999999999999999999999999
Q ss_pred cCCCCccccccCchHHHHhhcCcccccchHHHHHHHHHHHcCC-CCCCCceEEecCCCCcccCCCccccccccchhhhcc
Q 046825 396 SPDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGA-EIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSR 474 (1208)
Q Consensus 396 spDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni~~L~~lv~nG~-~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~ 474 (1208)
||||+|++||||||..||++||+| ||+ ++||.||+ ..+++|+.++...+ +
T Consensus 372 ~pdP~L~i~evGvP~~~A~~L~~P-----~~~---~~lv~~g~~~~i~~ak~~i~~~~---------------------~ 422 (1265)
T 1hqm_D 372 VVGPQLKLHQCGLPKRMALELFKP-----FLL---KKMEEKAFAPNVKAARRMLERQR---------------------D 422 (1265)
T ss_dssp EECCSSSSSBCCCBHHHHHHHHHH-----HHH---HHHHHTTCSSCSHHHHHHHCSSS---------------------C
T ss_pred ecCCCcccccccChHHHHHHhCcH-----HHH---HHHHHcCCcchhhhhhhhhhhcc---------------------c
Confidence 999999999999999999999998 564 77899997 34455443321100 0
Q ss_pred cccccCCCCCCCcccCceeehhhcccceEEEecCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccC
Q 046825 475 GAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFP 554 (1208)
Q Consensus 475 ~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~p 554 (1208)
....+|.|+||++|||+|||||||||||+|||||+|+++++ +||||||+||+||||||||||||+|+|
T Consensus 423 -----------~~~~~~~v~~~v~~gd~VLlNRqPTLHr~sIma~~~~l~~~-ktirlhp~vC~~yNADFDGDeMnvHvP 490 (1265)
T 1hqm_D 423 -----------IKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEG-QSIQLHPLVCEAFNADFDGDQMAVHVP 490 (1265)
T ss_dssp -----------CCHHHHTTTTTTTTTCCEECCCSSCCSGGGSCEEBCCCBSS-SSEEECGGGHHHHCCCSSSCBCCCCCC
T ss_pred -----------cCCccceeEEEeccCcEEEEecCcccccccccceeEEecCC-CeEEechhhcCCcCCCcccceEEEecC
Confidence 00235778999999999999999999999999999999886 999999999999999999999999999
Q ss_pred CCHHHHHHHHHhcccCCceecCCCCCCcccchhhhhhhhhhcccCc--------cccCHHHHHHHHHhcCccCCCCCCCC
Q 046825 555 QDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQDHIVSAALLTKKD--------TFLNRDEFCQLLYSSGVSSSGLGSFT 626 (1208)
Q Consensus 555 qs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~QD~l~g~~lLT~~d--------~f~~~~~~~~l~~~~~~~~~~~~~~~ 626 (1208)
||++|||||++||++++||+||++|+|++|++||+|+|+|+||++| +|+++++++++++...+
T Consensus 491 qs~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~~i--------- 561 (1265)
T 1hqm_D 491 LSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEV--------- 561 (1265)
T ss_dssp CSTHHHHTTSSSSBSSSSSSSCSSSSCSSCCCTTHHHHHHHTTCCCCCCCCCCCCSSCCTHHHHHTTSSCC---------
T ss_pred CCHHHHHHHHHHhCccccEecCCCCCeeEeeeccccceeEEeccccCCccCCCcccCCHHHHHHHHHCCCC---------
Confidence 9999999999999999999999999999999999999999999999 79999999987664321
Q ss_pred CCCCceeeeecccceeeccCCC----ccCCCCCCC-----------CCe---EEEEee-c----cccCCCcceeeccCCC
Q 046825 627 GKPGQRVLISRSEQEVLPLLPA----IWKPEPLWT-----------GKQ---VITAVL-N----HITRGRPPFVVERGGK 683 (1208)
Q Consensus 627 ~~~~~~~~~~~~~~~~~~~~Pa----Ilkp~~lwT-----------GKq---v~s~~l-~----~~~~~~~~~n~~~~~k 683 (1208)
+.+..+.+.+|+ |++ ++|| |+| ++++++ + .++.|+..||+..+..
T Consensus 562 ----------~l~a~i~~~~~~~~~g~~k--~~~t~P~k~I~~~~~g~~~~q~~~~~~~k~~~~~t~~Gr~if~~~lp~~ 629 (1265)
T 1hqm_D 562 ----------ALNAPIVVAGRETSVGRLK--FVFANPDEALLAVAHGLLDLQDTVTTRYLGRRLETNPGRILFARIVGEA 629 (1265)
T ss_dssp ----------SSCCCSSSCCSTTSSCCCC--CTTTCSHHHHHHHHTTSSCSSSCCCCEESSSEECCCHHHHHHHHHHHHH
T ss_pred ----------CCCCceEEecccccccccc--cccccccccccccccCccccccccceeccccceeccCCceEEeeecccc
Confidence 111122222222 222 4565 443 333332 1 1111222222111000
Q ss_pred CCcccccccccccccccccccccCccccccccccccCCCccccccCCCCchhhhhhhcccccccCCceEEEecceeeeee
Q 046825 684 LPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGV 763 (1208)
Q Consensus 684 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ 763 (1208)
+. .+ ..+++ +.+ ++|+
T Consensus 630 ~~--~~-------------------------------------------------------~~p~~--~~~-----~ngv 645 (1265)
T 1hqm_D 630 VG--DE-------------------------------------------------------KVAQE--LIQ-----MDVP 645 (1265)
T ss_dssp TT--CT-------------------------------------------------------TTTTT--SSC-----CSSC
T ss_pred cc--cc-------------------------------------------------------CCCCC--Cce-----Eeee
Confidence 00 00 00111 111 4689
Q ss_pred cCccccCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHcC-ceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHH
Q 046825 764 IDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHG-FTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEA 842 (1208)
Q Consensus 764 ldK~~iG~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~~~G-fSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ 842 (1208)
