Query 001532
Match_columns 1058
No_of_seqs 168 out of 1543
Neff 6.9
Searched_HMMs 29240
Date Tue Mar 26 15:51:08 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/001532.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_835-839//hhsearch_pdb/001532hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_B DNA-directed RNA polyme 1.0 1 1 2376.3 38.6 1018 24-1058 10-1118(1210)
2 1twf_B DNA-directed RNA polyme 1.0 1 1 2342.3 69.8 1027 12-1058 13-1129(1224)
3 4ayb_B DNA-directed RNA polyme 1.0 1 1 2161.1 70.2 1008 23-1057 5-1029(1131)
4 2a6h_C DNA-directed RNA polyme 1.0 1 1 1780.6 42.2 867 28-1057 2-1030(1119)
5 3lu0_C DNA-directed RNA polyme 1.0 1 1 1593.4 42.2 882 24-1058 7-1269(1342)
6 3mlq_A DNA-directed RNA polyme 1.0 1 1 236.4 12.3 120 43-198 2-133 (188)
7 3tbi_B DNA-directed RNA polyme 1.0 1 1 108.4 5.7 99 778-882 2-108 (228)
8 3lti_A DNA-directed RNA polyme 1.0 1 1 65.1 16.0 68 192-264 4-78 (296)
9 3mlq_A DNA-directed RNA polyme 1.0 1 1 45.2 3.6 66 363-433 120-185 (188)
10 2g7j_A Putative cytoplasmic pr 1.0 1 1 15.7 2.7 39 921-959 76-114 (124)
No 1
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=1.00 E-value=1 Score=2376.33 Aligned_cols=1018 Identities=37% Similarity=0.619 Sum_probs=932.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHCCCCEECCC-----------CCEEEEEEEEEECCCCC
Q ss_conf 7764001222462111443517999999999998477999870476110589-----------94999994899928701
Q 001532 24 PVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGID-----------PSIFLRFKDVRIGQPSM 92 (1058)
Q Consensus 24 ~~~~~~~~~~~i~~~f~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~~-----------~~~~l~f~~i~i~~P~~ 92 (1058)
..++.+|+|.++++||+.++||+|||||||+|++++|++|+++.++|+.+.+ .++.|+|+++++++|++
T Consensus 10 ~~~~~ed~w~li~aff~~~gLV~qHIdSFN~FI~~~Lq~IV~~~~~I~~~~~~~~~~~~~~~~~~~~l~f~~i~v~kP~~ 89 (1210)
T 3h0g_B 10 ETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPTM 89 (1210)
T ss_dssp CCCCHHHHHHHHHHHHHHTCTTCSSSSSSSSSTTTTHHHHSSTTCCCC-------------------CEEEEEECCCCCC
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCEEEEEEEEEEECCCCE
T ss_conf 66798898898999864302588998899999997499997414847766766766444467754999997899858840
Q ss_pred CCCC-CCCCCCHHHHHHCCCCCCCEEEEEEEEEECCCC----------C---CEEEEEEEEEEEEECCCCCCCCCCCCCC
Q ss_conf 3588-667899144763299547409999999999875----------4---2024786899965202013565227999
Q 001532 93 TVDG-VSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHT----------E---KTTMEKNDVVIGRIPIMLRSCRCVLYGK 158 (1058)
Q Consensus 93 ~~~~-~~~~l~P~eaR~r~lTYsa~l~v~i~~~~~~~~----------~---~~~~~~~~v~iG~iPIMv~S~~C~L~~~ 158 (1058)
.+++ ..+++||+|||+|++||+||++|++++..++.. + .......++.||+|||||||++|||+++
T Consensus 90 ~e~d~~~~~l~P~EcRlR~lTYsapl~Vdi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IG~iPIMlrS~~C~L~g~ 169 (1210)
T 3h0g_B 90 TEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGV 169 (1210)
T ss_dssp BCTTSCBCCCCTTTTTTTCCCCEEEEEEEEEC---------------------CCSSCCCEEEEEEECCSSSTTSSSSSC
T ss_pred ECCCCCCCCCCHHHHHHCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCEEECCCCCCCCCC
T ss_conf 05778646558899971399635268999999975756443333333444433333300488711898847783327897
Q ss_pred CHHHHHHCCCCCCCCCCEEEECCCEEEEEEEECCCCCEEEEEECCC---CCEEEEEEECCCCCC----EEEEEEEE----
Q ss_conf 9888976299989999489991913478642003598799995799---757999982589950----08999955----
Q 001532 159 DEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKK---GNINASVTSSTETVK----SKTVIQME---- 227 (1058)
Q Consensus 159 s~~el~~~gE~~~d~GGYFIInG~EKVIi~q~~~~~N~i~~~~~~~---g~~~~~v~s~~~~~~----~~~~~~~~---- 227 (1058)
+++||+++||||+|+||||||||+||||++||++++|+|++++++. ..+.+.++|++++.+ +.++.+..
T Consensus 170 s~~eL~~~gEcp~D~GGYFIING~EKVII~qerla~N~~iv~~~~~~~~~~~~a~irS~~~~~~~~~s~~~v~~~~~~~~ 249 (1210)
T 3h0g_B 170 SDSELYDLNECPYDQGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTE 249 (1210)
T ss_dssp CHHHHHHTTCCTTCCCCCBCGGGSCBCCCBCBCCCCSCCCCCCCCCSSSCCCCCCCCCCCCSSSCCCCCCCCCCCCCCTT
T ss_pred CHHHHHHCCCCCCCCCCEEEEECEEEEEEECHHHCCCEEEEEEECCCCCCEEEEEEEEEECCCCCCEEEEEEEEEECCCC
T ss_conf 98999756888789997899908788898321230565799962588874079999998358862005899999851566
Q ss_pred --CCEEEEEECCEECCCCHHHHHHHHCCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCC
Q ss_conf --8899999811001323856899828998889998817---94467863566199988428768899999985003346
Q 001532 228 --KGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVG---RDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRS 302 (1058)
Q Consensus 228 --~g~i~~~~~~~~~~IPi~illrALg~~sD~eI~~~i~---~~~~~~~~l~~~l~~~~~~~~~t~~~al~yig~~~~~~ 302 (1058)
++.+++++++++..||++++|||||.+||+||++.|. .+..+.+.+.++++++. .++|+++|++|||++++..
T Consensus 250 ~~~~~i~~~~~~~~~~IPi~ivlkALg~~sD~EI~~~I~~~~~d~~~~~~l~~slee~~--~i~tq~~aL~yIG~r~~~~ 327 (1210)
T 3h0g_B 250 NSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAF--VIQDKDIALDYIGKRGSTT 327 (1210)
T ss_dssp SCSCCCCCCCTTSCSCCCSHHHHTTTTCCSTTHHHHHHCCSSCCHHHHHTHHHHHHTTS--SCCSSHHHHHTTCCCSSSC
T ss_pred CCCCEEEEEEECCCCCCCHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHH--HCCCHHHHHHHHHHHCCCC
T ss_conf 78955999970422677699999870798899999997178884899999999999865--0588999999998754346
Q ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEECCHHHHHHHHHHH
Q ss_conf 78999998178999998764316878788888973024889999999862398777884643460871127889999999
Q 001532 303 TFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFED 382 (1058)
Q Consensus 303 ~~~~~~~~~~e~~~~~L~~~llpHl~~~~~~~~~K~~~L~~Mv~kLl~l~~g~~~~Dd~D~l~NKRv~l~G~Ll~~lfr~ 382 (1058)
..++++ ++++|+++|++++|||++..+.++.+||.||++|++||++++.|.+.+||+|||+||||+|+|+||+.+||+
T Consensus 328 -~~~~~~-~~~~a~~iL~~~lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~l~G~Ll~~lfr~ 405 (1210)
T 3h0g_B 328 -GVTREK-RLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRM 405 (1210)
T ss_dssp -CCCHHH-HHHHHHHHHTTTSSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBCCHHHHHHHHHHH
T ss_pred -CCCCHH-HHHHHHHHHHHHEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECHHHHHHHHHHH
T ss_conf -888144-799999998741884769874450589999999999999986799878898422471773378999999999
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC-CCCCCCCCCCCEEECCCCCCCCCCCCCC
Q ss_conf 999999999999876723999888775223433344206454530248775-1011343345428713334000023544
Q 001532 383 LFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFD-VKRFKMHRKGMTQVLARLSFIGTLGHMT 461 (1058)
Q Consensus 383 ~l~~~~~~i~~~l~k~~~~~~~~~~~~~~~~i~~~~It~~l~~~lsTGnw~-~~~~~~q~sG~sq~l~Rln~ls~LShlR 461 (1058)
.|++|++.+++.+++.+.+. ..+++...++++.||++|+||||||||+ .++++++++|+||+|+|+||+|+|||||
T Consensus 406 ~~~~~~~~i~~~l~k~~~~~---~~~~~~~~i~~~~It~~l~~~laTGNW~~~kk~~~~~sGvsqvl~R~n~~s~lShlR 482 (1210)
T 3h0g_B 406 LFRKMTRDVYKYMQKCVETN---REFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLR 482 (1210)
T ss_dssp HHHHHHHHHHHHHHHHHTTC---CSCCCTTSSCSTTTSHHHHHHHSSSCSSTTSSCCSCCCCSCCBCCCSSHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHCC---CCCCHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHH
T ss_conf 99999999999888876137---766889960600567899988611786555666557677799833687899888888
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHCCCEECCCCCCCCCCC
Q ss_conf 23653234543358986799976443347799987632222355115541489970599998641974412468545679
Q 001532 462 RVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHN 541 (1058)
Q Consensus 462 rv~~~~~~~~k~t~~R~Lhps~wGfICPveTPEG~~cGLi~~LA~~a~Is~~~~~~~i~~~l~~~G~~~l~~~~~~~~~~ 541 (1058)
|+++||++++|+++||+|||||||||||+|||||++|||+||||++|.||++.+.+||.++|.++||++++...+...
T Consensus 483 rv~~p~~~~~K~~~~R~Lhpt~WG~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~pI~~~l~~~gme~le~~~~~~~-- 560 (1210)
T 3h0g_B 483 RTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLEDYNPSAS-- 560 (1210)
T ss_dssp BBCCSCCSSCCSSSSSSCCGGGTTTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSSHHHHHHHSSSCCCCSCCCSSSS--
T ss_pred HCCCCHHHCCCCCCCCCCCHHHHEEECCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHCCCCHHHCCCCCC--
T ss_conf 606840002666656644731631335666878774443003540036678998188999999848741544276568--
Q ss_pred CCCEEEEECCEEEEECCCHHHHHHHHHHHHHCCCCCCEEEEEECCCCCEEEEECCCCEEEEEEEEEECC-------CCCC
Q ss_conf 980799997948763269244899999876438767315998614563499953998234439997248-------3121
Q 001532 542 PNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKG-------ISRI 614 (1058)
Q Consensus 542 ~~~~~V~lnG~~iG~~~~~~~~~~~lr~lrr~~~i~~~v~i~~~~~~~~i~I~td~gRl~RPll~v~~~-------~~~~ 614 (1058)
++.++|||||+|||++.+|..|+++||.|||.+.|+.+||+++|...++++||||+||++|||++|+|+ ++.+
T Consensus 561 ~~~tkVfvNG~wVGvh~dp~~Lv~~lR~lRR~g~Is~eVSIvrdir~rE~~IfTDaGRv~RPLfvVen~~~~~~~g~L~l 640 (1210)
T 3h0g_B 561 PNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCI 640 (1210)
T ss_dssp SSSCCCCSTTCCCCCCSCHHHHHHHHHHHHTTTSSCTTCCCCCCTTTCCCCCCCSSCCBCCEEEECCCSSCSSSSCCCSS
T ss_pred CCCEEEEECCEEEEEECCHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEECCCCCCCCEEEEECCCCCCCCCCCCCC
T ss_conf 98429999999999948999999999998606899994698753889869996678714641799716876444565245
Q ss_pred HHHHHHHHHCC----------CCCCHHHHCCCCEEEECCCCCCCEEEEEECCCCC-------------------------
Q ss_conf 06568876317----------7650121015815576044332258995139999-------------------------
Q 001532 615 KEHHMKELLDG----------VRSFDDFLREGLIEYLDVNEENNALIALYEGDAT------------------------- 659 (1058)
Q Consensus 615 ~~~~~~~~~~~----------~~~~~~ll~~g~iE~id~~Eq~~~~Ia~~~~~~~------------------------- 659 (1058)
+++|++++..+ ..+|++|+..|+|||||++||++++|||+++|+.
