Query psy4067
Match_columns 1384
No_of_seqs 414 out of 2198
Neff 5.4
Searched_HMMs 29240
Date Sat Aug 17 00:29:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4067.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/4067hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_B DNA-directed RNA polyme 100.0 9E-191 3E-195 1818.1 28.6 789 39-1377 252-1118(1210)
2 1twf_B DNA-directed RNA polyme 100.0 2E-184 7E-189 1777.3 40.7 787 39-1377 266-1129(1224)
3 4ayb_B DNA-directed RNA polyme 100.0 1E-162 4E-167 1581.1 33.9 771 38-1377 209-1030(1131)
4 2a6h_C DNA-directed RNA polyme 100.0 2E-151 6E-156 1444.3 29.6 739 339-1377 71-1031(1119)
5 3lu0_C DNA-directed RNA polyme 100.0 4E-139 1E-143 1316.5 30.5 642 477-1377 420-1269(1342)
6 3h0g_B DNA-directed RNA polyme 100.0 3E-72 1E-76 721.6 13.5 336 339-685 82-629 (1210)
7 2a6h_C DNA-directed RNA polyme 100.0 4.4E-69 1.5E-73 687.5 8.6 231 32-290 171-463 (1119)
8 1twf_B DNA-directed RNA polyme 100.0 1.9E-64 6.3E-69 656.0 3.7 335 339-684 95-642 (1224)
9 4ayb_B DNA-directed RNA polyme 100.0 4.4E-59 1.5E-63 608.1 13.1 486 339-966 66-709 (1131)
10 3lu0_C DNA-directed RNA polyme 100.0 1E-54 3.5E-59 550.0 11.6 142 137-290 422-583 (1342)
11 3mlq_A DNA-directed RNA polyme 99.4 2.9E-13 9.8E-18 144.1 6.7 58 356-413 63-121 (188)
12 3tbi_B DNA-directed RNA polyme 98.7 3E-09 1E-13 114.9 3.8 72 1021-1098 3-78 (228)
No 1
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=8.6e-191 Score=1818.09 Aligned_cols=789 Identities=33% Similarity=0.572 Sum_probs=671.2
Q ss_pred cceeeEeccchhe-----eccccccccchHHHHhhhccccc-----------------cceeccccccccccccccccee
Q psy4067 39 GLQAILFLPLFKQ-----VDFGDSKVVSLRELLSHVTYQKR-----------------LYRLTVQPNWLGTVKAVHGTYL 96 (1384)
Q Consensus 39 ~~~~~~~~~~~~~-----~~~~~~~~~sd~~~~~~i~~~~~-----------------~~~~~~~~~~~~~~~~~~g~~~ 96 (1384)
|..+.+.+||+++ |+|||||++||+||++||+||.+ +++|++||+|||+|....|
T Consensus 252 ~~~i~~~~~~~~~~IPi~ivlkALg~~sD~EI~~~I~~~~~d~~~~~~l~~slee~~~i~tq~~aL~yIG~r~~~~~--- 328 (1210)
T 3h0g_B 252 GQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQDKDIALDYIGKRGSTTG--- 328 (1210)
T ss_dssp SCCCCCCCTTSCSCCCSHHHHTTTTCCSTTHHHHHHCCSSCCHHHHHTHHHHHHTTSSCCSSHHHHHTTCCCSSSCC---
T ss_pred CceEEEEEeccccCCcHHHHHHHcCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHhhhcCCHHHHHHHHHHhccccC---
Confidence 7788999999998 99999999999999999998763 6899999999999986556
Q ss_pred eeeccccccCCCCHHHHHHHHHHHHHHHhcCccccccCh-------hhHHHHHHHHHHHHHhcCcCC-CCChhhhhhHHh
Q psy4067 97 TMVTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDS-------FDYFINVEIKKLMQANANIYS-DVDPLFYLKYLD 168 (1384)
Q Consensus 97 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~~kgl~~~hi~~-------~~~f~~~~i~~~~~~~~~~~~-d~~d~f~~k~~d 168 (1384)
+.+|. +++.+.++.++. ++|||+. |.+||++|+++++++..+... |++|||.+||++
T Consensus 329 --~~~~~-~~~~a~~iL~~~------------lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~ 393 (1210)
T 3h0g_B 329 --VTREK-RLRYAHDILQKE------------LLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLD 393 (1210)
T ss_dssp --CCHHH-HHHHHHHHHTTT------------SSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBC
T ss_pred --CCchh-HHHHHHHHHHhh------------EEeCcCCCccchhHHHHHHHHHHHHHHHHhCCCCCCCCCccccCeEEe
Confidence 44552 333333333333 9999975 789999999999999887655 888999999999
Q ss_pred hhhcchh-----------h----hccc--ccccccccccccchhhHHHHHHHHHHhCCcc-cccccccccceeeeecccc
Q psy4067 169 IHVGIAD-----------K----IIPK--IKAAQFDIVNHMRQDTITNALTAAIQTGNWT-IRRFKMERQGVTQVLSRLS 230 (1384)
Q Consensus 169 ~~~~~~~-----------k----~~~~--~~~~~~~~~~~~~~~~IT~~l~~alsTGNW~-~~~~~~~r~GvsQvL~Rln 230 (1384)
++|..+. | .+.+ .+...||+..+++++.||++|+||||||||+ .+++.++|+||||||+|+|
T Consensus 394 l~G~Ll~~lfr~~~~~~~~~i~~~l~k~~~~~~~~~~~~~i~~~~It~~l~~~laTGNW~~~kk~~~~~sGvsqvl~R~n 473 (1210)
T 3h0g_B 394 LAGPLLASLFRMLFRKMTRDVYKYMQKCVETNREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYT 473 (1210)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCCTTSSCSTTTSHHHHHHHSSSCSSTTSSCCSCCCCSCCBCCCSS
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCccCHHHhcchhhhHHHHHHHhhcCCcccccccccCcCCEEEEcccCC
Confidence 9985332 1 1111 1245789999999999999999999999997 6678899999999999999
Q ss_pred hhhcccccccccccccccccccCCCcCCCCCcccccCCCCCCCccccchhhcccccccccCCChHHHHHHHHHcCceecc
Q psy4067 231 YISGLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTENDEKNMLKIMYNIGIEHIA 310 (1384)
Q Consensus 231 ~ls~lshlrRv~s~~~~~~K~~~pR~LhpsqwG~iCP~eTPEG~~cGLVKnLAl~a~It~~~~~~~i~~~l~~lG~~~~~ 310 (1384)
|+|+||||||+|+|+++++|+++||+||||||||+||+|||||++||||||||+||+||++++++||.++|.++||++++
T Consensus 474 ~~s~lShlRrv~~p~~~~~K~~~~R~Lhpt~WG~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~pI~~~l~~~gme~le 553 (1210)
T 3h0g_B 474 FASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLE 553 (1210)
T ss_dssp HHHHHHHTTBBCCSCCSSCCSSSSSSCCGGGTTTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSSHHHHHHHSSSCCCCS
T ss_pred HHHHHHHHHhccCchhhccccccccccChhhheeeccccCCCCCcccccccccceeeeECCCCcHHHHHHHHHhCCcchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCcccCCCCeEEEEECCEEEEEeecCcccCCcccccccccccccCCcccccccccccceEEEEEEEeeCCceeeeeee
Q psy4067 311 MFNGEELSSPGVYLVFVNGILAGITCHHKEVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDL 390 (1384)
Q Consensus 311 ~~~~~~~~~~~~~~VflNG~~vG~~~~~i~ig~Psv~e~~~~~R~i~P~EcRlrd~TYsa~i~V~v~~~~~~~~~~~~~V 390 (1384)
++.+.. .+++++|||||+|||+|++|..+ .+.++.+| ++
T Consensus 554 ~~~~~~--~~~~tkVfvNG~wVGvh~dp~~L-----v~~lR~lR--------------------------------R~-- 592 (1210)
T 3h0g_B 554 DYNPSA--SPNATKVFVNGVWLGVHRDPAHL-----TETLRSLR--------------------------------RR-- 592 (1210)
T ss_dssp CCCSSS--SSSSCCCCSTTCCCCCCSCHHHH-----HHHHHHHH--------------------------------TT--
T ss_pred hcCccc--CCCceEEEECCEEEEEeCCHHHH-----HHHHHHHh--------------------------------hc--
Confidence 876643 36789999999999999999888 77777776 22
Q ss_pred eeccccceeccccccccCCcccccccceeeeeEEEeccccccchhhhHHhhccccccccCCChhhHHHHhhhcccccccc
Q psy4067 391 VIGRMPIMLQSSKCVLRNKTEYTSSSRRASTSSVTMHSQRTSPLLSCKKLRQKRFQTYKKTPVDDARDFLSSTCIAHIPV 470 (1384)
Q Consensus 391 ~IG~iPIMLrS~~CvL~g~~~~is~~~~~s~t~i~~~~~~~~P~~e~~~~~~~~~~~~~~~~~~ea~e~L~~~~LpHv~v 470 (1384)
|.||- ++| ++.+.