+||+++| +|||.+|++||++.|+.|||.+++|+++|++.+| ||||++|+++++++ +++|++|++++.+++++|
T Consensus 646 ldKk~lG--~LI~~i~~~~G~~~a~~~ld~l~~l~~~~lt~~G~fSigi~D~~~~~~k----~~~i~~a~~~v~~i~~~y 719 (1265)
T 1hqm_D 646 QEKNSLK--DLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGIITIGIDDAVIPEEK----QRYLEEADRKLRQIEQAY 719 (1265)
T ss_dssp CCSSHHH--HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHTTCCCCSSSSCCCCSTT----TTHHHHHHHHHHHHHTTT
T ss_pred ecHHHHH--HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhCCCceEeeccccCCHHH----HHHHHHHHHHHHHHHHHH
Confidence 9999999 9999999999999999999999999999999999 99999999999874 578999988888777766
Q ss_pred HhhccCCCCChhhHHHHHHHHhcCCcchhhHHHHHHHHHHHHhhhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcc
Q 046825 843 LELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKV 922 (1208)
Q Consensus 843 ~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~ln~~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~v 922 (1208)
.. + .++.. ++ ...+...|++++++ +.+.++ ..+.+.+++|++++|+.||||||.+
T Consensus 720 ~~---g-~lt~~---e~----------------~~~v~~~~~~~~d~-~~~~~~-~~l~~~~~~N~i~~Ma~SGAKGS~~ 774 (1265)
T 1hqm_D 720 EM---G-FLTDR---ER----------------YDQVIQLWTETTEK-VTQAVF-NNFEENYPFNPLYVMAQSGARGNPQ 774 (1265)
T ss_dssp TS---S-SSCHH---HH----------------HHHHHHHHHHHHHH-HHHHHH-HHHHHSCSSSCTTTTTTTSSSCCHH
T ss_pred Hc---C-CCcHH---HH----------------HHHHHHHHHHHHHH-HHHHHH-HHhcccCCCCcHHHHHHhcCCcCHH
Confidence 32 1 11221 11 22333445555555 544444 2233446899999999999999999
Q ss_pred cHHHHHhhcccccccCcccCCCCCCccccCCCCCCCCccccccccccccCCCCchhhhhhcccccccchhccccccCCch
Q 046825 923 NFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGY 1002 (1208)
Q Consensus 923 N~~Qi~~~lGQQ~leG~Rip~~~~grtLP~f~~~d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGY 1002 (1208)
|++||+||+|||. ..+|+++| +||.|||++||+|+|||||||||||||||||||||+|||
T Consensus 775 ni~Ql~g~~G~ma--------~~~G~~i~------------~pI~ssF~eGLtp~EyFfhtmggReGLiDTAvKTA~SGY 834 (1265)
T 1hqm_D 775 QIRQLCGMRGLMQ--------KPSGETFE------------VPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGY 834 (1265)
T ss_dssp HHHHHSSCCCCCC--------CTTSCCCS------------CCCCCCBTTBCTTCTHHHHHHHHTTHHHHHTHHHHTSSS
T ss_pred HHHHHHhhccccc--------cCCCCccC------------cccccccccCCChHHhheecccccccchhhhhhcccCCc
Confidence 9999999999996 23444543 569999999999999999999999999999999999999
Q ss_pred hhHHHHhhhceeeeecccEEEcCCCCEEEeeecCCcceeccccccccch--------hhhhhhcccccccccc---ccCC
Q 046825 1003 LQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFD--------ALAARERGRGRGRNKF---CDKG 1071 (1208)
Q Consensus 1003 LqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGedGld~~k~~~~~~~~--------~~~~~~~~~~~~~~~~---~~~~ 1071 (1208)
|||||||+|||+.|.||.+ ||+||+|++.....+.++ .+.+++.||+.+.+.. .++.
T Consensus 835 LqRRLVkv~qDv~V~~ddc------------~t~dGi~v~~~~~~~~i~~~~~~~~~~L~~ri~gr~~~~~i~~~~~~p~ 902 (1265)
T 1hqm_D 835 LTRKLVDVAHEIVVREADC------------GTTKYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREVEALGRRLE 902 (1265)
T ss_dssp THHHHHHHSCSCCCCSCCC------------CCCCCEECCSEECCSTTCCCEECCTTTTHHHHTTCEESSCEEETTEEEC
T ss_pred ceeeeeeecceEEEEECCC------------CCCCCEEEEEeecCceeechhhhhhhHHHHHHHhhhhhhcccccccCCC
Confidence 9999999999999888874 689999998654311112 2567777877554330 1222
Q ss_pred CceeeechhHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHHHHhhhcchhHHHHHHHHHHHHhhh-----cCCCCCCch
Q 046825 1072 SHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVL-----SLAQPGEPV 1146 (1208)
Q Consensus 1072 ~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~f~~l~~~~y~~-----slv~pGeaV 1146 (1208)
...+....|...+ .+++.++ .. -....++.+||+.+..+|..||.+ ++|+|||||
T Consensus 903 ~~~~i~~~~~~i~--------------~~~i~~~---gi---~~v~iRs~ltc~s~~gvc~~CYgr~La~~~lV~~GEaV 962 (1265)
T 1hqm_D 903 EGRYLSLEDVHFL--------------IKAAEAG---EV---REVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAV 962 (1265)
T ss_dssp SSCBCCTTHHHHH--------------HHHHHTT---SC---SSCEEECGGGCSCTTSCCSSSSCSCSSSSSCCCTTCCH
T ss_pred CccEEecCcchhh--------------HHHHHHc---CC---CEEEeecCcCHHHHHHHHHHHhhhhhccCCEeccCcee
Confidence 2222222232110 0000000 00 000126789999999999999987 799999999
Q ss_pred hhhhhccCCCcccccccccccccCcc-ccccccccchHHHHHHHhhcCCCCCeEEEecCCC
Q 046825 1147 GLLASQSVGEPSTQMTLNTFHLAGRG-EMNVTLGIPRLQEILTIASKDIKTPVITCPLLVG 1206 (1208)
Q Consensus 1147 GiIAAQSIGEP~TQMTLnTFH~AGv~-~~nVTlGvPRlkEIi~~ask~ikTP~~~~~l~~~ 1206 (1208)
|+|||||||||+|||||||||+||++ ++|||+|+||++||| .| .+||||.|++++...