T Consensus 641 ~k~hi~~L~~~~~~~~~~~~~~~~w~~Lv~~GvIEylDaeEEet~mIamtpeDL~~~r~~~~g~~~~~~~d~~~r~k~~~ 720 (1210)
T 3h0g_B 641 RKEHIQQLIEDKDRYDIDPEQRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAP 720 (1210)
T ss_dssp CHHHHHHHHHHHTCCCSCTTCCCSSTTTTTTTSEEECCTTTGGGCCEESCHHHHHHHHHHTTCCCCCCSSCCSSCCCCCS
T ss_pred CHHHHHHHHCCCCCCCCCCCCCCCHHHHHHCCCEEEECHHHHHCEEEEECHHHHHHHHHHHCCCCCCCCCCCHHHCCCCC
T ss_conf 69999998614334433322357888897679789846766202258745899534554322566544446101102567
Q ss_pred ----CCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEECCCCCEEECHHHHH
Q ss_conf ----9730144237600032236677889999986410111245776531575310013520552079953132302322
Q 001532 660 ----PDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLLTTRTIEL 735 (1058)
Q Consensus 660 ----~~~th~Ei~p~~ilsv~AsliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~r~d~~~y~L~ypQ~PlV~t~~~~~ 735 (1058)
..||||||||++|||||||+||||||||||||||||||+|||||++++|+..|+||++|+|+|||+|||+|+++++
T Consensus 721 ~~~~~~~THcEIhPsmILGIcASiIPFpdHNQSPRNtYQ~aMgKQamG~~~~n~~~R~Dt~~~~L~yPQkPlv~T~~~e~ 800 (1210)
T 3h0g_B 721 NPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEY 800 (1210)
T ss_dssp CCSCCSCSEECSCGGGSSCSSSTTSSSSTTSCSHHHHHHHHHHTTCCSCCCTTTTTSCCSSEEEESSCBCCSSBCTTSTT
T ss_pred CCCCCCCCCCCCCCHHHHHHEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCHHHHH
T ss_conf 77654555335441034453000466865555605554333303555543224232447500276268176543256787
Q ss_pred HCCCCCCCCCCEEEEEEECCCCCCCCCEEEECCEEECCCEEEEEEEEEEEEEECCCCCCCCEECCCCCCCC---CCCCCC
Q ss_conf 16898889840379996147888777199854311014347999999999962036986312319999999---510011
Q 001532 736 VGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGP---GAERMQ 812 (1058)
Q Consensus 736 ~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~---~~~~~~ 812 (1058)
++++++|+|+||+||||||+|||||||||+||+|++||+|||+||++|++++++...+..|.|..|+.+.. +...|+
T Consensus 801 ~~~~elp~G~NaiVAvmsy~GYn~EDAiIink~sv~rg~~~s~~~~~y~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~ 880 (1210)
T 3h0g_B 801 LKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYD 880 (1210)
T ss_dssp TTCTTSCSCCEECBEECCCSSSSCSSCEEEEHHHHTTTTTCEEEEEEEEECCCCCSSSCCCCCCCCCTTSCCSCCSCCGG
T ss_pred HCCCCCCCCCCEEEEEECCCCCCHHHHEEEEHHHEECCCEEEEEEEEEEEEEEECCCCCEEEECCCCCCHHCCCCHHHHH
T ss_conf 48886668622389996667887446302302140048659999998887743147986049718983120133313476
Q ss_pred CCCCCCCCCCCCEECCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEEEEECCCCCEEEEEEE
Q ss_conf 49998300689376899989997358988788789999878653223177207999713999999851899977999998
Q 001532 813 ILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLI 892 (1058)
Q Consensus 813 ~ld~~Gl~~~g~~v~~gdili~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~e~~~g~v~~v~~~~~~~~~~~v~v~i 892 (1058)
+||+||||++|++|++|||||||++|+....+.+. ...+...++|+|++++++| .|+||+|.++.+++|.+.|||++
T Consensus 881 ~LD~dGi~~~G~~v~~gDiligK~~p~~~~~~~~~-~~~~~~~~rd~s~~~~~~e--~g~Vd~V~~~~~~~g~~~vkv~~ 957 (1210)
T 3h0g_B 881 KLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELG-QRTQLHAKRDVSTPLRSTE--SGIVDQVMVTTNQEGLKFVKVRM 957 (1210)
T ss_dssp GCCTTSSCCTTCCCCTTCCCCCCCCCC------------CCCCCCCCCCCCCTTC--CCCCCEEEEEECSSSSEEEEEEE
T ss_pred HCCCCCCCCCCCEECCCCEEEEEECCCCCCCHHHC-CCCCCCCCCEEEEEECCCC--CEEEEEEEEEEECCCCEEEEEEE
T ss_conf 46888883788796689989998458887720112-3445665531458953899--75999999977068976999999
Q ss_pred EECCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHCCCHHCCCCEEEEECCC
Q ss_conf 32279964430002379822797541467889989999882870899998865388999984100000279403430014
Q 001532 893 RHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFG 972 (1058)
Q Consensus 893 r~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~~~tpF~ 972 (1058)
|+.|+|+||||||||||||||||++||+|||||++||++||||||||||||||||||++|+++||++++.|.+.|+|||+
T Consensus 958 ~~~R~~~~GDK~a~RhGqKGvi~~i~~~edmPf~~~G~~pDii~NP~~~PSRMtigq~~E~~~g~~~~~~g~~~~~tpF~ 1037 (1210)
T 3h0g_B 958 RSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFT 1037 (1210)
T ss_dssp CCCBCCCTTCEEECTTCCCEEEEEEECTTTSCCBTTTBCCSEECCGGGSTTSCCHHHHHHHHHHHHSSSSCCCCBCCSSC
T ss_pred EEECCCCCHHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEECCCC
T ss_conf 87517886366503257873056785320188677897874987887577776203365768779998559831305688
Q ss_pred CCCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCEEEEEEEEEEEEEECCCCCCCCCEEEECCCCCCCCCCCCCCCCC
Q ss_conf 79999998999999999839999994599828889476556966342122035634861078412784333237867434
Q 001532 973 EPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRA 1052 (1058)
Q Consensus 973 ~~~~~~~~~~~~~~~l~~~g~~~~G~e~l~~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~ 1052 (1058)
+...+++++.|.++||+++|+++||||+||++|+++||+|++|||||+|||+||+|||++|||+.+||||++||+
T Consensus 1038 -----~~~~~~~~~~l~~~g~~~~G~~~l~~g~tg~~~~~~i~~G~~yy~kL~Hmv~dK~h~r~~gp~~~~t~QP~~gr~ 1112 (1210)
T 3h0g_B 1038 -----DVTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRS 1112 (1210)
T ss_dssp -----SCCHHHHHHHHHTTTSCTTSCBCCBCSSSCCBCSSCBEECCEECEECSCCSTTTCEECSSCCBCSSSCSBCCSST
T ss_pred -----CCCHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCEEEEEHHHHCCHHHCCCCCEEECCCCCCHHCCCCCCCCC
T ss_conf -----873999999999769698998897848989771033798714742314111547578655887120248865432
Q ss_pred CCCCCC
Q ss_conf 989999
Q 001532 1053 RNGGFP 1058 (1058)
Q Consensus 1053 ~~GG~~ 1058 (1058)
|+|||-
T Consensus 1113 ~~GG~r 1118 (1210)
T 3h0g_B 1113 RDGGLR 1118 (1210)
T ss_dssp TCCCCC
T ss_pred CCCCEE
T ss_conf 568732
No 2
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Probab=1.00 E-value=1 Score=2342.26 Aligned_cols=1027 Identities=36% Similarity=0.619 Sum_probs=929.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHCCCCEECCC-----------CCEEE
Q ss_conf 8888311112487764001222462111443517999999999998477999870476110589-----------94999
Q 001532 12 DEQLPDKQKLAAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGID-----------PSIFL 80 (1058)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~i~~~f~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~~-----------~~~~l 80 (1058)
++.+.++..+ ++ ++.+|+|.++++||+.++|++|||||||||+++||+++++++++|+.+.+ .++.|
T Consensus 13 ~~~~~~~~~~-~~-~~~~d~w~li~~~~~~~~Lv~~qidSFn~Fi~~gL~~iv~~~~~I~~~~~~~~~~~~~~~~~~~~l 90 (1224)
T 1twf_B 13 EDPYGFEDES-AP-ITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEI 90 (1224)
T ss_dssp -----CCCTT-CC-CCTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHTHHHHHHHTTCBCC------------------CC
T ss_pred CCCCCCCCCC-CC-CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCEEEEE
T ss_conf 4455661115-84-578898886899872844789899999999997089999855966503754455554556607999
Q ss_pred EEEEEEECCCCCCCCC-CCCCCCHHHHHHCCCCCCCEEEEEEEEEE-CCCCCC---E-------E--EE--EEEEEEEEE
Q ss_conf 9948999287013588-66789914476329954740999999999-987542---0-------2--47--868999652
Q 001532 81 RFKDVRIGQPSMTVDG-VSEKLNPHMCRLSDMTYAAPILVNIEYVQ-GSHTEK---T-------T--ME--KNDVVIGRI 144 (1058)
Q Consensus 81 ~f~~i~i~~P~~~~~~-~~~~l~P~eaR~r~lTYsa~l~v~i~~~~-~~~~~~---~-------~--~~--~~~v~iG~i 144 (1058)
+|+++++++|++.+.+ ..++++|+|||+|++||+|||+|++++.. ++.+.. . + ++ +++|++|+|
T Consensus 91 ~f~~i~l~~P~~~e~~~~~~~l~P~EcRlR~lTYsapl~v~v~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~v~iG~i 170 (1224)
T 1twf_B 91 SFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRL 170 (1224)
T ss_dssp EECCCEEEEEEECCSSSCCEECCHHHHHHTTCCCEEEEECCEECCCCC-------------------------CCEEEEE
T ss_pred EEEEEEEECCCEECCCCCCCCCCHHHHHHCCCCCCEEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEECCC
T ss_conf 99789995880103677546689899962389534158999999999688655554332332210022334113671789
Q ss_pred CCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCEEEEEEEECCCCCEEEEEECCCCC---EEEEEEECCCCC---
Q ss_conf 02013565227999988897629998999948999191347864200359879999579975---799998258995---
Q 001532 145 PIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGN---INASVTSSTETV--- 218 (1058)
Q Consensus 145 PIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIInG~EKVIi~q~~~~~N~i~~~~~~~g~---~~~~v~s~~~~~--- 218 (1058)
||||||++|||++++++||+++||||+|+||||||||+||||++||++++|++++++++++. +.+.++|...+.
T Consensus 171 PIMlrS~~C~L~~~s~~el~~~gEcp~D~GGYFIING~ERVIv~Qe~~s~N~i~~~~~~~~~~~~~~~~irsv~~~~~~~ 250 (1224)
T 1twf_B 171 PIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRF 250 (1224)
T ss_dssp ECCTTSTTSGGGTCCHHHHHHTTCCTTCCCCSEEETTEEEEECEEEEECSSCCEEEECCTTSSEEEEEEEECCCSSSCCC
T ss_pred CEEECCCCCCCCCCCHHHHHHHCCCCCCCCCEEEEECCEEEEEEEEECCCCEEEEEECCCCCCCEEEEEEEEEECCCCCC
T ss_conf 75706684347898989998616675689977999085888877650057717999616898635899999886268864
Q ss_pred -CEEEEEEEE-----CCEEEEEECCEECCCCHHHHHHHHCCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf -008999955-----8899999811001323856899828998889998817---9446786356619998842876889
Q 001532 219 -KSKTVIQME-----KGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVG---RDPRYSALLLPSIEECANLDIYTQE 289 (1058)
Q Consensus 219 -~~~~~~~~~-----~g~i~~~~~~~~~~IPi~illrALg~~sD~eI~~~i~---~~~~~~~~l~~~l~~~~~~~~~t~~ 289 (1058)
.+..+.+.+ ++.+++++++++.+||++++|||||.+||+||++.++ .+..+.+.+.++|+++. .+++++
T Consensus 251 ~~~~~l~~~~~~~~~~~~i~vr~~~~k~~IPi~illkALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~e~~--~~~t~~ 328 (1224)
T 1twf_B 251 ISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGF--VIQDRE 328 (1224)
T ss_dssp CCEEEEEEESCSSCSSCCEEEECTTCSSCEEHHHHHHHTTCCSHHHHHHHHCCCTTCHHHHHHHHHHHHHTT--TCCSHH
T ss_pred EEEEEEEEECCCCCCCCEEEEEEECCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHH--HCCCHH
T ss_conf 168999994356678977999981556645299999986699899999986466785899999999999765--138999
Q ss_pred HHHHHHHHC-CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEE
Q ss_conf 999998500-3346789999981789999987643168787888889730248899999998623987778846434608
Q 001532 290 KALEYLEGK-VKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKR 368 (1058)
Q Consensus 290 ~al~yig~~-~~~~~~~~~~~~~~e~~~~~L~~~llpHl~~~~~~~~~K~~~L~~Mv~kLl~l~~g~~~~Dd~D~l~NKR 368 (1058)
+|+.|||++ ++++ .+++. +.+.|+++|++++|||++..+.+..+|++||++|++||+.+..|.+.+||+|||+|||
T Consensus 329 ~AL~yIg~r~~~~g--~~~~~-~~~~a~~iL~~~~l~Hvg~~~~~~~~K~~~L~~mi~kLl~~~~g~~~~DD~DhlgnkR 405 (1224)
T 1twf_B 329 TALDFIGRRGTALG--IKKEK-RIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKR 405 (1224)
T ss_dssp HHHHHHHHTTSCTT--SCHHH-HHHHHHHHHHHTSSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEE
T ss_pred HHHHHHHHHHCCCC--CCCCC-HHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCE
T ss_conf 99999987622679--88730-8999999997520154698754443188999999999999856997777875302628
Q ss_pred ECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC-CCCCCCCCCEEE
Q ss_conf 7112788999999999999999999987672399988877522343334420645453024877510-113433454287
Q 001532 369 LELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVK-RFKMHRKGMTQV 447 (1058)
Q Consensus 369 v~l~G~Ll~~lfr~~l~~~~~~i~~~l~k~~~~~~~~~~~~~~~~i~~~~It~~l~~~lsTGnw~~~-~~~~q~sG~sq~ 447 (1058)
|+++|+||+++||..|+++++.+++.+++..++. ..+++..++++++||++|+||||||||+.+ .++++++|+||+
T Consensus 406 v~l~G~Ll~~lfr~~~~r~~~~i~~~l~~~~~~~---~~~~~~~~i~~~~It~~lk~~~aTGNw~~~k~~~~~~sGvSQv 482 (1224)
T 1twf_B 406 LDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEA---HDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQV 482 (1224)
T ss_dssp EECHHHHHHHHHHHHHHHHHHHHHHHHHSCCC-----------CCCCTHHHHHHHHHHHHHCCCC---------CCCEEE
T ss_pred EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHCCCCHHHCCHHHEEECCCCCCCCCCCCCCCEEEE
T ss_conf 8026589999999999999999999998876214---3214566505653210426343413445555432356644575
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHCC
Q ss_conf 13334000023544236532345433589867999764433477999876322223551155414899705999986419
Q 001532 448 LARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLG 527 (1058)
Q Consensus 448 l~Rln~ls~LShlRrv~~~~~~~~k~t~~R~Lhps~wGfICPveTPEG~~cGLi~~LA~~a~Is~~~~~~~i~~~l~~~G 527 (1058)
|+|+||+|+|||+||+|+++++++|+++||+|||||||||||+|||||+|||||||||++|+|+++.++++|.++|.++|
T Consensus 483 ldr~n~ls~LSH~RRi~~~~~r~~k~~~~R~LHpshwG~iCPiETPEG~~cGLVknLAl~a~Is~g~~~~pi~~~l~~~G 562 (1224)
T 1twf_B 483 LNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWG 562 (1224)
T ss_dssp CCCSSHHHHHHHHTEEECCC------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCHHHHHHHHHTT
T ss_pred ECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHCC
T ss_conf 11134566654544025652434666665424676352446889989863141555773275567998799999999839
Q ss_pred CEECCCCCCCCCCCCCCEEEEECCEEEEECCCHHHHHHHHHHHHHCCCCCCEEEEEECCCCCEEEEECCCCEEEEEEEEE
Q ss_conf 74412468545679980799997948763269244899999876438767315998614563499953998234439997
Q 001532 528 VEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIA 607 (1058)
Q Consensus 528 ~~~l~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~lrr~~~i~~~v~i~~~~~~~~i~I~td~gRl~RPll~v 607 (1058)
|.++++.++..+. +.++|||||+|||++.+|..++..||.+||.+.|+.++|++++...++++||||+||++|||++|
T Consensus 563 ~~~l~e~~~~~~~--~~~kVfvnG~~vG~~~~p~~lv~~lr~lRR~g~i~~evsiv~d~r~~ei~I~TD~GRv~RPl~vV 640 (1224)
T 1twf_B 563 MEPLEDYVPHQSP--DATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIV 640 (1224)
T ss_dssp CEEGGGCCGGGCT--TCEEEEETTEEEEEESCHHHHHHHHHHHHHHTSSCTTCEEEEETTTTEEEEECCSCCEEEEEEEE
T ss_pred CCCEEECCCCCCC--CCEEEEECCEEEEEECCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCEEEEECCCCEEEEEEEEE
T ss_conf 9630312665578--85599999999999688899999999887536778707999964667179960586355467782
Q ss_pred ECC------CCCCHHHHHHHHHCC-------------CCCCHHHHCCCCEEEECCCCCCCEEEEEECCCCCC--------
Q ss_conf 248------312106568876317-------------76501210158155760443322589951399999--------
Q 001532 608 DKG------ISRIKEHHMKELLDG-------------VRSFDDFLREGLIEYLDVNEENNALIALYEGDATP-------- 660 (1058)
Q Consensus 608 ~~~------~~~~~~~~~~~~~~~-------------~~~~~~ll~~g~iE~id~~Eq~~~~Ia~~~~~~~~-------- 660 (1058)
+++ ++.++++|++++..+ ..+|++|+..|+|||+|++||++++||++++++..