T Consensus 593 --g~Is~--------------eVS--------Ivrdi------------------------------------------- 605 (1210)
T 3h0g_B 593 --LDISA--------------EVS--------IVRDI------------------------------------------- 605 (1210)
T ss_dssp --TSSCT--------------TCC--------CCCCT-------------------------------------------
T ss_pred --CCCCC--------------ceE--------EEecC-------------------------------------------
Confidence 11221 111 00000
Q ss_pred ccccchhhhHHHHHHHHHHHHhhcCCCCCCCCccccCcEeeehhhHHHHHHHHHHHHHHHHHHhhccccceeccccceee
Q psy4067 471 INMRFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKETNLSGVVNLVSGWWFE 550 (1384)
Q Consensus 471 ~~~~~~~Ka~yLg~MvRr~l~~~~~~~~~DDrD~ygNKRlelAG~Lls~lFe~~fk~~~~~~k~~~~~~i~sl~~g~w~~ 550 (1384)
T Consensus 606 -------------------------------------------------------------------------------- 605 (1210)
T 3h0g_B 606 -------------------------------------------------------------------------------- 605 (1210)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred cccCceeEeecCcccccccCCCCCCCcccccCCCCCeEEEeccccc--CCcchhhhHHHhhcccccccccccceeeccCC
Q psy4067 551 LKYGNKIYIRSPSRKLLAAGFSGPHSGRVRLMPEGPTILLNSCLRS--GGKAQHEALYNAVQRHATKCCTLNFLFFLGGG 628 (1384)
Q Consensus 551 ~~~~n~~~i~t~~r~~~a~Gvh~sh~GRicp~pEgp~i~~~~~~~~--~~~~~~~~~~~~lk~~~~~~~~~~~~~fl~~g 628 (1384)
..++++|.|| +||+| ||+++|.....+ .|++ .++++|+
T Consensus 606 --r~rE~~IfTD-------------aGRv~----RPLfvVen~~~~~~~g~L-------~l~k~hi-------------- 645 (1210)
T 3h0g_B 606 --REKELRLFTD-------------AGRIC----RPLFIVDNNPNSERRGEL-------CIRKEHI-------------- 645 (1210)
T ss_dssp --TTCCCCCCCS-------------SCCBC----CEEEECCCSSCSSSSCCC-------SSCHHHH--------------
T ss_pred --CCCeEEEecC-------------CCccc----ceEEEEccCCcccccccc-------cccHHHH--------------
Confidence 0123889999 99999 999998421111 1233 3444444
Q ss_pred CCcccccccccceeeeEeeeccccccccccccccccCCCCCCCCCCCCCcccccccccccccccccccccCcEEEeccCC
Q psy4067 629 GILPSIQRQTTCLLTLILFSLNGDGKRGARNSQQYCDCPDGYSSGCQPRPTFLNMHQFLGFKRFDDFLYEGKIEYLDVNE 708 (1384)
Q Consensus 629 ~i~~~~~~~~~~~l~~v~v~~~~~l~~~~r~~r~~~d~~~~~~~gr~~rPl~~~~~~~~~~~~~~~~~~~~~~e~~~~~e 708 (1384)
+.|+.... .+ . ......+.|++|+.+|.|||||++|
T Consensus 646 ----------------------~~L~~~~~-----~~------~-----------~~~~~~~~w~~Lv~~GvIEylDaeE 681 (1210)
T 3h0g_B 646 ----------------------QQLIEDKD-----RY------D-----------IDPEQRFGWTALVSSGLIEYLDAEE 681 (1210)
T ss_dssp ----------------------HHHHHHHT-----CC------C-----------SCTTCCCSSTTTTTTTSEEECCTTT
T ss_pred ----------------------HHHhcccc-----cc------c-----------ccccccCCHHHHHhCCCEEEecHhh
Confidence 33322000 00 0 0001347899999999999999999
Q ss_pred CcceEEEeCCCCCCC----------------------------ccceeecccCcccccccchhhhhhcccccCCCCCCCC
Q psy4067 709 GNDSHIAVSESGIRP----------------------------GVTTHLEIAPFTLLGVCAGIELLQYNKRFHSPGLVPY 760 (1384)
Q Consensus 709 ~~~~~ia~~~~~~~~----------------------------~~~th~ei~p~~~l~v~a~~~~~~~~~~~~~~~lipf 760 (1384)
|++++||++++++.. ..||||||+|++||||||| +|||
T Consensus 682 Eet~mIamtpeDL~~~r~~~~g~~~~~~~d~~~r~k~~~~~~~~~~THcEIhPsmILGIcAS--------------iIPF 747 (1210)
T 3h0g_B 682 EETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPHVHAWTHCEIHPAMILGILAS--------------IIPF 747 (1210)
T ss_dssp GGGCCEESCHHHHHHHHHHTTCCCCCCSSCCSSCCCCCSCCSCCSCSEECSCGGGSSCSSST--------------TSSS
T ss_pred hhceeEEecHHHhhhhhhhhccccccccccchhhccccCCCcccccccccccchhhhhheee--------------cccC
Confidence 999999999877631 3689999999999999999 9999
Q ss_pred CCCCCCccchhhhhhccccccccccccccccccceeeeccCCCceeeccccccccCCCCCCCccccCCCCccchhhcccc
Q psy4067 761 PHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITNFHKLPAGKCQISPGGAEELTARESC 840 (1384)
Q Consensus 761 ~~hNqspRn~yq~~m~kQ~~g~~~~~~~~R~D~~~~~l~~pQ~Piv~t~~~~~~~~~~~p~G~n~~~~~g~e~~~~~~~~ 840 (1384)
|||||||||||||||+|||||+|++||++|+||++|+|+|||+|||+|++++.++
T Consensus 748 pdHNQSPRNtYQ~aMgKQamG~~~~n~~~R~Dt~~~~L~yPQkPlv~T~~~e~~~------------------------- 802 (1210)
T 3h0g_B 748 PDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLK------------------------- 802 (1210)
T ss_dssp STTSCSHHHHHHHHHHTTCCSCCCTTTTTSCCSSEEEESSCBCCSSBCTTSTTTT-------------------------
T ss_pred ccccccchhhhhhhhhcccccccccccccccCccccEeecCcCccccchhHHHhC-------------------------
Confidence 9999999999999999999999999999999999999999999999996666654
Q ss_pred cceeEEeecccceeeecccccccccccccccccccchhhcccccccccchhhhhhhccccceeeccccCCCCccccCCCC
Q psy4067 841 HEVLKIISFSISVAVFDSVWLGDVKQGVHQLSEEKEPRLLRKFQYFDVRTPYRLRRLLCWECVLYNKRFHSPGLVPYPHH 920 (1384)
Q Consensus 841 ~~vva~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~k~s~s~glIPF~~H 920 (1384)
T Consensus 803 -------------------------------------------------------------------------------- 802 (1210)
T 3h0g_B 803 -------------------------------------------------------------------------------- 802 (1210)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCccchhhhcccccccceeeeccccceeeeeeeeeccCCceeeeeeEeecccCCCCCCcceEEEEeeecccccccceee
Q psy4067 921 NQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITNFHKLPAGQNATIAVMSYSGYDIEDALIM 1000 (1384)
Q Consensus 921 NqSPRntyq~~M~KQAiG~~~yN~~~RiDt~~~~L~ypQkPLV~T~~i~~~~~~elp~GqN~iVAvmsy~GYN~EDAIIi 1000 (1384)
++++|+|+|++||||||+||||||||||
T Consensus 803 ----------------------------------------------------~~elp~G~NaiVAvmsy~GYn~EDAiIi 830 (1210)
T 3h0g_B 803 ----------------------------------------------------FRELPAGQNAIVAILCYSGYNQEDSIIM 830 (1210)
T ss_dssp ----------------------------------------------------CTTSCSCCEECBEECCCSSSSCSSCEEE
T ss_pred ----------------------------------------------------CCcccCccceEEEEeccCCCChhhheee
Confidence 4456677788899999999999999999
Q ss_pred cccccccCCceeeEEecceeeeeecCCCccceeeCCccccCCCCCcccccccCCCCcccCCceeecCceEEeeeccCccc
Q psy4067 1001 NKASLDRGFGRCLVYRNSKCVLKQYPNQTHDRILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISV 1080 (1384)
Q Consensus 1001 NkssidRG~~rs~~yr~~~~~i~~~~~~~~d~i~~p~~~~~~~~p~~~~~~LDedGiv~~G~~V~~gDILIgKvsp~~~~ 1080 (1384)
||+|+|||||||++|++|.++++++..+..|.+..|..+...+.+...|++||+||||.+|++|++|||||||++|..+.
T Consensus 831 nk~sv~rg~~~s~~~~~y~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gDiligK~~p~~~~ 910 (1210)
T 3h0g_B 831 NQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLD 910 (1210)
T ss_dssp EHHHHTTTTTCEEEEEEEEECCCCCSSSCCCCCCCCCTTSCCSCCSCCGGGCCTTSSCCTTCCCCTTCCCCCCCCCC---
T ss_pred ehhheecCceEEEEEEEEEEEeeecCCCceeEEcCCCcchhcccchhhHhhcCCCCCcCCCCEecCCCEEEEEecCCCCC
Confidence 99999999999999999999999988877888888875543344455799999999999999999999999999996532
Q ss_pred cccccCCCccccccccccccccccceEEEEecCcchhhhHHHhhhccccccccccccccCCCcceeeeEeecCCCCCCCC
Q psy4067 1081 SAISMATPEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNES 1160 (1384)
Q Consensus 1081 ~~~~~~~~e~k~~~~~~k~~~p~~vd~Vii~~~~~~~~~vki~irq~R~p~IGDKfssRHGqKGVis~ilp~eDMPfte~ 1160 (1384)
. .+ .|
T Consensus 911 ~---------~~---------------------------------------~~--------------------------- 915 (1210)
T 3h0g_B 911 H---------EE---------------------------------------LG--------------------------- 915 (1210)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred c---------hh---------------------------------------hc---------------------------
Confidence 1 00 00
Q ss_pred CCcCceeeCCCCCCCcccccceeeecccccCCccceeeEEEEecCCCCcEEEEEEEEeecCCCcCCcccccCCCceeEEE
Q psy4067 1161 GICPDIIMNPHGLKGCDRITEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGL 1240 (1384)
Q Consensus 1161 Gi~pDIIiNP~gvpsr~~i~~~~e~s~~~k~~e~~~vd~V~i~~~~~~~~~vkV~ir~~R~p~iGDKfsSRHGQKGvvg~ 1240 (1384)
.+.+...++|+|+.+++.|.|+||+|+++.++++.++|||++|++|+|++|||||||||||||||+
T Consensus 916 --------------~~~~~~~~rd~s~~~~~~e~g~Vd~V~~~~~~~g~~~vkv~~~~~R~~~~GDK~a~RhGqKGvi~~ 981 (1210)
T 3h0g_B 916 --------------QRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGM 981 (1210)
T ss_dssp -----------------CCCCCCCCCCCCCTTCCCCCCEEEEEECSSSSEEEEEEECCCBCCCTTCEEECTTCCCEEEEE
T ss_pred --------------ccccccccceeeEEecCCCCeEEEEEEEEEecCCCeEEEEEEEEecCCCchhhhhcccCCCceeeE
Confidence 001123468899999999999999999999999999999999999999999999999999999999
Q ss_pred EeecCCCCCCCCCCcceEeeCCCCCCCccchhhhHHhhhhHHHhhcCCeeeeccCCCCCHHHHHHHHHHcCCCCCCceEE
Q psy4067 1241 IVEQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQGKDIF 1320 (1384)
Q Consensus 1241 i~~qeDMPft~dGi~PDIIiNPhg~PSRMTIGql~E~l~Gk~~~~~g~~~d~t~F~~~~~~~i~~~L~~~G~~~~Gke~l 1320 (1384)
|+|+|||||++||++|||||||||||||||||||+|+++||++++.|.+.|+|||++.+++++++.|.++||+++|+|.|