T Consensus 963 GiIAAQSIGEPGTQlTLrTFH~gGvas~~dIT~GLPRv~El~-eA-rkpk~p~i~a~~~g~ 1021 (1265)
T 1hqm_D 963 GVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF-EA-RRPKAKAVISEIDGV 1021 (1265)
T ss_dssp HHHHHHHHHGGGTTSCCCC--------CCTTSSHHHHHHHHH-HC-CCCSSCBCCCSSSCB
T ss_pred eeeeccccCCCCceeeeEEEEEcceecccccccCchhHHHHH-hh-cCCCCceEEEeccce
Confidence 99999999999999999999999999 599999999999999 45 569999999887543
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=100.00 E-value=1.2e-165 Score=1568.22 Aligned_cols=724 Identities=24% Similarity=0.304 Sum_probs=554.6
Q ss_pred CCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhc
Q 046825 275 KKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFD 353 (1208)
Q Consensus 275 ~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d 353 (1208)
..++|+||||++|||||+++||++.+++ .+++||+|.+|++||+.|++|++++..+ ++...+.+.|.+||.+|++|||
T Consensus 505 ~~~rPewmil~vlPVpPp~lRP~v~ldgg~~~~sDLn~ly~~II~~Nn~Lk~~~~~g-ap~~ii~~e~~~LQ~~V~~liD 583 (1524)
T 2a6h_D 505 SGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQG-APEIIIRNEKRMLQEAVDALLD 583 (1524)
T ss_dssp SSCCTTTTEEEEEEECCSTTSCEEECSTTCEEECTHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHC
T ss_pred cCCCccEEEEecccCCCCCCCCceecCCCceecchHHHHHHHHHHHHHHHHHHHHhc-chHHHHHHHHHHHHHHHHHHhc
Confidence 3589999999999999999999999876 5789999999999999999999998875 7777778899999999999999
Q ss_pred CCCCCc-----CCCC-hhhHHHHhhcccccccccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHH
Q 046825 354 GKNAAG-----QRDM-ASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNV 427 (1208)
Q Consensus 354 ~~~~~~-----~~~~-~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni 427 (1208)
|+.... .++| ++||+||||||+||||+|||||||||||||||||||+|++||||||..||++||+|+
T Consensus 584 N~~~g~p~~~~~~Rp~lKslsq~LkGKeGRFRqNLlGKRVDySgRSVI~pdP~L~l~evGvP~~mA~eLt~Pf------- 656 (1524)
T 2a6h_D 584 NGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPF------- 656 (1524)
T ss_dssp SSSSSCCBCSSSCCCBCCCHHHHHSTTTCHHHHHHHCEEESSEEEEEEEECTTSCTTEEEEEHHHHHHHTHHH-------
T ss_pred CCCCCCCccCCCCCCcCcchhhhccccccccccccccccccccCcceEecCCCccccccCCcHHHHHHhccHH-------
Confidence 987631 2788 999999999999999999999999999999999999999999999999999999984
Q ss_pred HHHHHHHHcCCCCC-CCceEEecCCCCcccCCCccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEe
Q 046825 428 VKLRDSIINGAEIH-PGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVN 506 (1208)
Q Consensus 428 ~~L~~lv~nG~~~~-pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~N 506 (1208)
.|++||.||+..+ ++|+.++...+ + ....+|.|+||+++||+||||
T Consensus 657 -~~r~Lv~nG~a~nik~AK~li~~~~---------------~-----------------~~~~v~dVlr~vidgd~VLlN 703 (1524)
T 2a6h_D 657 -LLKKMEEKGIAPNVKAARRMLERQR---------------D-----------------IKDEVWDALEEVIHGKVVLLN 703 (1524)
T ss_dssp -HHHHHHHSTTCSSHHHHHHHHSSGG---------------G-----------------CCHHHHHHHHHHSTTCCEEEE
T ss_pred -HHHHHHHcCCccchhhhhHHHhhhc---------------c-----------------ccccchhhheeeccCceEEEc
Confidence 3788999997422 33332211000 0 012367889999999999999
Q ss_pred cCCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccch
Q 046825 507 RQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLI 586 (1208)
Q Consensus 507 RqPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~ 586 (1208)
|||||||+|||||+|+++++ +||||||+||+||||||||||||+|||||++|||||++||++++||+||++|+|+++++
T Consensus 704 RqPTLHRlSIqAf~~kl~~g-kTiRLhplVC~pyNADFDGDEMnvHvPqS~eAraEA~~LM~~~~nilsP~~G~Pi~~~~ 782 (1524)
T 2a6h_D 704 RAPTLHRLGIQAFQPVLVEG-QSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPS 782 (1524)
T ss_dssp CSSCCSGGGEEEEEEEEESS-SCEEECSGGGTTTTCCTTTCEEEEECCCSHHHHHHHHHHSBTTTCCBCSSSSSBSSCCC
T ss_pred cCCcccccccceeEEEEcCC-ccceeChhhcCCccCCcccceeeEecCCCHHHHHHHHHHhCCccceecCCCCCeeeeec
Confidence 99999999999999999887 99999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhhcccCc--------cccCHHHHHHHHHhcCccCCCCCCCCCCCCceeeeeccc---ceeeccCC--CccCCC
Q 046825 587 QDHIVSAALLTKKD--------TFLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSE---QEVLPLLP--AIWKPE 653 (1208)
Q Consensus 587 QD~l~g~~lLT~~d--------~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~P--aIlkp~ 653 (1208)
||+|+|+|+||.++ +|+++++++.+++...++ .... ..+...+.. ....+|+| +|+||
T Consensus 783 QD~vlG~y~LT~~~~~~~~~g~~F~~~~e~~~ay~~~~~~------l~~~--i~v~~~~~~~~~~~~~~p~P~~aIlKp- 853 (1524)
T 2a6h_D 783 RDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVA------LNAP--IKVAGRETSVGRLKYVFANPDEALLAV- 853 (1524)
T ss_dssp HHHHHHHHHHHCCCCCCCCSCCCTTSCHHHHHHHHHHHHT------TSSC--SSCCCSSCCHHHHHCEESSHHHHHHHH-
T ss_pred ccchhhheecccccccccCCCceeCCHHHHHHHHhcCCcC------cCCc--eEEecccccccccccccCCchhhhcCC-
Confidence 99999999999984 899999998775532110 0000 000000000 00123445 48888
Q ss_pred CCCCCCeEEEEe----ec----cccCCCcceeeccCCCCCcccccccccccccccccccccCccccccccccccCCCccc
Q 046825 654 PLWTGKQVITAV----LN----HITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKE 725 (1208)
Q Consensus 654 ~lwTGKqv~s~~----l~----~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~ 725 (1208)
|||||+++.+ ++ ..+.|+..||... |....
T Consensus 854 --wtGKQi~~~~~~~~I~~~~~~tt~Gr~ifn~~l----p~~l~------------------------------------ 891 (1524)
T 2a6h_D 854 --AHGIVDLQDVVTVRYMGKRLETSPGRILFARIV----AEAVE------------------------------------ 891 (1524)
T ss_dssp --HTTSSCTTSCCEEECSSCEECCCHHHHHHHHHH----HHHSS------------------------------------
T ss_pred --CCCccccccccccceecceeecccchhhHHHHh----hhhcc------------------------------------
Confidence 9999988742 11 1122222222110 00000
Q ss_pred cccCCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHc
Q 046825 726 VVEGKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMH 805 (1208)
Q Consensus 726 ~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~~~ 805 (1208)
....+++ -..++|+|||+++| +|||.+|++||++.|+.|||++++|+++|++.+
T Consensus 892 -----------------~~~~P~d-------~~~inGvLdKk~LG--~LI~~i~~~yG~~~t~~fLD~lk~Lg~~~lt~~ 945 (1524)
T 2a6h_D 892 -----------------DEKVAWE-------LIQLDVPQEKNSLK--DLVYQAFLRLGMEKTARLLDALKYYGFTFSTTS 945 (1524)
T ss_dssp -----------------CHHHHHH-------TCCTTSCCCHHHHH--HHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred -----------------cccCCCc-------ccceeceecHHHHH--HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhc
Confidence 0000111 01235899999999 899999999999999999999999999999999
Q ss_pred CceeeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcchhhHHHHHHHHHHHHh
Q 046825 806 GFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNK 885 (1208)
Q Consensus 806 GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~ln~ 885 (1208)
||||||+|++++++ +.++|++|++++.+++++|.. + .++.. ++ ...+...|++
T Consensus 946 GfSIGI~Dlii~~~----K~eiI~eA~~~v~~i~~~y~~---G-~lt~~---Er----------------~~~Vi~iw~~ 998 (1524)
T 2a6h_D 946 GITIGIDDAVIPEE----KKQYLEEADRKLLQIEQAYEM---G-FLTDR---ER----------------YDQILQLWTE 998 (1524)
T ss_dssp TCCCCSTTSCCCTT----HHHHHHHHHHHHHHHHHHHHT---T-CSCHH---HH----------------HHHHHHHHHH
T ss_pred CceeehhhccCCHH----HHHHHHHHHHHHHHHHHHHHc---C-CCCHH---HH----------------HHHHHHHHHH
Confidence 99999999999986 468999999999888888743 1 11111 11 1233456666
Q ss_pred hhhhHHHHHHhhcCCCCCCCCCcchhhhhcCCCCCcccHHHHHhhccccc-ccCcccCCCCCCccccCCCCCCCCccccc
Q 046825 886 HTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQE-LEGKRVPRMVSGKTLPSFHPWDWAPRAGG 964 (1208)
Q Consensus 886 ~~~~~~~~~~~~~~l~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~-leG~Rip~~~~grtLP~f~~~d~~~~a~G 964 (1208)
++++ +.+.|+ .++.+.+++|++++|+.||||||.+|++||+||+|||. .+|++ +|.