T Consensus 641 ~~~~~~~~~~l~l~k~hi~~L~~~~~~~~~~~~~~~~~~~w~~Lv~~G~iEyldaeEEe~~~Ia~~~~dl~~~~~~~~~~ 720 (1224)
T 1twf_B 641 EDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEND 720 (1224)
T ss_dssp ECCCTTSSCEESCCHHHHHHHHHHHHCC---------CCCHHHHHHTTSEEEEEHHHHTTCCEESSGGGGCC--------
T ss_pred CCCCCCCCCCCEECHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHCCCCCEEECCHHHHCCCEEECCCCCCCCCCCCCCCC
T ss_conf 47875554542012999998651322234432222223556573237937982766614857843650137223424555
Q ss_pred ----------------CCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEECCC
Q ss_conf ----------------7301442376000322366778899999864101112457765315753100135205520799
Q 001532 661 ----------------DTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQ 724 (1058)
Q Consensus 661 ----------------~~th~Ei~p~~ilsv~AsliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~r~d~~~y~L~ypQ 724 (1058)
.||||||||+++|||+||+|||+||||||||||||||+|||||++.+|+..|+|++.|+|+|||
T Consensus 721 ~~~~~~~R~~~~~~~~~~Th~EI~Ps~ILgV~ASlIPF~dHNqSpRn~yqs~M~kQA~g~~~~n~~~r~dt~~~~l~ypQ 800 (1224)
T 1twf_B 721 LDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQ 800 (1224)
T ss_dssp -CCCTTSCCCCCCCCSCCCEECSCGGGGSCTTGGGSSSGGGSCHHHHHHHHHHGGGBCBCSCTTTTTCCCSEEEEESSCB
T ss_pred CCCCCCCCCCCCCCCHHHCCCCCCCCCCCCEEECCCCCCCCCCCCHHHHCCCCCCCCCCCCCCEEEEECCCCCCEEECCC
T ss_conf 44444333468767512022256885222132114687434543133322344334356532114442145541523582
Q ss_pred CCEEECHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCEEEECCEEECCCEEEEEEEEEEEEEECCCCCCCCEECCCCCC
Q ss_conf 53132302322168988898403799961478887771998543110143479999999999620369863123199999
Q 001532 725 RPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRT 804 (1058)
Q Consensus 725 ~PlV~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~ 804 (1058)
+|||+|+.++.++++|+|+|+||+||||||+||||||||||||+|++||+|||+||++|++++++...+..|.|..|+.+
T Consensus 801 kPlV~t~~~~~~~~~elp~G~N~iVAvm~y~GYN~EDAiIin~~sv~rg~~~s~~~~~y~~~~~~~~~~~~e~~~~P~~~ 880 (1224)
T 1twf_B 801 KPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRT 880 (1224)
T ss_dssp CCSEECTTHHHHTTTTSCCCEEEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCS
T ss_pred CCEEECCCCCCCCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEEEEEEEEEEEECCCCCEEEECCCCHH
T ss_conf 78277565200145557797647999961357664025562132775488158999999998640788854675278802
Q ss_pred -C--CCCCCCCCCCCCCCCCCCCEECCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEEEEEC
Q ss_conf -9--9510011499983006893768999899973589887887899998786532231772079997139999998518
Q 001532 805 -G--PGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSD 881 (1058)
Q Consensus 805 -~--~~~~~~~~ld~~Gl~~~g~~v~~gdili~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~e~~~g~v~~v~~~~~ 881 (1058)
. .+...|++||+||||++|++|++|||||||++|+...+.... ...+...++|+|++++++| .|+||+|.++.+
T Consensus 881 ~~~~~~~~~~~~LD~dGiv~~G~~V~~gDilvgK~~p~~~~~~~~~-~~~~~~~~rd~s~~~~~~e--~g~Vd~V~~~~~ 957 (1224)
T 1twf_B 881 NTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELG-QRTAYHSKRDASTPLRSTE--NGIVDQVLVTTN 957 (1224)
T ss_dssp SSCBCCSSCGGGCCTTSBCCTTCEECTTCEEECEECCCC--------------CCBBCCEECCTTC--CEEEEEEEEEEC
T ss_pred HCCCCCHHHHHHCCCCCCCCCCCEECCCCEEEEEECCCCCCCCCCC-CCCCCCCCCEEEEEEECCC--CEEEEEEEEEEC
T ss_conf 0357557777643558744775274599989999658876643334-4555676543689940898--749977899851
Q ss_pred CCCCEEEEEEEEECCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHCCCHHC
Q ss_conf 99977999998322799644300023798227975414678899899998828708999988653889999841000002
Q 001532 882 KNGDLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVS 961 (1058)
Q Consensus 882 ~~~~~~v~v~ir~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~ 961 (1058)
.+|.+.|||++|++|+|+||||||||||||||||++||+||||||+||++|||||||||||||||||||+|+++||+|++
T Consensus 958 ~~g~~~vkV~ir~~R~p~iGDKfasRHGqKGvis~i~p~eDMPf~~dG~~pDiIiNPhg~PSRMtiGqllE~~lgka~~~ 1037 (1224)
T 1twf_B 958 QDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAAL 1037 (1224)
T ss_dssp SSSCEEEEEEEEEEECCCTTCEEECTTSCEEEEEEEECTTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHH
T ss_pred CCCCEEEEEEEEECCCCCCHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 79978999999833788744654332068640301314025996788977638868875766654210578876589985
Q ss_pred CCCEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCEEEEEEEEEEEEEECCCCCCCCCEEEECCCCCC
Q ss_conf 79403430014799999989999999998399999945998288894765569663421220356348610784127843
Q 001532 962 CGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRV 1041 (1058)
Q Consensus 962 ~g~~~~~tpF~~~~~~~~~~~~~~~~l~~~g~~~~G~e~l~~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~ 1041 (1058)
.|.+.|+|||+ +..++++++.|.++||+++|+|+||||+||++|+++||+||+|||||+|||+||+|||++|||+
T Consensus 1038 ~G~~~datpF~-----~~~~~~i~~~L~~~g~~~~G~e~ly~G~TG~~~~~~i~vG~~YyqkL~HmV~DKihaRs~GP~~ 1112 (1224)
T 1twf_B 1038 SGNEGDASPFT-----DITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQ 1112 (1224)
T ss_dssp HCSCEECCSSS-----SCCHHHHHHHHHTTTSCTTSEECEECTTTCCBCSSCEEEEEEEEEEBSSCGGGTCEEECCCC--
T ss_pred CCCEEECCCCC-----CCCHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCEEEEEHHHHHCCHHHCCCCCEEEEECCCC
T ss_conf 49644237889-----8659999999998698988978966289898732117874567440131206675697208975
Q ss_pred CCCCCCCCCCCCCCCCC
Q ss_conf 33237867434989999
Q 001532 1042 MLTRQPTEGRARNGGFP 1058 (1058)
Q Consensus 1042 ~lT~QP~~Gr~~~GG~~ 1058 (1058)
.|||||++||+|+|||-
T Consensus 1113 ~lT~QP~~Gr~r~GG~R 1129 (1224)
T 1twf_B 1113 VLTRQPVEGRSRDGGLR 1129 (1224)
T ss_dssp --------------CCC
T ss_pred CCCCCCCCCCCCCCCEE
T ss_conf 43108974300477610
No 3
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Probab=1.00 E-value=1 Score=2161.14 Aligned_cols=1008 Identities=36% Similarity=0.621 Sum_probs=922.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHCCCCEECCCCCEEEEEEEEEECCCCCCCCC-CCCCC
Q ss_conf 87764001222462111443517999999999998477999870476110589949999948999287013588-66789
Q 001532 23 APVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDG-VSEKL 101 (1058)
Q Consensus 23 ~~~~~~~~~~~~i~~~f~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~~~~~~l~f~~i~i~~P~~~~~~-~~~~l 101 (1058)
+..++.+|+|.++++||+.++||+|||||||||+++||++++++++||+.. .+++.|+|+++++++|++.+.+ ..+++
T Consensus 5 ~~~~~~~d~w~~i~~~f~~~gLV~~qidSfn~Fl~~gL~~i~~~~~pI~~~-~~~~~l~f~~~~l~~P~~~e~d~~~~~l 83 (1131)
T 4ayb_B 5 SSNLSIDERWKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTE-IPGLKVRLGKIRIGKPRVRESDRGEREI 83 (1131)
T ss_dssp --CCCHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHTTTHHHHHHHCSCCCS-STTCEEEEEEEEECCSEEEETTTEEEEC
T ss_pred CCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCHHHHHHHCCCEEEC-CCCEEEEEEEEEEECCEEECCCCCCCCC
T ss_conf 345986477998999868899728999999999986879999835975635-8988999988999078363488876745
Q ss_pred CHHHHHHCCCCCCCEEEEEEEEEECCCCCCEEEEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECC
Q ss_conf 91447632995474099999999998754202478689996520201356522799998889762999899994899919
Q 001532 102 NPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKG 181 (1058)
Q Consensus 102 ~P~eaR~r~lTYsa~l~v~i~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIInG 181 (1058)
+|+|||+|++||+|||+|++.+..++ .++++++|++|+|||||+|++|||+++++++|++.||||+|+||||||||
T Consensus 84 ~P~EcR~r~~TYsapl~v~v~~~~~~----~~~~~~~v~lG~iPiM~~S~~C~L~~~s~~el~~~gEc~~D~GGyFIING 159 (1131)
T 4ayb_B 84 SPMEARLRNLTYAAPLWLTMIPVENN----IEAEPEEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNG 159 (1131)
T ss_dssp CHHHHHHHTCCCEEEEEEEEEEEETT----EECCCEEEEEEEEECCTTSTTSGGGGCCHHHHHHHTCCTTCCCCCEEETT
T ss_pred CHHHHHHCCCCCCCEEEEEEEEEECC----CEEEEEEEEEEECCEEECCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECC
T ss_conf 99999704997363489999999999----08899999998797896888544779898999862888679973898698
Q ss_pred CEEEEEEEECCCCCEEEEEECCCC-C--EEEEEEECCCCCC-EEEEEEEECCEEEEEECCEECCCCHHHHHHHHCCCCHH
Q ss_conf 134786420035987999957997-5--7999982589950-08999955889999981100132385689982899888
