Query 002545
Match_columns 910
No_of_seqs 157 out of 1738
Neff 6.8
Searched_HMMs 29240
Date Tue Mar 26 16:52:27 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/002545.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_1262-1266//hhsearch_pdb/002545hhsearch_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 1912.2 26.5 840 9-909 24-1023(1210)
2 1twf_B DNA-directed RNA polyme 1.0 1 1 1859.5 64.7 839 9-909 37-1034(1224)
3 4ayb_B DNA-directed RNA polyme 1.0 1 1 1657.2 59.9 825 9-909 20-935 (1131)
4 2a6h_C DNA-directed RNA polyme 1.0 1 1 1402.8 41.0 735 8-909 11-893 (1119)
5 3lu0_C DNA-directed RNA polyme 1.0 1 1 1238.8 27.6 749 9-909 21-1120(1342)
6 3mlq_A DNA-directed RNA polyme 1.0 1 1 188.2 6.2 89 14-127 2-132 (188)
7 3lti_A DNA-directed RNA polyme 1.0 1 1 83.8 12.0 162 139-311 22-296 (296)
8 3tbi_B DNA-directed RNA polyme 1.0 1 1 77.8 6.2 68 763-830 18-108 (228)
9 3mlq_A DNA-directed RNA polyme 1.0 1 1 30.0 5.1 65 315-391 120-184 (188)
10 3ddc_B RAS association domain- 1.0 1 1 16.0 1.2 41 14-58 10-50 (163)
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=1912.18 Aligned_cols=840 Identities=27% Similarity=0.395 Sum_probs=736.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHH---------------------------------------------------HH
Q ss_conf 437033499999979999997699999---------------------------------------------------99
Q 002545 9 FEPLRELVRHHIESFDYMLDEGLSEMF---------------------------------------------------DH 37 (910)
Q Consensus 9 ~~~~~~lv~~hi~SFn~Fi~~gl~~ii---------------------------------------------------~e 37 (910)
+...++||+|||||||+|++++|++|+ +|
T Consensus 24 ff~~~gLV~qHIdSFN~FI~~~Lq~IV~~~~~I~~~~~~~~~~~~~~~~~~~~l~f~~i~v~kP~~~e~d~~~~~l~P~E 103 (1210)
T 3h0g_B 24 FFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPTMTEADGSTTTMFPQE 103 (1210)
T ss_dssp HHHHTCTTCSSSSSSSSSTTTTHHHHSSTTCCCC-------------------CEEEEEECCCCCCBCTTSCBCCCCTTT
T ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCEEEEEEEEEEECCCCEECCCCCCCCCCHHH
T ss_conf 86430258899889999999749999741484776676676644446775499999789985884005778646558899
Q ss_pred HHHCCCEEEEEEEEEEEEEEECCC----------C-----CEEEEEEEECCCCEEECCCCCCCCCCCHHHHHHCCCCCCC
Q ss_conf 997299043689999999995399----------9-----6255376540451030579744899995778721332125
Q 002545 38 CRQAKISYTGKLMADVEFQYLDAG----------S-----PVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAE 102 (910)
Q Consensus 38 aR~r~~TYs~~l~v~i~~~~~~~~----------~-----~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D 102 (910)
||+|++||+||++|+++++++... . .....++.||+|||||||++|||++++++|+++.||||+|
T Consensus 104 cRlR~lTYsapl~Vdi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IG~iPIMlrS~~C~L~g~s~~eL~~~gEcp~D 183 (1210)
T 3h0g_B 104 ARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYD 183 (1210)
T ss_dssp TTTTCCCCEEEEEEEEEC---------------------CCSSCCCEEEEEEECCSSSTTSSSSSCCHHHHHHTTCCTTC
T ss_pred HHHCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCEEECCCCCCCCCCCHHHHHHCCCCCCC
T ss_conf 97139963526899999997575644333333344443333330048871189884778332789798999756888789
Q ss_pred CCCEEEECCCEEEEEEEEEECCCCCEEEEECCCCCCCCCCEEEEEEEEEEECCCCCE--EEEEEEEE------CCEEEEE
Q ss_conf 894899939400999998404994089971254478985102389999665199823--99999982------8908999
Q 002545 103 MGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSV--TLKLYYLL------NGSVRLG 174 (910)
Q Consensus 103 ~GGYFIInG~EKVIr~~i~~~~N~~~~~~r~~~~~~~~~~t~~~v~ir~~~~~~~~~--~~~l~~~~------~g~~~l~ 174 (910)
|||||||||+||||+.|+..++|+|+++. +++..++.+++.+||+++++++. ...+++.. ++.+.++
T Consensus 184 ~GGYFIING~EKVII~qerla~N~~iv~~-----~~~~~~~~~~a~irS~~~~~~~~~s~~~v~~~~~~~~~~~~~i~~~ 258 (1210)
T 3h0g_B 184 QGGYFIINGSEKVIIAQERSAANIVQVFK-----KAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTENSGQTIRAT 258 (1210)
T ss_dssp CCCCBCGGGSCBCCCBCBCCCCSCCCCCC-----CCCSSSCCCCCCCCCCCCSSSCCCCCCCCCCCCCCTTSCSCCCCCC
T ss_pred CCCEEEEECEEEEEEECHHHCCCEEEEEE-----ECCCCCCEEEEEEEEEECCCCCCEEEEEEEEEECCCCCCCCEEEEE
T ss_conf 99789990878889832123056579996-----2588874079999998358862005899999851566789559999
Q ss_pred EEEECCCCCCCHHHHHHHCCCCCHHHHHHHHCCCCCCHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC
Q ss_conf 99606433310977998614798889998710122100100027889811678999999999840231298999998503
Q 002545 175 FWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEH 254 (910)
Q Consensus 175 ~~~~k~~~~IPi~illkALg~~sD~eI~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~i~t~~~al~yig~~ 254 (910)
|++.+. .||++++|||||.+||+||++.|+. +.++..+.+.+..+++++. .++|+++||+|||++
T Consensus 259 ~~~~~~--~IPi~ivlkALg~~sD~EI~~~I~~-----------~~~d~~~~~~l~~slee~~--~i~tq~~aL~yIG~r 323 (1210)
T 3h0g_B 259 LPYIRS--DIPIVIVFRALGVVPDRDILEHICY-----------DPNDFQMLEMMKPCIEEAF--VIQDKDIALDYIGKR 323 (1210)
T ss_dssp CTTSCS--CCCSHHHHTTTTCCSTTHHHHHHCC-----------SSCCHHHHHTHHHHHHTTS--SCCSSHHHHHTTCCC
T ss_pred EECCCC--CCCHHHHHHHCCCCCHHHHHHHHHC-----------CCCCHHHHHHHHHHHHHHH--HCCCHHHHHHHHHHH
T ss_conf 704226--7769999987079889999999717-----------8884899999999999865--058899999999875
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCC----CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECCCCHHHHH
Q ss_conf 465446888861799999999767435799984----3289999999999861079988899431126077453030699
Q 002545 255 FQPVIDGLQSESYYAVAETVIRDYIFVHLNDNN----DKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITI 330 (910)
Q Consensus 255 f~~~~~~~~~~~~~~~g~~~L~~~ll~Hi~~~~----~K~~~L~~Mv~kLl~~~~g~~~~Dd~D~~~nkrv~l~G~Ll~~ 330 (910)
|+.. ..++.++.++|+++|++++|||++... +||+||+||++||++++.|.+.+||+|||+|||++++|+||+.
T Consensus 324 ~~~~--~~~~~~~~~~a~~iL~~~lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~l~G~Ll~~ 401 (1210)
T 3h0g_B 324 GSTT--GVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLAS 401 (1210)
T ss_dssp SSSC--CCCHHHHHHHHHHHHTTTSSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBCCHHHHHHH
T ss_pred CCCC--CCCCHHHHHHHHHHHHHHEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECHHHHHHH
T ss_conf 4346--88814479999999874188476987445058999999999999998679987889842247177337899999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECC
Q ss_conf 99999999999999999998862698413410688999872189724289998674146766444554443454189804
Q 002545 331 YLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAE 410 (910)
Q Consensus 331 lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~l~~~lsTGnw~~~~~~~~~q~sGvsqvle 410 (910)
+||+.|+++++++++.+++.+.+ ++.+++. .+++ ++.||++|++|||||||+++++ +++|++||||+|+
T Consensus 402 lfr~~~~~~~~~i~~~l~k~~~~-~~~~~~~------~~i~---~~~It~~l~~~laTGNW~~~kk-~~~~~sGvsqvl~ 470 (1210)
T 3h0g_B 402 LFRMLFRKMTRDVYKYMQKCVET-NREFNLT------LAVK---SNIITNGLRYSLATGNWGDQKR-SMVNRVGVSQVLN 470 (1210)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTT-CCSCCCT------TSSC---STTTSHHHHHHHSSSCSSTTSS-CCSCCCCSCCBCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHC-CCCCCHH------HHCC---HHHHHHHHHHHHHCCCCCCCCC-CCCCCCCEEEECC
T ss_conf 99999999999999988887613-7766889------9606---0056789998861178655566-6557677799833
Q ss_pred CCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCHHHH
Q ss_conf 30256685530001369855665556664247777521014789998544544456612699200389886433201168
Q 002545 411 RLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRT 490 (910)
Q Consensus 411 RlN~~~~lSh~Rrv~rg~~~~~~K~t~~R~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is~~~~~~~~~~~~~~~~~ 490 (910)
|+||+|+|||||||+ +++++++|+++||+||||||||+||+|||||++||||||||++|+||++.+.+
T Consensus 471 R~n~~s~lShlRrv~-~p~~~~~K~~~~R~Lhpt~WG~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~----------- 538 (1210)
T 3h0g_B 471 RYTFASTLSHLRRTN-TPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSA----------- 538 (1210)
T ss_dssp CSSHHHHHHHTTBBC-CSCCSSCCSSSSSSCCGGGTTTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSS-----------
T ss_pred CCCHHHHHHHHHHCC-CCHHHCCCCCCCCCCCHHHHEEECCCCCCCCCCCCCCCCCCCEEEEECCCCCH-----------
T ss_conf 687899888888606-84000266665664473163133566687877444300354003667899818-----------
Q ss_pred HHHHHHHHCCCEECCCCCCCCCCCCEEEEEECCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCC
Q ss_conf 89999984698125875435899960699989899945449518999999999888168888998447999867899888
Q 002545 491 SILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYP 570 (910)
Q Consensus 491 ~i~~~L~~lg~~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~~~~~~~lr~lk~~~~~~i~~~~ei~~v~~~~~~~~~ 570 (910)
+|.++|.++||+++. +......++.++|||||+|+|++ .+|..|++.||.+||.+ .|+.+++|+ ++...+
T Consensus 539 pI~~~l~~~gme~le-~~~~~~~~~~tkVfvNG~wVGvh--~dp~~Lv~~lR~lRR~g--~Is~eVSIv-----rdir~r 608 (1210)
T 3h0g_B 539 PIIEFLEEWGLETLE-DYNPSASPNATKVFVNGVWLGVH--RDPAHLTETLRSLRRRL--DISAEVSIV-----RDIREK 608 (1210)
T ss_dssp HHHHHHHSSSCCCCS-CCCSSSSSSSCCCCSTTCCCCCC--SCHHHHHHHHHHHHTTT--SSCTTCCCC-----CCTTTC
T ss_pred HHHHHHHHHCCCCHH-HCCCCCCCCCEEEEECCEEEEEE--CCHHHHHHHHHHHHHCC--CCCCCEEEE-----ECCCCC
T ss_conf 899999984874154-42765689842999999999994--89999999999986068--999946987-----538898
Q ss_pred CEEEECCCCCEECEEEEECCC-------CC-------------------------------CCCCEEEECCCCEEEEEEE
Q ss_conf 059654999200007750589-------98-------------------------------8875666475430534642
Q 002545 571 GLYLFTSPPKFVRPVRNISLP-------SE-------------------------------ESQNIELIGPFEQVFMEIR 612 (910)
Q Consensus 571 ~i~I~td~gR~~RPv~~~~~~-------~~-------------------------------~~g~iE~id~~Eq~~~~Ia 612 (910)
|++||||+||+||||++++++ +. ..|.|||||++||++++||
T Consensus 609 E~~IfTDaGRv~RPLfvVen~~~~~~~g~L~l~k~hi~~L~~~~~~~~~~~~~~~~w~~Lv~~GvIEylDaeEEet~mIa 688 (1210)
T 3h0g_B 609 ELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPEQRFGWTALVSSGLIEYLDAEEEETVMIA 688 (1210)
T ss_dssp CCCCCCSSCCBCCEEEECCCSSCSSSSCCCSSCHHHHHHHHHHHTCCCSCTTCCCSSTTTTTTTSEEECCTTTGGGCCEE
T ss_pred EEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCHHHHHHCCCEEEECHHHHHCEEEE
T ss_conf 69996678714641799716876444565245699999986143344333223578888976797898467662022587
Q ss_pred CCCCCCCC----------------C--------CCCCCCEECCCCCCCCCCCEEECCCCCCCCCCCHHHHHHHCCCCCCC
Q ss_conf 38999999----------------8--------78877300124787653202212548999984011111000012344
Q 002545 613 CPDGGDGG----------------R--------RNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMG 668 (910)
Q Consensus 613 ~~~~~~~~----------------~--------~~~~~~th~Ei~p~~ils~~asliPF~~hNqspRn~yq~~M~KQaig 668 (910)
|+++|+.. . ...+.||||||||++|||+|||+||||||||||||||||||+|||||
T Consensus 689 mtpeDL~~~r~~~~g~~~~~~~d~~~r~k~~~~~~~~~~THcEIhPsmILGIcASiIPFpdHNQSPRNtYQ~aMgKQamG 768 (1210)
T 3h0g_B 689 MSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMG 768 (1210)
T ss_dssp SCHHHHHHHHHHTTCCCCCCSSCCSSCCCCCSCCSCCSCSEECSCGGGSSCSSSTTSSSSTTSCSHHHHHHHHHHTTCCS
T ss_pred ECHHHHHHHHHHHCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCHHHHHHEEECCCCCCCCCCCHHHHHHHHHCCCCC