T Consensus 999 a~d~-v~~~~~-~~L~~~~~~N~i~~Ma~SGAKGS~~NI~Ql~gmrGqma~p~Gki---------Ip~------------ 1055 (1524)
T 2a6h_D 999 TTEK-VTQAVF-KNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGET---------FEV------------ 1055 (1524)
T ss_dssp HHHH-HHHHHH-HHHHHTCTTCHHHHHHHSSSSCCHHHHHHHTSCCCCCBCSSSCB---------CSS------------
T ss_pred HHHH-HHHHHH-HhhcccCCCCCHHHHHHhcCCcCHHHHHHHHhhccccccCCCCC---------ccc------------
Confidence 7776 666665 45555578999999999999999999999999999975 45554 442
Q ss_pred cccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEEEeeecCCcceeccc
Q 046825 965 FIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQT 1044 (1208)
Q Consensus 965 fI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGedGld~~k~ 1044 (1208)
+|.|||++||+|+|||||||||||||||||||||+||||||||||+|||++|.||.+ +|+||+|++..
T Consensus 1056 PI~ssF~eGLtp~EyFfhtmGgReGLvDTAvKTAdSGYLqRRLVkv~qDviVr~dDc------------gt~dGi~v~~~ 1123 (1524)
T 2a6h_D 1056 PVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADC------------GTTNYISVPLF 1123 (1524)
T ss_dssp CCCCCSSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCSCC------------CCCCCEEEESB
T ss_pred ccccccccCCChHHhheecccccCCccccceeeccCCcceeeeeeecceeEEEeCCC------------CCCCCeEEEEe
Confidence 399999999999999999999999999999999999999999999998888777654 58999999764
Q ss_pred cccc--------cchhhhhhhcccccccccc---ccCCCceeeechhHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHH
Q 046825 1045 SFIS--------KFDALAARERGRGRGRNKF---CDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKF 1113 (1208)
Q Consensus 1045 ~~~~--------~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1113 (1208)
.... .+..+.+++.||+...+.. .++....+....|...+ ++++......
T Consensus 1124 ~~g~~~~~~~~~~i~~l~~ri~gR~~~~di~~~~~~p~~~e~i~~~~~~I~-----------------~~~i~~~gi~-- 1184 (1524)
T 2a6h_D 1124 QPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLL-----------------IKAAEAGEIQ-- 1184 (1524)
T ss_dssp CSCSSSSCCCBCCHHHHHHHHTTCBBSSCEECSSCEECTTCBCCTTTTTHH-----------------HHHHHHTSCS--
T ss_pred ecCCccccchhHHHHHHHHHHhcccchhhhhhhccCCCcCcEEeCCCCeeh-----------------HHHHHHcCCC--
Confidence 3332 3345566777887665431 22222223333332110 1111111100
Q ss_pred HHhhhcchhHHHHHHHHHHHHhhhc-----CCCCCCchhhhhhccCCCcccccccccccccCcc-ccccccccchHHHHH
Q 046825 1114 ADKFLSNEMAKQDFLKLVKHKFVLS-----LAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRG-EMNVTLGIPRLQEIL 1187 (1208)
Q Consensus 1114 ~~~~~~~~l~~~~f~~l~~~~y~~s-----lv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~-~~nVTlGvPRlkEIi 1187 (1208)
....++.++|+.+..+|..||.++ +|+||||||||||||||||+|||||||||+||++ ++|||+|+||++||+
T Consensus 1185 -~v~iRS~ltC~s~~gvc~~CYgr~La~~~~v~~GeaVGiiaAQSIGEPgTQlTlrTFH~gGv~~~~dIt~GlPRv~El~ 1263 (1524)
T 2a6h_D 1185 -EVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELF 1263 (1524)
T ss_dssp -EEEECCGGGCCCSSCBCHHHHCSCSSSSSSCCTTCCHHHHHHHHHHSGGGTCCCC-----------CCCCSHHHHHHHH
T ss_pred -cccccccccHHHHHHHHHHHhccccccCCccccccceeehhhhccCCCcccccceeeeeccccccccccccCcchhhhe
Confidence 011267899999999999999987 8999999999999999999999999999999998 789999999999999
Q ss_pred HHhhcCCCCCeEE
Q 046825 1188 TIASKDIKTPVIT 1200 (1208)
Q Consensus 1188 ~~ask~ikTP~~~ 1200 (1208)
.|.+...||+++
T Consensus 1264 -eARkpk~~aiI~ 1275 (1524)
T 2a6h_D 1264 -EARRPKAKAVIS 1275 (1524)
T ss_dssp -TTCCCSSBCCBC
T ss_pred -ecccCCCcceEE
Confidence 577777777654
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=100.00 E-value=5.3e-160 Score=1494.44 Aligned_cols=670 Identities=24% Similarity=0.349 Sum_probs=525.8
Q ss_pred CCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhh
Q 046825 274 GKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLF 352 (1208)
Q Consensus 274 ~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~ 352 (1208)
...++|+||||++|||||+++||++.+++ .+.+||+|++|++||+.|++|++++..+ ++...+.+.|.+||.+|++||
T Consensus 229 ~s~~rPewmil~~lPVpPp~lRP~v~l~gg~~~~~DLn~ly~~II~~N~~Lk~~~~~~-ap~~ii~~~~~~LQ~~V~~l~ 307 (1407)
T 3lu0_D 229 QSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLA-APDIIVRNEKRMLQEAVDALL 307 (1407)
T ss_dssp SSSCCGGGSSEEEEECCCSTTSCCCBCSTTCBCCCTTTTTHHHHHHTTTTTGGGTSSC-CCTTTHHHHHHHHHHHHHHHH
T ss_pred hcCCCHHHhhhheeecCCCCCCCcEEeCCCccccCchHHHHHHHHHHHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHHhc
Confidence 34689999999999999999999999976 6889999999999999999999988764 666667889999999999999
Q ss_pred cCCCCCc-----CCCChhhHHHHhhcccccccccccCccCCccceeeecCCCCccccccCchHHHHhhcCcccccchHHH
Q 046825 353 DGKNAAG-----QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGIPPYFALRLTYPERVTPWNV 427 (1208)
Q Consensus 353 d~~~~~~-----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~saRsVIspDP~l~~~evgvP~~~A~~Lt~pe~Vt~~Ni 427 (1208)
||+.... .++|++||+||||||+||||+|||||||||||||||||||+|++||||||..||++||+| ||+
T Consensus 308 Dn~~~g~~~~~~~~rplksl~qrLkGKeGrfR~NLmGKRVDfSaRSVIspdP~L~i~evGvP~~~A~~L~~P-----f~i 382 (1407)
T 3lu0_D 308 DNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKP-----FIY 382 (1407)
T ss_dssp CSSSSCCCCBTTBCCCCCCTTHHHHTSSSTHHHHTTCCCCSSBCEEEEEECSSCCTTEEEEESHHHHHHTCH-----HHH
T ss_pred CCCCCCCcccCCCCCcccchHHHhccccchhhcccccCCCCCcCceEEeCCCCccceeeeCCHHHHHHhcch-----HHH
Confidence 9987631 278999999999999999999999999999999999999999999999999999999987 788
Q ss_pred HHHHHHHHcCCCCCCCceEEecCCCCcccCCCccccccccchhhhcccccccCCCCCCCcccCceeehhhcccceEEEec
Q 046825 428 VKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNR 507 (1208)
Q Consensus 428 ~~L~~lv~nG~~~~pGa~~i~~~~g~~~~~l~~~~~~~~~~r~~~a~~l~l~~~~~~~~~~~g~~v~Rhl~dgD~Vl~NR 507 (1208)
++|++ +|+.. .+. .|+.+ +... ....|.|+||+++||+|||||
T Consensus 383 ~~L~~---~g~~~--------------~i~--------------~ak~~-v~~~-----~~~v~~vl~~vi~gd~VLlNR 425 (1407)
T 3lu0_D 383 GKLEL---RGLAT--------------TIK--------------AAKKM-VERE-----EAVVWDILDEVIREHPVLLNR 425 (1407)
T ss_dssp HHHTT---SSSCS--------------STT--------------TTTTT-TTSS-----CSSHHHHHHTTTTSCCEEEEE
T ss_pred HHHHH---cCccc--------------cHH--------------HHHHH-HHhc-----CCchhhHHHHHhhceeeeecC
Confidence 77664 45421 000 11122 1110 123567889999999999999
Q ss_pred CCCCCcCcccceeEEEeCCCCeEEEeccCCCCCCCCCCCCceecccCCCHHHHHHHHHhcccCCceecCCCCCCcccchh
Q 046825 508 QPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQ 587 (1208)
Q Consensus 508 qPsLHk~simah~v~vl~~~~t~rln~~~c~~yNADFDGDemn~h~pqs~~a~~Ea~~L~~~~~~~~sp~~g~pi~gl~Q 587 (1208)
||||||+|||||+++++++ +||||||+||+||||||||||||+|+|||++|+|||++||.+++||+||++|+|+++++|
T Consensus 426 qPTLHr~sIma~~~~l~~~-ktirlnp~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~Q 504 (1407)
T 3lu0_D 426 APTLHRLGIQAFEPVLIEG-KAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQ 504 (1407)
T ss_dssp SSCCSGGGEEEEEEEEESS-SSEEECTGGGGTTTCCSSSCEEEEECCCSSHHHHTTTTSSBTTTCCSCSSSSSCSSCCCS
T ss_pred CcccccccceeeeEEecCC-ceEEeChhhcccccCCcccceeeeecCCCHHHHHHHHHHHhCccccccCCCCCceeeecc
Confidence 9999999999999999986 999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhcccCcc--------ccCHHHHHHHHHhcCccCCCCCCCCCCCCceeeeecccceeeccCC-----------C
Q 046825 588 DHIVSAALLTKKDT--------FLNRDEFCQLLYSSGVSSSGLGSFTGKPGQRVLISRSEQEVLPLLP-----------A 648 (1208)
Q Consensus 588 D~l~g~~lLT~~d~--------f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P-----------a 648 (1208)
|+|+|+|+||+++. |.+.+++++++....+. .+.++.+..| .