Q 001532 182 TEKVLLIQEQLSKNRVIIDTDKKG-N--INASVTSSTETVK-SKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQ 257 (1058)
Q Consensus 182 ~EKVIi~q~~~~~N~i~~~~~~~g-~--~~~~v~s~~~~~~-~~~~~~~~~g~i~~~~~~~~~~IPi~illrALg~~sD~ 257 (1058)
+||||++|++++||.+++.+.+.+ . +.+.++|++..++ +..+.+.+++.+++++++.+.+||+++||||||..||+
T Consensus 160 ~ERVIv~Q~~~spn~~~~~~~~~~~~~~~~a~ii~~~~~~~~~~~i~~~~~~~~~v~~~~~~~~iPi~illrALG~~sD~ 239 (1131)
T 4ayb_B 160 SERVIVTQEDLAPNRVLVDTGKTGSNITHTAKIISSTAGYRVPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTDR 239 (1131)
T ss_dssp EEEEECEEEEECCSSCEEEECCTTCSEEEEEECEEECSSCEEECCEEEETTTCCEECCSSSCCCEEHHHHHHHHTCCSHH
T ss_pred EEEEEEEEECCCCCEEEEEECCCCCCEEEEEEEEECCCCCEEEEEEEEECCCEEEEEECCCCCEEEHHHHHHHHCCCCHH
T ss_conf 89899986426798699984168991789999988888752349999937987999991747566499999985876346
Q ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 99988179446786356619998842876889999998500334678999998178999998764316878788888973
Q 001532 258 EVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPK 337 (1058)
Q Consensus 258 eI~~~i~~~~~~~~~l~~~l~~~~~~~~~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L~~~llpHl~~~~~~~~~K 337 (1058)
||++.++.+.++.+.+..+++++ ..+.++++|+.||+++++.. .++.+ ..+.++++|++++|||++....++..|
T Consensus 240 eI~~~i~~~~~~~~~l~~~~~~~--~~i~~~~~al~~i~~r~~~~--~~~~~-~~~~a~~il~~~~l~hl~~~~~~~~~K 314 (1131)
T 4ayb_B 240 DIVYAVSLDPEIQNELFPSLEQA--SSIANVDDALDFIGSRVAIG--QKREN-RIEKAQQIIDKYFLPHLGTSADDRRKK 314 (1131)
T ss_dssp HHHHHHCSCHHHHTTTHHHHHHH--TTTCCSSHHHHHHHHHHHCS--SCHHH-HHHHHHHHHHTTSSTTSCSSTTSHHHH
T ss_pred HHHHHHCCCHHHHHHHHHHHHHH--CCCCCHHHHHHHHHHHHHCC--CCCCH-HHHHHHHHHHHHHCCCCCCCCCCHHHH
T ss_conf 57878513088899988779874--14123899998776665328--88741-578999999986201245433203677
Q ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 02488999999986239877788464346087112788999999999999999999987672399988877522343334
Q 001532 338 CFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRD 417 (1058)
Q Consensus 338 ~~~L~~Mv~kLl~l~~g~~~~Dd~D~l~NKRv~l~G~Ll~~lfr~~l~~~~~~i~~~l~k~~~~~~~~~~~~~~~~i~~~ 417 (1058)
+.+|++|+++|+.+..|.+.+||+|||+||||+++|+||+++||..|.++++.+++++.+...+. ..+++..+++++
T Consensus 315 ~~~L~~mi~~Ll~l~~g~~~~DD~Dhl~NkRvr~vGeLl~~~fr~~l~r~~r~ir~~~~~~~~~~---~~~~~~~li~~~ 391 (1131)
T 4ayb_B 315 AYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRG---RKLALKALVRPD 391 (1131)
T ss_dssp HHHHHHHHHHHHHHHHTSSCCCCTTSGGGEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTC---SCCCHHHHCCTH
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCHHCCEECCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHCC---CCCCHHHHCCCC
T ss_conf 88899999999999729999888854422110414689999999999988777664122101002---311446534786
Q ss_pred CCHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 42064545302487751011343345428713334000023544236532345433589867999764433477999876
Q 001532 418 SITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEA 497 (1058)
Q Consensus 418 ~It~~l~~~lsTGnw~~~~~~~q~sG~sq~l~Rln~ls~LShlRrv~~~~~~~~k~t~~R~Lhps~wGfICPveTPEG~~ 497 (1058)
.||++|++|||||||.. +++|+||++||+||+|+|||+||+++++++++|.++||+|||||||||||+|||||+|
T Consensus 392 ~it~~i~~~~aTGn~~~-----~~sglSQ~mdq~NpLs~lsH~RRlsagl~rera~~evRdlHpShyGriCPIETPEG~n 466 (1131)
T 4ayb_B 392 IVTERIRHALATGNWVG-----GRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPN 466 (1131)
T ss_dssp HHHHHHHHHHHTTBCSS-----SCBCCEEECCCSSHHHHHHHHTEEEECSCSSSCCHHHHSCCGGGTTTBCSSCCCSSTT
T ss_pred HHHHHHHHHHHHCCCCC-----CCCCEEEEECCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCC
T ss_conf 05565677774145556-----8772689814677889877566315775335666644026775664302565999865
Q ss_pred CCCCCCCCCEEEEECCCCCHHHHHHHHHCCCEECCCC----CCCC---CCCCCCEEEEECCEEEEECCCHHHHHHHHHHH
Q ss_conf 3222235511554148997059999864197441246----8545---67998079999794876326924489999987
Q 001532 498 CGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELL----SGEE---LHNPNSFLVIFNGLILGKHRRPKCFADVMRKL 570 (1058)
Q Consensus 498 cGLi~~LA~~a~Is~~~~~~~i~~~l~~~G~~~l~~~----~~~~---~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~l 570 (1058)
||||||||++|+|+.+.++.++.+++.++|+.+++.. +... .......+||+||+|+|++.++..++..+|.+
T Consensus 467 iGLI~sLA~~a~I~~g~~e~~i~~~l~~~g~~~~e~~~~~~~~~~~~~~~~~~~~~v~lng~~vg~~~~~~~~~~~~~~~ 546 (1131)
T 4ayb_B 467 SGLVKNLALMAQIAVGINEKIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLVGYYRDGEELAKKIRER 546 (1131)
T ss_dssp BTTEEEBBSSCEECCCCCHHHHHHHHHHTTCEEHHHHHHTTTTC-----CCCCCCEEEETTEEEEECSCHHHHHHHHHHH
T ss_pred CCCCCCCEEEEEEECCCCCCCEEEEHHHCCCEEEEEEEHHHCCCCCCCCHHHHHCCEEECCCEEEEECCCHHHHHHHHHH
T ss_conf 33446620467882488873333313644934503230021235333330121000464371578850433102226645
Q ss_pred HHCCCCCCEEEEEECC--CCCEEEEECCCCEEEEEEEEEECCCCCCHHHHHHHHHCCCCCCHHHHCCCCEEEECCCCCCC
Q ss_conf 6438767315998614--56349995399823443999724831210656887631776501210158155760443322
Q 001532 571 RRAGKIGEFVSVFVNE--KQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENN 648 (1058)
Q Consensus 571 rr~~~i~~~v~i~~~~--~~~~i~I~td~gRl~RPll~v~~~~~~~~~~~~~~~~~~~~~~~~ll~~g~iE~id~~Eq~~ 648 (1058)
|+.+.++.++++.+.. ..+++++++|+||++|||++++++++.+..++++.+..+...|.+++..|.+||+|++|+++
T Consensus 547 ~~~~~i~~~vsi~~~~~~~~~~~~i~~d~~r~~rpv~~~~~~~p~v~~~~~~~~~~g~~~~~~~~~~g~veyvd~~e~~~ 626 (1131)
T 4ayb_B 547 RRKGEISDEVNVGHIVTDFINEVHVNCDSGRVRRPLIIVSNGNPLVTREDIEKLDSGSITFDDLVRQGKIEYLDAEEEEN 626 (1131)
T ss_dssp HHHTSSCTTCEEEEECTTTCCEEEEECCTTCEEEEEEEBSSSSBSCCHHHHHHHHTTTCCHHHHHHTTSEEEEEHHHHTT
T ss_pred HCCCCCCCEEEEEECCCCCCCEEEEECCCCCCCCCEEEEECCCCCCCHHHHHHHHCCCHHHHHHHHCCCEEEEECCCCCE
T ss_conf 10476585688741125543304665378640265688634664235889999864870477786278324420134520
Q ss_pred EEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEECCCCCEE
Q ss_conf 58995139999973014423760003223667788999998641011124577653157531001352055207995313
Q 001532 649 ALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLL 728 (1058)
Q Consensus 649 ~~Ia~~~~~~~~~~th~Ei~p~~ilsv~AsliPF~~hNqspRn~yq~~M~KQaiG~~~~n~~~r~d~~~y~L~ypQ~PlV 728 (1058)
++||+.++++...+||+||+|+.++|++|++|||++|||||||+|||||+|||||++.+|+..|+|+++|+|+|||+|||
T Consensus 627 ~~ia~~~~~~~~~~th~ei~p~~il~v~a~lipf~~~NqspRn~yq~~m~KQa~G~~~~~~~~r~D~~~~~l~ypQ~PlV 706 (1131)
T 4ayb_B 627 AYVALEPSDLTPEHTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLV 706 (1131)
T ss_dssp CCEESSGGGCCTTCSEECSCGGGGSBTTGGGCSSGGGSCHHHHHHHHHHGGGBCSCCCGGGGTCCCSEEEEESSCCCCSS
T ss_pred EEEEEECCCCCCCCCCEEECCCCCCCCCCCEECCCCCCCCCHHEECCCCCCCCCCCEEECCEEEECCCCCEEECCCCCCC
T ss_conf 27986334345433313641442233346554332457663102225555036883110130563144436652875520
Q ss_pred ECHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCEEEECCEEECCCEEEEEEEEEEEEEECCCCCCCCEECCCCCCC---
Q ss_conf 23023221689888984037999614788877719985431101434799999999996203698631231999999---
Q 001532 729 TTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTG--- 805 (1058)
Q Consensus 729 ~t~~~~~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~--- 805 (1058)
+|+.++.++++++|+|+|++||||||+||||||||||||++++||+|||+||++|++++++++.|..|.++.|..+.
T Consensus 707 ~t~~~~~~~~~e~p~G~N~lVA~m~w~GYN~EDAIIine~~v~rg~ftSihi~~y~~e~r~~~~g~~e~it~~~p~v~~~ 786 (1131)
T 4ayb_B 707 QTRALDIIGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGY 786 (1131)
T ss_dssp BCHHHHHHTCTTSCCSEEEEEEECCCSSCCCTTCEEEEHHHHTTTTTCEEEEEEEEEECCCCTTSCCCCCCCCCSSCSSC
T ss_pred CCCHHHHHCCCCCCCCEEEEEEEECCCCCCHHHHHHHHCCHHHCCCCEEEEEEEEEEEEEECCCCCCEEEECCCCCCCCC
T ss_conf 11212220667788744589999746785677766550303323653045788899999964899833870477532110
Q ss_pred CCCCCCCCCCCCCCCCCCCEECCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEEEEECCCCC
Q ss_conf 95100114999830068937689998999735898878878999987865322317720799971399999985189997
Q 001532 806 PGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGD 885 (1058)
Q Consensus 806 ~~~~~~~~ld~~Gl~~~g~~v~~gdili~k~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~e~~~g~v~~v~~~~~~~~~ 885 (1058)
.+...+++||+||||++|++|++|||||||++|+...+...... .....+|+|+++++++ .|+||.|.++.+.+|.