T ss_conf 45899534554322566544446101102567776545553354410344530004668655556055543333035555
Q ss_pred CCEEEEEEECCCCEEECCCCCEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCCCCEEEEEEEE
Q ss_conf 31138998415742552799810583464001386436898401689973368885532544200001476112499999
Q 002545 669 FSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTE 748 (910)
Q Consensus 669 ~~~~n~~~R~d~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~ 748 (910)
++++|+..|+||++|+|+|||+|||+|+.+++++++++|+|+||+||||||+|||||||||+||+|+||||||+++|++|
T Consensus 769 ~~~~n~~~R~Dt~~~~L~yPQkPlv~T~~~e~~~~~elp~G~NaiVAvmsy~GYn~EDAiIink~sv~rg~~~s~~~~~y 848 (1210)
T 3h0g_B 769 VYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTY 848 (1210)
T ss_dssp CCCTTTTTSCCSSEEEESSCBCCSSBCTTSTTTTCTTSCSCCEECBEECCCSSSSCSSCEEEEHHHHTTTTTCEEEEEEE
T ss_pred CCCCCCCCCCCCCCCEEECCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHEEEEHHHEECCCEEEEEEEEE
T ss_conf 43224232447500276268176543256787488866686223899966678874463023021400486599999988
Q ss_pred EEEEECCCCCCCCCCEEECCCCCC------HHHHCCCCCCCCCCCCCEECCCCCEEEEECCCC--------------CCE
Q ss_conf 997302478767650110059887------021102699998554706659994998321689--------------934
Q 002545 749 TIDLSDDGNKVDRGQKLFRRNKDA------KSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT--------------NSW 808 (910)
Q Consensus 749 ~~~~~~~~~~~~~~~~~f~~~~~~------~~~~~~ld~dG~~~~G~~v~~gdil~~~~~~~~--------------~~~ 808 (910)
.++.... .....+.|+.|+.. ...+++||+||||.+|++|++||||+||..|+. .++
T Consensus 849 ~~~~~~~---~~~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gDiligK~~p~~~~~~~~~~~~~~~~~rd 925 (1210)
T 3h0g_B 849 TDQEKKI---GMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRD 925 (1210)
T ss_dssp EECCCCC---SSSCCCCCCCCCTTSCCSCCSCCGGGCCTTSSCCTTCCCCTTCCCCCCCCCC-----------CCCCCCC
T ss_pred EEEEEEC---CCCCEEEECCCCCCHHCCCCHHHHHHCCCCCCCCCCCEECCCCEEEEEECCCCCCCHHHCCCCCCCCCCE
T ss_conf 8774314---7986049718983120133313476468888837887966899899984588877201123445665531
Q ss_pred EEEEECCCCCEEEEEEEEEECCCCCCCEEEEEEEEEEECCCCCCCEECCCCCCCEEEEEECCCCCCCCCCCCCCCCEEEC
Q ss_conf 34550699856999999970579999708999992240897664000247982378532047676844899996829738
Q 002545 809 RTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIIN 888 (910)
Q Consensus 809 ~~~~~~~~e~g~v~~v~~~~~~~g~~~~~~~i~~r~~r~p~iGDKf~sRHGqKGv~s~~~~~~dmPf~~~~G~~pDiI~N 888 (910)
.|++++++|+|+||+|.++.+++| ...++|++|+.|.|++|||||||||||||||++||+|||||+ ++|++||||+|
T Consensus 926 ~s~~~~~~e~g~Vd~V~~~~~~~g--~~~vkv~~~~~R~~~~GDK~a~RhGqKGvi~~i~~~edmPf~-~~G~~pDii~N 1002 (1210)
T 3h0g_B 926 VSTPLRSTESGIVDQVMVTTNQEG--LKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFS-AQGIVPDIIIN 1002 (1210)
T ss_dssp CCCCCCTTCCCCCCEEEEEECSSS--SEEEEEEECCCBCCCTTCEEECTTCCCEEEEEEECTTTSCCB-TTTBCCSEECC
T ss_pred EEEEECCCCCEEEEEEEEEEECCC--CEEEEEEEEEECCCCCHHHHHCCCCCCCEEEEEECCCCCCCC-CCCCCCEEEEC
T ss_conf 458953899759999999770689--769999998751788636650325787305678532018867-78978749878
Q ss_pred CCCCCCCCCHHHHHHHHHCCC
Q ss_conf 998665564889998730246
Q 002545 889 PHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 889 Ph~~PSRMtiGql~E~~~gK~ 909 (910)
||||||||||||++|+++||+
T Consensus 1003 P~~~PSRMtigq~~E~~~g~~ 1023 (1210)
T 3h0g_B 1003 PHAIPSRMTVAHLVECQLSKV 1023 (1210)
T ss_dssp GGGSTTSCCHHHHHHHHHHHH
T ss_pred CCCCCCCCCCHHHHHHHHHHH
T ss_conf 875777762033657687799
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=1859.48 Aligned_cols=839 Identities=27% Similarity=0.403 Sum_probs=735.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHH---------------------------------------------------HH
Q ss_conf 437033499999979999997699999---------------------------------------------------99
Q 002545 9 FEPLRELVRHHIESFDYMLDEGLSEMF---------------------------------------------------DH 37 (910)
Q Consensus 9 ~~~~~~lv~~hi~SFn~Fi~~gl~~ii---------------------------------------------------~e 37 (910)
+..+++|++||+||||+|+++||++++ +|
T Consensus 37 ~~~~~~Lv~~qidSFn~Fi~~gL~~iv~~~~~I~~~~~~~~~~~~~~~~~~~~l~f~~i~l~~P~~~e~~~~~~~l~P~E 116 (1224)
T 1twf_B 37 FFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQE 116 (1224)
T ss_dssp HHHHHTTCHHHHHHHHHHHHTHHHHHHHTTCBCC------------------CCEECCCEEEEEEECCSSSCCEECCHHH
T ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCEEEEEEEEEEEEECCCEECCCCCCCCCCHHH
T ss_conf 87284478989999999999708999985596650375445555455660799999789995880103677546689899
Q ss_pred HHHCCCEEEEEEEEEEEEEE-ECCCC------------C--EE--EEEEEECCCCEEECCCCCCCCCCCHHHHHHCCCCC
Q ss_conf 99729904368999999999-53999------------6--25--53765404510305797448999957787213321
Q 002545 38 CRQAKISYTGKLMADVEFQY-LDAGS------------P--VV--RERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEA 100 (910)
Q Consensus 38 aR~r~~TYs~~l~v~i~~~~-~~~~~------------~--~~--~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~ 100 (910)
||+|++||+|||+|++++.+ +..+. + ++ .++|++|+|||||||++|||+|++++||++.||||
T Consensus 117 cRlR~lTYsapl~v~v~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~v~iG~iPIMlrS~~C~L~~~s~~el~~~gEcp 196 (1224)
T 1twf_B 117 ARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECP 196 (1224)
T ss_dssp HHHTTCCCEEEEECCEECCCCC-------------------------CCEEEEEECCTTSTTSGGGTCCHHHHHHTTCCT
T ss_pred HHHCCCCCCEEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEEECCCCCCCCCCCHHHHHHHCCCC
T ss_conf 96238953415899999999968865555433233221002233411367178975706684347898989998616675
Q ss_pred CCCCCEEEECCCEEEEEEEEEECCCCCEEEEECCCCCCCCCCEEEEEEEEEEECC--CCCEEEEEEEEE-----CCEEEE
Q ss_conf 2589489993940099999840499408997125447898510238999966519--982399999982-----890899
Q 002545 101 AEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKD--QSSVTLKLYYLL-----NGSVRL 173 (910)
Q Consensus 101 ~D~GGYFIInG~EKVIr~~i~~~~N~~~~~~r~~~~~~~~~~t~~~v~ir~~~~~--~~~~~~~l~~~~-----~g~~~l 173 (910)
+|+||||||||+||||++|+++++|+++++.. ++..++.|++.+||+.++ +++.|+.+++++ ++.+|+
T Consensus 197 ~D~GGYFIING~ERVIv~Qe~~s~N~i~~~~~-----~~~~~~~~~~~irsv~~~~~~~~~~~~l~~~~~~~~~~~~i~v 271 (1224)
T 1twf_B 197 FDMGGYFIINGSEKVLIAQERSAGNIVQVFKK-----AAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKA 271 (1224)
T ss_dssp TCCCCSEEETTEEEEECEEEEECSSCCEEEEC-----CTTSSEEEEEEEECCCSSSCCCCCEEEEEEESCSSCSSCCEEE
T ss_pred CCCCCEEEEECCEEEEEEEEECCCCEEEEEEC-----CCCCCCEEEEEEEEEECCCCCCEEEEEEEEECCCCCCCCEEEE
T ss_conf 68997799908588887765005771799961-----6898635899999886268864168999994356678977999
Q ss_pred EEEEECCCCCCCHHHHHHHCCCCCHHHHHHHHCCCCCCHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 99960643331097799861479888999871012210010002788981167899999999984023129899999850
Q 002545 174 GFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGE 253 (910)
Q Consensus 174 ~~~~~k~~~~IPi~illkALg~~sD~eI~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~i~t~~~al~yig~ 253 (910)
++++.++ +||+++||||||.+||+||++.|+ ++ .+++.+.+.+..+|++.. .++|+++||.|||+
T Consensus 272 r~~~~k~--~IPi~illkALG~~sD~eI~~~i~--~~---------~~d~~~~~~l~~~l~e~~--~~~t~~~AL~yIg~ 336 (1224)
T 1twf_B 272 TLPYIKQ--DIPIVIIFRALGIIPDGEILEHIC--YD---------VNDWQMLEMLKPCVEDGF--VIQDRETALDFIGR 336 (1224)
T ss_dssp ECTTCSS--CEEHHHHHHHTTCCSHHHHHHHHC--CC---------TTCHHHHHHHHHHHHHTT--TCCSHHHHHHHHHH
T ss_pred EEECCCC--CCCHHHHHHHHCCCCHHHHHHHHC--CC---------CCCHHHHHHHHHHHHHHH--HCCCHHHHHHHHHH
T ss_conf 9815566--452999999866998999999864--66---------785899999999999765--13899999999987
Q ss_pred C-CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCC----CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECCCCHHH
Q ss_conf 3-46544688886179999999976743579998----432899999999998610799888994311260774530306
Q 002545 254 H-FQPVIDGLQSESYYAVAETVIRDYIFVHLNDN----NDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLI 328 (910)
Q Consensus 254 ~-f~~~~~~~~~~~~~~~g~~~L~~~ll~Hi~~~----~~K~~~L~~Mv~kLl~~~~g~~~~Dd~D~~~nkrv~l~G~Ll 328 (910)
+ +++. .++.++.+.|+.+|++++|||++.. ..|++||++|++||+.++.|.+.+||+|||+||||+++|+||
T Consensus 337 r~~~~g---~~~~~~~~~a~~iL~~~~l~Hvg~~~~~~~~K~~~L~~mi~kLl~~~~g~~~~DD~DhlgnkRv~l~G~Ll 413 (1224)
T 1twf_B 337 RGTALG---IKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLL 413 (1224)
T ss_dssp TTSCTT---SCHHHHHHHHHHHHHHTSSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEECHHHHH
T ss_pred HHCCCC---CCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEHHHHHH
T ss_conf 622679---88730899999999752015469875444318899999999999985699777787530262880265899
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf 99999999999999999999988626984134106889998721897242899986741467664445544434541898
Q 002545 329 TIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQ 408 (910)
Q Consensus 329 ~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~l~~~lsTGnw~~~~~~~~~q~sGvsqv 408 (910)
+.+||+.|+++.+.++..+++.+.+ ++.++ ++.++ +++.||++|++|||||||+++. .++++++||||+
T Consensus 414 ~~lfr~~~~r~~~~i~~~l~~~~~~-~~~~~------~~~~i---~~~~It~~lk~~~aTGNw~~~k-~~~~~~sGvSQv 482 (1224)
T 1twf_B 414 AQLFKTLFKKLTKDIFRYMQRTVEE-AHDFN------MKLAI---NAKTITSGLKYALATGNWGEQK-KAMSSRAGVSQV 482 (1224)
T ss_dssp HHHHHHHHHHHHHHHHHHHHSCCC---------------CCC---CTHHHHHHHHHHHHHCCCC----------CCCEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHC-CCCCC------HHHHH---CCCCHHHCCHHHEEECCCCCCC-CCCCCCCCEEEE
T ss_conf 9999999999999999999887621-43214------56650---5653210426343413445555-432356644575
Q ss_pred CCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCHH
Q ss_conf 04302566855300013698556655566642477775210147899985445444566126992003898864332011
Q 002545 409 AERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKM 488 (910)
Q Consensus 409 leRlN~~~~lSh~Rrv~rg~~~~~~K~t~~R~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is~~~~~~~~~~~~~~~ 488 (910)
|+|+||+|+|||+||+|+ ++++++|+++||+|||||||||||+|||||++||||||||+||+|+++.+.+
T Consensus 483 ldr~n~ls~LSH~RRi~~-~~~r~~k~~~~R~LHpshwG~iCPiETPEG~~cGLVknLAl~a~Is~g~~~~--------- 552 (1224)
T 1twf_B 483 LNRYTYSSTLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPM--------- 552 (1224)
T ss_dssp CCCSSHHHHHHHHTEEEC-CC------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCH---------
T ss_pred ECCCCHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCHHHHHHHHCCCCCCCCHH---------
T ss_conf 111345666545440256-5243466666542467635244688998986314155577327556799879---------
Q ss_pred HHHHHHHHHHCCCEECCCCCCCCCCCCEEEEEECCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCC
Q ss_conf 68899999846981258754358999606999898999454495189999999998881688889984479998678998
Q 002545 489 RTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGA 568 (910)
Q Consensus 489 ~~~i~~~L~~lg~~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~~~~~~~lr~lk~~~~~~i~~~~ei~~v~~~~~~~ 568 (910)
+|.++|.++||+++. +......++.++|||||+|+|++ .+|..++..||.+||.+ .|+.+++|+++ ..