T Consensus 505 D~llG~y~lT~~~~~~~~~~~~F~~~~ev~~al~~g~v~-------------------l~a~i~vr~~~~~~~~~g~~~~ 565 (1407)
T 3lu0_D 505 DVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLAS-------------------LHARVKVRITEYEKDANGELVA 565 (1407)
T ss_dssp HHHHHHHHHSCCCCCSCCSCCCCSSCSHHHHHHHHSSSS-------------------SSSCSSSSCCCCSCSHHHHHHH
T ss_pred cchheeEEeecccccccCCcceeCCHHHHHHHHHcCCCC-------------------CCCeeEEecCccccCcCCcccc
Confidence 99999999999996 77888988876543221 1111111111 1
Q ss_pred ccCCCCCCCCCeEEEEeeccccCCCcceeeccCCCCCcccccccccccccccccccccCccccccccccccCCCcccccc
Q 046825 649 IWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKGKLSKTNKMHKDKSGKKKEVVE 728 (1208)
Q Consensus 649 Ilkp~~lwTGKqv~s~~l~~~~~~~~~~n~~~~~k~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~ 728 (1208)
..++.++|+|||+|+.+||. .+++
T Consensus 566 ~~~~~~tt~Gr~ifs~ilP~------~~~~-------------------------------------------------- 589 (1407)
T 3lu0_D 566 KTSLKDTTVGRAILWMIVPK------GLPY-------------------------------------------------- 589 (1407)
T ss_dssp TTTSCCSSSHHHHHHHHGGG------SSCC--------------------------------------------------
T ss_pred cceeeecCCccccHHhhCCC------CCCc--------------------------------------------------
Confidence 23456789999999998874 1110
Q ss_pred CCCCchhhhhhhcccccccCCceEEEecceeeeeecCccccCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHcCce
Q 046825 729 GKPGEEKEAEKNKSKEKELSEEKLLIYKNDLVRGVIDKAQFADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFT 808 (1208)
Q Consensus 729 ~~~~~~~~~~~~~~~~~~~~d~~v~i~~gell~G~ldK~~iG~~~Lih~i~~~yG~~~a~~~l~~l~~l~~~~l~~~GfS 808 (1208)
++++|++||+.+| +|||.+|++||++.|+.|||.+++|+++|++.+|||
T Consensus 590 -----------------------------~~ing~l~KK~lg--~LI~~i~~~~G~~~t~~flD~lk~Lgf~~at~~GfS 638 (1407)
T 3lu0_D 590 -----------------------------SIVNQALGKKAIS--KMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGAS 638 (1407)
T ss_dssp -----------------------------TTTTTCCSSSTTT--THHHHHHHHSCSHHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred -----------------------------eeeecccchhhHH--HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeE
Confidence 1456899999999 999999999999999999999999999999999999
Q ss_pred eeecccccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHhcCCcchhhHHHHHHHHHHHHhhhh
Q 046825 809 CGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTS 888 (1208)
Q Consensus 809 igi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~ln~~~~ 888 (1208)
||++|+++|+++ .++|++|++++.+++++|.. + .+++.+.+.+ +..+|+++++
T Consensus 639 IgI~D~~ip~~K----~~iI~~A~~eV~ei~~~y~~---G-~lt~~er~~k-------------------Vi~iw~~a~e 691 (1407)
T 3lu0_D 639 VGIDDMVIPEKK----HEIISEAEAEVAEIQEQFQS---G-LVTAGERYNK-------------------VIDIWAAAND 691 (1407)
T ss_dssp CCSTTSCCCTTH----HHHHHHHHTHHHHHHHHHHH---T-SCCSSTTTTT-------------------HHHHHHTHHH
T ss_pred EeeccCccChHH----HHHHHHHHHHHHHHHHHHHc---C-CCccchHHHH-------------------HHHHHHHHHH
Confidence 999999999876 48999999999988888854 1 1111111111 1222333333
Q ss_pred hHHHHHHhhcCC------------CCCCCCCcchhhhhcCCCCCcccHHHHHhhcccccccCcccCCCCCCccccCCCCC
Q 046825 889 SSVINELLSEGL------------LKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPW 956 (1208)
Q Consensus 889 ~~~~~~~~~~~l------------~~~~~~N~~~~M~~SGaKGS~vN~~Qi~~~lGQQ~leG~Rip~~~~grtLP~f~~~ 956 (1208)
+ +.+.++. .+ ....++|++++|+.||||||.+|++||+||+|||... +|+..
T Consensus 692 ~-v~~~m~~-~l~~~~~~d~~G~~~~l~~~N~i~mMa~SGARGS~~qI~QLaGmrGlmakp--------dG~ii------ 755 (1407)
T 3lu0_D 692 R-VSKAMMD-NLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKP--------DGSII------ 755 (1407)
T ss_dssp H-HHHHHHT-THHHH------------CSCCHHHHHHHSSSSCCTTHHHHHSSCCCCCBCS--------SSCBC------
T ss_pred H-HHHHHHH-hccccccccccccccccCCCCChheeeeccccCCHHHHHHHHHhcCCccCC--------CCCCc------
Confidence 2 2222221 11 1224689999999999999999999999999998632 22221
Q ss_pred CCCccccccccccccCCCCchhhhhhcccccccchhccccccCCchhhHHHHhhhceeeeecccEEEcCCCCEEEeeecC
Q 046825 957 DWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGE 1036 (1208)
Q Consensus 957 d~~~~a~GfI~~sF~~GL~p~EfFfH~maGReGLiDTAvKTa~SGYLqRrLvK~lEdl~V~YD~TVR~~~g~IvQF~YGe 1036 (1208)
.++|.|||++||+|+|||||||||||||+|||||||+||||||||||+||||.|. ..||.. .
T Consensus 756 ------e~PI~ssFreGLtp~EyFfst~GaRKGL~DTALKTAdSGYLTRRLVdv~QDviV~------e~DCGT------~ 817 (1407)
T 3lu0_D 756 ------ETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVT------EDDCGT------H 817 (1407)
T ss_dssp ------SSCCCCCSSSCCCHHHHHHHHHHHHHHHHHTTTTTTCTTTTTHHHHTTSTTCCBC------CCSCCC------C
T ss_pred ------chhhhcccccCCCHHHhhhhcccchhhhhhhhhhcccchhHHHHHHHhhcceEEE------ecCCCC------C
Confidence 2468999999999999999999999999999999999999999999999888755 445422 4
Q ss_pred Ccceeccc-cccccchhhhhhhccccccccccccCCCceeeechhHHHHHhhhcchhhhHHHHHHhHHHHHHHhHHHHHH
Q 046825 1037 DGVDVHQT-SFISKFDALAARERGRGRGRNKFCDKGSHTFVMGRNQEMIYKKCSGQLDASNAYIMELPDALKDNAEKFAD 1115 (1208)
Q Consensus 1037 dGld~~k~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1115 (1208)
+|+.+... +..+..+.+.+++.||+.+.+.+. +....+.+.+|...- . +..++ |.+. -++
T Consensus 818 ~Gi~v~~~~~~~~vi~~L~~ri~GRv~a~di~~-p~tgevi~~~n~~I~-e----------~~a~~----i~~~---gi~ 878 (1407)
T 3lu0_D 818 EGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLK-PGTADILVPRNTLLH-E----------QWCDL----LEEN---SVD 878 (1407)
T ss_dssp SSCEEEESSCCCSSSSCCCCCCSSCBBSSCBCC-SSSCCBCSSCBCCHH-H----------HHHHH----HTTT---TCS
T ss_pred CCEEEEEeecCCeEEeehhhheeeeeeHhHeec-CCCCcEEEeCCCcCC-H----------HHHHH----HHHc---CCC
Confidence 56555321 111224456778899988776553 334455555563321 0 00000 0000 001
Q ss_pred h-hhcchhHHHHHHHHHHHHhhhc-----CCCCCCchhhhhhccCCCcccccccccccccCccc
Q 046825 1116 K-FLSNEMAKQDFLKLVKHKFVLS-----LAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGE 1173 (1208)
Q Consensus 1116 ~-~~~~~l~~~~f~~l~~~~y~~s-----lv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~ 1173 (1208)
+ ..++.+||+.-..+|..||++. +|+.|||||||||||||||||||||||||++|+++
T Consensus 879 ~V~IRS~LTC~s~~GVC~~CYGrdLa~g~~V~iGEAVGiIAAQSIGEPGTQLTMRTFHtGGvas 942 (1407)
T 3lu0_D 879 AVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAAS 942 (1407)
T ss_dssp EEEECCSSSCSCSSSBCSTTTCSCSSSSSCCCSSCCTTHHHHHHHHSGGGSSCCSCTTCCCCCC
T ss_pred EEEEcCceeecCCCcccHHHhCccccCCCCcccCceeeeeeeeccCCCcceeeeeeeeeccccc
Confidence 1 1279999999999999999984 68999999999999999999999999999999875
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=100.00 E-value=3.1e-63 Score=581.26 Aligned_cols=274 Identities=26% Similarity=0.349 Sum_probs=201.8
Q ss_pred CCCCCCCCCCCCCccceeeccccccchhcHHHHHHHHHHhhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhcccC
Q 046825 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPLLFNLLYTLLKRICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDLDLP 80 (1208)
Q Consensus 1 C~TCg~~~~~CPGHFGHIELa~PVynP~ff~~l~kLLr~iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~i~~ 80 (1208)
|+|||++..+||||||||||++|||||+||+.+++||+|+|++||||++++.+...|..+++.+...