T Consensus 787 ~~~~~~~~LDe~Gii~iGa~V~~gDilvGKvtP~~~~~~~~~~~--~~~~~~d~sl~~~~g~--~g~Vd~v~~~~~~~~~ 862 (1131)
T 4ayb_B 787 KGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELS--PEQAKRDTSIVTRHGE--MGIVDLVLITETAEGN 862 (1131)
T ss_dssp CCGGGGTTCCTTSBCCTTCEECTTCEEECCCCCCC-------------CCCCCCCEECCTTC--CEEEEEEEEEECSSSC
T ss_pred CHHHHHHCCCCCCCCCCCCEECCCCEEEEEECCCCCHHHHHHCC--CCEEEEEEEEECCCCC--CEEEEEEEEEECCCCC
T ss_conf 03777505786666568847448998999855875122343037--6200046558724897--3589999996615785
Q ss_pred EEEEEEEEECCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHCCCHHCCCCE
Q ss_conf 79999983227996443000237982279754146788998999988287089999886538899998410000027940
Q 001532 886 LCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRF 965 (1058)
Q Consensus 886 ~~v~v~ir~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~ 965 (1058)
+.|||++|+.|+|+||||||||||||||||+|||+|||||++||++||||+|||||||||||||++|+++||+|++.|.+
T Consensus 863 ~~vkV~i~~~R~~~vGDK~agRHGnKGvvs~i~p~eDMPf~~dG~~~DiilNP~gvPSRMniGqilE~~~gk~~~~~g~~ 942 (1131)
T 4ayb_B 863 KLVKVRVRDLRIPSIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALSGNI 942 (1131)
T ss_dssp EEEEEEEEEEECCCTTCEEEETTSCEEEEEEEECTTTSEEETTSCCCSEECCTTSSTTTTCHHHHHHHHHHHHHHHHCCC
T ss_pred EEEEEEEECCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf 37999983244676566025466664244301352129948899875088899878666739999999988999847983
Q ss_pred EEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCEEEEEEEEEEEEEECCCCCCCCCEEEECCCCCCCCCC
Q ss_conf 34300147999999899999999983999999459982888947655696634212203563486107841278433323
Q 001532 966 HYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTR 1045 (1058)
Q Consensus 966 ~~~tpF~~~~~~~~~~~~~~~~l~~~g~~~~G~e~l~~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~ 1045 (1058)
.|+|||. ....+++.+.|.++||+++|+++||||+||++|+++||+|++|||||+|||+||+||||+|||+++||
T Consensus 943 ~~atpf~-----~~~~e~~~~~l~~~g~~~~g~~~lydG~TGe~~~~~i~vG~~Yy~kL~HmV~DKihaRs~GP~s~~Tq 1017 (1131)
T 4ayb_B 943 VDATPFY-----KTPIEQLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQILTR 1017 (1131)
T ss_dssp CBCCTTS-----SCCTHHHHHHHHHTTSCTTSEECEEETTTCCBCSSCEEEEEEEEEEBSCCHHHHCEEESSCCBCTTTC
T ss_pred EECCCCC-----CCCHHHHHHHHHHCCCCCCCCEEEECCCCCCEECCCEEEEHHHHHCCCHHHCCCCEEECCCCCCCCCC
T ss_conf 1547657-----98379999999974799999878857999988067089975463305113053877213089977425
Q ss_pred CCCCCCCCCCCC
Q ss_conf 786743498999
Q 001532 1046 QPTEGRARNGGF 1057 (1058)
Q Consensus 1046 QP~~Gr~~~GG~ 1057 (1058)
||++||+|+|||
T Consensus 1018 QPl~Gra~~GG~ 1029 (1131)
T 4ayb_B 1018 QPTEGRAREGGL 1029 (1131)
T ss_dssp CBCSSGGGTCCC
T ss_pred CCCCCCCCCCCC
T ss_conf 899975568983
No 4
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...
Probab=1.00 E-value=1 Score=1780.56 Aligned_cols=867 Identities=24% Similarity=0.396 Sum_probs=722.4
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHH----------HHCHHHHHHHCCCCEEC--CCCCEEEEEEEEEECCCCCCCC
Q ss_conf 00122246211144351799999999999----------84779998704761105--8994999994899928701358
Q 001532 28 VVDKFQLLPEFLKVRGLVKQHLDSFNYFV----------NTGIRKIVRANDRIVSG--IDPSIFLRFKDVRIGQPSMTVD 95 (1058)
Q Consensus 28 ~~~~~~~i~~~f~~~~lv~~qi~SFn~Fi----------~~gl~~ii~~~~~i~~~--~~~~~~l~f~~i~i~~P~~~~~ 95 (1058)
++..|+.++.+|+.++|+++|++|||||+ ++||++++++++||+.+ .+.++.|+|.++++++|.+
T Consensus 2 ~r~~~~~~~~~~~~p~Lv~~QidSFn~Fl~~~~~~~~~~~~GL~~i~~~~~pI~~~~~~~~~~~l~f~~~~l~~P~~--- 78 (1119)
T 2a6h_C 2 EIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPF--- 78 (1119)
T ss_dssp EEEECCCCCCCSCCCCTTHHHHHHHHHHSCTTSCTTSSCCCHHHHHHHHHCSEEECCSSSCCEEEEECCCCBCCCSS---
T ss_pred CCEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCEECCCCCCCEEEEEEEEEEECCCCC---
T ss_conf 52201234312468578999999999997067764432110179999866977514778980899999899768989---
Q ss_pred CCCCCCCHHHHHHCCCCCCCEEEEEEEEEECCCCCCEEEEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHCCCCCCCCCC
Q ss_conf 86678991447632995474099999999998754202478689996520201356522799998889762999899994
Q 001532 96 GVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGG 175 (1058)
Q Consensus 96 ~~~~~l~P~eaR~r~lTYsa~l~v~i~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GG 175 (1058)
+|.|||+|++||+|||+|++++..++. +++++++|++|+||+|+ +||
T Consensus 79 ------~p~Ecr~r~lTYsapL~V~v~l~~~~~---~~ik~~~V~iG~iPiMt------------------------~gG 125 (1119)
T 2a6h_C 79 ------PQDECREKDLTYQAPLYARLQLIHKDT---GLIKEDEVFLGHIPLMT------------------------EDG 125 (1119)
T ss_dssp ------CHHHHHHTTCCCEEEBCCCEEECCSSS---CCEECCCCCCCEEECCC------------------------TTS
T ss_pred ------CHHHHHHCCCCCCCEEEEEEEEEECCC---CEEEEEEEEECCCCEEC------------------------CCC
T ss_conf ------999998529943621799999998787---32554588950797688------------------------886
Q ss_pred EEEECCCEEEEEEEECCCCCEEEEEE-CCCCC--EEEEEEECCCCCCEEEEEEEECCEEEEEECCEECCCCHHHHHHHHC
Q ss_conf 89991913478642003598799995-79975--7999982589950089999558899999811001323856899828
Q 001532 176 YFIIKGTEKVLLIQEQLSKNRVIIDT-DKKGN--INASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMG 252 (1058)
Q Consensus 176 YFIInG~EKVIi~q~~~~~N~i~~~~-~~~g~--~~~~v~s~~~~~~~~~~~~~~~g~i~~~~~~~~~~IPi~illrALg 252 (1058)
||||||+||||++|++++||.++... ++.|. +.+.+.+.+. .|..+...+++.+|+++++ .+||++++|||||
T Consensus 126 yFIING~ERVIVsQ~~rspgv~~~~~~~~~g~~~ysa~ii~~rg--s~l~~~~d~~~~i~vri~r--~kIPi~ilLrALG 201 (1119)
T 2a6h_C 126 SFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRG--PWIDLEVEPNGVVSMKVNK--RKFPLVLLLRVLG 201 (1119)
T ss_dssp CCCSSSSCEEECEEEEECSCEEEECCSSCSSCCEEEECCCSSSS--CCEEEEEETTTEEEEESSS--SEECHHHHHHHHT
T ss_pred EEEEECEEEEEEEEEECCCCEEEEEECCCCCCEEEEEEEEECCC--CEEEEEECCCCEEEEEEEC--CCEEHHHHHHHHC
T ss_conf 79994818999999804895999861367896579999983268--5699998579879999927--6000999998878
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH-------CC
Q ss_conf 99888999881794467863566199988428768899999985003346789999981789999987643-------16
Q 001532 253 MESDQEVVQMVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVF-------LA 325 (1058)
Q Consensus 253 ~~sD~eI~~~i~~~~~~~~~l~~~l~~~~~~~~~t~~~al~yig~~~~~~~~~~~~~~~~e~~~~~L~~~l-------lp 325 (1058)
. ||+||++.++.+..+.+.+.... ..+.++++|+.+|+++++++ ... ..+.++.+|.+.+ |+
T Consensus 202 ~-sD~eIl~~~~~~~~~~~tl~~d~-----~~~~~~~eAl~~i~~~lr~g----~~~-~~e~a~~~l~~~ff~~~rydl~ 270 (1119)
T 2a6h_C 202 Y-DQETLARELGAYGELVQGLMDES-----VFAMRPEEALIRLFTLLRPG----DPP-KRDKAVAYVYGLIADPRRYDLG 270 (1119)
T ss_dssp C-CHHHHHHHHHSSCTTHHHHSSCH-----HHHTCHHHHHHHHHHHSSSC----CCS-CCSSHHHHHTSSSSSSCCSCTT
T ss_pred C-CHHHHHHHHCCCHHHHHHHHHHH-----CCCCCHHHHHHHHHHHHCCC----CCC-CHHHHHHHHHHHHCCCCCCCCH
T ss_conf 9-99999999746899999998532-----24679999999999974578----998-4999999998760785344301
Q ss_pred CCCCCCCCC-----------------CCCCHHHHHHHHHHHHHHCCCC--CCCCCCCCCCEEECCHHHHHHHHHHHHHHH
Q ss_conf 878788888-----------------9730248899999998623987--778846434608711278899999999999
Q 001532 326 NVPVHNNNF-----------------RPKCFYVAVMLRRMVEAMLNKD--AMDDKDYVGNKRLELSGQLVSLLFEDLFKT 386 (1058)
Q Consensus 326 Hl~~~~~~~-----------------~~K~~~L~~Mv~kLl~l~~g~~--~~Dd~D~l~NKRv~l~G~Ll~~lfr~~l~~ 386 (1058)
|+|....+. .-+...+++|+++|+.+..|.+ .+||+|||+||||+++|+||+++||..|.+
T Consensus 271 ~vGr~~ln~kl~l~~~~~~~~~~~~~~l~~~di~~mi~~Ll~l~~G~~~~~~DD~DhlgNkRv~~~GeLl~~~fr~~l~r 350 (1119)
T 2a6h_C 271 EAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLAR 350 (1119)
T ss_dssp TSSHHHHHTTSCSCCSTTTTCCCSSSCCCCTTHHHHHHHHHHHHTSCSSCCCCCTTSTTTEEEECHHHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHCEEEHHHHHHHHHHHHHHHHH
T ss_conf 14512221220568752223443324332999999999999863488777776744111347534569999999999999
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCC-
Q ss_conf 9999999987672399988877522343334420645453024877510113433454287133340000235442365-
Q 001532 387 MISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP- 465 (1058)
Q Consensus 387 ~~~~i~~~l~k~~~~~~~~~~~~~~~~i~~~~It~~l~~~lsTGnw~~~~~~~q~sG~sq~l~Rln~ls~LShlRrv~~- 465 (1058)
+.+.+++.+.+.. ...+++..++++++||++|++||+||| +||+|+|+||+|+|||+||+++
T Consensus 351 ~~~~i~~~~~~~~-----~~~~~~~~~i~~~~It~~lk~ff~tg~------------lSQ~Ldq~N~ls~LsH~RRissl 413 (1119)
T 2a6h_C 351 LARGVRERMLMGS-----EDSLTPAKLVNSRPLEAAIREFFSRSQ------------LSQFKDETNPLSSLRHKRRISAL 413 (1119)
T ss_dssp HHHHHHHHHHHSC-----SSCCSSTTTCCSHHHHHHHHHHHHTCS------------SEEECCCSSTHHHHHHHHEEESS
T ss_pred HHHHHHHHHHHHC-----CCCCCHHHHHCCCHHHHHHHHHHHCCC------------CCCCCCCCCHHHHHHHHHEECCC
T ss_conf 9999998752310-----011145775146216899999860367------------40102552067664320200345
Q ss_pred ---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHCCCEECCCCCCCCCCCC
Q ss_conf ---32345433589867999764433477999876322223551155414899705999986419744124685456799
Q 001532 466 ---QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCYCLGVEDLELLSGEELHNP 542 (1058)
Q Consensus 466 ---~~~~~~k~t~~R~Lhps~wGfICPveTPEG~~cGLi~~LA~~a~Is~~~~~~~i~~~l~~~G~~~l~~~~~~~~~~~ 542 (1058)
++++++|+++||+|||||||||||+|||||+|||||||||++|+|+. +|+.. .