T Consensus 982 i~~~edmPf~~~G~~pDii~NP~~~PSRMtigq~~E~~~g~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~~~l 1061 (1210)
T 3h0g_B 982 TYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHGFQSRGFEVM 1061 (1210)
T ss_dssp EECTTTSCCBTTTBCCSEECCGGGSTTSCCHHHHHHHHHHHHSSSSCCCCBCCSSCSCCHHHHHHHHHTTTSCTTSCBCC
T ss_pred EeccccCCcCCCCCCCeEEECCCcCCCCccchhhhHhHHHHHHHhcCCceeeccCCCCcHHHHHHHHHHcCcCCCCCEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeCCCCcEEEeeEeEeeehhhccccccCccceeeccCCccccccCCCccccccCCCc
Q psy4067 1321 YSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTGRRWKLTFTP 1377 (1384)
Q Consensus 1321 ydG~TGe~l~~~IfiGp~YYqRLkHMV~DKiHaRsrGP~~~LTrQP~eGRsr~~~~~ 1377 (1384)
|||+|||+|+++||+||+|||||+|||+|||||||+|||+.|||||++||||.|||-
T Consensus 1062 ~~g~tg~~~~~~i~~G~~yy~kL~Hmv~dK~h~r~~gp~~~~t~QP~~gr~~~GG~r 1118 (1210)
T 3h0g_B 1062 YHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLR 1118 (1210)
T ss_dssp BCSSSCCBCSSCBEECCEECEECSCCSTTTCEECSSCCBCSSSCSBCCSSTTCCCCC
T ss_pred EcCCCCCCccccEEEEehHhhcchhhcccCcEEeccCCCchhccCCcccccccCCee
Confidence 999999999999999999999999999999999999999999999999999999984
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=100.00 E-value=1.9e-184 Score=1777.32 Aligned_cols=787 Identities=34% Similarity=0.575 Sum_probs=628.8
Q ss_pred cceeeEeccchhe-----eccccccccchHHHHhhhcccc-----------------ccceeccccccccccccccccee
Q psy4067 39 GLQAILFLPLFKQ-----VDFGDSKVVSLRELLSHVTYQK-----------------RLYRLTVQPNWLGTVKAVHGTYL 96 (1384)
Q Consensus 39 ~~~~~~~~~~~~~-----~~~~~~~~~sd~~~~~~i~~~~-----------------~~~~~~~~~~~~~~~~~~~g~~~ 96 (1384)
+..+.+.+|++++ |+|||||++||+||+++|+|+. .+++|++||+|||+++.++|
T Consensus 266 ~~~i~vr~~~~k~~IPi~illkALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~e~~~~~t~~~AL~yIg~r~~~~g--- 342 (1224)
T 1twf_B 266 ARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALG--- 342 (1224)
T ss_dssp SCCEEEECTTCSSCEEHHHHHHHTTCCSHHHHHHHHCCCTTCHHHHHHHHHHHHHTTTCCSHHHHHHHHHHTTSCTT---
T ss_pred CCEEEEEEecccccccHHHHHHHhcCCCHHHHHHHhcccCCcHHHHHHHHHHHHHhhhcCCHHHHHHHHHHhhccCC---
Confidence 5678899999987 9999999999999999999764 16689999999999966677
Q ss_pred eeeccccccCCCCHHHHHHHHHHHHHHHhcCccccccCh-------hhHHHHHHHHHHHHHhcCcCC-CCChhhhhhHHh
Q psy4067 97 TMVTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDS-------FDYFINVEIKKLMQANANIYS-DVDPLFYLKYLD 168 (1384)
Q Consensus 97 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~~kgl~~~hi~~-------~~~f~~~~i~~~~~~~~~~~~-d~~d~f~~k~~d 168 (1384)
+.++ .++..+.+..++. +++||+. +.+||++|+++++.+..+... ||.|||.|||++
T Consensus 343 --~~~~-~~~~~a~~iL~~~------------~l~Hvg~~~~~~~~K~~~L~~mi~kLl~~~~g~~~~DD~DhlgnkRv~ 407 (1224)
T 1twf_B 343 --IKKE-KRIQYAKDILQKE------------FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLD 407 (1224)
T ss_dssp --SCHH-HHHHHHHHHHHHT------------SSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEE
T ss_pred --CCCc-cHHHHHHHHHHhh------------cccccCCCccccccHHHHHHHHHHHHHHHhcCCCCCCCCccccccEEe
Confidence 4444 2333333333333 7899975 579999999999999887655 888999999999
Q ss_pred hhhcchhh-----------h----cccc--cccccccccccchhhHHHHHHHHHHhCCcccc-cccccccceeeeecccc
Q psy4067 169 IHVGIADK-----------I----IPKI--KAAQFDIVNHMRQDTITNALTAAIQTGNWTIR-RFKMERQGVTQVLSRLS 230 (1384)
Q Consensus 169 ~~~~~~~k-----------~----~~~~--~~~~~~~~~~~~~~~IT~~l~~alsTGNW~~~-~~~~~r~GvsQvL~Rln 230 (1384)
++|..++. . +.+. +.+.|++..+++++.||++|+||||||||+.+ .+.++++||||||+|+|
T Consensus 408 l~G~Ll~~lfr~~~~r~~~~i~~~l~~~~~~~~~~~~~~~i~~~~It~~lk~~~aTGNw~~~k~~~~~~sGvSQvldr~n 487 (1224)
T 1twf_B 408 LAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYT 487 (1224)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHSCCC--------CCCCTHHHHHHHHHHHHHCCCC---------CCCEEECCCSS
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhcccchhhcchhheeeccccccccccccccceeEeecccc
Confidence 99854331 1 1111 24578899999999999999999999999754 46799999999999999
Q ss_pred hhhcccccccccccccccccccCCCcCCCCCcccccCCCCCCCccccchhhcccccccccCCChHHHHHHHHHcCceecc
Q psy4067 231 YISGLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTENDEKNMLKIMYNIGIEHIA 310 (1384)
Q Consensus 231 ~ls~lshlrRv~s~~~~~~K~~~pR~LhpsqwG~iCP~eTPEG~~cGLVKnLAl~a~It~~~~~~~i~~~l~~lG~~~~~ 310 (1384)
|+|+|||+||+|+|+++++|.++||+||||||||+||+|||||+|||||||||+||+||++++++||.++|.++||++++
T Consensus 488 ~ls~LSH~RRi~~~~~r~~k~~~~R~LHpshwG~iCPiETPEG~~cGLVknLAl~a~Is~g~~~~pi~~~l~~~G~~~l~ 567 (1224)
T 1twf_B 488 YSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLE 567 (1224)
T ss_dssp HHHHHHHHTEEECCC------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCHHHHHHHHHTTCEEGG
T ss_pred hhhhhhhhhcccccccccccccccccccCccceeecCCCCCCCcccchhhhHHhhCcccCCCCHHHHHHHHHHcCCccee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccCCcccCCCCeEEEEECCEEEEEeecCcccCCcccccccccccccCCcccccccccccceEEEEEEEeeCCceeeeeee
Q psy4067 311 MFNGEELSSPGVYLVFVNGILAGITCHHKEVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDL 390 (1384)
Q Consensus 311 ~~~~~~~~~~~~~~VflNG~~vG~~~~~i~ig~Psv~e~~~~~R~i~P~EcRlrd~TYsa~i~V~v~~~~~~~~~~~~~V 390 (1384)
+.++..+ ++.++|||||+|+|+|++|..+ .+.++.+| ++
T Consensus 568 e~~~~~~--~~~~kVfvnG~~vG~~~~p~~l-----v~~lr~lR--------------------------------R~-- 606 (1224)
T 1twf_B 568 DYVPHQS--PDATRVFVNGVWHGVHRNPARL-----METLRTLR--------------------------------RK-- 606 (1224)
T ss_dssp GCCGGGC--TTCEEEEETTEEEEEESCHHHH-----HHHHHHHH--------------------------------HH--
T ss_pred ecccccC--CCceEEEECCEEEEEeCCHHHH-----HHHHHHHH--------------------------------hc--
Confidence 7765443 4679999999999999999888 77777776 21
Q ss_pred eeccccceeccccccccCCcccccccceeeeeEEEeccccccchhhhHHhhccccccccCCChhhHHHHhhhcccccccc
Q psy4067 391 VIGRMPIMLQSSKCVLRNKTEYTSSSRRASTSSVTMHSQRTSPLLSCKKLRQKRFQTYKKTPVDDARDFLSSTCIAHIPV 470 (1384)
Q Consensus 391 ~IG~iPIMLrS~~CvL~g~~~~is~~~~~s~t~i~~~~~~~~P~~e~~~~~~~~~~~~~~~~~~ea~e~L~~~~LpHv~v 470 (1384)
|.||- ++| ++.+.+
T Consensus 607 --g~i~~--------------evs--------iv~d~r------------------------------------------ 620 (1224)
T 1twf_B 607 --GDINP--------------EVS--------MIRDIR------------------------------------------ 620 (1224)
T ss_dssp --TSSCT--------------TCE--------EEEETT------------------------------------------
T ss_pred --cCCCC--------------eEE--------EEEecc------------------------------------------
Confidence 11111 000 111000
Q ss_pred ccccchhhhHHHHHHHHHHHHhhcCCCCCCCCccccCcEeeehhhHHHHHHHHHHHHHHHHHHhhccccceeccccceee
Q psy4067 471 INMRFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKETNLSGVVNLVSGWWFE 550 (1384)
Q Consensus 471 ~~~~~~~Ka~yLg~MvRr~l~~~~~~~~~DDrD~ygNKRlelAG~Lls~lFe~~fk~~~~~~k~~~~~~i~sl~~g~w~~ 550 (1384)
T Consensus 621 -------------------------------------------------------------------------------- 620 (1224)
T 1twf_B 621 -------------------------------------------------------------------------------- 620 (1224)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred cccCceeEeecCcccccccCCCCCCCcccccCCCCCeEEEecccccCC------cchhhhHHHhhcccccccccccceee
Q psy4067 551 LKYGNKIYIRSPSRKLLAAGFSGPHSGRVRLMPEGPTILLNSCLRSGG------KAQHEALYNAVQRHATKCCTLNFLFF 624 (1384)
Q Consensus 551 ~~~~n~~~i~t~~r~~~a~Gvh~sh~GRicp~pEgp~i~~~~~~~~~~------~~~~~~~~~~lk~~~~~~~~~~~~~f 624 (1384)
-+.++|.|| +||+| ||+++|. ++ ++ .++.+|+
T Consensus 621 ---~~ei~I~TD-------------~GRv~----RPl~vV~-----~~~~~~~~~l-------~l~k~hi---------- 658 (1224)
T 1twf_B 621 ---EKELKIFTD-------------AGRVY----RPLFIVE-----DDESLGHKEL-------KVRKGHI---------- 658 (1224)
T ss_dssp ---TTEEEEECC-------------SCCEE----EEEEEEE-----CCCTTSSCEE-------SCCHHHH----------
T ss_pred ---cCeEEEecc-------------Cceee----eeEEEec-----CCCccccccc-------eecHHHH----------
Confidence 123889999 99999 9999883 33 33 3333333
Q ss_pred ccCCCCcccccccccceeeeEeeeccccccccccccccccCCCCCCCCCCCCCcccccccccccccccccccccCcEEEe
Q psy4067 625 LGGGGILPSIQRQTTCLLTLILFSLNGDGKRGARNSQQYCDCPDGYSSGCQPRPTFLNMHQFLGFKRFDDFLYEGKIEYL 704 (1384)
Q Consensus 625 l~~g~i~~~~~~~~~~~l~~v~v~~~~~l~~~~r~~r~~~d~~~~~~~gr~~rPl~~~~~~~~~~~~~~~~~~~~~~e~~ 704 (1384)
..|+... ..+.+..+ .+ ...++|++|+.+|.||||
T Consensus 659 --------------------------~~L~~~~-----~~~~~~~~-------------~~-~~~~~w~~Lv~~G~iEyl 693 (1224)
T 1twf_B 659 --------------------------AKLMATE-----YQDIEGGF-------------ED-VEEYTWSSLLNEGLVEYI 693 (1224)
T ss_dssp --------------------------HHHHHHH-----HCC-----------------------CCCHHHHHHTTSEEEE
T ss_pred --------------------------HHhhhcc-----cccccccc-------------cc-ccccchhHhccCCcEEEc