T Consensus 121 C~TCg~~~~~CpGHfGhIeL~~PVfh~gF~~~I~kILr~vC~~C~klll~~~~~~~f~~~lr~~~~~------------- 187 (436)
T 3qqc_A 121 CETCGGRAGECPGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNR------------- 187 (436)
T ss_dssp CSSSCCCSSSCCCCEEEEEEEEEEECGGGHHHHHHHHHHSCSTTCCCSSCHHHHHHHHHHHHHTSSC-------------
T ss_pred CCCCCCCCCcCCCCceeEeechHHHHHHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHhhhhc-------------
Confidence 9999999999999999999999999999999999999999999999999988887888888753210
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCccCCCCcccchhhHHHHHHHHHHHHHhc--ccCCCCCCCCCCceecccceEE
Q 046825 81 SESSNPEDSDVSNKSSCSMVTPRGNYDNVRNLKPQEWTSLQFAEAKLALLQFLKIE--TTKCGNCKAKNPRISKPTFGWI 158 (1208)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ii~eflk~~--~~kC~~Cg~~~p~Irk~g~~ki 158 (1208)
...++.+++++++.| .+.|++||+.||+|+++++..+
T Consensus 188 -----------------------------------------~~~~k~~~~~i~~~~k~~~~C~gCG~~qp~Ir~e~~~~~ 226 (436)
T 3qqc_A 188 -----------------------------------------RSEFNEIIKEIHKKAKERMVCPHCGAPQYPIKFEKPTIY 226 (436)
T ss_dssp -----------------------------------------HHHHHHHHHHHHHHHHTCCSCC-------CCCBCSSSCE
T ss_pred -----------------------------------------cccHHHHHHHHHHHcccCCcCcccCCcCceEEEecceee
Confidence 113455666676665 6789999999999999998755
Q ss_pred EEecCCchhhhhhhhccCCcCCCcCCCccccccCCCCCCCCCCCCCCCCCCCCCcchhhhhcccCCCCCCCCcccccccc
Q 046825 159 HMNGMPHADIRANLIRGCNLGETFSGGEEEKDLGASSDVDAPETHSFNGTFPGTQDTAARRHQKGSGAVPSGFKKQKDLF 238 (1208)
Q Consensus 159 ~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (1208)
+... + +++.. ..++
T Consensus 227 ~~~~--~----------------------------------~~~~~----------------------~~k~-------- 240 (436)
T 3qqc_A 227 WEIR--K----------------------------------DEQGN----------------------EYRH-------- 240 (436)
T ss_dssp EEEC--C----------------------------------C---C----------------------CCEE--------
T ss_pred eecc--c----------------------------------ccccc----------------------cccc--------
Confidence 4321 0 00000 0123
Q ss_pred CCCCCHHHHHHHHHhcCHhHHHHccccccccccCCCCCCCCceEEEeeeecCCCcccCCcccCC-CccCchhHHHHHHHH
Q 046825 239 SGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVVLVPPIKFRLPSKGGD-SVMEHPQTVLLSKVL 317 (1208)
Q Consensus 239 ~~~L~P~eV~~iLkkI~~~d~~lL~ll~~~~~~~~~~~~~Pe~ffL~~lpVpP~~~RP~~~~~~-~~~eddlt~~l~~Ii 317 (1208)
.|+|++|+++|++||++|.++|++. +..++||||||++|||||+++||++.+++ .++|||||++|++||
T Consensus 241 --~LtP~~vl~ifk~IsdeD~~lLGl~--------~~~~rPewmIlt~LPVpPp~vRPsv~~~~g~~~edDLT~kl~~II 310 (436)
T 3qqc_A 241 --RLMPTEVRDWLEKIPDKDLPLLGLD--------PEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDLTHKLVDII 310 (436)
T ss_dssp --EECHHHHHHHHHHSCTTTGGGSSCC--------TTTCCGGGGEEEEEEECCGGGSCCBCC---CCBCCHHHHHHHHHH
T ss_pred --ccCHHHHHHHHHhCCHHHHHHhccc--------ccCCCcceeEeeccccCCCcCcccEEeCCCcCCCChHHHHHHHHH
Confidence 7999999999999999999999874 34689999999999999999999999865 789999999999999
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHHhhHHHHHHhhhcCCCCC--c----CCCChhhHHHHhhcccccccccccCccCCccc
Q 046825 318 QANIYLANAYVNQPDNAKVIVARWMNLQQSVNVLFDGKNAA--G----QRDMASGICQLLEKKEGLFRQKLMGKRVNYAC 391 (1208)
Q Consensus 318 ~~n~~l~~~~~~~~~~~~~i~~~~~~LQ~~v~~~~d~~~~~--~----~~~~~~~i~q~L~gK~G~fR~nlmGKRvd~sa 391 (1208)
+.|++|++.+..+ ++...+.+.|..||.+|++||||+.+. . .++|++||+|||||||||||+||||||||||+
T Consensus 311 ~~N~~L~~~~~~g-ap~~~i~~~~~lLQ~~V~~~~dn~~~g~~~~~~~~~rp~ksi~~rLkGKeGRfR~NL~GKRVdy~~ 389 (436)
T 3qqc_A 311 RINNRLKQNIEAG-APQLIIEDLWDLLQYHVTTYINNEAPGVPPAKHKSGRPLKTLAQRLKGKEGRFRGNLSGGAGSGAG 389 (436)
T ss_dssp HHHHHHHHHHHSC-CCSHHHHHHHHHHHHHHHHHHCTTCTTCCCCBCTTSCBCCCHHHHHCC------------------
T ss_pred HHHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHhhccCCCCCCCccccCCCCCccchHhhhccccceecCcCCCCCCCccc
Confidence 9999999999885 777778899999999999999999873 1 27899999999999999999999999999999
Q ss_pred e-eeecCCCCccccccCchHHHHhhcCcc
Q 046825 392 R-SVISPDPYLAVNEIGIPPYFALRLTYP 419 (1208)
Q Consensus 392 R-sVIspDP~l~~~evgvP~~~A~~Lt~p 419 (1208)
| ||| ..+|-+||+|
T Consensus 390 ~~s~~--------------~~~~~e~~~~ 404 (436)
T 3qqc_A 390 SGSVL--------------ARAAFEITVQ 404 (436)