T Consensus 414 gpggl~re~k~~~vRdlHpShwGriCPiETPEG~ncGLVknLAl~a~I~~-------------~G~~e------~----- 469 (1119)
T 2a6h_C 414 GPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDE-------------LGFIR------T----- 469 (1119)
T ss_dssp SSSSSCCSSCCHHHHSCCGGGTTTBCSSCSCSSSSCSSEEEBCSSCEECS-------------SSCEE------E-----
T ss_pred CCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCHHHHHHHEEECC-------------CCCCC------C-----
T ss_conf 87752344656754626774576527874889975311543431215423-------------67646------7-----
Q ss_pred CCEEEEECCEEEEECCCHHHHHHHHHHHHHCCCCCCEEEEEECCCCCEEEEECCCCEEEEEEEEEECCCCCCHHHHHHHH
Q ss_conf 80799997948763269244899999876438767315998614563499953998234439997248312106568876
Q 001532 543 NSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGISRIKEHHMKEL 622 (1058)
Q Consensus 543 ~~~~V~lnG~~iG~~~~~~~~~~~lr~lrr~~~i~~~v~i~~~~~~~~i~I~td~gRl~RPll~v~~~~~~~~~~~~~~~ 622 (1058)
.+.+.+||+|.+.+. .+.. ... ... -+ ....+.+ +.||++||++.++++
T Consensus 470 -p~~~V~nG~v~~~i~---yl~a-~ee---~~~-----~i----~~~~~~l--~~gr~~r~~i~~r~~------------ 518 (1119)
T 2a6h_C 470 -PYRRVVGGVVTDEVV---YMTA-TEE---DRY-----TI----AQANTPL--EGNRIAAERVVARRK------------ 518 (1119)
T ss_dssp -EEEEEETTEEEEEEE---EECH-HHH---HHS-----CE----ECTTSCB--SSSBBCCSSEEEESS------------
T ss_pred -CCEEEECCEEEEEEE---EECH-HCC---CCE-----EE----ECCCEEE--CCCCCCCCCEEEEEC------------
T ss_conf -758999998951157---7671-006---666-----99----4175621--578303672567741------------
Q ss_pred HCCCCCCHHHHCCCCEEEECCCCCCCEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 31776501210158155760443322589951399999730144237600032236677889999986410111245776
Q 001532 623 LDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAM 702 (1058)
Q Consensus 623 ~~~~~~~~~ll~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~th~Ei~p~~ilsv~AsliPF~~hNqspRn~yq~~M~KQai 702 (1058)
.||+ .+.+ ..+|||||||+++||++||+|||+||||||||||||||+||||
T Consensus 519 ---------------~e~~----------~~~~----~~~~~~ei~P~~ilsv~aslIPF~ehn~s~R~lmgsnM~kQAv 569 (1119)
T 2a6h_C 519 ---------------GEPV----------IVSP----EEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAV 569 (1119)
T ss_dssp ---------------SSEE----------EECT----TTCCEEECCTTTTSCHHHHTCTTGGGBCHHHHHHHHHHHTTBC
T ss_pred ---------------CCEE----------EECH----HHEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf ---------------6305----------5165----5869998425431342012578744577764222211010223
Q ss_pred CCEEEE-----------------------------------EEECCC---CCEEEE----------ECCCCCEEECHHH-
Q ss_conf 531575-----------------------------------310013---520552----------0799531323023-
Q 001532 703 GNIAFN-----------------------------------QLCRMD---SLLYLL----------VYPQRPLLTTRTI- 733 (1058)
Q Consensus 703 G~~~~n-----------------------------------~~~r~d---~~~y~L----------~ypQ~PlV~t~~~- 733 (1058)
|++.++ +..|.| ++.|.| +|||+|||+++.+
T Consensus 570 ~l~~~~~p~vgTg~e~~~a~ds~~~~~a~~~G~v~~vd~~~i~ir~~~~~~~~y~L~~~~rsnq~t~~~QkPiV~~g~~v 649 (1119)
T 2a6h_C 570 PLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRV 649 (1119)
T ss_dssp CBSSCCCCSEECSCHHHHHHHTTCSEECSSSEEEEEECSSBEEEEETTTEEECCBCCCSEECTTSCEECCEECCCSSCCB
T ss_pred CCCCCCCCEEECCCCCEEEECCCCEEEECCCCEEEEECCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCEEEECCEE
T ss_conf 33456798444365520135467626863587899832846999816886126774023243610036503467207531
Q ss_pred ---H------HHCCCCCCCCCCEEEEEEECCCCCCCCCEEEECCEEECCCEEEEEEEEEEEEEECCCCCCCCEEC-CCCC
Q ss_conf ---2------21689888984037999614788877719985431101434799999999996203698631231-9999
Q 001532 734 ---E------LVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRIL-RPDR 803 (1058)
Q Consensus 734 ---~------~~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~-~p~~ 803 (1058)
+ .++++|+|+|+|++||||||+||||||||||||++++||+|+|+|+++|++++++++.|..|.+. .|+.
T Consensus 650 ~~g~~ladg~~~~~gel~lG~N~lVA~m~~~GYN~EDAiiine~~v~rg~~tSihi~~~e~~~r~~~~g~eeit~~ip~~ 729 (1119)
T 2a6h_C 650 RKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHL 729 (1119)
T ss_dssp CTTCEEEECTTBSSSSBCCSEEEEEECSCCSSTTSSSEEEEETHHHHTTCSEEEEEEEEEEEEECCTTCCCBCCSCCSSS
T ss_pred ECCCEECCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCEEEEEEEEEEEEEECCCCCEEEECCCCCC
T ss_conf 01423214533578756686447999952567761025563320775498458999998766441678852431258886
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEECCCCCCCCCCC------CCCCCCCCCCCCEEEEECCCCCCEEEEEEE
Q ss_conf 99951001149998300689376899989997358988788789------999878653223177207999713999999
Q 001532 804 TGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMS------PTGQTDSRYRSARQTYKGPDGETCVVDRVA 877 (1058)
Q Consensus 804 ~~~~~~~~~~ld~~Gl~~~g~~v~~gdili~k~~~~~~~~~~~~------~~~~~~~~~~~~s~~~~~~e~~~g~v~~v~ 877 (1058)
+ ...+++||+||||++|++|++|||||||++|+.+.+.... -++++....+|+|+++++++ .|+|+.|.
T Consensus 730 ~---~~~~~~LD~dGiv~iG~~V~~gDiLvgK~tP~~~~~~~~ee~ll~aifg~k~~~~rd~Sl~~~~~e--~G~V~~V~ 804 (1119)
T 2a6h_C 730 S---EAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGE--GGIVVRTV 804 (1119)
T ss_dssp C---SGGGSSCCSSSBCCTTCBCCTTSEEECCEEESSSSSCCHHHHHHHHHHHSCCCCEEECCEECCSSC--CCEEEEEE
T ss_pred C---HHHHHCCCCCCCCCCCCEECCCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCC--CEEEEEEE
T ss_conf 5---355533488706688789879998999965776566782554455453134664311038825876--37999999
Q ss_pred EEECCC-CC-------EEEEEEEEECCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCHHH
Q ss_conf 851899-97-------7999998322799644300023798227975414678899899998828708999988653889
Q 001532 878 LCSDKN-GD-------LCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGK 949 (1058)
Q Consensus 878 ~~~~~~-~~-------~~v~v~ir~~R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNPh~~PSRMtiGq 949 (1058)
++.+++ |. +.|||++|+.|+|+||||||||||||||||+|||+|||||++||++||||+|||||||||||||
T Consensus 805 ~~~~~~~g~~l~~~~~~~vkV~i~~~R~~~vGDKfasRHGqKGVis~i~p~eDMPf~~dG~~pDiIlNPhgvPSRMtiGq 884 (1119)
T 2a6h_C 805 RLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQ 884 (1119)
T ss_dssp EECSSCSSCCCCTTEEEEEEEEEEEEEECCTTCEEECTTSCEEEEEEEECTTTSCBCSSSCBCSEECCSTTTTTTTBTHH
T ss_pred EECCCCCCCCCCCCCCEEEEEEECCCCCCCCCCHHHHCCCCCCEEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCHHH
T ss_conf 98268888655788635999997434876638521001478745876505677766667987668967886853232235
Q ss_pred HHHHHHCCCHHCCCCEEEEEC-CCCCCCCCCCHHHHHHHHHHC-----------------------------CC------
Q ss_conf 999841000002794034300-147999999899999999983-----------------------------99------
Q 001532 950 MIELLGGKAGVSCGRFHYGSA-FGEPSGHADTVESISETLVKH-----------------------------GF------ 993 (1058)
Q Consensus 950 l~E~~~gk~~~~~g~~~~~tp-F~~~~~~~~~~~~~~~~l~~~-----------------------------g~------ 993 (1058)
++|+++||||++.|... +|| |+ +...+++.+.|.++ ||
T Consensus 885 llE~~lG~a~~~~g~~~-atp~F~-----~~~~~~i~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~ 958 (1119)
T 2a6h_C 885 ILETHLGLAGYFLGQRY-ISPIFD-----GAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKT 958 (1119)
T ss_dssp HHHHHHHHHHHHTTEEE-ECCTTT-----SCCHHHHHHHHHHHHHHHHHHHHHHTCCCBHHHHHHHHHHHTTTSSCTTSC
T ss_pred HHHHHHHHHHHHCCCCE-EECCCC-----CCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCC
T ss_conf 56777546776369805-721558-----988999999999856520232211111110235555544420796543344
Q ss_pred --------CCCCCEEEEECCCCCEEEEEEEEEEEEEECCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCC
Q ss_conf --------9999459982888947655696634212203563486107841278433323786743498999
Q 001532 994 --------SYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057 (1058)
Q Consensus 994 --------~~~G~e~l~~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~ 1057 (1058)
+++|+++||||+||++|+++||+|++|||||+|||+||+|||++|||+.+||||++||+|+|||
T Consensus 959 ~~~~~~~~~~~Gk~~lydG~TGe~~~~~I~vG~~Yy~kL~HmVdDKihaRs~GP~s~lTqQP~~Gra~~GGq 1030 (1119)
T 2a6h_C 959 PEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQ 1030 (1119)
T ss_dssp HHHHHHHHHHTTEECCBCSSSCCBCSSCEEEEEEEEEEBCCCTTTSCEEESSCCBCSSSCSBCCCSSSCCCE
T ss_pred CHHHHCCCCCCCCEEEECCCCCCCCCCEEEEEHHHHHCCHHHCCCCCEEEECCCCCEEECCCCCCCCCCCCE
T ss_conf 012201358877369661899988011489875774511312054857850366320501897654467884
No 5
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C*
Probab=1.00 E-value=1 Score=1593.40 Aligned_cols=882 Identities=22% Similarity=0.365 Sum_probs=722.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH------HCHHHHHHHCCCCEECCCCCEEEEEEEEEECCCCCCCCCC
Q ss_conf 7764001222462111443517999999999998------4779998704761105899499999489992870135886
Q 001532 24 PVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVN------TGIRKIVRANDRIVSGIDPSIFLRFKDVRIGQPSMTVDGV 97 (1058)
Q Consensus 24 ~~~~~~~~~~~i~~~f~~~~lv~~qi~SFn~Fi~------~gl~~ii~~~~~i~~~~~~~~~l~f~~i~i~~P~~~~~~~ 97 (1058)
...+.+..|+.++..++.++|++.|++||+||++ +||++++++++||+.. +..+.|+|.++++++|.+.
T Consensus 7 ~~~~~R~~f~k~~~~~~~P~Ll~iQ~~Sf~~Fl~~~~r~~~GL~evf~~~fPI~d~-~~~~~Lef~~y~l~~Pk~~---- 81 (1342)
T 3lu0_C 7 EKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSY-SGNSELQYVSYRLGEPVFD---- 81 (1342)
T ss_dssp -CCCCCCCSSCCCCSSCCCCGGGTTHHHHHHHSCSSSCSCSTTHHHHTTTSSCEET-TTTEECCEEEECCCCCSCC----
T ss_pred CCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCEECC-CCCEEEEEEEEEECCCCCC----
T ss_conf 88505753356776778998899999999999738864121399999863987878-9978999866782798899----
Q ss_pred CCCCCHHHHHHCCCCCCCEEEEEEEEEECCCC----CCEEEEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHCCCCCCCC
Q ss_conf 67899144763299547409999999999875----42024786899965202013565227999988897629998999
Q 001532 98 SEKLNPHMCRLSDMTYAAPILVNIEYVQGSHT----EKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDP 173 (1058)
Q Consensus 98 ~~~l~P~eaR~r~lTYsa~l~v~i~~~~~~~~----~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~ 173 (1058)
+.||++|++||++||+|++.++..+.. .++++++++|++|+||+|+ .
T Consensus 82 -----~~Ec~~r~lTYsapL~v~~rL~~~~~d~~~~~~~eikeq~Vy~GdiPLMT------------------------~ 132 (1342)
T 3lu0_C 82 -----VQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMT------------------------D 132 (1342)
T ss_dssp -----SSTTTSSCCCCCCCCBEEECCEECCCSSCCCCCCCCCBCCCBCCCCCCCC------------------------S
T ss_pred -----HHHHHHCCCCCCCCEEEEEEEEEECCCCCCCCCCCEEEEEEEEECCCEEC------------------------C
T ss_conf -----99999618976642699999998136555566564179999983273087------------------------8
Q ss_pred CCEEEECCCEEEEEEEECCCCCEEEEEEC--C---CC--CEEEEEEECCCCCCEEEEEEEECCEEEEEECCEECCCCHHH
Q ss_conf 94899919134786420035987999957--9---97--57999982589950089999558899999811001323856
Q 001532 174 GGYFIIKGTEKVLLIQEQLSKNRVIIDTD--K---KG--NINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMV 246 (1058)
Q Consensus 174 GGYFIInG~EKVIi~q~~~~~N~i~~~~~--~---~g--~~~~~v~s~~~~~~~~~~~~~~~g~i~~~~~~~~~~IPi~i 246 (1058)
+|||||||+||||++|++++|+ +++..+ + .| .+.|.+.+.+. .|.-+..+.++.+|+++++ +.++|+++
T Consensus 133 ~GtFIING~ERVIVsQl~RSPG-Vyf~~~~~k~~~~gk~lysa~IIP~RG--sWlefe~D~kd~l~vrIdr-~rKipvt~ 208 (1342)
T 3lu0_C 133 NGTFVINGTERVIVSQLHRSPG-VFFDSDKGKTHSSGKVLYNARIIPYRG--SWLDFEFDPKDNLFVRIDR-RRKLPATI 208 (1342)
T ss_dssp SSCEESSSSEEECCEEEECCSS-CCCCSCCSCSSSCCCSCCEEEECCSSS--CCEEEEEETTTEEEEEESS-CSCEETTH
T ss_pred CCEEEECCCEEEEEEEECCCCC-EEEECCCCCCCCCCCEEEEEEEECCCC--CCEEEEECCCCEEEEEECC-CCCEEEEH
T ss_conf 8679985835899984212675-168514566577884689999944898--6289998689859999668-88534333
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHH------------H--------------------------------------------
Q ss_conf 89982899888999881794467------------8--------------------------------------------
Q 001532 247 VMKAMGMESDQEVVQMVGRDPRY------------S-------------------------------------------- 270 (1058)
Q Consensus 247 llrALg~~sD~eI~~~i~~~~~~------------~-------------------------------------------- 270 (1058)
||||||++ +++|++.++....+ .