T Consensus 553 --pi~~~l~~~G~~~l~-e~~~~~~~~~~kVfvnG~~vG~~--~~p~~lv~~lr~lRR~g--~i~~evsiv~d-----~r 620 (1224)
T 1twf_B 553 --PIITFLSEWGMEPLE-DYVPHQSPDATRVFVNGVWHGVH--RNPARLMETLRTLRRKG--DINPEVSMIRD-----IR 620 (1224)
T ss_dssp --HHHHHHHHTTCEEGG-GCCGGGCTTCEEEEETTEEEEEE--SCHHHHHHHHHHHHHHT--SSCTTCEEEEE-----TT
T ss_pred --HHHHHHHHCCCCCEE-ECCCCCCCCCEEEEECCEEEEEE--CCHHHHHHHHHHHHHCC--CCCCEEEEEEE-----CC
T ss_conf --999999983996303-12665578855999999999996--88899999999887536--77870799996-----46
Q ss_pred CCCEEEECCCCCEECEEEEECCCC------C----------------------------------CCCCEEEECCCCEEE
Q ss_conf 880596549992000077505899------8----------------------------------887566647543053
Q 002545 569 YPGLYLFTSPPKFVRPVRNISLPS------E----------------------------------ESQNIELIGPFEQVF 608 (910)
Q Consensus 569 ~~~i~I~td~gR~~RPv~~~~~~~------~----------------------------------~~g~iE~id~~Eq~~ 608 (910)
.++++||||+||++|||++++++. . ..|.|||+|++||++
T Consensus 621 ~~ei~I~TD~GRv~RPl~vV~~~~~~~~~~l~l~k~hi~~L~~~~~~~~~~~~~~~~~~~w~~Lv~~G~iEyldaeEEe~ 700 (1224)
T 1twf_B 621 EKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEES 700 (1224)
T ss_dssp TTEEEEECCSCCEEEEEEEEECCCTTSSCEESCCHHHHHHHHHHHHCC---------CCCHHHHHHTTSEEEEEHHHHTT
T ss_pred CCEEEEECCCCEEEEEEEEECCCCCCCCCCCEECHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHCCCCCEEECCHHHHCC
T ss_conf 67179960586355467782478755545420129999986513222344322222235565732379379827666148
Q ss_pred EEEECCCCCCCCCC-------------------CCCCCEECCCCCCCCCCCEEECCCCCCCCCCCHHHHHHHCCCCCCCC
Q ss_conf 46423899999987-------------------88773001247876532022125489999840111110000123443
Q 002545 609 MEIRCPDGGDGGRR-------------------NAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGF 669 (910)
Q Consensus 609 ~~Ia~~~~~~~~~~-------------------~~~~~th~Ei~p~~ils~~asliPF~~hNqspRn~yq~~M~KQaig~ 669 (910)
++||++++++.... ....||||||||++|||++||+|||+||||||||||||||+|||||+
T Consensus 701 ~~Ia~~~~dl~~~~~~~~~~~~~~~~~R~~~~~~~~~~Th~EI~Ps~ILgV~ASlIPF~dHNqSpRn~yqs~M~kQA~g~ 780 (1224)
T 1twf_B 701 ILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGV 780 (1224)
T ss_dssp CCEESSGGGGCC---------CCCTTSCCCCCCCCSCCCEECSCGGGGSCTTGGGSSSGGGSCHHHHHHHHHHGGGBCBC
T ss_pred CEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCEEECCCCCCCCCCCCHHHHCCCCCCCCCCC
T ss_conf 57843650137223424555444443334687675120222568852221321146874345431333223443343565
Q ss_pred CEEEEEEECCCCEEECCCCCEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCCCCEEEEEEEEE
Q ss_conf 11389984157425527998105834640013864368984016899733688855325442000014761124999999
Q 002545 670 SVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTET 749 (910)
Q Consensus 670 ~~~n~~~R~d~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~ 749 (910)
+.+|+..|+|++.|+|+|||+|||+|+.++.++++|+|+|+||+||||||+||||||||||||+|++||+|++++|+++.
T Consensus 781 ~~~n~~~r~dt~~~~l~ypQkPlV~t~~~~~~~~~elp~G~N~iVAvm~y~GYN~EDAiIin~~sv~rg~~~s~~~~~y~ 860 (1224)
T 1twf_B 781 FLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYM 860 (1224)
T ss_dssp SCTTTTTCCCSEEEEESSCBCCSEECTTHHHHTTTTSCCCEEEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEE
T ss_pred CCCEEEEECCCCCCEEECCCCCEEECCCCCCCCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEEEEEEE
T ss_conf 32114442145541523582782775652001455577976479999613576640255621327754881589999999
Q ss_pred EEEECCCCCCCCCCEEECCCCC------CHHHHCCCCCCCCCCCCCEECCCCCEEEEECCCC--------------CCEE
Q ss_conf 9730247876765011005988------7021102699998554706659994998321689--------------9343
Q 002545 750 IDLSDDGNKVDRGQKLFRRNKD------AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT--------------NSWR 809 (910)
Q Consensus 750 ~~~~~~~~~~~~~~~~f~~~~~------~~~~~~~ld~dG~~~~G~~v~~gdil~~~~~~~~--------------~~~~ 809 (910)
++..... ....+.|++|+. .+..+++||+||||++|++|++||||+||++|+. .++.
T Consensus 861 ~~~~~~~---~~~~e~~~~P~~~~~~~~~~~~~~~LD~dGiv~~G~~V~~gDilvgK~~p~~~~~~~~~~~~~~~~~rd~ 937 (1224)
T 1twf_B 861 DQEKKYG---MSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDA 937 (1224)
T ss_dssp ECCCCSC---TTCCCEESCCCCSSSCBCCSSCGGGCCTTSBCCTTCEECTTCEEECEECCCC-------------CCBBC
T ss_pred EEEEECC---CCCEEEECCCCHHHCCCCCHHHHHHCCCCCCCCCCCEECCCCEEEEEECCCCCCCCCCCCCCCCCCCCEE
T ss_conf 9864078---8854675278802035755777764355874477527459998999965887664333445556765436
Q ss_pred EEEECCCCCEEEEEEEEEECCCCCCCEEEEEEEEEEECCCCCCCEECCCCCCCEEEEEECCCCCCCCCCCCCCCCEEECC
Q ss_conf 45506998569999999705799997089999922408976640002479823785320476768448999968297389
Q 002545 810 TNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINP 889 (910)
Q Consensus 810 ~~~~~~~e~g~v~~v~~~~~~~g~~~~~~~i~~r~~r~p~iGDKf~sRHGqKGv~s~~~~~~dmPf~~~~G~~pDiI~NP 889 (910)
|++++.+|.|+||+|.++.+++|. +.++|++|+.|.|+||||||||||||||||++||+|||||+ ++|++|||||||
T Consensus 938 s~~~~~~e~g~Vd~V~~~~~~~g~--~~vkV~ir~~R~p~iGDKfasRHGqKGvis~i~p~eDMPf~-~dG~~pDiIiNP 1014 (1224)
T 1twf_B 938 STPLRSTENGIVDQVLVTTNQDGL--KFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFT-AEGIVPDLIINP 1014 (1224)
T ss_dssp CEECCTTCCEEEEEEEEEECSSSC--EEEEEEEEEEECCCTTCEEECTTSCEEEEEEEECTTTSCEE-TTSCCCSEEECG
T ss_pred EEEEECCCCEEEEEEEEEECCCCC--EEEEEEEEECCCCCCHHHHHHHCCCCCEEEEECCCCCCCCC-CCCCCCCEEECC
T ss_conf 899408987499778998517997--89999998337887446543320686403013140259967-889776388688
Q ss_pred CCCCCCCCHHHHHHHHHCCC
Q ss_conf 98665564889998730246
Q 002545 890 HAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 890 h~~PSRMtiGql~E~~~gK~ 909 (910)
|||||||||||++|+++||+
T Consensus 1015 hg~PSRMtiGqllE~~lgka 1034 (1224)
T 1twf_B 1015 HAIPSRMTVAHLIECLLSKV 1034 (1224)
T ss_dssp GGSTTTTCHHHHHHHHHHHH
T ss_pred CCCCCCCCCCHHHHHHHHHH
T ss_conf 75766654210578876589
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=1657.20 Aligned_cols=825 Identities=26% Similarity=0.412 Sum_probs=706.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHH---------------------------------------HHHHHCCCEEEEEE
Q ss_conf 437033499999979999997699999---------------------------------------99997299043689
Q 002545 9 FEPLRELVRHHIESFDYMLDEGLSEMF---------------------------------------DHCRQAKISYTGKL 49 (910)
Q Consensus 9 ~~~~~~lv~~hi~SFn~Fi~~gl~~ii---------------------------------------~eaR~r~~TYs~~l 49 (910)
+...++||+|||||||||+++||++++ +|||+|++||+|||
T Consensus 20 ~f~~~gLV~~qidSfn~Fl~~gL~~i~~~~~pI~~~~~~~~l~f~~~~l~~P~~~e~d~~~~~l~P~EcR~r~~TYsapl 99 (1131)
T 4ayb_B 20 YFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEIPGLKVRLGKIRIGKPRVRESDRGEREISPMEARLRNLTYAAPL 99 (1131)
T ss_dssp HHHHSCSSCHHHHHHHHHHHTTTHHHHHHHCSCCCSSTTCEEEEEEEEECCSEEEETTTEEEECCHHHHHHHTCCCEEEE
T ss_pred HHCCCCCCHHHHHHHHHHHHHCHHHHHHHCCCEEECCCCEEEEEEEEEEECCEEECCCCCCCCCCHHHHHHCCCCCCCEE
T ss_conf 86889972899999999998687999983597563589889999889990783634888767459999970499736348
Q ss_pred EEEEEEEEECCCCCEEEEEEEECCCCEEECCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCEEEEEEEEEECCCCCEE
Q ss_conf 99999999539996255376540451030579744899995778721332125894899939400999998404994089
Q 002545 50 MADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMS 129 (910)
Q Consensus 50 ~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~~i~~~~N~~~~ 129 (910)
+|++.+..+ +.+++.++|++|+|||||+|++|||++++++++++.||||+||||||||||+||||++|+.+++|.++.