T ss_dssp -----------------------CCCCHH
T ss_pred chhHH--------------HHHHHHHHHH
Confidence 9 999 8899999998
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=99.96 E-value=1.4e-30 Score=305.96 Aligned_cols=87 Identities=46% Similarity=0.657 Sum_probs=69.7
Q ss_pred cchhHHHHHHHHHHHHhhhcCCCCCCchhhhhhccCCCcccccccccccccCccccccccccchHHHHHHHhhcCCCCCe
Q 046825 1119 SNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPV 1198 (1208)
Q Consensus 1119 ~~~l~~~~f~~l~~~~y~~slv~pGeaVGiIAAQSIGEP~TQMTLnTFH~AGv~~~nVTlGvPRlkEIi~~ask~ikTP~ 1198 (1208)
.+..+++.+..+|..||.|++|+||||||+|||||||||||||||||||+||+|++|||+|+|||+||+ +|+|+++||+
T Consensus 43 ~~~~~~~~~~~~~~~~y~r~lv~pGEAVGiIAAQSIGEPgTQlTLrTFH~gGva~~nvT~GlPRl~Ei~-~a~k~~~tp~ 121 (395)
T 4ayb_C 43 VTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIV-DAKKVPSTPM 121 (395)
T ss_dssp CCHHHHHHHHHHHHHHHHHTBCCTTCCHHHHHHHHHHHHHHTCC-------------CCCSHHHHHHHH-TCCSSCSSCE
T ss_pred cCHHHHHHHHHHHHHHHHHhcCCCCchHhHHHHhhcCCchhhhccccceeeeecceeeecCccceEEec-ccccCCCCCc
Confidence 567778889999999999999999999999999999999999999999999999999999999999999 5999999999
Q ss_pred EEEecCCC
Q 046825 1199 ITCPLLVG 1206 (1208)
Q Consensus 1199 ~~~~l~~~ 1206 (1208)
|+++|.++
T Consensus 122 ~~i~l~~~ 129 (395)
T 4ayb_C 122 MTIYLTDE 129 (395)
T ss_dssp EEECCTTT
T ss_pred eEEEeccc
Confidence 99999764
No 9
>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=94.46 E-value=0.0066 Score=79.76 Aligned_cols=49 Identities=22% Similarity=0.419 Sum_probs=40.4
Q ss_pred CCCCCCCCCCCC---CccceeeccccccchhcHHHH-----------HHHHHHhhhhcccccc
Q 046825 1 CKTCGQRQFLCP---GHFGHIDLVVPVYNPLLFNLL-----------YTLLKRICFFCHHFKA 49 (1208)
Q Consensus 1 C~TCg~~~~~CP---GHFGHIELa~PVynP~ff~~l-----------~kLLr~iC~~C~rfll 49 (1208)
|+.||-...+|. .+||||+|+.||.|+.||+.+ .+.|+.+|.++.-+..
T Consensus 73 C~~Cgve~t~s~VRR~rmG~I~La~PV~HiWylk~~PS~l~~LLd~s~k~le~i~yf~~y~v~ 135 (1524)
T 2a6h_D 73 CERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVL 135 (1524)
T ss_dssp CSSSCCCCSSTHHHHHCEEEEEEEEEEECHHHHSSSSCHHHHHTTSCTTHHHHHHHHSCCEEE
T ss_pred CCCCCCccccchHHhhhcCeeeecCceeehhhhcCCchHHHHHhcCCHHHHhHhhcceeeEee
Confidence 666666666666 999999999999999999977 8889999988865444
No 10
>2j7n_A RNA-dependent RNA polymerase; RNAI response, RNA-directed RNA polymerase, hydrolase; 2.30A {Neurospora crassa} PDB: 2j7o_A
Probab=33.94 E-value=14 Score=47.82 Aligned_cols=54 Identities=24% Similarity=0.164 Sum_probs=35.8
Q ss_pred hcccceEEEecCCCCCcCcccceeEEEeCCCCeE-----------EEeccCCCCCCCCCCCCceecc
Q 046825 497 LQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTL-----------RMHYANCSTYNADFDGDEMNVH 552 (1208)
Q Consensus 497 l~dgD~Vl~NRqPsLHk~simah~v~vl~~~~t~-----------rln~~~c~~yNADFDGDemn~h 552 (1208)
+..|..||+-|.|+||..-|+=.++.-.|.-+-+ |=+|.-| =..|+|||+-+|-
T Consensus 572 ~l~gg~VlVtRnP~lhPGDIrvv~AV~~PeL~hL~DvIVFp~kG~Rplps~l--SGGDLDGD~Y~Vi 636 (1022)
T 2j7n_A 572 LLSDCDVLVARSPAHFPSDIQRVRAVFKPELHSLKDVIIFSTKGDVPLAKKL--SGGDYDGDMAWVC 636 (1022)
T ss_dssp EECSEEEEEECSSCCSGGGEEEEEECCCGGGTTCCSEEEECSCSSSCHHHHT--TTCCSSSCEEEEE
T ss_pred eecCceEEEEeCCCcCcCceeEEEeccChhhhccCCeEEccCCCCCCChhHh--cCCCCCCCeEEEE
Confidence 4556679999999999999987776544432111 1111112 1689999998765
No 11
>1twf_J DNA-directed RNA polymerases I, II, and III 8.3 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.11.1 PDB: 1i3q_J 1i6h_J 1k83_J* 1nik_J 1nt9_J 1pqv_J 1r5u_J 1r9s_J* 1r9t_J* 1sfo_J* 1twa_J* 1twc_J* 1i50_J* 1twg_J* 1twh_J* 1wcm_J 1y1v_J 1y1w_J 1y1y_J 1y77_J* ...
Probab=23.94 E-value=32 Score=30.10 Aligned_cols=33 Identities=18% Similarity=0.411 Sum_probs=22.7
Q ss_pred hhhhccccccChhhHHHHHHHHHHhhcCChHHHhhhhc
Q 046825 40 ICFFCHHFKASRREVEKCVRKLELIIKGDIIAAKSLDL 77 (1208)
Q Consensus 40 iC~~C~rfll~~~~~~~~~~kL~ll~~G~~~~a~~L~~ 77 (1208)
.||+|+++.-+.|+. |.. +++.|.+.+.+-||+
T Consensus 6 RCFTCGkvi~~~we~--y~~---~~~~g~l~~~~~LD~ 38 (70)
T 1twf_J 6 RCFSCGKVVGDKWES--YLN---LLQEDELDEGTALSR 38 (70)
T ss_dssp BCTTTCCBCTTCHHH--HHH---HHHTSCCCHHHHHHH
T ss_pred ecCCCCCChHHHHHH--HHH---HHHcCCCCHHHHHHH
Confidence 599999999888874 543 455665455555664
Done!