Confidence 2222100 00000000 00 023689999999999999
Q ss_pred ccCCCcceEEEeCCCCCCCc-----------------------cceeecccCcccccccchhhhhhcccccCCCCCCCCC
Q psy4067 705 DVNEGNDSHIAVSESGIRPG-----------------------VTTHLEIAPFTLLGVCAGIELLQYNKRFHSPGLVPYP 761 (1384)
Q Consensus 705 ~~~e~~~~~ia~~~~~~~~~-----------------------~~th~ei~p~~~l~v~a~~~~~~~~~~~~~~~lipf~ 761 (1384)
|++||++++||++++++... .+|||||+|++||||||| |||||
T Consensus 694 daeEEe~~~Ia~~~~dl~~~~~~~~~~~~~~~~~R~~~~~~~~~~Th~EI~Ps~ILgV~AS--------------lIPF~ 759 (1224)
T 1twf_B 694 DAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAAS--------------IIPFP 759 (1224)
T ss_dssp EHHHHTTCCEESSGGGGCC---------CCCTTSCCCCCCCCSCCCEECSCGGGGSCTTGG--------------GSSSG
T ss_pred ChhhhcCcEEeccccccCcccccccccccccccccccCCcCchhhcccccCCccccceeec--------------ccCCc
Confidence 99999999999999887651 689999999999999999 99999
Q ss_pred CCCCCccchhhhhhccccccccccccccccccceeeeccCCCceeeccccccccCCCCCCCccccCCCCccchhhccccc
Q psy4067 762 HHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITNFHKLPAGKCQISPGGAEELTARESCH 841 (1384)
Q Consensus 762 ~hNqspRn~yq~~m~kQ~~g~~~~~~~~R~D~~~~~l~~pQ~Piv~t~~~~~~~~~~~p~G~n~~~~~g~e~~~~~~~~~ 841 (1384)
||||||||||||||+|||||++.+|+..|.||++|+|+|||+|||+|..+
T Consensus 760 dHNqSpRn~yqs~M~kQA~g~~~~n~~~r~dt~~~~l~ypQkPlV~t~~~------------------------------ 809 (1224)
T 1twf_B 760 DHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAM------------------------------ 809 (1224)
T ss_dssp GGSCHHHHHHHHHHGGGBCBCSCTTTTTCCCSEEEEESSCBCCSEECTTH------------------------------
T ss_pred cccccchhhhcccccccccccccceeeeecccccceeecCcCCeEEcccc------------------------------
Confidence 99999999999999999999999999999999999999999999998211
Q ss_pred ceeEEeecccceeeecccccccccccccccccccchhhcccccccccchhhhhhhccccceeeccccCCCCccccCCCCC
Q psy4067 842 EVLKIISFSISVAVFDSVWLGDVKQGVHQLSEEKEPRLLRKFQYFDVRTPYRLRRLLCWECVLYNKRFHSPGLVPYPHHN 921 (1384)
Q Consensus 842 ~vva~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~k~s~s~glIPF~~HN 921 (1384)
T Consensus 810 -------------------------------------------------------------------------------- 809 (1224)
T 1twf_B 810 -------------------------------------------------------------------------------- 809 (1224)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCccchhhhcccccccceeeeccccceeeeeeeeeccCCceeeeeeEeecccCCCCCCcceEEEEeeecccccccceeec
Q psy4067 922 QAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITNFHKLPAGQNATIAVMSYSGYDIEDALIMN 1001 (1384)
Q Consensus 922 qSPRntyq~~M~KQAiG~~~yN~~~RiDt~~~~L~ypQkPLV~T~~i~~~~~~elp~GqN~iVAvmsy~GYN~EDAIIiN 1001 (1384)
++++++++|+|+|++||||||+|||||||||||
T Consensus 810 -----------------------------------------------~~~~~~elp~G~N~iVAvm~y~GYN~EDAiIin 842 (1224)
T 1twf_B 810 -----------------------------------------------EYLKFRELPAGQNAIVAIACYSGYNQEDSMIMN 842 (1224)
T ss_dssp -----------------------------------------------HHHTTTTSCCCEEEEEEECBSSSTTTTTEEEEE
T ss_pred -----------------------------------------------cccccccCCCCeeEEEEEecccCcccchhhhhh
Confidence 123578899999999999999999999999999
Q ss_pred ccccccCCceeeEEecceeeeeecCCCccceeeCCccccCCCCCcccccccCCCCcccCCceeecCceEEeeeccCcccc
Q psy4067 1002 KASLDRGFGRCLVYRNSKCVLKQYPNQTHDRILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVS 1081 (1384)
Q Consensus 1002 kssidRG~~rs~~yr~~~~~i~~~~~~~~d~i~~p~~~~~~~~p~~~~~~LDedGiv~~G~~V~~gDILIgKvsp~~~~~ 1081 (1384)
|+++|||+|||++|++|.+++++...+..+.+..|......+.....|++||+||||++|++|++|||||||++|+.+++
T Consensus 843 ~~sv~rg~~~s~~~~~y~~~~~~~~~~~~e~~~~P~~~~~~~~~~~~~~~LD~dGiv~~G~~V~~gDilvgK~~p~~~~~ 922 (1224)
T 1twf_B 843 QSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDE 922 (1224)
T ss_dssp HHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCSSSCBCCSSCGGGCCTTSBCCTTCEECTTCEEECEECCCC---
T ss_pred hhHHhcCCeeEEEEEEEEEEeeeCCCCceeEecCCChhhccCccHHHHhhcccCCccCCccEecCCCEEEEEecCCCccc
Confidence 99999999999999999998877554566778877653333334456999999999999999999999999999976431
Q ss_pred ccccCCCccccccccccccccccceEEEEecCcchhhhHHHhhhccccccccccccccCCCcceeeeEeecCCCCCCCCC
Q psy4067 1082 AISMATPEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESG 1161 (1384)
Q Consensus 1082 ~~~~~~~e~k~~~~~~k~~~p~~vd~Vii~~~~~~~~~vki~irq~R~p~IGDKfssRHGqKGVis~ilp~eDMPfte~G 1161 (1384)
+. +.
T Consensus 923 -------~~--~~------------------------------------------------------------------- 926 (1224)
T 1twf_B 923 -------EE--LG------------------------------------------------------------------- 926 (1224)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred -------cc--cc-------------------------------------------------------------------
Confidence 00 00
Q ss_pred CcCceeeCCCCCCCcccccceeeecccccCCccceeeEEEEecCCCCcEEEEEEEEeecCCCcCCcccccCCCceeEEEE
Q psy4067 1162 ICPDIIMNPHGLKGCDRITEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLI 1241 (1384)
Q Consensus 1162 i~pDIIiNP~gvpsr~~i~~~~e~s~~~k~~e~~~vd~V~i~~~~~~~~~vkV~ir~~R~p~iGDKfsSRHGQKGvvg~i 1241 (1384)
.+.+...++|+|+.++..+.|+||+|+++.+++|.++|||++|++|+|+||||||||||||||||+|
T Consensus 927 -------------~~~~~~~~rd~s~~~~~~e~g~Vd~V~~~~~~~g~~~vkV~ir~~R~p~iGDKfasRHGqKGvis~i 993 (1224)
T 1twf_B 927 -------------QRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGIT 993 (1224)
T ss_dssp -------------------CCBBCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEEEECCCTTCEEECTTSCEEEEEEE
T ss_pred -------------cccccCccceeEEEeeCCCCeEEEEEEEEecCCCCEEEEEEEEecCCCCchhhhhhhccCcceeeee
Confidence 0011234688999999999999999999999999999999999999999999999999999999999
Q ss_pred eecCCCCCCCCCCcceEeeCCCCCCCccchhhhHHhhhhHHHhhcCCeeeeccCCCCCHHHHHHHHHHcCCCCCCceEEe
Q psy4067 1242 VEQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQGKDIFY 1321 (1384)
Q Consensus 1242 ~~qeDMPft~dGi~PDIIiNPhg~PSRMTIGql~E~l~Gk~~~~~g~~~d~t~F~~~~~~~i~~~L~~~G~~~~Gke~ly 1321 (1384)
+||||||||+||++|||||||||||||||||||+||++||||++.|...|+|||++.+++++++.|.++||+++|+|+||
T Consensus 994 ~p~eDMPf~~dG~~pDiIiNPhg~PSRMtiGqllE~~lgka~~~~G~~~datpF~~~~~~~i~~~L~~~g~~~~G~e~ly 1073 (1224)
T 1twf_B 994 YRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMY 1073 (1224)
T ss_dssp ECTTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSCCHHHHHHHHHTTTSCTTSEECEE
T ss_pred cccccCCcCCCCCCccEEeCCCcCccccccchhHHHHhhHHHHhcCceeecCCCCCccHHHHHHHHHHcCCCCCCCEEee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCCCcEEEeeEeEeeehhhccccccCccceeeccCCccccccCCCccccccCCCc
Q psy4067 1322 SGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTGRRWKLTFTP 1377 (1384)
Q Consensus 1322 dG~TGe~l~~~IfiGp~YYqRLkHMV~DKiHaRsrGP~~~LTrQP~eGRsr~~~~~ 1377 (1384)
||+|||+|+++||+||+|||||+|||+|||||||||||++|||||++||||.|||-
T Consensus 1074 ~G~TG~~~~~~i~vG~~YyqkL~HmV~DKihaRs~GP~~~lT~QP~~Gr~r~GG~R 1129 (1224)
T 1twf_B 1074 NGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLR 1129 (1224)
T ss_dssp CTTTCCBCSSCEEEEEEEEEEBSSCGGGTCEEECCCC----------------CCC
T ss_pred cCCCCCCccceEEEehhHhhcchhhcccCceEEeeCCCcccccCCCcccccCCcee
Confidence 99999999999999999999999999999999999999999999999999999984
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=100.00 E-value=1.1e-162 Score=1581.06 Aligned_cols=771 Identities=34% Similarity=0.560 Sum_probs=642.4
Q ss_pred ecceeeEeccchhe-----eccccccccchHHHHhhhccccc--------------cceecccccccccccccccceeee
Q psy4067 38 EGLQAILFLPLFKQ-----VDFGDSKVVSLRELLSHVTYQKR--------------LYRLTVQPNWLGTVKAVHGTYLTM 98 (1384)
Q Consensus 38 ~~~~~~~~~~~~~~-----~~~~~~~~~sd~~~~~~i~~~~~--------------~~~~~~~~~~~~~~~~~~g~~~~~ 98 (1384)
..-.+.+.+|++++ |+|||||++||+||+++|++|++ +++++.||+|||++.. +|
T Consensus 209 ~~~~~~v~~~~~~~~iPi~illrALG~~sD~eI~~~i~~~~~~~~~l~~~~~~~~~i~~~~~al~~i~~r~~-~~----- 282 (1131)
T 4ayb_B 209 KDGTFHVSFPAVPGKIPFVILMRALGILTDRDIVYAVSLDPEIQNELFPSLEQASSIANVDDALDFIGSRVA-IG----- 282 (1131)
T ss_dssp TTTCCEECCSSSCCCEEHHHHHHHHTCCSHHHHHHHHCSCHHHHTTTHHHHHHHTTTCCSSHHHHHHHHHHH-CS-----
T ss_pred CCCEEEEEEcCcCceeeHHHHHHHhCCcchhhHHHHhcccHHHHHHHHHHHHHhcccccHHHHHHHHhhhhh-cC-----
Confidence 33456788899886 99999999999999999999874 7889999999998854 56
Q ss_pred eccccccCCCCHHHHHHHHHHHHHHHhcCccccccCh-------hhHHHHHHHHHHHHHhcCcCC-CCChhhhhhHHhhh
Q psy4067 99 VTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDS-------FDYFINVEIKKLMQANANIYS-DVDPLFYLKYLDIH 170 (1384)
Q Consensus 99 ~~~e~~~~~~~~~~~~~~~~~~~~~~~kgl~~~hi~~-------~~~f~~~~i~~~~~~~~~~~~-d~~d~f~~k~~d~~ 170 (1384)
..++. ++..+. ++.. -.+++|++. +.+|+.+|+++++.+..+... ||.|||.|||+++.