T Consensus 100 ~v~v~~~~~--~~~~~~~~v~lG~iPiM~~S~~C~L~~~s~~el~~~gEc~~D~GGyFIING~ERVIv~Q~~~spn~~~~ 177 (1131)
T 4ayb_B 100 WLTMIPVEN--NIEAEPEEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLV 177 (1131)
T ss_dssp EEEEEEEET--TEECCCEEEEEEEEECCTTSTTSGGGGCCHHHHHHHTCCTTCCCCCEEETTEEEEECEEEEECCSSCEE
T ss_pred EEEEEEEEC--CCEEEEEEEEEEECCEEECCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCEEEEEEEEECCCCCEEEE
T ss_conf 999999999--908899999998797896888544779898999862888679973898698898999864267986999
Q ss_pred EEECCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEEEECCEEEEEEEEECCCCCCCHHHHHHHCCCCCHHHHHHHHCCCC
Q ss_conf 97125447898510238999966519982399999982890899999606433310977998614798889998710122
Q 002545 130 MVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCY 209 (910)
Q Consensus 130 ~~r~~~~~~~~~~t~~~v~ir~~~~~~~~~~~~l~~~~~g~~~l~~~~~k~~~~IPi~illkALg~~sD~eI~~~I~~~~ 209 (910)
... +++..++..+..+++ +..+ +..+.+++++++.++++++..+. +||+++||||||..||+||++.++.
T Consensus 178 ~~~----~~~~~~~~~a~ii~~-~~~~-~~~~~i~~~~~~~~~v~~~~~~~--~iPi~illrALG~~sD~eI~~~i~~-- 247 (1131)
T 4ayb_B 178 DTG----KTGSNITHTAKIISS-TAGY-RVPVTIERLKDGTFHVSFPAVPG--KIPFVILMRALGILTDRDIVYAVSL-- 247 (1131)
T ss_dssp EEC----CTTCSEEEEEECEEE-CSSC-EEECCEEEETTTCCEECCSSSCC--CEEHHHHHHHHTCCSHHHHHHHHCS--
T ss_pred EEC----CCCCCEEEEEEEEEC-CCCC-EEEEEEEEECCCEEEEEECCCCC--EEEHHHHHHHHCCCCHHHHHHHHCC--
T ss_conf 841----689917899999888-8875-23499999379879999917475--6649999998587634657878513--
Q ss_pred CCHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCC---
Q ss_conf 10010002788981167899999999984023129899999850346544688886179999999976743579998---
Q 002545 210 DEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDN--- 286 (910)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~i~t~~~al~yig~~f~~~~~~~~~~~~~~~g~~~L~~~ll~Hi~~~--- 286 (910)
+. .+.+.+...+++ ...+.++++|+.|++++++.. .+..+..+.++.+|++++|||++..
T Consensus 248 ~~------------~~~~~l~~~~~~--~~~i~~~~~al~~i~~r~~~~---~~~~~~~~~a~~il~~~~l~hl~~~~~~ 310 (1131)
T 4ayb_B 248 DP------------EIQNELFPSLEQ--ASSIANVDDALDFIGSRVAIG---QKRENRIEKAQQIIDKYFLPHLGTSADD 310 (1131)
T ss_dssp CH------------HHHTTTHHHHHH--HTTTCCSSHHHHHHHHHHHCS---SCHHHHHHHHHHHHHTTSSTTSCSSTTS
T ss_pred CH------------HHHHHHHHHHHH--HCCCCCHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 08------------889998877987--414123899998776665328---8874157899999998620124543320
Q ss_pred -CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf -4328999999999986107998889943112607745303069999999999999999999998862698413410688
Q 002545 287 -NDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLAN 365 (910)
Q Consensus 287 -~~K~~~L~~Mv~kLl~~~~g~~~~Dd~D~~~nkrv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~ 365 (910)
..|+.+|++|+++|+.+..|.+.+||+|||+||||+++|+||+++||..|.++.+.++..+.+...+ .+.+.
T Consensus 311 ~~~K~~~L~~mi~~Ll~l~~g~~~~DD~Dhl~NkRvr~vGeLl~~~fr~~l~r~~r~ir~~~~~~~~~-~~~~~------ 383 (1131)
T 4ayb_B 311 RRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVR-GRKLA------ 383 (1131)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTSSCCCCTTSGGGEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHSTT-CSCCC------
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHCCEECCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHC-CCCCC------
T ss_conf 36778889999999999972999988885442211041468999999999998877766412210100-23114------
Q ss_pred HHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99987218972428999867414676644455444345418980430256685530001369855665556664247777
Q 002545 366 IKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPES 445 (910)
Q Consensus 366 ~~~~~~~~~~~~It~~l~~~lsTGnw~~~~~~~~~q~sGvsqvleRlN~~~~lSh~Rrv~rg~~~~~~K~t~~R~Lhps~ 445 (910)
++.++ +++.||+++++|||||||.. +++|+||+++|+||+|+|||+||||+| +++++|+++||+|||||
T Consensus 384 ~~~li---~~~~it~~i~~~~aTGn~~~-------~~sglSQ~mdq~NpLs~lsH~RRlsag-l~rera~~evRdlHpSh 452 (1131)
T 4ayb_B 384 LKALV---RPDIVTERIRHALATGNWVG-------GRTGVSQLLDRTNWLSMLSHLRRVISS-LARGQPNFEARDLHGTQ 452 (1131)
T ss_dssp HHHHC---CTHHHHHHHHHHHHTTBCSS-------SCBCCEEECCCSSHHHHHHHHTEEEEC-SCSSSCCHHHHSCCGGG
T ss_pred HHHHC---CCCHHHHHHHHHHHHCCCCC-------CCCCEEEEECCCCHHHHHHHHHHHCCC-CCCCCCCCCCCCCCHHH
T ss_conf 46534---78605565677774145556-------877268981467788987756631577-53356666440267756
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHCCCEECCCCC---C-----CCCCCCEE
Q ss_conf 521014789998544544456612699200389886433201168899999846981258754---3-----58999606
Q 002545 446 WGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKL---V-----KSGPPAVL 517 (910)
Q Consensus 446 wG~iCPveTPEG~~cGLvk~LA~~a~Is~~~~~~~~~~~~~~~~~~i~~~L~~lg~~~~~~~~---~-----~~~~~~~~ 517 (910)
||||||+|||||+||||+||||++|+|+.+.+.. .+.+.+.++|+.++.... . ........
T Consensus 453 yGriCPIETPEG~niGLI~sLA~~a~I~~g~~e~-----------~i~~~l~~~g~~~~e~~~~~~~~~~~~~~~~~~~~ 521 (1131)
T 4ayb_B 453 WGRMCPFETPEGPNSGLVKNLALMAQIAVGINEK-----------IVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWS 521 (1131)
T ss_dssp TTTBCSSCCCSSTTBTTEEEBBSSCEECCCCCHH-----------HHHHHHHHTTCEEHHHHHHTTTTC-----CCCCCC
T ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCC-----------CEEEEHHHCCCEEEEEEEHHHCCCCCCCCHHHHHC
T ss_conf 6430256599986533446620467882488873-----------33331364493450323002123533333012100
Q ss_pred EEEECCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCEEEECCCCCEECEEEEECCCCC----
Q ss_conf 9998989994544951899999999988816888899844799986789988805965499920000775058998----
Q 002545 518 SVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE---- 593 (910)
Q Consensus 518 ~VflnG~~iG~~~~~~~~~~~~~lr~lk~~~~~~i~~~~ei~~v~~~~~~~~~~i~I~td~gR~~RPv~~~~~~~~---- 593 (910)
+||+||+|+|++ .++..++..+|.+|+.+ .++..++|+++.. ...+++++++|+||++|||..++++..
T Consensus 522 ~v~lng~~vg~~--~~~~~~~~~~~~~~~~~--~i~~~vsi~~~~~---~~~~~~~i~~d~~r~~rpv~~~~~~~p~v~~ 594 (1131)
T 4ayb_B 522 KVILNGRLVGYY--RDGEELAKKIRERRRKG--EISDEVNVGHIVT---DFINEVHVNCDSGRVRRPLIIVSNGNPLVTR 594 (1131)
T ss_dssp EEEETTEEEEEC--SCHHHHHHHHHHHHHHT--SSCTTCEEEEECT---TTCCEEEEECCTTCEEEEEEEBSSSSBSCCH
T ss_pred CEEECCCEEEEE--CCCHHHHHHHHHHHCCC--CCCCEEEEEECCC---CCCCEEEEECCCCCCCCCEEEEECCCCCCCH
T ss_conf 046437157885--04331022266451047--6585688741125---5433046653786402656886346642358
Q ss_pred -----------------CCCCEEEECCCCEEEEEEECCCCCCCCCCCCCCCEECCCCCCCCCCCEEECCCCCCCCCCCHH
Q ss_conf -----------------887566647543053464238999999878877300124787653202212548999984011
Q 002545 594 -----------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRN 656 (910)
Q Consensus 594 -----------------~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~th~Ei~p~~ils~~asliPF~~hNqspRn 656 (910)
..|.+||+|++||+++.||+.++++... +||+||+|+.++|++|++|||++|||||||
T Consensus 595 ~~~~~~~~g~~~~~~~~~~g~veyvd~~e~~~~~ia~~~~~~~~~-----~th~ei~p~~il~v~a~lipf~~~NqspRn 669 (1131)
T 4ayb_B 595 EDIEKLDSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTPE-----HTHLEIWSPAILGITASIIPYPEHNQSPRN 669 (1131)
T ss_dssp HHHHHHHTTTCCHHHHHHTTSEEEEEHHHHTTCCEESSGGGCCTT-----CSEECSCGGGGSBTTGGGCSSGGGSCHHHH
T ss_pred HHHHHHHCCCHHHHHHHHCCCEEEEECCCCCEEEEEEECCCCCCC-----CCCEEECCCCCCCCCCCEECCCCCCCCCHH
T ss_conf 899998648704777862783244201345202798633434543-----331364144223334655433245766310
Q ss_pred HHHHHCCCCCCCCCEEEEEEECCCCEEECCCCCEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEECCCCC
Q ss_conf 11100001234431138998415742552799810583464001386436898401689973368885532544200001
Q 002545 657 MYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVD 736 (910)
Q Consensus 657 ~yq~~M~KQaig~~~~n~~~R~d~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~ 736 (910)
+|||||+|||||++.+|++.|+|++.|+|.|||+|+|+|+.++.++++++|+|+|++||||||+||||||||||||++++
T Consensus 670 ~yq~~m~KQa~G~~~~~~~~r~D~~~~~l~ypQ~PlV~t~~~~~~~~~e~p~G~N~lVA~m~w~GYN~EDAIIine~~v~ 749 (1131)
T 4ayb_B 670 TYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVE 749 (1131)
T ss_dssp HHHHHHGGGBCSCCCGGGGTCCCSEEEEESSCCCCSSBCHHHHHHTCTTSCCSEEEEEEECCCSSCCCTTCEEEEHHHHT
T ss_pred EECCCCCCCCCCCEEECCEEEECCCCCEEECCCCCCCCCCHHHHHCCCCCCCCEEEEEEEECCCCCCHHHHHHHHCCHHH
T ss_conf 22255550368831101305631444366528755201121222066778874458999974678567776655030332
Q ss_pred CCCCEEEEEEEEEEEEECCCCCCCCCCEEEC--CCCC----CHHHHCCCCCCCCCCCCCEECCCCCEEEEECCCC-----
Q ss_conf 4761124999999973024787676501100--5988----7021102699998554706659994998321689-----
Q 002545 737 RGMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKD----AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT----- 805 (910)
Q Consensus 737 rG~~~~~~~~~~~~~~~~~~~~~~~~~~~f~--~~~~----~~~~~~~ld~dG~~~~G~~v~~gdil~~~~~~~~----- 805 (910)
||+|++++|+.|.++..+.+. +..+.+. .|+. .+..+++||+|||+++|++|++||||+||++|+.