T Consensus 209 lLrALG~~-~~~Il~~f~~~~~~~~~~~~~~~~~~~e~~~g~~~~~di~~~g~vi~~~g~~it~~~~~~l~~~g~~~i~v 287 (1342)
T 3lu0_C 209 ILRALNYT-TEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEV 287 (1342)
T ss_dssp HHHTTTCC-HHHHHTTTSCEEEECEETTEEEECCCGGGGTTEECCSCEEETTEEEECSSSEECSHHHHHHHHTTCCCEEC
T ss_pred HHHHHCCC-HHHHHHHHCCCCEEEECCCCEEEECCHHHHCCCCCCCCHHCCCCCEECCCCCCCHHHHHHHHHCCCCCCCC
T ss_conf 48673899-99999985555147741674023126455325421100002451000215501099999988626741025
Q ss_pred -------------------------------HHHHHHHHHHH-----------------------HCCCCCHHHHHHHHH
Q ss_conf -------------------------------63566199988-----------------------428768899999985
Q 001532 271 -------------------------------ALLLPSIEECA-----------------------NLDIYTQEKALEYLE 296 (1058)
Q Consensus 271 -------------------------------~~l~~~l~~~~-----------------------~~~~~t~~~al~yig 296 (1058)
+.+...+.++. .....++++|+.+|+
T Consensus 288 ~~~~l~g~~la~divd~~tge~~~~~~~~i~~~~l~~l~~~~i~~~~~l~~~~~~~~~~i~~tl~~d~~~~~~eAl~~iy 367 (1342)
T 3lu0_C 288 PVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIY 367 (1342)
T ss_dssp CSHHHHTSEECSCEECTTTCCEEECSSCBCCTTHHHHHHHHTCSCEEEECCCSSSSCCSGGGTTTTCCCCSSHHHHHHHH
T ss_pred CHHHHHCCHHHHEEEECCCCEEEECCCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf 77885120101104636787088627861489999999976983799884046654379999986345789999999999
Q ss_pred HCCCCCCCCCCCCCHHHHHHHHHHHHHC-------CCCCC---------C--CCCCCCCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf 0033467899999817899999876431-------68787---------8--8888973024889999999862398777
Q 001532 297 GKVKRSTFGSPPNDREGRAFSILRDVFL-------ANVPV---------H--NNNFRPKCFYVAVMLRRMVEAMLNKDAM 358 (1058)
Q Consensus 297 ~~~~~~~~~~~~~~~~e~~~~~L~~~ll-------pHl~~---------~--~~~~~~K~~~L~~Mv~kLl~l~~g~~~~ 358 (1058)
++++++ ... ..+.|+.++++.|| +|+|. . +.+..-+...++.++++|+.+..|.+.+
T Consensus 368 r~lrpg----ep~-t~e~a~~l~~~lFf~~~rYdL~~VGR~k~N~kL~l~~~~~~~~Lt~~DIi~~i~~Li~l~~g~~~~ 442 (1342)
T 3lu0_C 368 RMMRPG----EPP-TREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEV 442 (1342)
T ss_dssp HHHSCS----SCC-CTTHHHHHHHHHHSCTTTCCCTTTHHHHHHTTTTCSCCCCCSSCCTTHHHHHHHHHHHHHHTSSCC
T ss_pred HHCCCC----CCC-CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCC
T ss_conf 853799----998-789999999986068433451133167776531887676664741999999999999886089987
Q ss_pred CCCCCCCCEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf 88464346087112788999999999999999999987672399988877522343334420645453024877510113
Q 001532 359 DDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFK 438 (1058)
Q Consensus 359 Dd~D~l~NKRv~l~G~Ll~~lfr~~l~~~~~~i~~~l~k~~~~~~~~~~~~~~~~i~~~~It~~l~~~lsTGnw~~~~~~ 438 (1058)
||+|||+||||+++|+||+++||.+|.++.+.+++++.+. ....+.+..++++++++.++++||+
T Consensus 443 DDiDHLgNrRvr~vGeLl~~qfr~~l~r~~r~i~~~~~~~-----~~~~~~~~~lin~~~i~~~~k~ffg---------- 507 (1342)
T 3lu0_C 443 DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLG-----DLDTLMPQDMINAKPISAAVKEFFG---------- 507 (1342)
T ss_dssp CCSSSTTTSEEECHHHHHHHTHHHHHHHHHHHHTTHHHHC-----CSSCCSSTTTCCSSTTHHHHTTTTT----------
T ss_pred CCHHHHHCCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHC-----CCCCCCHHHHHCCCHHHHHHHHHHC----------
T ss_conf 6145564021030999999999999999999999997230-----2546788897356458999998847----------
Q ss_pred CCCCCCEEECCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf 43345428713334000023544236----53234543358986799976443347799987632222355115541489
Q 001532 439 MHRKGMTQVLARLSFIGTLGHMTRVS----PQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDE 514 (1058)
Q Consensus 439 ~q~sG~sq~l~Rln~ls~LShlRrv~----~~~~~~~k~t~~R~Lhps~wGfICPveTPEG~~cGLi~~LA~~a~Is~~~ 514 (1058)
++|+||++||+|++|.|||+||++ +.+.++++.+.+|+|||||||||||+|||||+|||||+|||++|+|+.
T Consensus 508 --~s~lSQ~lDqtNpLseltHkRRlsalGPGGLsr~~a~fevRdvH~thyGRiCPiETPEG~niGLI~sLA~~a~in~-- 583 (1342)
T 3lu0_C 508 --SSQLSQFMVQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNE-- 583 (1342)
T ss_dssp --TCSSCEECCCSSHHHHHHHHSBEESCCSTTSCCSSCCTTTSSCCTTCSSSSCTTCCCSSSCSSSCCBCCSSCCBCS--
T ss_pred --CCCCCEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCEEEECCHHHEEEECC--
T ss_conf --5640326037788888765530034578875434567520115732134224555898875001000032078645--
Q ss_pred CCHHHHHHHHHCCCEECCCCCCCCCCCCCCEEEEECCEEEEECCCHHHHHHHHHHHHHCCCCCCEEEEEECCCCCEEEEE
Q ss_conf 97059999864197441246854567998079999794876326924489999987643876731599861456349995
Q 001532 515 EEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFVNEKQRCVYIA 594 (1058)
Q Consensus 515 ~~~~i~~~l~~~G~~~l~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~lr~lrr~~~i~~~v~i~~~~~~~~i~I~ 594 (1058)
+|+.. ..|.+..||++-.-+. .+ . .....+.+- +..... .
T Consensus 584 -----------~Gfie------------tPyr~V~~g~v~~~i~---yL-s---A~eE~~~~I---------Aqan~~-l 623 (1342)
T 3lu0_C 584 -----------YGFLE------------TPYRKVTDGVVTDEIH---YL-S---AIEEGNYVI---------AQANSN-L 623 (1342)
T ss_dssp -----------SSCBC------------EEEEEEETTEEEEEEE---EE-C---TTTGGGSCB---------CCSSSC-C
T ss_pred -----------CCCCC------------CCCEEEECCEECCCEE---EC-C---HHHHCCCEE---------EECCCC-C
T ss_conf -----------78455------------7868988988758356---67-8---678558468---------754764-6
Q ss_pred CCCCEEEEEEEEEECCCCCCHHHHHHHHHCCCCCCHHHHCCCCEEEECCCCCCCEEEEEECCCCCCCCEEEEECCCCCCC
Q ss_conf 39982344399972483121065688763177650121015815576044332258995139999973014423760003
Q 001532 595 SDGGRVCRPLVIADKGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIEPFTILG 674 (1058)
Q Consensus 595 td~gRl~RPll~v~~~~~~~~~~~~~~~~~~~~~~~~ll~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~th~Ei~p~~ils 674 (1058)
.+.|++.++++.++.. + ||+- +.+ ...+|++++|.+++|
T Consensus 624 ~~~g~~~~~~v~~R~~-------------------------~--e~~~----------~~~----~~v~~~dvsP~qivS 662 (1342)
T 3lu0_C 624 DEEGHFVEDLVTCRSK-------------------------G--ESSL----------FSR----DQVDYMDVSTQQVVS 662 (1342)
T ss_dssp SSSSCCSCSSEEEECS-------------------------S--CEEE----------ECT----TTCCEEESCTTTTSC
T ss_pred CCCCCCCCCEEEEEEC-------------------------C--CEEE----------ECH----HHCEEEECCHHHHCC
T ss_conf 7789665775778866-------------------------9--6578----------586----887068617778301
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE-----------------------------------EEEEEECCCC----
Q ss_conf 2236677889999986410111245776531-----------------------------------5753100135----
Q 001532 675 VIAGLIPYPHHNQSPRNTYQCAMGKQAMGNI-----------------------------------AFNQLCRMDS---- 715 (1058)
Q Consensus 675 v~AsliPF~~hNqspRn~yq~~M~KQaiG~~-----------------------------------~~n~~~r~d~---- 715 (1058)
|+||+|||++||||||++|||||||||+|+. +.++..|.|.
T Consensus 663 vaaslIPFLEhdDAnRaLMGsNMQRQAVPLl~~e~p~VgTG~E~~~a~dsg~~i~a~~~G~v~~vda~~I~Ir~~~~~~~ 742 (1342)
T 3lu0_C 663 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMY 742 (1342)
T ss_dssp HHHHSCTTSTTBCHHHHHHHHHTTTTBCCCSSCCCCSSBCSCHHHHHHHTTTSCBCSSCBEECCCCSSBCCEEECSSSSS
T ss_pred HHHCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCEEECCCCHHEEECCCCEEEECCCCEEEEECCCEEEEEECCCCCC
T ss_conf 13204787445875566512415144623056889737545430004647865896379789996388599984787555
Q ss_pred ------CEEE----------EECCCCCEEECHHH----HH------HCCCCCCCCCCEEEEEEECCCCCCCCCEEEECCE
Q ss_conf ------2055----------20799531323023----22------1689888984037999614788877719985431
Q 001532 716 ------LLYL----------LVYPQRPLLTTRTI----EL------VGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSS 769 (1058)
Q Consensus 716 ------~~y~----------L~ypQ~PlV~t~~~----~~------~~~~~~~~G~N~iVAv~~y~Gyn~EDaiiink~s 769 (1058)
..|. +||+|+|+|+++.. +. +..+|+|+|+|++||||||.|||||||||||+++
T Consensus 743 ~~~~~~~~y~L~kf~RSNq~Tc~~QrPiV~~G~~V~~GdilADG~st~~GElaLG~N~lVAfMpW~GYNfEDAIlISErl 822 (1342)
T 3lu0_C 743 PGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERV 822 (1342)
T ss_dssp SSCCEEECCBCCCSCBCSSSCBCCCCBCCCSSCCBCTTCBCBCCSSCSSSSCCCSEECCEECCCCSSTTSSSEEEECTHH
T ss_pred CCCCCCEEEEECCCCCCCCCCCCCCCCEEECCCEEECCCEECCCCCCCCCEEECCCCCEEEEECCCCCCCCCCHHHHHHH
T ss_conf 56676137874032444455566530046559888527386046545689552425208999513376514350120335
Q ss_pred EECCCEEEEEEEEEEEEEECCCCCCCCEECC-CCCCCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEECCCCCCCCCC--
Q ss_conf 1014347999999999962036986312319-9999995100114999830068937689998999735898878878--
Q 001532 770 LDRGFGRCIVVKKYTAINQKYANSTSDRILR-PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIM-- 846 (1058)
Q Consensus 770 ~~rg~~~s~~~~~~~~~~~~~~~~~~e~~~~-p~~~~~~~~~~~~ld~~Gl~~~g~~v~~gdili~k~~~~~~~~~~~-- 846 (1058)
+++|+|||+|+++|++++++++.|.+|++.. |+.+ ...+++||++||+++|++|++|||||||++|+.+.+.+.
T Consensus 823 V~eD~fTSIHIee~e~~aRdtklG~EeiTrdIPnv~---e~al~~LDe~GIv~iGa~V~~GDILVGKvtPkge~~~tpEe 899 (1342)
T 3lu0_C 823 VQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVG---EAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEE 899 (1342)
T ss_dssp HHTTTSCEEEEEEEEEECCEETTEECCCCSCCSSCC---HHHHHSBCSSSCBCTTCCCCTTCEEECCCCBCCTTTCCHHH
T ss_pred HHCCCCEEEEEEEEEEEEEECCCCCCEECCCCCCCC---HHHHHCCCCCCCEECCCEECCCCEEEECCCCCCCCCCCHHH
T ss_conf 524872038999876653205899743445699988---68873478789761675877898798605799877678478
Q ss_pred ----CCCCCCCCCCCCCEEEEECCCCCCEEEEEEEEEECC----------------------------------------
Q ss_conf ----999987865322317720799971399999985189----------------------------------------
Q 001532 847 ----SPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDK---------------------------------------- 882 (1058)
Q Consensus 847 ----~~~~~~~~~~~~~s~~~~~~e~~~g~v~~v~~~~~~---------------------------------------- 882 (1058)
.-++++....+|+|+++++++ .|+|..|.+.+..
T Consensus 900 kLLraIFGeka~~vkDtSL~vp~g~--~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~ 977 (1342)
T 3lu0_C 900 KLLRAIFGEKASDVKDSSLRVPNGV--SGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRA 977 (1342)
T ss_dssp HHGGGTSCSSSSSBCCCCEECCTTC--CCEEEECCCCCCGGGCCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHCCCCCCCCCCCEECCCCC--CEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8899986675665345717638999--38999989971245320045667788899887776777888888889999887
Q ss_pred -------------------------------------------------------------------CCCEEEEEEEEEC
Q ss_conf -------------------------------------------------------------------9977999998322
Q 001532 883 -------------------------------------------------------------------NGDLCIKFLIRHT 895 (1058)
Q Consensus 883 -------------------------------------------------------------------~~~~~v~v~ir~~ 895 (1058)
...++|||++|+.