T Consensus 283 ~~~~~-~~~~a~-----------~il~-~~~l~hl~~~~~~~~~K~~~L~~mi~~Ll~l~~g~~~~DD~Dhl~NkRvr~v 349 (1131)
T 4ayb_B 283 QKREN-RIEKAQ-----------QIID-KYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLA 349 (1131)
T ss_dssp SCHHH-HHHHHH-----------HHHH-TTSSTTSCSSTTSHHHHHHHHHHHHHHHHHHHHTSSCCCCTTSGGGEEEECH
T ss_pred CCCch-hHHHHH-----------HHHH-HhhcccccccccchhHHHHHHHHHHHHHHHHHcCCCCCCCCcchhcceecch
Confidence 22221 111111 1222 248899854 569999999999999877665 88899999999998
Q ss_pred hcchh-----------hhc----cc--ccccccccccccchhhHHHHHHHHHHhCCcccccccccccceeeeecccchhh
Q psy4067 171 VGIAD-----------KII----PK--IKAAQFDIVNHMRQDTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYIS 233 (1384)
Q Consensus 171 ~~~~~-----------k~~----~~--~~~~~~~~~~~~~~~~IT~~l~~alsTGNW~~~~~~~~r~GvsQvL~Rln~ls 233 (1384)
|..++ |.+ .+ .+...+++..+++++.||++|++|||||||.. +++||||+|+|+||+|
T Consensus 350 GeLl~~~fr~~l~r~~r~ir~~~~~~~~~~~~~~~~~li~~~~it~~i~~~~aTGn~~~-----~~sglSQ~mdq~NpLs 424 (1131)
T 4ayb_B 350 GDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVTERIRHALATGNWVG-----GRTGVSQLLDRTNWLS 424 (1131)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHSTTCSCCCHHHHCCTHHHHHHHHHHHHTTBCSS-----SCBCCEEECCCSSHHH
T ss_pred hHHHHHHHHHHHHHHHHHhhhhcccchhcccccchhhhcCCchhhhhhHHHHhhccccc-----CCCceEEEeccCCHHH
Confidence 85433 111 11 12345777888999999999999999999963 6899999999999999
Q ss_pred cccccccccccccccccccCCCcCCCCCcccccCCCCCCCccccchhhcccccccccCCChHHHHHHHHHcCceecccc-
Q psy4067 234 GLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTENDEKNMLKIMYNIGIEHIAMF- 312 (1384)
Q Consensus 234 ~lshlrRv~s~~~~~~K~~~pR~LhpsqwG~iCP~eTPEG~~cGLVKnLAl~a~It~~~~~~~i~~~l~~lG~~~~~~~- 312 (1384)
+|||+||+++++++++|.++||+|||||||||||+|||||+|||||||||++|+|+.++++.++.+++.++|+.++++.
T Consensus 425 ~lsH~RRlsagl~rera~~evRdlHpShyGriCPIETPEG~niGLI~sLA~~a~I~~g~~e~~i~~~l~~~g~~~~e~~~ 504 (1131)
T 4ayb_B 425 MLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINEKIVEKTLYEMGVVPVEEVI 504 (1131)
T ss_dssp HHHHHTEEEECSCSSSCCHHHHSCCGGGTTTBCSSCCCSSTTBTTEEEBBSSCEECCCCCHHHHHHHHHHTTCEEHHHHH
T ss_pred HHHhhhhhcCCcccccccccccccCHhhccccccccCCCCccccccccceeeEEEecCCCCcceeeehhhcCceeeeeee
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999887642
Q ss_pred ---CCc---ccCCCCeEEEEECCEEEEEeecCcccCCcccccccccccccCCcccccccccccceEEEEEEEeeCCceee
Q psy4067 313 ---NGE---ELSSPGVYLVFVNGILAGITCHHKEVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVV 386 (1384)
Q Consensus 313 ---~~~---~~~~~~~~~VflNG~~vG~~~~~i~ig~Psv~e~~~~~R~i~P~EcRlrd~TYsa~i~V~v~~~~~~~~~~ 386 (1384)
... ........+||+||+|+|+++++..+ ....+..|
T Consensus 505 ~~~~~~~~~~~~~~~~~~v~lng~~vg~~~~~~~~-----~~~~~~~~-------------------------------- 547 (1131)
T 4ayb_B 505 RRVTEGGEDQNEYLKWSKVILNGRLVGYYRDGEEL-----AKKIRERR-------------------------------- 547 (1131)
T ss_dssp HTTTTC-----CCCCCCEEEETTEEEEECSCHHHH-----HHHHHHHH--------------------------------
T ss_pred hhhcccccccchhhhhcceeecCceEEEeccchhh-----hhhhhhhh--------------------------------
Confidence 111 11112457899999999999887655 33222222
Q ss_pred eeeeeeccccceeccccccccCCcccccccceeeeeEEEeccccccchhhhHHhhccccccccCCChhhHHHHhhhcccc
Q psy4067 387 RSDLVIGRMPIMLQSSKCVLRNKTEYTSSSRRASTSSVTMHSQRTSPLLSCKKLRQKRFQTYKKTPVDDARDFLSSTCIA 466 (1384)
Q Consensus 387 ~~~V~IG~iPIMLrS~~CvL~g~~~~is~~~~~s~t~i~~~~~~~~P~~e~~~~~~~~~~~~~~~~~~ea~e~L~~~~Lp 466 (1384)
+ -|.++-.+ ++.
T Consensus 548 ~----~~~i~~~v-----------------------si~----------------------------------------- 559 (1131)
T 4ayb_B 548 R----KGEISDEV-----------------------NVG----------------------------------------- 559 (1131)
T ss_dssp H----HTSSCTTC-----------------------EEE-----------------------------------------
T ss_pred c----cCccCceE-----------------------EEe-----------------------------------------
Confidence 0 11111000 000
Q ss_pred ccccccccchhhhHHHHHHHHHHHHhhcCCCCCCCCccccCcEeeehhhHHHHHHHHHHHHHHHHHHhhccccceecccc
Q psy4067 467 HIPVINMRFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKETNLSGVVNLVSG 546 (1384)
Q Consensus 467 Hv~v~~~~~~~Ka~yLg~MvRr~l~~~~~~~~~DDrD~ygNKRlelAG~Lls~lFe~~fk~~~~~~k~~~~~~i~sl~~g 546 (1384)
T Consensus 560 -------------------------------------------------------------------------------- 559 (1131)
T 4ayb_B 560 -------------------------------------------------------------------------------- 559 (1131)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred ceeecccCceeEeecCcccccccCCCCCCCcccccCCCCCeEEEecccccCCcchhhhHHHhhcccccccccccceeecc
Q psy4067 547 WWFELKYGNKIYIRSPSRKLLAAGFSGPHSGRVRLMPEGPTILLNSCLRSGGKAQHEALYNAVQRHATKCCTLNFLFFLG 626 (1384)
Q Consensus 547 ~w~~~~~~n~~~i~t~~r~~~a~Gvh~sh~GRicp~pEgp~i~~~~~~~~~~~~~~~~~~~~lk~~~~~~~~~~~~~fl~ 626 (1384)
|.....-+..++.++ +||+| +|.+++ +.+.+ .+.+++.