T Consensus 750 rg~ftSihi~~y~~e~r~~~~---g~~e~it~~~p~v~~~~~~~~~~~LDe~Gii~iGa~V~~gDilvGKvtP~~~~~~~ 826 (1131)
T 4ayb_B 750 RGMYRSTFFRLYSTEEVKYPG---GQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEF 826 (1131)
T ss_dssp TTTTCEEEEEEEEEECCCCTT---SCCCCCCCCCSSCSSCCCGGGGTTCCTTSBCCTTCEECTTCEEECCCCCCC-----
T ss_pred CCCCEEEEEEEEEEEEEECCC---CCCEEEECCCCCCCCCCHHHHHHCCCCCCCCCCCCEECCCCEEEEEECCCCCHHHH
T ss_conf 365304578889999996489---98338704775321100377750578666656884744899899985587512234
Q ss_pred --------CCEEEEEECCCCCEEEEEEEEEECCCCCCCEEEEEEEEEEECCCCCCCEECCCCCCCEEEEEECCCCCCCCC
Q ss_conf --------934345506998569999999705799997089999922408976640002479823785320476768448
Q 002545 806 --------NSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSG 877 (910)
Q Consensus 806 --------~~~~~~~~~~~e~g~v~~v~~~~~~~g~~~~~~~i~~r~~r~p~iGDKf~sRHGqKGv~s~~~~~~dmPf~~ 877 (910)
.++.|+++++++.|+||.|.++.+.+|. +.++|++|+.|.|+||||||||||||||||+|||+|||||+
T Consensus 827 ~~~~~~~~~~d~sl~~~~g~~g~Vd~v~~~~~~~~~--~~vkV~i~~~R~~~vGDK~agRHGnKGvvs~i~p~eDMPf~- 903 (1131)
T 4ayb_B 827 KELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGN--KLVKVRVRDLRIPSIGDKFASRHGQKGVIGMLIPQVDMPYT- 903 (1131)
T ss_dssp ------CCCCCCCEECCTTCCEEEEEEEEEECSSSC--EEEEEEEEEEECCCTTCEEEETTSCEEEEEEEECTTTSEEE-
T ss_pred HHCCCCEEEEEEEEECCCCCCEEEEEEEEEECCCCC--EEEEEEEECCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCC-
T ss_conf 303762000465587248973589999996615785--37999983244676566025466664244301352129948-
Q ss_pred CCCCCCCEEECCCCCCCCCCHHHHHHHHHCCC
Q ss_conf 99996829738998665564889998730246
Q 002545 878 VTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 878 ~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
+||++||||+|||||||||||||++|+++||+
T Consensus 904 ~dG~~~DiilNP~gvPSRMniGqilE~~~gk~ 935 (1131)
T 4ayb_B 904 VKGVVPDVILNPHALPSRMTLGQIMEGIAGKY 935 (1131)
T ss_dssp TTSCCCSEECCTTSSTTTTCHHHHHHHHHHHH
T ss_pred CCCCCCCEEECCCCCCCCCCHHHHHHHHHHHH
T ss_conf 89987508889987866673999999998899
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=1402.82 Aligned_cols=735 Identities=19% Similarity=0.263 Sum_probs=574.3
Q ss_pred CCCCCHHHHHHHHHHHHHHH----------HHHHHHHH--------------------------------HHHHHCCCEE
Q ss_conf 84370334999999799999----------97699999--------------------------------9999729904
Q 002545 8 DFEPLRELVRHHIESFDYML----------DEGLSEMF--------------------------------DHCRQAKISY 45 (910)
Q Consensus 8 ~~~~~~~lv~~hi~SFn~Fi----------~~gl~~ii--------------------------------~eaR~r~~TY 45 (910)
.+..+++|+++|++|||||+ ++||++++ +|||+|++||
T Consensus 11 ~~~~~p~Lv~~QidSFn~Fl~~~~~~~~~~~~GL~~i~~~~~pI~~~~~~~~~~~l~f~~~~l~~P~~~p~Ecr~r~lTY 90 (1119)
T 2a6h_C 11 EVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTY 90 (1119)
T ss_dssp CCSCCCCTTHHHHHHHHHHSCTTSCTTSSCCCHHHHHHHHHCSEEECCSSSCCEEEEECCCCBCCCSSCHHHHHHTTCCC
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCEECCCCCCCEEEEEEEEEEECCCCCCHHHHHHCCCCC
T ss_conf 12468578999999999997067764432110179999866977514778980899999899768989999998529943
Q ss_pred EEEEEEEEEEEEECCCCCEEEEEEEECCCCEEECCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCEEEEEEEEEECCC
Q ss_conf 36899999999953999625537654045103057974489999577872133212589489993940099999840499
Q 002545 46 TGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQN 125 (910)
Q Consensus 46 s~~l~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~~i~~~~N 125 (910)
+|||+|++.+..+ .+++++.++|++|+||+|+. ||||||||+||||++|+.+++|
T Consensus 91 sapL~V~v~l~~~-~~~~ik~~~V~iG~iPiMt~------------------------gGyFIING~ERVIVsQ~~rspg 145 (1119)
T 2a6h_C 91 QAPLYARLQLIHK-DTGLIKEDEVFLGHIPLMTE------------------------DGSFIINGADRVIVSQIHRSPG 145 (1119)
T ss_dssp EEEBCCCEEECCS-SSCCEECCCCCCCEEECCCT------------------------TSCCCSSSSCEEECEEEEECSC
T ss_pred CCEEEEEEEEEEC-CCCEEEEEEEEECCCCEECC------------------------CCEEEEECEEEEEEEEEECCCC
T ss_conf 6217999999987-87325545889507976888------------------------8679994818999999804895
Q ss_pred CCEEEEECCCCCCC-CCCEEEEEEEEEEECCCCCEEEEEEEEECCEEEEEEEEECCCCCCCHHHHHHHCCCCCHHHHHHH
Q ss_conf 40899712544789-85102389999665199823999999828908999996064333109779986147988899987
Q 002545 126 YPMSMVRSSFRDRR-EGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNH 204 (910)
Q Consensus 126 ~~~~~~r~~~~~~~-~~~t~~~v~ir~~~~~~~~~~~~l~~~~~g~~~l~~~~~k~~~~IPi~illkALg~~sD~eI~~~ 204 (910)
.++ +..+.+++ ..|+...+..|| .|+.+.+++++.+|+++.. .+||+++||||||. ||+||++.
T Consensus 146 v~~---~~~~~~~g~~~ysa~ii~~rg-------s~l~~~~d~~~~i~vri~r----~kIPi~ilLrALG~-sD~eIl~~ 210 (1119)
T 2a6h_C 146 VYF---TPDPARPGRYIASIIPLPKRG-------PWIDLEVEPNGVVSMKVNK----RKFPLVLLLRVLGY-DQETLARE 210 (1119)
T ss_dssp EEE---ECCSSCSSCCEEEECCCSSSS-------CCEEEEEETTTEEEEESSS----SEECHHHHHHHHTC-CHHHHHHH
T ss_pred EEE---EEECCCCCCEEEEEEEEECCC-------CEEEEEECCCCEEEEEEEC----CCEEHHHHHHHHCC-CHHHHHHH
T ss_conf 999---861367896579999983268-------5699998579879999927----60009999988789-99999999
Q ss_pred HCCCCCCHH-HCCCCCCCCH-HHHHHHHHHHHHHHHC---CCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 101221001-0002788981-1678999999999840---2312989999985034654468888617999999997674
Q 002545 205 LTCCYDEKY-KKEKGAVGSP-LVSERVKIILAEVQDL---SLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYI 279 (910)
Q Consensus 205 I~~~~~~~~-~~~~~~~~~~-~~~~~~~~~L~~~~~~---~i~t~~~al~yig~~f~~~~~~~~~~~~~~~g~~~L~~~l 279 (910)
++. +... .++. .+. ...+..+++++.+... ...+.+.|+++|++.| +.++++++..+|+..+++++
T Consensus 211 ~~~--~~~~~~tl~---~d~~~~~~~~eAl~~i~~~lr~g~~~~~e~a~~~l~~~f----f~~~rydl~~vGr~~ln~kl 281 (1119)
T 2a6h_C 211 LGA--YGELVQGLM---DESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLI----ADPRRYDLGEAGRYKAEEKL 281 (1119)
T ss_dssp HHS--SCTTHHHHS---SCHHHHTCHHHHHHHHHHHSSSCCCSCCSSHHHHHTSSS----SSSCCSCTTTSSHHHHHTTS
T ss_pred HCC--CHHHHHHHH---HHHCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH----CCCCCCCCHHCCHHHHHHHH
T ss_conf 746--899999998---532246799999999999745789984999999998760----78534430114512221220
Q ss_pred CCCCC------C--CCCHHHHHHHHHHHHHHHCCCCC--CCCCCCCCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 35799------9--84328999999999986107998--88994311260774530306999999999999999999999
Q 002545 280 FVHLN------D--NNDKFNLLIFMLQKLFSLVDHTS--VSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQD 349 (910)
Q Consensus 280 l~Hi~------~--~~~K~~~L~~Mv~kLl~~~~g~~--~~Dd~D~~~nkrv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~ 349 (910)
-...+ . ...+..++++|+++|+.+..|.+ .+||+|||+||||+++|+||+.+|+..|+++.+.++..+++
T Consensus 282 ~l~~~~~~~~~~~~~~l~~~di~~mi~~Ll~l~~G~~~~~~DD~DhlgNkRv~~~GeLl~~~fr~~l~r~~~~i~~~~~~ 361 (1119)
T 2a6h_C 282 GIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERMLM 361 (1119)
T ss_dssp CSCCSTTTTCCCSSSCCCCTTHHHHHHHHHHHHTSCSSCCCCCTTSTTTEEEECHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 56875222344332433299999999999986348877777674411134753456999999999999999999987523
Q ss_pred HHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHCCCC---C
Q ss_conf 8862698413410688999872189724289998674146766444554443454189804302566855300013---6
Q 002545 350 EIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVH---R 426 (910)
Q Consensus 350 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~l~~~lsTGnw~~~~~~~~~q~sGvsqvleRlN~~~~lSh~Rrv~---r 426 (910)
. . ...+.. +.++ +++.||+++++||+|||| ||+|+|+||+|+|||+||++ |
T Consensus 362 ~--~-~~~~~~------~~~i---~~~~It~~lk~ff~tg~l--------------SQ~Ldq~N~ls~LsH~RRisslgp 415 (1119)
T 2a6h_C 362 G--S-EDSLTP------AKLV---NSRPLEAAIREFFSRSQL--------------SQFKDETNPLSSLRHKRRISALGP 415 (1119)
T ss_dssp S--C-SSCCSS------TTTC---CSHHHHHHHHHHHHTCSS--------------EEECCCSSTHHHHHHHHEEESSSS
T ss_pred H--C-CCCCCH------HHHH---CCCHHHHHHHHHHHCCCC--------------CCCCCCCCHHHHHHHHHEECCCCC
T ss_conf 1--0-011145------7751---462168999998603674--------------010255206766432020034587
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHCCCEECCC
Q ss_conf 98556655566642477775210147899985445444566126992003898864332011688999998469812587
Q 002545 427 GASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLP 506 (910)
Q Consensus 427 g~~~~~~K~t~~R~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is~~~~~~~~~~~~~~~~~~i~~~L~~lg~~~~~~ 506 (910)
|++++++|+++||+|||||||||||+|||||++||||||||++|+|+. +|+... +
T Consensus 416 ggl~re~k~~~vRdlHpShwGriCPiETPEG~ncGLVknLAl~a~I~~------------------------~G~~e~-p 470 (1119)
T 2a6h_C 416 GGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDE------------------------LGFIRT-P 470 (1119)
T ss_dssp SSSCCSSCCHHHHSCCGGGTTTBCSSCSCSSSSCSSEEEBCSSCEECS------------------------SSCEEE-E
T ss_pred CCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCHHHHHHHEEECC------------------------CCCCCC-C
T ss_conf 752344656754626774576527874889975311543431215423------------------------676467-7
Q ss_pred CCCCCCCCCEEEEEECCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCEEEECCCCCEECEEE
Q ss_conf 54358999606999898999454495189999999998881688889984479998678998880596549992000077
Q 002545 507 KLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVR 586 (910)
Q Consensus 507 ~~~~~~~~~~~~VflnG~~iG~~~~~~~~~~~~~lr~lk~~~~~~i~~~~ei~~v~~~~~~~~~~i~I~td~gR~~RPv~ 586 (910)
+.+++||+|.+.+..-.+ ..... + -| . ...+.+ |.||++||+.