T Consensus 978 ~l~~~g~t~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gd~l~~gv~k~VkV~ia~k 1057 (1342)
T 3lu0_C 978 VLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVK 1057 (1342)
T ss_dssp HHHTTSCCHHHHTTSCGGGTTTCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCCCSSSSCEEEEEEEEE
T ss_pred HHHHCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEEE
T ss_conf 77654888999864888774024568699999999999999999999999999998722367666767746999999775
Q ss_pred CCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHCCCHHCCCCEE---------
Q ss_conf 79964430002379822797541467889989999882870899998865388999984100000279403---------
Q 001532 896 RRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFH--------- 966 (1058)
Q Consensus 896 R~p~iGDKf~sRhGqKGvvs~i~~~~DmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~--------- 966 (1058)
|+|++|||||||||||||||+|||+|||||++||++||||+|||||||||||||++|+++||+++..|...
T Consensus 1058 Rk~qvGDK~AgRHGnKGVis~I~p~EDMPf~~dG~~pDIIlNP~gvPSRMnIGqilE~~lG~aa~~~G~~i~~~~~~~~~ 1137 (1342)
T 3lu0_C 1058 RRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQE 1137 (1342)
T ss_dssp ECCCTTCEEECSSSCCEEECCCCCTTTSCEETTEEECSEECCGGGTTSSCBTHHHHHHHHHHGGGTSSTHHHHTTTHHHH
T ss_pred CCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 16877887013468874477772456799898898984886888787766333566876557777417238877776555
Q ss_pred --------------------------------------------EEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEE
Q ss_conf --------------------------------------------430014799999989999999998399999945998
Q 001532 967 --------------------------------------------YGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIY 1002 (1058)
Q Consensus 967 --------------------------------------------~~tpF~~~~~~~~~~~~~~~~l~~~g~~~~G~e~l~ 1002 (1058)
.+|| .+++...+++.+.|.++||+++|+++||
T Consensus 1138 ~~~~r~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~aTP----vFdga~~~~i~~~L~~aG~~~~Gk~~Ly 1213 (1342)
T 3lu0_C 1138 VAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATP----VFDGAKEAEIKELLKLGDLPTSGQIRLY 1213 (1342)
T ss_dssp CTTTHHHHHHHTTTTCCCSSSCCTTTSCHHHHHHTTTTTSSCTTCBCC----SSSSCCHHHHHHHTSSSSSCSSSCBCCB
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCCC----CCCCCCHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 678999999986314320000111024357788876643037741588----8899889999999997397999978988
Q ss_pred ECCCCCEEEEEEEEEEEEEECCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 28889476556966342122035634861078412784333237867434989999
Q 001532 1003 SGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGFP 1058 (1058)
Q Consensus 1003 ~g~tG~~~~~~if~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~~ 1058 (1058)
||+||++|+++||+|++|||||+|||+||+||||+|||+.+||||++||+++|||-
T Consensus 1214 dGrTGe~f~~~V~vG~~YylKL~HmVdDKiHaRs~GPysllTqQPl~Gkaq~GGqR 1269 (1342)
T 3lu0_C 1214 DGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQR 1269 (1342)
T ss_dssp CSSSCSBCSSCBCEECCEEEEBCCCGGGSCCCBSSCCBCSSSCCBCCCSSSCCCCC
T ss_pred CCCCCCCCCCCEEEEEHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEE
T ss_conf 49989870353663105674103104641378614897543569887442578833
No 6
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus}
Probab=1.00 E-value=1 Score=236.41 Aligned_cols=120 Identities=26% Similarity=0.555 Sum_probs=108.5
Q ss_pred CHHHHHHHHHHHHH----------HHCHHHHHHHCCCCEECC--CCCEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHCC
Q ss_conf 51799999999999----------847799987047611058--994999994899928701358866789914476329
Q 001532 43 GLVKQHLDSFNYFV----------NTGIRKIVRANDRIVSGI--DPSIFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSD 110 (1058)
Q Consensus 43 ~lv~~qi~SFn~Fi----------~~gl~~ii~~~~~i~~~~--~~~~~l~f~~i~i~~P~~~~~~~~~~l~P~eaR~r~ 110 (1058)
+|+++|++|||||+ ++||++++++++||+... +.++.|+|.++++++|.+ +|+|||+|+
T Consensus 2 ~Lv~~Q~~SF~~Flq~~~~~~~r~~~GL~ei~~~~~pI~~~~~~~~~~~L~f~~~~l~~P~~---------~p~Ecr~r~ 72 (188)
T 3mlq_A 2 PLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPF---------SQDECREKD 72 (188)
T ss_dssp CCHHHHHHHHHHHHCTTSCGGGCCSCHHHHHHHHHCCEEECCSSSCCEEEEEEEEEECCCSS---------CHHHHHHTT
T ss_pred CHHHHHHHHHHHHHHCCCCCCCCHHHCHHHHHHHCCCEEECCCCCCEEEEEEEEEEECCCCC---------CHHHHHHCC
T ss_conf 77899999999998577654443110589999755976512677973999998899648878---------999999649
Q ss_pred CCCCCEEEEEEEEEECCCCCCEEEEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCEEEEEEEE
Q ss_conf 95474099999999998754202478689996520201356522799998889762999899994899919134786420
Q 001532 111 MTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQE 190 (1058)
Q Consensus 111 lTYsa~l~v~i~~~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~gE~~~d~GGYFIInG~EKVIi~q~ 190 (1058)
+||+|||+|++++..++. +++++++|++|+||+|+ +||||||||+||||++||
T Consensus 73 lTYsapl~v~v~l~~~~~---~~i~~~~v~iG~iPlMt------------------------~gGyFIING~ERVIVsQe 125 (188)
T 3mlq_A 73 LTYQAPLYARLQLIHKDT---GLIKEDEVFLGHLPLMT------------------------EDGSFIINGADRVIVSQG 125 (188)
T ss_dssp CCCEEEEEEEEEEEETTT---CCEEEEEEEEEEEECCC------------------------TTSCEEETTEEEECCCCS
T ss_pred CCCCEEEEEEEEEEECCC---CEEEEEEEEECCCCEEC------------------------CCCEEEECCEEEEEEEEE
T ss_conf 976605899999998788---51789889973508899------------------------998899978899999830
Q ss_pred CCCCCEEE
Q ss_conf 03598799
Q 001532 191 QLSKNRVI 198 (1058)
Q Consensus 191 ~~~~N~i~ 198 (1058)
++++|-.+
T Consensus 126 ~r~~gell 133 (188)
T 3mlq_A 126 GRTVGELM 133 (188)
T ss_dssp SSCHHHHH
T ss_pred CCCCCEEE
T ss_conf 36688126
No 7
>3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory protein, transcription; 3.00A {Escherichia coli}
Probab=1.00 E-value=1 Score=108.38 Aligned_cols=99 Identities=14% Similarity=0.213 Sum_probs=79.7
Q ss_pred EEEEEEEEEEECCCCCCCCEECC--CCCCCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEECCCCCCCCCCC------CC
Q ss_conf 99999999962036986312319--99999951001149998300689376899989997358988788789------99
Q 001532 778 IVVKKYTAINQKYANSTSDRILR--PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSIMS------PT 849 (1058)
Q Consensus 778 ~~~~~~~~~~~~~~~~~~e~~~~--p~~~~~~~~~~~~ld~~Gl~~~g~~v~~gdili~k~~~~~~~~~~~~------~~ 849 (1058)
+|+..|++++++++.|. |.|+. |+.+ ...+++||++||+++|++|++|||||||++|+...+.+.. -+
T Consensus 2 iHIeeyei~~r~tk~G~-EeIT~dIPnv~---e~~l~~LDe~GIV~iGs~V~~GDILVGKvTPk~~~~~tpEekLL~aIf 77 (228)
T 3tbi_B 2 IHIQELACVSRDTKLGP-EEITADIPNVG---EAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIF 77 (228)
T ss_dssp CEEEEEEEEEEEETTEE-CEESSCCSSCC---HHHHHTBCTTSBBCTTCCCBTTCEEECEEEECCGGGCCHHHHHHHHHH
T ss_pred CCEEEEEEEEEECCCCC-EEEECCCCCCC---HHHHHCCCCCCCEECCCEECCCCEEEECCCCCCCCCCCHHHHHHHHHH
T ss_conf 32799999999769997-27716899966---999850798898056789789988985468998787783788899986
Q ss_pred CCCCCCCCCCEEEEECCCCCCEEEEEEEEEECC
Q ss_conf 987865322317720799971399999985189
Q 001532 850 GQTDSRYRSARQTYKGPDGETCVVDRVALCSDK 882 (1058)
Q Consensus 850 ~~~~~~~~~~s~~~~~~e~~~g~v~~v~~~~~~ 882 (1058)
+.+....+|+|++.++++ .|+|..|.+.+..
T Consensus 78 g~k~~~vkDtSL~vp~G~--~G~VidV~if~r~ 108 (228)
T 3tbi_B 78 GEKASDVKDSSLRVPNGV--SGTVIDVQVFTRD 108 (228)
T ss_dssp CTTSSCEEECCEECCSSC--BEEEEEEEEEEBT
T ss_pred CCCCCCCEECCEECCCCC--CEEEEEEEEEECC
T ss_conf 776665016807638999--5799999998137
No 8
>3lti_A DNA-directed RNA polymerase subunit beta; BBM2, nucleotidyltransferase, transcription, transferase; HET: MLY MSE; 1.60A {Escherichia coli} PDB: 3e7h_A
Probab=1.00 E-value=1 Score=65.13 Aligned_cols=68 Identities=18% Similarity=0.359 Sum_probs=49.8
Q ss_pred CCCCEEEEEECC-----CC--CEEEEEEECCCCCCEEEEEEEECCEEEEEECCEECCCCHHHHHHHHCCCCHHHHHHHHC
Q ss_conf 359879999579-----97--57999982589950089999558899999811001323856899828998889998817
Q 001532 192 LSKNRVIIDTDK-----KG--NINASVTSSTETVKSKTVIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQMVG 264 (1058)
Q Consensus 192 ~~~N~i~~~~~~-----~g--~~~~~v~s~~~~~~~~~~~~~~~g~i~~~~~~~~~~IPi~illrALg~~sD~eI~~~i~ 264 (1058)
+||+ +++..+. .| .+.|.+.+.+. .|.-...+.++.+|+++++. .++|+.+||||||.+ ++||++.++
T Consensus 4 ~SPG-v~f~~~~~~ths~g~~~y~~~iIP~RG--sWlefe~d~~d~~~vrIdr~-rK~p~t~lLrAlG~~-~edIL~~Fy 78 (296)
T 3lti_A 4 MSPG-VFFDSDKGKTHSSGKVLYNARIIPYRG--SWLDFEFDPKDNLFVRIDRR-RKLPATIILRALNYT-TEQILDLFF 78 (296)
T ss_dssp CCCE-EEEEEC---------CCEEEEEECSBS--CCEEEEECTTSCEEEEETTC-CCEETHHHHHHTTCC-HHHHHHHHC
T ss_pred CCCE-EEEECCCCCCCCCCCEEEEEEEECCCC--CEEEEEECCCCEEEEEECCC-CCCHHHHHHHHCCCC-HHHHHHHCC
T ss_conf 8987-877346677677884789999905997--51899985887499997674-121088999980898-699998614
No 9
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus}
Probab=1.00 E-value=1 Score=45.21 Aligned_cols=66 Identities=9% Similarity=0.140 Sum_probs=56.2
Q ss_pred CCCCEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf 43460871127889999999999999999999876723999888775223433344206454530248775
Q 001532 363 YVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFD 433 (1058)
Q Consensus 363 ~l~NKRv~l~G~Ll~~lfr~~l~~~~~~i~~~l~k~~~~~~~~~~~~~~~~i~~~~It~~l~~~lsTGnw~ 433 (1058)
-..+|+.+++|+||+..++.+|.++++.++.++.-. +...+.+.+++|+++++..++.||.|++++
T Consensus 120 VIVsQe~r~~gell~~q~r~gl~r~ek~~~e~~~~~-----~~~~~~~~~l~n~kp~~~~ik~ff~ss~Ls 185 (188)
T 3mlq_A 120 VIVSQGGRTVGELMADQFRVGLARLARGVRERMVMG-----SPDTLTPAKLVNSRPLEAALREFFSRSQLS 185 (188)
T ss_dssp ECCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHS-----CGGGCCHHHHCCCHHHHHHHHHHHHTCEEC
T ss_pred EEEEEECCCCCEEEEEEHHHHHHHHHHHHHHHHCCC-----CCCCCCCCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf 999830366881268731167789999998651413-----100137334402478999998741645334
No 10
>2g7j_A Putative cytoplasmic protein; STR72, autostructure, structural genomics, PSI, protein STRU initiative; NMR {Salmonella typhimurium} SCOP: d.198.5.1
Probab=1.00 E-value=1 Score=15.70 Aligned_cols=39 Identities=28% Similarity=0.480 Sum_probs=32.7
Q ss_pred CCCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHCCCH
Q ss_conf 788998999988287089999886538899998410000
Q 001532 921 EDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAG 959 (1058)
Q Consensus 921 ~DmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~ 959 (1058)
..+|---.|-.++-.==||||.|||-+-..++++.|-+.
T Consensus 76 ~~FPlyl~g~~~~~yGIpHGFSSR~~L~r~l~~~F~~~~ 114 (124)
T 2g7j_A 76 QNFPLYLGGETHEHYGIPHGFSSRIALERYLNGLFGDEK 114 (124)
T ss_dssp CCSCCCCSSSSCCEEECEECCSCHHHHHHHHHHHHTC--
T ss_pred HCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCC
T ss_conf 707742366760100778673469999999988624533
Done!