T Consensus 560 -~~~~~~~~~~~i~~d-------------~~r~~----rpv~~~-----~~~~p-------~v~~~~~------------ 597 (1131)
T 4ayb_B 560 -HIVTDFINEVHVNCD-------------SGRVR----RPLIIV-----SNGNP-------LVTREDI------------ 597 (1131)
T ss_dssp -EECTTTCCEEEEECC-------------TTCEE----EEEEEB-----SSSSB-------SCCHHHH------------
T ss_pred -eccccccceeeeecC-------------Ccccc----cceEEe-----ecccc-------cccHHHH------------
Confidence 000001123667788 99999 888877 45555 2222222
Q ss_pred CCCCcccccccccceeeeEeeeccccccccccccccccCCCCCCCCCCCCCcccccccccccccccccccccCcEEEecc
Q psy4067 627 GGGILPSIQRQTTCLLTLILFSLNGDGKRGARNSQQYCDCPDGYSSGCQPRPTFLNMHQFLGFKRFDDFLYEGKIEYLDV 706 (1384)
Q Consensus 627 ~g~i~~~~~~~~~~~l~~v~v~~~~~l~~~~r~~r~~~d~~~~~~~gr~~rPl~~~~~~~~~~~~~~~~~~~~~~e~~~~ 706 (1384)
..+. .+...|++++..|.|||+|+
T Consensus 598 ------------------------~~~~--------------------------------~g~~~~~~~~~~g~veyvd~ 621 (1131)
T 4ayb_B 598 ------------------------EKLD--------------------------------SGSITFDDLVRQGKIEYLDA 621 (1131)
T ss_dssp ------------------------HHHH--------------------------------TTTCCHHHHHHTTSEEEEEH
T ss_pred ------------------------HHHh--------------------------------cCChhHHHHhhCCceeeeec
Confidence 1111 15567899999999999999
Q ss_pred CCCcceEEEeCCCCCCCccceeecccCcccccccchhhhhhcccccCCCCCCCCCCCCCCccchhhhhhccccccccccc
Q psy4067 707 NEGNDSHIAVSESGIRPGVTTHLEIAPFTLLGVCAGIELLQYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYN 786 (1384)
Q Consensus 707 ~e~~~~~ia~~~~~~~~~~~th~ei~p~~~l~v~a~~~~~~~~~~~~~~~lipf~~hNqspRn~yq~~m~kQ~~g~~~~~ 786 (1384)
+|++++.||+.++++.. .+||+||+|+++||++|+ +|||++|||||||+|||||+|||||++.+|
T Consensus 622 ~e~~~~~ia~~~~~~~~-~~th~ei~p~~il~v~a~--------------lipf~~~NqspRn~yq~~m~KQa~G~~~~~ 686 (1131)
T 4ayb_B 622 EEEENAYVALEPSDLTP-EHTHLEIWSPAILGITAS--------------IIPYPEHNQSPRNTYQSAMAKQALGLYAAN 686 (1131)
T ss_dssp HHHTTCCEESSGGGCCT-TCSEECSCGGGGSBTTGG--------------GCSSGGGSCHHHHHHHHHHGGGBCSCCCGG
T ss_pred cccceeEEEeecccccc-cccceeeccccccccccc--------------eecccccCccchheeccccccccCCceeec
Confidence 99999999999999887 699999999999999999 999999999999999999999999999999
Q ss_pred cccccccceeeeccCCCceeeccccccccCCCCCCCccccCCCCccchhhcccccceeEEeecccceeeecccccccccc
Q psy4067 787 QQNRIDTLMYNLVYAQRPMVESKTIRITNFHKLPAGKCQISPGGAEELTARESCHEVLKIISFSISVAVFDSVWLGDVKQ 866 (1384)
Q Consensus 787 ~~~R~D~~~~~l~~pQ~Piv~t~~~~~~~~~~~p~G~n~~~~~g~e~~~~~~~~~~vva~~~~~~~~~~~~~~~~~~~~~ 866 (1384)
++.|+|+++|+|+|||+|||+|+.++.+
T Consensus 687 ~~~r~D~~~~~l~ypQ~PlV~t~~~~~~---------------------------------------------------- 714 (1131)
T 4ayb_B 687 YQLRTDTRAHLLHYPQRPLVQTRALDII---------------------------------------------------- 714 (1131)
T ss_dssp GGTCCCSEEEEESSCCCCSSBCHHHHHH----------------------------------------------------
T ss_pred ceeeeccccceeecCCccccccchhhhh----------------------------------------------------
Confidence 9999999999999999999998444332
Q ss_pred cccccccccchhhcccccccccchhhhhhhccccceeeccccCCCCccccCCCCCCCccchhhhcccccccceeeecccc
Q psy4067 867 GVHQLSEEKEPRLLRKFQYFDVRTPYRLRRLLCWECVLYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQN 946 (1384)
Q Consensus 867 ~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~k~s~s~glIPF~~HNqSPRntyq~~M~KQAiG~~~yN~~~ 946 (1384)
T Consensus 715 -------------------------------------------------------------------------------- 714 (1131)
T 4ayb_B 715 -------------------------------------------------------------------------------- 714 (1131)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred ceeeeeeeeeccCCceeeeeeEeecccCCCCCCcceEEEEeeecccccccceeecccccccCCceeeEEecceeeeeecC
Q psy4067 947 RIDTLMYNLVYAQRPMVESKTIRITNFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYP 1026 (1384)
Q Consensus 947 RiDt~~~~L~ypQkPLV~T~~i~~~~~~elp~GqN~iVAvmsy~GYN~EDAIIiNkssidRG~~rs~~yr~~~~~i~~~~ 1026 (1384)
+++++|+|+|++||||||+||||||||||||++++||+|+|++|++|+++++++.
T Consensus 715 -------------------------~~~e~p~G~N~lVA~m~w~GYN~EDAIIine~~v~rg~ftSihi~~y~~e~r~~~ 769 (1131)
T 4ayb_B 715 -------------------------GYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYP 769 (1131)
T ss_dssp -------------------------TCTTSCCSEEEEEEECCCSSCCCTTCEEEEHHHHTTTTTCEEEEEEEEEECCCCT
T ss_pred -------------------------ccCCCCCceeEEEEEEccCCccHHHhhhhhcchhhcccceeeEEEEEEEEEEecC
Confidence 2456778999999999999999999999999999999999999999999999888
Q ss_pred CCccceeeCCccccCCCCCcccccccCCCCcccCCceeecCceEEeeeccCccccccccCCCccccccccccccccccce
Q psy4067 1027 NQTHDRILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEYKEVPVSYKGSVPSYLE 1106 (1384)
Q Consensus 1027 ~~~~d~i~~p~~~~~~~~p~~~~~~LDedGiv~~G~~V~~gDILIgKvsp~~~~~~~~~~~~e~k~~~~~~k~~~p~~vd 1106 (1384)
.+..|.+..|...+........+++||+||||++|++|++|||||||++|+.+.. +.+.
T Consensus 770 ~g~~e~it~~~p~v~~~~~~~~~~~LDe~Gii~iGa~V~~gDilvGKvtP~~~~~-------~~~~-------------- 828 (1131)
T 4ayb_B 770 GGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQ-------EFKE-------------- 828 (1131)
T ss_dssp TSCCCCCCCCCSSCSSCCCGGGGTTCCTTSBCCTTCEECTTCEEECCCCCCC----------------------------
T ss_pred CCCceEEecCCccccccchHHHhhcCCccccccCCcEecCCCEEEEEecCCcchh-------hhhh--------------
Confidence 8878878777655544445556899999999999999999999999999965431 0000
Q ss_pred EEEEecCcchhhhHHHhhhccccccccccccccCCCcceeeeEeecCCCCCCCCCCcCceeeCCCCCCCcccccceeeec
Q psy4067 1107 KVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGLKGCDRITEYKEVP 1186 (1384)
Q Consensus 1107 ~Vii~~~~~~~~~vki~irq~R~p~IGDKfssRHGqKGVis~ilp~eDMPfte~Gi~pDIIiNP~gvpsr~~i~~~~e~s 1186 (1384)
+ . + ....+|+|
T Consensus 829 -------------------------------------------------------~------~----~----~~~~~d~s 839 (1131)
T 4ayb_B 829 -------------------------------------------------------L------S----P----EQAKRDTS 839 (1131)
T ss_dssp -------------------------------------------------------------------------CCCCCCC
T ss_pred -------------------------------------------------------c------C----c----ceeeeeee
Confidence 0 0 0 01236788
Q ss_pred ccccCCccceeeEEEEecCCCCcEEEEEEEEeecCCCcCCcccccCCCceeEEEEeecCCCCCCCCCCcceEeeCCCCCC
Q psy4067 1187 VSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYP 1266 (1384)
Q Consensus 1187 ~~~k~~e~~~vd~V~i~~~~~~~~~vkV~ir~~R~p~iGDKfsSRHGQKGvvg~i~~qeDMPft~dGi~PDIIiNPhg~P 1266 (1384)
+.++..+.|+||.|.++.+++++++|||++|++|+|+||||||||||||||||+|+|+|||||++||++|||||||||||
T Consensus 840 l~~~~g~~g~Vd~v~~~~~~~~~~~vkV~i~~~R~~~vGDK~agRHGnKGvvs~i~p~eDMPf~~dG~~~DiilNP~gvP 919 (1131)
T 4ayb_B 840 IVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALP 919 (1131)
T ss_dssp EECCTTCCEEEEEEEEEECSSSCEEEEEEEEEEECCCTTCEEEETTSCEEEEEEEECTTTSEEETTSCCCSEECCTTSST
T ss_pred EEccCCCceEEEEEEEeeccCCceEEEEEEeccccCcccccccccccccceeeeecccccCCcCCCCCCccEEECCCCCc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccchhhhHHhhhhHHHhhcCCeeeeccCCCCCHHHHHHHHHHcCCCCCCceEEeeCCCCcEEEeeEeEeeehhhccccc
Q psy4067 1267 SRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQGKDIFYSGITGEALEAYIYSGPVYYQKLKHM 1346 (1384)
Q Consensus 1267 SRMTIGql~E~l~Gk~~~~~g~~~d~t~F~~~~~~~i~~~L~~~G~~~~Gke~lydG~TGe~l~~~IfiGp~YYqRLkHM 1346 (1384)
||||||||+|+++||+|++.|.+.|+|||.+...+++.+.|.++||+++|+|.||||+|||+|+++|||||+|||||+||
T Consensus 920 SRMniGqilE~~~gk~~~~~g~~~~atpf~~~~~e~~~~~l~~~g~~~~g~~~lydG~TGe~~~~~i~vG~~Yy~kL~Hm 999 (1131)
T 4ayb_B 920 SRMTLGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLHHM 999 (1131)
T ss_dssp TTTCHHHHHHHHHHHHHHHHCCCCBCCTTSSCCTHHHHHHHHHTTSCTTSEECEEETTTCCBCSSCEEEEEEEEEEBSCC
T ss_pred ccCcHHHHHHHHHHHHHHhCCCceecCccCCCcHHHHHHHHHHcCCCCCCCEEEeCCCCCCEecCcEEEEhhhhhccchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCccceeeccCCccccccCCCccccccCCCc
Q psy4067 1347 VQDKIHARSRGPRVVLTRQPTGRRWKLTFTP 1377 (1384)
Q Consensus 1347 V~DKiHaRsrGP~~~LTrQP~eGRsr~~~~~ 1377 (1384)
|+|||||||||||++|||||++||||+|||-
T Consensus 1000 V~DKihaRs~GP~s~~TqQPl~Gra~~GG~R 1030 (1131)
T 4ayb_B 1000 VADKIHARARGPVQILTRQPTEGRAREGGLR 1030 (1131)
T ss_dssp HHHHCEEESSCCBCTTTCCBCSSGGGTCCCE
T ss_pred hccCCEeeccCCCCCcccCCCCCcccCCCcc
Confidence 9999999999999999999999999999994
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=100.00 E-value=1.8e-151 Score=1444.27 Aligned_cols=739 Identities=24% Similarity=0.369 Sum_probs=568.2
Q ss_pred cccCCcccccccccccccCCcccccccccccceEEEEEEEeeCC-ceeeeeeeeeccccceeccccccccCCcccc----
Q psy4067 339 KEVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGS-QRVVRSDLVIGRMPIMLQSSKCVLRNKTEYT---- 413 (1384)
Q Consensus 339 i~ig~Psv~e~~~~~R~i~P~EcRlrd~TYsa~i~V~v~~~~~~-~~~~~~~V~IG~iPIMLrS~~CvL~g~~~~i---- 413 (1384)
+++|+|.+ +|+|||+||+||+|||||+++++.++ ..+.+++|+||+||||+..+.|++||..+.+
T Consensus 71 ~~l~~P~~----------~p~Ecr~r~lTYsapL~V~v~l~~~~~~~ik~~~V~iG~iPiMt~gGyFIING~ERVIVsQ~ 140 (1119)
T 2a6h_C 71 YRLGEPPF----------PQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFIINGADRVIVSQI 140 (1119)
T ss_dssp CCBCCCSS----------CHHHHHHTTCCCEEEBCCCEEECCSSSCCEECCCCCCCEEECCCTTSCCCSSSSCEEECEEE
T ss_pred EEEcCCCC----------CHHHHHhcCCcccceEEEEEEEEECCCceeeeeEEEecCCCeECCCcEEEEeCeEEEEEEEE
Confidence 56777764 79999999999999999999999864 4456678999999999999999999988874
Q ss_pred --c------------ccceeeeeEEEeccc------------------cccch---hhh------HH---hh--------
Q psy4067 414 --S------------SSRRASTSSVTMHSQ------------------RTSPL---LSC------KK---LR-------- 441 (1384)
Q Consensus 414 --s------------~~~~~s~t~i~~~~~------------------~~~P~---~e~------~~---~~-------- 441 (1384)
| +...++.+++..+++ +.+|+ ..| ++ ..