T Consensus 471 ----------~~~V~nG~v~~~i~yl~a---------~ee~~-~------~i--~-------~~~~~l--~~gr~~r~~i 513 (1119)
T 2a6h_C 471 ----------YRRVVGGVVTDEVVYMTA---------TEEDR-Y------TI--A-------QANTPL--EGNRIAAERV 513 (1119)
T ss_dssp ----------EEEEETTEEEEEEEEECH---------HHHHH-S------CE--E-------CTTSCB--SSSBBCCSSE
T ss_pred ----------CEEEECCEEEEEEEEECH---------HCCCC-E------EE--E-------CCCEEE--CCCCCCCCCE
T ss_conf ----------589999989511577671---------00666-6------99--4-------175621--5783036725
Q ss_pred EECCCCCCCCCEEEECCCCEEEEEEECCCCCCCCCCCCCCCEECCCCCCCCCCCEEECCCCCCCCCCCHHHHHHHCCCCC
Q ss_conf 50589988875666475430534642389999998788773001247876532022125489999840111110000123
Q 002545 587 NISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQT 666 (910)
Q Consensus 587 ~~~~~~~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~th~Ei~p~~ils~~asliPF~~hNqspRn~yq~~M~KQa 666 (910)
.++.. .| + +.+.+++ +|||||||+++||++||+|||+||||||||||||||+|||
T Consensus 514 ~~r~~------~e--------~--~~~~~~~---------~~~~ei~P~~ilsv~aslIPF~ehn~s~R~lmgsnM~kQA 568 (1119)
T 2a6h_C 514 VARRK------GE--------P--VIVSPEE---------VEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQA 568 (1119)
T ss_dssp EEESS------SS--------E--EEECTTT---------CCEEECCTTTTSCHHHHTCTTGGGBCHHHHHHHHHHHTTB
T ss_pred EEEEC------CC--------E--EEECHHH---------EEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 67741------63--------0--5516558---------6999842543134201257874457776422221101022
Q ss_pred CCCCEE-----------------------------------EEEEECC---CCEEEC----------CCCCEEEEECCCC
Q ss_conf 443113-----------------------------------8998415---742552----------7998105834640
Q 002545 667 MGFSVQ-----------------------------------ALKFRAD---QKLYHL----------QTPQTPIVRTNTY 698 (910)
Q Consensus 667 ig~~~~-----------------------------------n~~~R~d---~~~y~L----------~~pQ~Plv~t~~~ 698 (910)
||+... ++..|+| ++.|.| .|||+|+|+++.+
T Consensus 569 v~l~~~~~p~vgTg~e~~~a~ds~~~~~a~~~G~v~~vd~~~i~ir~~~~~~~~y~L~~~~rsnq~t~~~QkPiV~~g~~ 648 (1119)
T 2a6h_C 569 VPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQR 648 (1119)
T ss_dssp CCBSSCCCCSEECSCHHHHHHHTTCSEECSSSEEEEEECSSBEEEEETTTEEECCBCCCSEECTTSCEECCEECCCSSCC
T ss_pred CCCCCCCCCEEECCCCCEEEECCCCEEEECCCCEEEEECCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCEEEECCE
T ss_conf 33345679844436552013546762686358789983284699981688612677402324361003650346720753
Q ss_pred CC----------CCCCCCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCCCCEEEEEEEEEEEEECCCCCCCCCCEEE--
Q ss_conf 01----------386436898401689973368885532544200001476112499999997302478767650110--
Q 002545 699 TK----------YGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLF-- 766 (910)
Q Consensus 699 ~~----------~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~f-- 766 (910)
.. ..++|+|+|+|++||||||+||||||||||||++++||+|++.+++.+.++..+.+. ..+.+
T Consensus 649 v~~g~~ladg~~~~~gel~lG~N~lVA~m~~~GYN~EDAiiine~~v~rg~~tSihi~~~e~~~r~~~~----g~eeit~ 724 (1119)
T 2a6h_C 649 VRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKL----GPERITR 724 (1119)
T ss_dssp BCTTCEEEECTTBSSSSBCCSEEEEEECSCCSSTTSSSEEEEETHHHHTTCSEEEEEEEEEEEEECCTT----CCCBCCS
T ss_pred EECCCEECCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCEEEEEEEEEEEEEECCC----CCEEEEC
T ss_conf 101423214533578756686447999952567761025563320775498458999998766441678----8524312
Q ss_pred CCCCCCHHHHCCCCCCCCCCCCCEECCCCCEEEEECCCC---------------------CCEEEEEECCCCCEEEEEEE
Q ss_conf 059887021102699998554706659994998321689---------------------93434550699856999999
Q 002545 767 RRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT---------------------NSWRTNSRKGSESVFVDYVA 825 (910)
Q Consensus 767 ~~~~~~~~~~~~ld~dG~~~~G~~v~~gdil~~~~~~~~---------------------~~~~~~~~~~~e~g~v~~v~ 825 (910)
..|+..+..+++||+||||++|++|++||||+||++|+. .++.|+++++++.|+|++|.
T Consensus 725 ~ip~~~~~~~~~LD~dGiv~iG~~V~~gDiLvgK~tP~~~~~~~~ee~ll~aifg~k~~~~rd~Sl~~~~~e~G~V~~V~ 804 (1119)
T 2a6h_C 725 DIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTV 804 (1119)
T ss_dssp CCSSSCSGGGSSCCSSSBCCTTCBCCTTSEEECCEEESSSSSCCHHHHHHHHHHHSCCCCEEECCEECCSSCCCEEEEEE
T ss_pred CCCCCCHHHHHCCCCCCCCCCCCEECCCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCCEEEEEEE
T ss_conf 58886535553348870668878987999899996577656678255445545313466431103882587637999999
Q ss_pred EEECCC-CCC-----CEEEEEEEEEEECCCCCCCEECCCCCCCEEEEEECCCCCCCCCCCCCCCCEEECCCCCCCCCCHH
Q ss_conf 970579-999-----70899999224089766400024798237853204767684489999682973899866556488
Q 002545 826 VDMKNS-KNL-----PQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIA 899 (910)
Q Consensus 826 ~~~~~~-g~~-----~~~~~i~~r~~r~p~iGDKf~sRHGqKGv~s~~~~~~dmPf~~~~G~~pDiI~NPh~~PSRMtiG 899 (910)
++.+++ |+. .+.|+|++|+.|+|+||||||||||||||||++||+|||||+ +||++||||+||||||||||||
T Consensus 805 ~~~~~~~g~~l~~~~~~~vkV~i~~~R~~~vGDKfasRHGqKGVis~i~p~eDMPf~-~dG~~pDiIlNPhgvPSRMtiG 883 (1119)
T 2a6h_C 805 RLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHL-PDGTPVDVILNPLGVPSRMNLG 883 (1119)
T ss_dssp EECSSCSSCCCCTTEEEEEEEEEEEEEECCTTCEEECTTSCEEEEEEEECTTTSCBC-SSSCBCSEECCSTTTTTTTBTH
T ss_pred EECCCCCCCCCCCCCCEEEEEEECCCCCCCCCCHHHHCCCCCCEEEEEECCCCCCCC-CCCCCCCEEECCCCCCCCCCHH
T ss_conf 982688886557886359999974348766385210014787458765056777666-6798766896788685323223
Q ss_pred HHHHHHHCCC
Q ss_conf 9998730246
Q 002545 900 MLLESVAAKE 909 (910)
Q Consensus 900 ql~E~~~gK~ 909 (910)
|++|+++||+
T Consensus 884 qllE~~lG~a 893 (1119)
T 2a6h_C 884 QILETHLGLA 893 (1119)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
T ss_conf 5567775467
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=1238.83 Aligned_cols=749 Identities=19% Similarity=0.269 Sum_probs=587.9
Q ss_pred CCCCHHHHHHHHHHHHHHHH------HHHHHHH-----------------------------HHHHHCCCEEEEEEEEEE
Q ss_conf 43703349999997999999------7699999-----------------------------999972990436899999
Q 002545 9 FEPLRELVRHHIESFDYMLD------EGLSEMF-----------------------------DHCRQAKISYTGKLMADV 53 (910)
Q Consensus 9 ~~~~~~lv~~hi~SFn~Fi~------~gl~~ii-----------------------------~eaR~r~~TYs~~l~v~i 53 (910)
...+++|+++|++||++|++ +||++++ .||++|++||++||+|++
T Consensus 21 ~~~~P~Ll~iQ~~Sf~~Fl~~~~r~~~GL~evf~~~fPI~d~~~~~~Lef~~y~l~~Pk~~~~Ec~~r~lTYsapL~v~~ 100 (1342)
T 3lu0_C 21 VLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKL 100 (1342)
T ss_dssp SSCCCCGGGTTHHHHHHHSCSSSCSCSTTHHHHTTTSSCEETTTTEECCEEEECCCCCSCCSSTTTSSCCCCCCCCBEEE
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCEECCCCCEEEEEEEEEECCCCCCHHHHHHCCCCCCCCEEEEE
T ss_conf 77899889999999999973886412139999986398787899789998667827988999999961897664269999
Q ss_pred EEEEECC------CCCEEEEEEEECCCCEEECCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCEEEEEEEEEECCCCC
Q ss_conf 9999539------9962553765404510305797448999957787213321258948999394009999984049940
Q 002545 54 EFQYLDA------GSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYP 127 (910)
Q Consensus 54 ~~~~~~~------~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~~i~~~~N~~ 127 (910)
.+...+. .+++++++|++|+||+|+. +|||||||+||||++|++++|+..
T Consensus 101 rL~~~~~d~~~~~~~eikeq~Vy~GdiPLMT~------------------------~GtFIING~ERVIVsQl~RSPGVy 156 (1342)
T 3lu0_C 101 RLVIYEREAPEGTVKDIKEQEVYMGEIPLMTD------------------------NGTFVINGTERVIVSQLHRSPGVF 156 (1342)
T ss_dssp CCEECCCSSCCCCCCCCCBCCCBCCCCCCCCS------------------------SSCEESSSSEEECCEEEECCSSCC
T ss_pred EEEEECCCCCCCCCCCEEEEEEEEECCCEECC------------------------CCEEEECCCEEEEEEEECCCCCEE
T ss_conf 99981365555665641799999832730878------------------------867998583589998421267516
Q ss_pred EEEEECCCCC-CCCCCEEEEEEEEEEECCCCCEEEEEEEEECCEEEEEEEEECCCCCCCHHHHHHHCCCCCHHHHHHHHC
Q ss_conf 8997125447-898510238999966519982399999982890899999606433310977998614798889998710
Q 002545 128 MSMVRSSFRD-RREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLT 206 (910)
Q Consensus 128 ~~~~r~~~~~-~~~~~t~~~v~ir~~~~~~~~~~~~l~~~~~g~~~l~~~~~k~~~~IPi~illkALg~~sD~eI~~~I~ 206 (910)
|...+.+.+. .+..|+...+..|+ .|+.+.++.++.+|+++..++ ++|+.+||||||+ +++||++.++
T Consensus 157 f~~~~~k~~~~gk~lysa~IIP~RG-------sWlefe~D~kd~l~vrIdr~r---Kipvt~lLrALG~-~~~~Il~~f~ 225 (1342)
T 3lu0_C 157 FDSDKGKTHSSGKVLYNARIIPYRG-------SWLDFEFDPKDNLFVRIDRRR---KLPATIILRALNY-TTEQILDLFF 225 (1342)
T ss_dssp CCSCCSCSSSCCCSCCEEEECCSSS-------CCEEEEEETTTEEEEEESSCS---CEETTHHHHTTTC-CHHHHHTTTS
T ss_pred EECCCCCCCCCCCEEEEEEEECCCC-------CCEEEEECCCCEEEEEECCCC---CEEEEHHHHHHCC-CHHHHHHHHC
T ss_conf 8514566577884689999944898-------628999868985999966888---5343334867389-9999999855
Q ss_pred CCCCCHHHC-------------CCC-----C-------------------------------------------------
Q ss_conf 122100100-------------027-----8-------------------------------------------------
Q 002545 207 CCYDEKYKK-------------EKG-----A------------------------------------------------- 219 (910)
Q Consensus 207 ~~~~~~~~~-------------~~~-----~------------------------------------------------- 219 (910)
. .+.... ..+ +
T Consensus 226 ~--~~~~~~~~~~~~~~~~~e~~~g~~~~~di~~~g~vi~~~g~~it~~~~~~l~~~g~~~i~v~~~~l~g~~la~divd 303 (1342)
T 3lu0_C 226 E--KVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYID 303 (1342)
T ss_dssp C--EEEECEETTEEEECCCGGGGTTEECCSCEEETTEEEECSSSEECSHHHHHHHHTTCCCEECCSHHHHTSEECSCEEC
T ss_pred C--CCEEEECCCCEEEECCHHHHCCCCCCCCHHCCCCCEECCCCCCCHHHHHHHHHCCCCCCCCCHHHHHCCHHHHEEEE
T ss_conf 5--51477416740231264553254211000024510002155010999999886267410257788512010110463
Q ss_pred ---------CCCHHHHHHHHHHHHH----------------------HHHCCCCCHHHHHHHHHHCCCCC----------
Q ss_conf ---------8981167899999999----------------------98402312989999985034654----------
Q 002545 220 ---------VGSPLVSERVKIILAE----------------------VQDLSLTTRLQCLQHIGEHFQPV---------- 258 (910)
Q Consensus 220 ---------~~~~~~~~~~~~~L~~----------------------~~~~~i~t~~~al~yig~~f~~~---------- 258 (910)
.++..-.+.+..+.+. +......++++|+.+|.+++|+.