T Consensus 141 ~rspgv~~~~~~~~~g~~~ysa~ii~~rgs~l~~~~d~~~~i~vri~r~kIPi~ilLrALG~sD~eIl~~~~~~~~~~~t 220 (1119)
T 2a6h_C 141 HRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQG 220 (1119)
T ss_dssp EECSCEEEECCSSCSSCCEEEECCCSSSSCCEEEEEETTTEEEEESSSSEECHHHHHHHHTCCHHHHHHHHHSSCTTHHH
T ss_pred ecCCcEEEEeeccCCCceEEEEEEEeccCceEEEEEcCCCEEEEEEeCcceeHHHHHHHHCCCHHHHHHHHccCHHHHHH
Confidence 1 111122322222111 23453 000 00 00
Q ss_pred --c----------------cccccccCCChhhHHHHhhhcc-------ccccccccccchhh--h---------------
Q psy4067 442 --Q----------------KRFQTYKKTPVDDARDFLSSTC-------IAHIPVINMRFKMK--A--------------- 479 (1384)
Q Consensus 442 --~----------------~~~~~~~~~~~~ea~e~L~~~~-------LpHv~v~~~~~~~K--a--------------- 479 (1384)
. +++........+.|+++|.+.+ |+||+...+|++.+ +
T Consensus 221 l~~d~~~~~~~~eAl~~i~~~lr~g~~~~~e~a~~~l~~~ff~~~rydl~~vGr~~ln~kl~l~~~~~~~~~~~~~~l~~ 300 (1119)
T 2a6h_C 221 LMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKD 300 (1119)
T ss_dssp HSSCHHHHTCHHHHHHHHHHHSSSCCCSCCSSHHHHHTSSSSSSCCSCTTTSSHHHHHTTSCSCCSTTTTCCCSSSCCCC
T ss_pred HHhhhcccCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHhhCCcccccchhcchhhhhhhhccCCccccccccccccccH
Confidence 0 0111111234588999999988 89998765554431 1
Q ss_pred HHHHHHHHHHHHhhcCCC--CCCCCccccCcEeeehhhHHHHHHHHHHHHHHHHHHhhc-------------------cc
Q psy4067 480 MYLAVMIRRMVLALSDPD--MLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKETN-------------------LS 538 (1384)
Q Consensus 480 ~yLg~MvRr~l~~~~~~~--~~DDrD~ygNKRlelAG~Lls~lFe~~fk~~~~~~k~~~-------------------~~ 538 (1384)
.+|+.|+|+++++..|.. .+||+|||||||+++||+||+.||+++|++|.+++++.. ++
T Consensus 301 ~di~~mi~~Ll~l~~G~~~~~~DD~DhlgNkRv~~~GeLl~~~fr~~l~r~~~~i~~~~~~~~~~~~~~~~~i~~~~It~ 380 (1119)
T 2a6h_C 301 EVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDSLTPAKLVNSRPLEA 380 (1119)
T ss_dssp TTHHHHHHHHHHHHTSCSSCCCCCTTSTTTEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHSCSSCCSSTTTCCSHHHHH
T ss_pred HHHHHHHHHHHHhhcCCCCCCCcCcchhhceEehhhhHHHHHHHHHHHHHHHHHHHHHhhhhcccccchHHhhccchhHH
Confidence 347889999999999999 999999999999999999999999999999999998733 11
Q ss_pred cc-eeccccceeecccC-ceeEeecCccccc---------------ccCCCCCCCcccccC--CCCCeEEEecccccCCc
Q psy4067 539 GV-VNLVSGWWFELKYG-NKIYIRSPSRKLL---------------AAGFSGPHSGRVRLM--PEGPTILLNSCLRSGGK 599 (1384)
Q Consensus 539 ~i-~sl~~g~w~~~~~~-n~~~i~t~~r~~~---------------a~Gvh~sh~GRicp~--pEgp~i~~~~~~~~~~~ 599 (1384)
++ +.|+||+|+.--.+ |.....|.+|+.+ ++.+|+||||||||+ ||||+|.+
T Consensus 381 ~lk~ff~tg~lSQ~Ldq~N~ls~LsH~RRisslgpggl~re~k~~~vRdlHpShwGriCPiETPEG~ncGL--------- 451 (1119)
T 2a6h_C 381 AIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGL--------- 451 (1119)
T ss_dssp HHHHHHHTCSSEEECCCSSTHHHHHHHHEEESSSSSSSCCSSCCHHHHSCCGGGTTTBCSSCSCSSSSCSS---------
T ss_pred HHHHHhhccCccccccccchHhhhhhhheecccCCCccccccccCcccccCHhhCcccCCCcCCCCCcccc---------
Confidence 22 23678888744322 2221112223333 455799999999999 99999733
Q ss_pred chhhhHHHhhcccccccccccceeeccCCCCcccccccccceeeeEeeeccccccccccccccccCCCCCCCCCCCCCcc
Q psy4067 600 AQHEALYNAVQRHATKCCTLNFLFFLGGGGILPSIQRQTTCLLTLILFSLNGDGKRGARNSQQYCDCPDGYSSGCQPRPT 679 (1384)
Q Consensus 600 ~~~~~~~~~lk~~~~~~~~~~~~~fl~~g~i~~~~~~~~~~~l~~v~v~~~~~l~~~~r~~r~~~d~~~~~~~gr~~rPl 679 (1384)
+++.+++|.... ++|+. .+ .. .| +|+.
T Consensus 452 ---------VknLAl~a~I~~-~G~~e--------~p-----~~--~V-~nG~--------------------------- 478 (1119)
T 2a6h_C 452 ---------ITSLAAYARVDE-LGFIR--------TP-----YR--RV-VGGV--------------------------- 478 (1119)
T ss_dssp ---------EEEBCSSCEECS-SSCEE--------EE-----EE--EE-ETTE---------------------------
T ss_pred ---------hhhhhhheeecc-cCccc--------CC-----cE--EE-ECCE---------------------------
Confidence 333333322111 11100 00 00 00 1111
Q ss_pred cccccccccccccccccccCcEEEeccCCCcceEEEeCCCCCC---------------------CccceeecccCccccc
Q psy4067 680 FLNMHQFLGFKRFDDFLYEGKIEYLDVNEGNDSHIAVSESGIR---------------------PGVTTHLEIAPFTLLG 738 (1384)
Q Consensus 680 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~e~~~~~ia~~~~~~~---------------------~~~~th~ei~p~~~l~ 738 (1384)
| .+.||||+++|++..+||..+..+. +..+||+||+|++|||
T Consensus 479 ------------v-----~~~i~yl~a~ee~~~~i~~~~~~l~~gr~~r~~i~~r~~~e~~~~~~~~~~~~ei~P~~ils 541 (1119)
T 2a6h_C 479 ------------V-----TDEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFS 541 (1119)
T ss_dssp ------------E-----EEEEEEECHHHHHHSCEECTTSCBSSSBBCCSSEEEESSSSEEEECTTTCCEEECCTTTTSC
T ss_pred ------------E-----eeeeEEeChhcccceEEecCceeecCCccccCceeEEeccceeeechhHeEEEEeccccccc
Confidence 1 1357777777777777777644332 1257999999999999
Q ss_pred ccchhhhhhcccccCCCCCCCCCCCCCCccchhhhhhccccccccccccccccccceeeeccCCCceeeccccccccCCC
Q psy4067 739 VCAGIELLQYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITNFHK 818 (1384)
Q Consensus 739 v~a~~~~~~~~~~~~~~~lipf~~hNqspRn~yq~~m~kQ~~g~~~~~~~~R~D~~~~~l~~pQ~Piv~t~~~~~~~~~~ 818 (1384)
|||| ||||+||||||||||||||+||||| |..|+.|+|.|
T Consensus 542 v~as--------------lIPF~ehn~s~R~lmgsnM~kQAv~----------------l~~~~~p~vgT---------- 581 (1119)
T 2a6h_C 542 VNTN--------------LIPFLEHDDANRALMGSNMQTQAVP----------------LIRAQAPVVMT---------- 581 (1119)
T ss_dssp HHHH--------------TCTTGGGBCHHHHHHHHHHHTTBCC----------------BSSCCCCSEEC----------
T ss_pred cccc--------------cCCCcccCCCccccccccccccccc----------------ccccCCCeeec----------
Confidence 9999 9999999999999999999999999 88899999999
Q ss_pred CCCCccccCCCCccchhhcccccceeEEeecccceeeecccccccccccccccccccchhhcccccccccchhhhhhhcc
Q psy4067 819 LPAGKCQISPGGAEELTARESCHEVLKIISFSISVAVFDSVWLGDVKQGVHQLSEEKEPRLLRKFQYFDVRTPYRLRRLL 898 (1384)
Q Consensus 819 ~p~G~n~~~~~g~e~~~~~~~~~~vva~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 898 (1384)
|+|.++|+||+.+|+|.-++.+.|++...|.+.........|.