T Consensus 304 ~~tge~~~~~~~~i~~~~l~~l~~~~i~~~~~l~~~~~~~~~~i~~tl~~d~~~~~~eAl~~iyr~lrpgep~t~e~a~~ 383 (1342)
T 3lu0_C 304 ESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAES 383 (1342)
T ss_dssp TTTCCEEECSSCBCCTTHHHHHHHHTCSCEEEECCCSSSSCCSGGGTTTTCCCCSSHHHHHHHHHHHSCSSCCCTTHHHH
T ss_pred CCCCEEEECCCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHHH
T ss_conf 67870886278614899999999769837998840466543799999863457899999999998537999987899999
Q ss_pred -----CCCCCCCCHHHHHHHHHHHHHCCC-CC-CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECCCCHHHHHH
Q ss_conf -----468888617999999997674357-99-98432899999999998610799888994311260774530306999
Q 002545 259 -----IDGLQSESYYAVAETVIRDYIFVH-LN-DNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIY 331 (910)
Q Consensus 259 -----~~~~~~~~~~~~g~~~L~~~ll~H-i~-~~~~K~~~L~~Mv~kLl~~~~g~~~~Dd~D~~~nkrv~l~G~Ll~~l 331 (910)
|+.+++|++.++||+.+|++|-.. .+ +...+..+++.++++|+.+..|....||+|||+||||+++|+||+++
T Consensus 384 l~~~lFf~~~rYdL~~VGR~k~N~kL~l~~~~~~~~Lt~~DIi~~i~~Li~l~~g~~~~DDiDHLgNrRvr~vGeLl~~q 463 (1342)
T 3lu0_C 384 LFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 463 (1342)
T ss_dssp HHHHHHSCTTTCCCTTTHHHHHHTTTTCSCCCCCSSCCTTHHHHHHHHHHHHHHTSSCCCCSSSTTTSEEECHHHHHHHT
T ss_pred HHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCHHCHHHHHHHHH
T ss_conf 99986068433451133167776531887676664741999999999999886089987614556402103099999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCC
Q ss_conf 99999999999999999988626984134106889998721897242899986741467664445544434541898043
Q 002545 332 LKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAER 411 (910)
Q Consensus 332 f~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~l~~~lsTGnw~~~~~~~~~q~sGvsqvleR 411 (910)
|+..|.++.+.++..+... . ...+. ++.++ +++.+|+++++||++ +|+||+++|
T Consensus 464 fr~~l~r~~r~i~~~~~~~--~-~~~~~------~~~li---n~~~i~~~~k~ffg~--------------s~lSQ~lDq 517 (1342)
T 3lu0_C 464 FRVGLVRVERAVKERLSLG--D-LDTLM------PQDMI---NAKPISAAVKEFFGS--------------SQLSQFMVQ 517 (1342)
T ss_dssp HHHHHHHHHHHHTTHHHHC--C-SSCCS------STTTC---CSSTTHHHHTTTTTT--------------CSSCEECCC
T ss_pred HHHHHHHHHHHHHHHHHHC--C-CCCCC------HHHHH---CCCHHHHHHHHHHCC--------------CCCCEEECC
T ss_conf 9999999999999997230--2-54678------88973---564589999988475--------------640326037
Q ss_pred CCHHHHHHHHCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCHH
Q ss_conf 02566855300013---698556655566642477775210147899985445444566126992003898864332011
Q 002545 412 LNFLRFISFFRAVH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKM 488 (910)
Q Consensus 412 lN~~~~lSh~Rrv~---rg~~~~~~K~t~~R~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is~~~~~~~~~~~~~~~ 488 (910)
+|+++.|||+||++ +|++.++++.++||++||||||+|||+|||||++||||+|||++|+|+.
T Consensus 518 tNpLseltHkRRlsalGPGGLsr~~a~fevRdvH~thyGRiCPiETPEG~niGLI~sLA~~a~in~-------------- 583 (1342)
T 3lu0_C 518 NNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNE-------------- 583 (1342)
T ss_dssp SSHHHHHHHHSBEESCCSTTSCCSSCCTTTSSCCTTCSSSSCTTCCCSSSCSSSCCBCCSSCCBCS--------------
T ss_pred CCHHHHHHHHHCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCEEEECCHHHEEEECC--------------
T ss_conf 788888765530034578875434567520115732134224555898875001000032078645--------------
Q ss_pred HHHHHHHHHHCCCEECCCCCCCCCCCCEEEEEECCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCC
Q ss_conf 68899999846981258754358999606999898999454495189999999998881688889984479998678998
Q 002545 489 RTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGA 568 (910)
Q Consensus 489 ~~~i~~~L~~lg~~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~~~~~~~lr~lk~~~~~~i~~~~ei~~v~~~~~~~ 568 (910)
+|++.. | |.++.||++-.-+. | +..+.|-.++-...+.
T Consensus 584 ----------~Gfiet-P----------yr~V~~g~v~~~i~------------y--------LsA~eE~~~~IAqan~- 621 (1342)
T 3lu0_C 584 ----------YGFLET-P----------YRKVTDGVVTDEIH------------Y--------LSAIEEGNYVIAQANS- 621 (1342)
T ss_dssp ----------SSCBCE-E----------EEEEETTEEEEEEE------------E--------ECTTTGGGSCBCCSSS-
T ss_pred ----------CCCCCC-C----------CEEEECCEECCCEE------------E--------CCHHHHCCCEEEECCC-
T ss_conf ----------784557-8----------68988988758356------------6--------7867855846875476-
Q ss_pred CCCEEEECCCCCEECEEEEECCCCCCCCCEEEECCCCEEEEEEECCCCCCCCCCCCCCCEECCCCCCCCCCCEEECCCCC
Q ss_conf 88059654999200007750589988875666475430534642389999998788773001247876532022125489
Q 002545 569 YPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYS 648 (910)
Q Consensus 569 ~~~i~I~td~gR~~RPv~~~~~~~~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~th~Ei~p~~ils~~asliPF~ 648 (910)
..++.|++.+++..+... +++..++. ++ ++|++++|.+++|++||||||+
T Consensus 622 -----~l~~~g~~~~~~v~~R~~--------------~e~~~~~~--~~---------v~~~dvsP~qivSvaaslIPFL 671 (1342)
T 3lu0_C 622 -----NLDEEGHFVEDLVTCRSK--------------GESSLFSR--DQ---------VDYMDVSTQQVVSVGASLIPFL 671 (1342)
T ss_dssp -----CCSSSSCCSCSSEEEECS--------------SCEEEECT--TT---------CCEEESCTTTTSCHHHHSCTTS
T ss_pred -----CCCCCCCCCCCEEEEEEC--------------CCEEEECH--HH---------CEEEECCHHHHCCHHHCCCCCC
T ss_conf -----467789665775778866--------------96578586--88---------7068617778301132047874
Q ss_pred CCCCCCHHHHHHHCCCCCCCCC-----------------------------------EEEEEEECCC----------CEE
Q ss_conf 9998401111100001234431-----------------------------------1389984157----------425
Q 002545 649 DHNQSPRNMYQCQMAKQTMGFS-----------------------------------VQALKFRADQ----------KLY 683 (910)
Q Consensus 649 ~hNqspRn~yq~~M~KQaig~~-----------------------------------~~n~~~R~d~----------~~y 683 (910)
+||||+|++|||||+|||+|+. +.++..|.|. ..|
T Consensus 672 EhdDAnRaLMGsNMQRQAVPLl~~e~p~VgTG~E~~~a~dsg~~i~a~~~G~v~~vda~~I~Ir~~~~~~~~~~~~~~~y 751 (1342)
T 3lu0_C 672 EHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIY 751 (1342)
T ss_dssp TTBCHHHHHHHHHTTTTBCCCSSCCCCSSBCSCHHHHHHHTTTSCBCSSCBEECCCCSSBCCEEECSSSSSSSCCEEECC
T ss_pred CCCCCCCCCHHHHCCCCCCCCCCCCCCEEECCCCHHEEECCCCEEEECCCCEEEEECCCEEEEEECCCCCCCCCCCCEEE
T ss_conf 45875566512415144623056889737545430004647865896379789996388599984787555566761378
Q ss_pred ECC----------CCCEEEEECCCCCCCC----------CCCCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCCCCEEE
Q ss_conf 527----------9981058346400138----------64368984016899733688855325442000014761124
Q 002545 684 HLQ----------TPQTPIVRTNTYTKYG----------IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQ 743 (910)
Q Consensus 684 ~L~----------~pQ~Plv~t~~~~~~~----------~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~ 743 (910)
.|. ++|+|+|+++.....| .+|+|+|+|++||||||.|||+|||||||++++++++|+++
T Consensus 752 ~L~kf~RSNq~Tc~~QrPiV~~G~~V~~GdilADG~st~~GElaLG~N~lVAfMpW~GYNfEDAIlISErlV~eD~fTSI 831 (1342)
T 3lu0_C 752 NLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831 (1342)
T ss_dssp BCCCSCBCSSSCBCCCCBCCCSSCCBCTTCBCBCCSSCSSSSCCCSEECCEECCCCSSTTSSSEEEECTHHHHTTTSCEE
T ss_pred EECCCCCCCCCCCCCCCCEEECCCEEECCCEECCCCCCCCCEEECCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCEEE
T ss_conf 74032444455566530046559888527386046545689552425208999513376514350120335524872038
Q ss_pred EEEEEEEEEECCCCCCCCCCEEECCCCCCHHHHCCCCCCCCCCCCCEECCCCCEEEEECCCC------------------
Q ss_conf 99999997302478767650110059887021102699998554706659994998321689------------------
Q 002545 744 IYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT------------------ 805 (910)
Q Consensus 744 ~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~ld~dG~~~~G~~v~~gdil~~~~~~~~------------------ 805 (910)
+...+.++..+.+.-.+..+ ...|+..+..+++||++||+++|++|++||||+||++|+.
T Consensus 832 HIee~e~~aRdtklG~EeiT--rdIPnv~e~al~~LDe~GIv~iGa~V~~GDILVGKvtPkge~~~tpEekLLraIFGek 909 (1342)
T 3lu0_C 832 HIQELACVSRDTKLGPEEIT--ADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEK 909 (1342)
T ss_dssp EEEEEEEECCEETTEECCCC--SCCSSCCHHHHHSBCSSSCBCTTCCCCTTCEEECCCCBCCTTTCCHHHHHGGGTSCSS
T ss_pred EEEEEEEEEEECCCCCCEEC--CCCCCCCHHHHHCCCCCCCEECCCEECCCCEEEECCCCCCCCCCCHHHHHHHHHHCCC
T ss_conf 99987665320589974344--5699988688734787897616758778987986057998776784788899986675
Q ss_pred ---CCEEEEEECCCCCEEEEEEEEEECC----------------------------------------------------
Q ss_conf ---9343455069985699999997057----------------------------------------------------
Q 002545 806 ---NSWRTNSRKGSESVFVDYVAVDMKN---------------------------------------------------- 830 (910)
Q Consensus 806 ---~~~~~~~~~~~e~g~v~~v~~~~~~---------------------------------------------------- 830 (910)
.++.|++.++++.|+|..|.++..+
T Consensus 910 a~~vkDtSL~vp~g~~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~l~~~g~t~~~l 989 (1342)
T 3lu0_C 910 ASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKL 989 (1342)
T ss_dssp SSSBCCCCEECCTTCCCEEEECCCCCCGGGCCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCHHHH
T ss_pred CCCCCCCCEECCCCCCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 66534571763899938999989971245320045667788899887776777888888889999887776548889998
Q ss_pred ------------------------------------------------CCC-----CCEEEEEEEEEEECCCCCCCEECC
Q ss_conf ------------------------------------------------999-----970899999224089766400024
Q 002545 831 ------------------------------------------------SKN-----LPQKANIRFRHTRNPIIGDKFSSR 857 (910)
Q Consensus 831 ------------------------------------------------~g~-----~~~~~~i~~r~~r~p~iGDKf~sR 857 (910)
.|+ ..+.|+|++|+.|.|++|||||||
T Consensus 990 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gd~l~~gv~k~VkV~ia~kRk~qvGDK~AgR 1069 (1342)
T 3lu0_C 990 DKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGR 1069 (1342)
T ss_dssp TTSCGGGTTTCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCCCSSSSCEEEEEEEEEECCCTTCEEECS
T ss_pred HHCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCC
T ss_conf 64888774024568699999999999999999999999999998722367666767746999999775168778870134
Q ss_pred CCCCCEEEEEECCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHCCC
Q ss_conf 7982378532047676844899996829738998665564889998730246
Q 002545 858 HGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE 909 (910)
Q Consensus 858 HGqKGv~s~~~~~~dmPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~ 909 (910)
||||||||++||+|||||+ +||++||||+|||||||||||||++|+++||+
T Consensus 1070 HGnKGVis~I~p~EDMPf~-~dG~~pDIIlNP~gvPSRMnIGqilE~~lG~a 1120 (1342)
T 3lu0_C 1070 HGNKGVISKINPIEDMPYD-ENGTPVDIVLNPLGVPSRMNIGQILETHLGMA 1120 (1342)
T ss_dssp SSCCEEECCCCCTTTSCEE-TTEEECSEECCGGGTTSSCBTHHHHHHHHHHG
T ss_pred CCCCCEEEEEECCCCCCCC-CCCCCCCEEECCCCCCCCCCHHHHHHHHHHHH
T ss_conf 6887447777245679989-88989848868887877663335668765577
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=188.21 Aligned_cols=89 Identities=26% Similarity=0.456 Sum_probs=80.1
Q ss_pred HHHHHHHHHHHHHH----------HHHHHHHH--------------------------------HHHHHCCCEEEEEEEE
Q ss_conf 34999999799999----------97699999--------------------------------9999729904368999
Q 002545 14 ELVRHHIESFDYML----------DEGLSEMF--------------------------------DHCRQAKISYTGKLMA 51 (910)
Q Consensus 14 ~lv~~hi~SFn~Fi----------~~gl~~ii--------------------------------~eaR~r~~TYs~~l~v 51 (910)
+|+++|++|||||+ ++||++++ +|||+|++||+|||+|
T Consensus 2 ~Lv~~Q~~SF~~Flq~~~~~~~r~~~GL~ei~~~~~pI~~~~~~~~~~~L~f~~~~l~~P~~~p~Ecr~r~lTYsapl~v 81 (188)
T 3mlq_A 2 PLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYA 81 (188)
T ss_dssp CCHHHHHHHHHHHHCTTSCGGGCCSCHHHHHHHHHCCEEECCSSSCCEEEEEEEEEECCCSSCHHHHHHTTCCCEEEEEE
T ss_pred CHHHHHHHHHHHHHHCCCCCCCCHHHCHHHHHHHCCCEEECCCCCCEEEEEEEEEEECCCCCCHHHHHHCCCCCCEEEEE
T ss_conf 77899999999998577654443110589999755976512677973999998899648878999999649976605899
Q ss_pred EEEEEEECCCCCEEEEEEEECCCCEEECCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCEEEEEEEEEECCCCC
Q ss_conf 9999995399962553765404510305797448999957787213321258948999394009999984049940
Q 002545 52 DVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYP 127 (910)
Q Consensus 52 ~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~~i~~~~N~~ 127 (910)
++.+... .+++++.++|++|+||+|+. ||||||||+||||++|+.+..|-.
T Consensus 82 ~v~l~~~-~~~~i~~~~v~iG~iPlMt~------------------------gGyFIING~ERVIVsQe~r~~gel 132 (188)
T 3mlq_A 82 RLQLIHK-DTGLIKEDEVFLGHLPLMTE------------------------DGSFIINGADRVIVSQGGRTVGEL 132 (188)
T ss_dssp EEEEEET-TTCCEEEEEEEEEEEECCCT------------------------TSCEEETTEEEECCCCSSSCHHHH
T ss_pred EEEEEEC-CCCEEEEEEEEECCCCEECC------------------------CCEEEECCEEEEEEEEECCCCCEE
T ss_conf 9999987-88517898899735088999------------------------988999788999998303668812
No 7
>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=83.83 Aligned_cols=162 Identities=15% Similarity=0.129 Sum_probs=109.6
Q ss_pred CCCCEEEEEEEEEEECCCCCEEEEEEEEECCEEEEEEEEECCCCCCCHHHHHHHCCCCCHHHHHHHHCCCCC--------
Q ss_conf 985102389999665199823999999828908999996064333109779986147988899987101221--------
Q 002545 139 REGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYD-------- 210 (910)
Q Consensus 139 ~~~~t~~~v~ir~~~~~~~~~~~~l~~~~~g~~~l~~~~~k~~~~IPi~illkALg~~sD~eI~~~I~~~~~-------- 210 (910)
...|+...+..|+ .|+.+.++.++.+|+|+..++ ++|+.+||||||. +++||++.+.....
T Consensus 22 ~~~y~~~iIP~RG-------sWlefe~d~~d~~~vrIdr~r---K~p~t~lLrAlG~-~~edIL~~Fy~~~~~~i~~~~~ 90 (296)
T 3lti_A 22 KVLYNARIIPYRG-------SWLDFEFDPKDNLFVRIDRRR---KLPATIILRALNY-TTEQILDLFFEKVIFEIRDNKL 90 (296)
T ss_dssp -CCEEEEEECSBS-------CCEEEEECTTSCEEEEETTCC---CEETHHHHHHTTC-CHHHHHHHHCCEEEEEEETTEE
T ss_pred CEEEEEEEECCCC-------CEEEEEECCCCEEEEEECCCC---CCHHHHHHHHCCC-CHHHHHHHCCCCEEEEECCCCE
T ss_conf 4789999905997-------518999858874999976741---2108899998089-8699998614645999808835
Q ss_pred ------CHHHCCC--------C----------------------------------------C------------CCCHH
Q ss_conf ------0010002--------7----------------------------------------8------------89811
Q 002545 211 ------EKYKKEK--------G----------------------------------------A------------VGSPL 224 (910)
Q Consensus 211 ------~~~~~~~--------~----------------------------------------~------------~~~~~ 224 (910)
+...... + + .++..
T Consensus 91 ~~~~~~~~~~g~~~~~di~~~g~v~~~~gk~it~r~~~~~~~~g~~~i~v~~~~l~g~~la~divd~~tGEvl~~a~~~i 170 (296)
T 3lti_A 91 QMELVPERLRGETASFDIEANGXVYVEXGRRITARHIRQLEKDDVKLIEVPVEYIAGXVVAXDYIDESTGELICAANMEL 170 (296)
T ss_dssp EEECCGGGGTTCBCSSCEEETTEEEECTTCBCCHHHHHHHHHTTCCEEECCHHHHHTSBBCSCEECTTTCCEEECTTCBC
T ss_pred EEECCHHHHCCCEEEEEECCCCCEEEECCCCHHHHHHHHHHHCCCCEEECCHHHHCCCEECCCEECCCCCCEEECCCCCC
T ss_conf 76427667447414654216773354046412199999998737732204778851420101001366661552355614
Q ss_pred HHHHHHH----------------------HHHHHHHCCCCCHHHHHHHHHHCCCCC---------------CCCCCCCCH
Q ss_conf 6789999----------------------999998402312989999985034654---------------468888617
Q 002545 225 VSERVKI----------------------ILAEVQDLSLTTRLQCLQHIGEHFQPV---------------IDGLQSESY 267 (910)
Q Consensus 225 ~~~~~~~----------------------~L~~~~~~~i~t~~~al~yig~~f~~~---------------~~~~~~~~~ 267 (910)
-.+.++. +...+.+....++++|+..|.+++|+. ++.+++|++
T Consensus 171 t~~~l~~l~~~gi~~i~~l~~~~~~~~~~i~~tL~~D~~~s~~eAl~eIYr~lRpgep~t~e~a~~l~~~lFF~~~RYDL 250 (296)
T 3lti_A 171 SLDLLAXLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDL 250 (296)
T ss_dssp CHHHHHHHHHTTCCEEEEECCCSSSSCCHHHHHHHHCCCCSHHHHHHHHHHHHSTTSCCCHHHHHHHHHHHHSCTTTCBC
T ss_pred CHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCEECH
T ss_conf 79999999865763578887236665489999998357999999999999737899999989999999986058672260
Q ss_pred HHHHHHHHHHHHCCCCCC--CCCHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 999999997674357999--84328999999999986107998889
Q 002545 268 YAVAETVIRDYIFVHLND--NNDKFNLLIFMLQKLFSLVDHTSVSD 311 (910)
Q Consensus 268 ~~~g~~~L~~~ll~Hi~~--~~~K~~~L~~Mv~kLl~~~~g~~~~D 311 (910)
.++||..||++|-..++. ......+++..+++|+.+..|....|
T Consensus 251 g~VGR~KlNkKL~l~~~~~~~~Lt~eDIl~~ikyLI~L~~g~~~vD 296 (296)
T 3lti_A 251 SAVGRMXFNRSLLREEIEGSGILSXDDIIDVMXXLIDIRNGXGEVD 296 (296)
T ss_dssp HHHHHHHHHHHTTCSCSCCCSSCCHHHHHHHHHHHHHHHHTSSCCC
T ss_pred HHHCHHHHHHHHCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 3544467666507677877547609999999999998652899999
No 8
>3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory protein, transcription; 3.00A {Escherichia coli}
Probab=1.00 E-value=1 Score=77.82 Aligned_cols=68 Identities=15% Similarity=0.077 Sum_probs=58.2
Q ss_pred CEEE--CCCCCCHHHHCCCCCCCCCCCCCEECCCCCEEEEECCCC---------------------CCEEEEEECCCCCE
Q ss_conf 0110--059887021102699998554706659994998321689---------------------93434550699856
Q 002545 763 QKLF--RRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT---------------------NSWRTNSRKGSESV 819 (910)
Q Consensus 763 ~~~f--~~~~~~~~~~~~ld~dG~~~~G~~v~~gdil~~~~~~~~---------------------~~~~~~~~~~~e~g 819 (910)
.+.+ ..|+.....+++||++||+++|++|.+||||+||.+|+. .++.|++.++++.|
T Consensus 18 ~EeIT~dIPnv~e~~l~~LDe~GIV~iGs~V~~GDILVGKvTPk~~~~~tpEekLL~aIfg~k~~~vkDtSL~vp~G~~G 97 (228)
T 3tbi_B 18 PEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSG 97 (228)
T ss_dssp ECEESSCCSSCCHHHHHTBCTTSBBCTTCCCBTTCEEECEEEECCGGGCCHHHHHHHHHHCTTSSCEEECCEECCSSCBE
T ss_pred CEEEECCCCCCCHHHHHCCCCCCCEECCCEECCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCEECCEECCCCCCE
T ss_conf 72771689996699985079889805678978998898546899878778378889998677666501680763899957
Q ss_pred EEEEEEEEECC
Q ss_conf 99999997057
Q 002545 820 FVDYVAVDMKN 830 (910)
Q Consensus 820 ~v~~v~~~~~~ 830 (910)
+|+.|.++...
T Consensus 98 ~VidV~if~r~ 108 (228)
T 3tbi_B 98 TVIDVQVFTRD 108 (228)
T ss_dssp EEEEEEEEEBT
T ss_pred EEEEEEEEECC
T ss_conf 99999998137
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=29.96 Aligned_cols=65 Identities=11% Similarity=0.119 Sum_probs=47.1
Q ss_pred CCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHCCCCC
Q ss_conf 11260774530306999999999999999999999886269841341068899987218972428999867414676
Q 002545 315 SLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRL 391 (910)
Q Consensus 315 ~~~nkrv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~l~~~lsTGnw 391 (910)
-.-+|+.+++|+||+..++ ..|.++++.++.++.... .. .-.+++++ +.+.++..++.||+|+++
T Consensus 120 VIVsQe~r~~gell~~q~r----~gl~r~ek~~~e~~~~~~-~~----~~~~~~l~---n~kp~~~~ik~ff~ss~L 184 (188)
T 3mlq_A 120 VIVSQGGRTVGELMADQFR----VGLARLARGVRERMVMGS-PD----TLTPAKLV---NSRPLEAALREFFSRSQL 184 (188)
T ss_dssp ECCCCSSSCHHHHHHHHHH----HHHHHHHHHHHHHHHHSC-GG----GCCHHHHC---CCHHHHHHHHHHHHTCEE
T ss_pred EEEEEECCCCCEEEEEEHH----HHHHHHHHHHHHHHCCCC-CC----CCCCCCCH---HHHHHHHHHHHHHCCCCC
T ss_conf 9998303668812687311----677899999986514131-00----13733440---247899999874164533
No 10
>3ddc_B RAS association domain-containing family protein; oncogene, tumorsuppressor, ubiquitin fold, RAS effector, RAP rassf1, rassf5, RAPL, NORE1, GMPPNP; HET: GNP; 1.80A {Mus musculus}
Probab=1.00 E-value=1 Score=15.98 Aligned_cols=41 Identities=15% Similarity=0.237 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEEEE
Q ss_conf 349999997999999769999999997299043689999999995
Q 002545 14 ELVRHHIESFDYMLDEGLSEMFDHCRQAKISYTGKLMADVEFQYL 58 (910)
Q Consensus 14 ~lv~~hi~SFn~Fi~~gl~~ii~eaR~r~~TYs~~l~v~i~~~~~ 58 (910)
.=+++-|+.||.-++..|. .---.+-||.|-+.|.+.+..-
T Consensus 10 ~ei~~kI~~YN~~~~~~l~----M~l~~dgsytGFIkV~l~L~RP 50 (163)
T 3ddc_B 10 QEIKQKIDSYNSREKHCLG----MKLSEDGTYTGFIKVHLKLRRP 50 (163)
T ss_dssp HHHHHHHHHHHHTSCGGGS----CEECGGGCEEEEEEEEEEEEEE
T ss_pred HHHHHHHHHHHHHCCCCCE----EEECCCCCCCCEEEEEEEECCC
T ss_conf 9999999999875335745----8877887321068999986168
Done!