T Consensus 582 -----------g~e~~~a~ds~~~~~a~~~G~v~~vd~~~i~ir~~~~~~~~y~-------------------------- 624 (1119)
T 2a6h_C 582 -----------GLEERVVRDSLAALYAEEDGEVAKVDGNRIVVRYEDGRLVEYP-------------------------- 624 (1119)
T ss_dssp -----------SCHHHHHHHTTCSEECSSSEEEEEECSSBEEEEETTTEEECCB--------------------------
T ss_pred -----------cccceeeeccCceeEeccCCEEEEecCceEEEEccCCcceeEE--------------------------
Confidence 9999999999999999444444333333333322111122222
Q ss_pred ccceeeccccCCCCccccCCCCCCCccchhhhcccccccceeeeccccceeeeeeeeeccCCceeeeeeE----e-----
Q psy4067 899 CWECVLYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTI----R----- 969 (1384)
Q Consensus 899 ~~~~~~~~k~s~s~glIPF~~HNqSPRntyq~~M~KQAiG~~~yN~~~RiDt~~~~L~ypQkPLV~T~~i----~----- 969 (1384)
|..|...||. ++|||+|||+++.+ +
T Consensus 625 ---------------L~~~~rsnq~-------------------------------t~~~QkPiV~~g~~v~~g~~ladg 658 (1119)
T 2a6h_C 625 ---------------LRRFYRSNQG-------------------------------TALDQRPRVVVGQRVRKGDLLADG 658 (1119)
T ss_dssp ---------------CCCSEECTTS-------------------------------CEECCEECCCSSCCBCTTCEEEEC
T ss_pred ---------------eecccccccc-------------------------------ccccccceEeeCceeeccceeccc
Confidence 4444444442 48999999999864 2
Q ss_pred -ecccCCCCCCcceEEEEeeecccccccceeecccccccCCceeeEEecceeeeeecCCCccceeeCCccccCCCCCccc
Q psy4067 970 -ITNFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDRILGPLLEADTRKPVYR 1048 (1384)
Q Consensus 970 -~~~~~elp~GqN~iVAvmsy~GYN~EDAIIiNkssidRG~~rs~~yr~~~~~i~~~~~~~~d~i~~p~~~~~~~~p~~~ 1048 (1384)
.++++++|+|+|++||||||+||||||||||||++++||+|+|++++.|+++.++...+.++ +.... .......
T Consensus 659 ~~~~~gel~lG~N~lVA~m~~~GYN~EDAiiine~~v~rg~~tSihi~~~e~~~r~~~~g~ee-it~~i----p~~~~~~ 733 (1119)
T 2a6h_C 659 PASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPER-ITRDI----PHLSEAA 733 (1119)
T ss_dssp TTBSSSSBCCSEEEEEECSCCSSTTSSSEEEEETHHHHTTCSEEEEEEEEEEEEECCTTCCCB-CCSCC----SSSCSGG
T ss_pred cccCCCcccCceeEEEEEecccCCcchhhhhhhhhHHhcCCceEEEEEEEEeeeeecCCCcee-eeccC----CCcchhh
Confidence 36789999999999999999999999999999999999999999999999988876544433 22111 1112345
Q ss_pred ccccCCCCcccCCceeecCceEEeeeccCccccccccCCCccccccccccccccccceEEEEecCcchhhhHHHhhhccc
Q psy4067 1049 HRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTR 1128 (1384)
Q Consensus 1049 ~~~LDedGiv~~G~~V~~gDILIgKvsp~~~~~~~~~~~~e~k~~~~~~k~~~p~~vd~Vii~~~~~~~~~vki~irq~R 1128 (1384)
|++||+||||++|++|++|||||||++|+.+++ ++||++++.+.|.
T Consensus 734 ~~~LD~dGiv~iG~~V~~gDiLvgK~tP~~~~~----~~~ee~ll~aifg------------------------------ 779 (1119)
T 2a6h_C 734 LRDLDEEGVVRIGAEVKPGDILVGRTSFKGESE----PTPEERLLRSIFG------------------------------ 779 (1119)
T ss_dssp GSSCCSSSBCCTTCBCCTTSEEECCEEESSSSS----CCHHHHHHHHHHH------------------------------
T ss_pred hhccCCCcccCCCCEECCCCEEEEEecCCcccc----CChhhhhhhhhhc------------------------------
Confidence 899999999999999999999999999987653 4555544443321
Q ss_pred cccccccccccCCCcceeeeEeecCCCCCCCCCCcCceeeCCCCCCCcccccceeeecccccCCccceeeEEEEecCCC-
Q psy4067 1129 RPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGLKGCDRITEYKEVPVSYKGSVPSYLEKVLVSSNSE- 1207 (1384)
Q Consensus 1129 ~p~IGDKfssRHGqKGVis~ilp~eDMPfte~Gi~pDIIiNP~gvpsr~~i~~~~e~s~~~k~~e~~~vd~V~i~~~~~- 1207 (1384)
+ +...++|+|+.++..+.|+||+|.++.+++
T Consensus 780 -----~-------------------------------------------k~~~~rd~Sl~~~~~e~G~V~~V~~~~~~~~ 811 (1119)
T 2a6h_C 780 -----E-------------------------------------------KARDVKDTSLRVPPGEGGIVVRTVRLRRGDP 811 (1119)
T ss_dssp -----S-------------------------------------------CCCCEEECCEECCSSCCCEEEEEEEECSSCS
T ss_pred -----c-------------------------------------------cccccceeeEEccCCccEEEEEEEEEccCCC
Confidence 0 113468899999999999999999988776
Q ss_pred Cc-------EEEEEEEEeecCCCcCCcccccCCCceeEEEEeecCCCCCCCCCCcceEeeCCCCCCCccchhhhHHhhhh
Q psy4067 1208 DA-------FLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAG 1280 (1384)
Q Consensus 1208 ~~-------~~vkV~ir~~R~p~iGDKfsSRHGQKGvvg~i~~qeDMPft~dGi~PDIIiNPhg~PSRMTIGql~E~l~G 1280 (1384)
|. ++|||++|++|+|++|||||||||||||||+|+|+|||||++||++|||||||||||||||||||+||++|
T Consensus 812 g~~l~~~~~~~vkV~i~~~R~~~vGDKfasRHGqKGVis~i~p~eDMPf~~dG~~pDiIlNPhgvPSRMtiGqllE~~lG 891 (1119)
T 2a6h_C 812 GVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLG 891 (1119)
T ss_dssp SCCCCTTEEEEEEEEEEEEEECCTTCEEECTTSCEEEEEEEECTTTSCBCSSSCBCSEECCSTTTTTTTBTHHHHHHHHH
T ss_pred CcccCCCcceEEEEEEcccCCcccCchhhhccCCCceEEeeeccCCCccccCCCCccEEeCCCcCccccchhhhhHHHhh
Confidence 53 89999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCCeeeecc-CCCCCHHHHHHHHHHc-----------------------------CC--------------CCCC
Q psy4067 1281 KAGLMEGNYKEGTA-FGGTKLVDVQEELIRH-----------------------------GY--------------NYQG 1316 (1384)
Q Consensus 1281 k~~~~~g~~~d~t~-F~~~~~~~i~~~L~~~-----------------------------G~--------------~~~G 1316 (1384)
|||++.|... +|| |++.+++++.+.|.++ || +++|
T Consensus 892 ~a~~~~g~~~-atp~F~~~~~~~i~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~G 970 (1119)
T 2a6h_C 892 LAGYFLGQRY-ISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQG 970 (1119)
T ss_dssp HHHHHTTEEE-ECCTTTSCCHHHHHHHHHHHHHHHHHHHHHHTCCCBHHHHHHHHHHHTTTSSCTTSCHHHHHHHHHHTT
T ss_pred hHHhhcCCce-EecccCCCCHHHHHHHHHHhhhhccccccccccccchhhhhhhhhhhcCCcccccccchhhhcccCCCC
Confidence 9999999877 999 9999999999999999 99 9999
Q ss_pred ceEEeeCCCCcEEEeeEeEeeehhhccccccCccceeeccCCccccccCCCccccccCCCc
Q psy4067 1317 KDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTGRRWKLTFTP 1377 (1384)
Q Consensus 1317 ke~lydG~TGe~l~~~IfiGp~YYqRLkHMV~DKiHaRsrGP~~~LTrQP~eGRsr~~~~~ 1377 (1384)
|++||||+|||+|+++||+||+|||||+|||+|||||||+|||++|||||++||||.|||-
T Consensus 971 k~~lydG~TGe~~~~~I~vG~~Yy~kL~HmVdDKihaRs~GP~s~lTqQP~~Gra~~GGqR 1031 (1119)
T 2a6h_C 971 KVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQR 1031 (1119)
T ss_dssp EECCBCSSSCCBCSSCEEEEEEEEEEBCCCTTTSCEEESSCCBCSSSCSBCCCSSSCCCEE
T ss_pred ceEeecCCCCCCccceEEEEhHHhhcchhhcccCcEEeeccccceeecCCCcccccCCCee
Confidence 9999999999999999999999999999999999999999999999999999999999983
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=100.00 E-value=4e-139 Score=1316.50 Aligned_cols=642 Identities=25% Similarity=0.361 Sum_probs=481.1
Q ss_pred hhhHHHHHHHHHHHHhhcCCCCCCCCccccCcEeeehhhHHHHHHHHHHHHHHHHHHhhc---------------cccce
Q psy4067 477 MKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKETN---------------LSGVV 541 (1384)
Q Consensus 477 ~Ka~yLg~MvRr~l~~~~~~~~~DDrD~ygNKRlelAG~Lls~lFe~~fk~~~~~~k~~~---------------~~~i~ 541 (1384)
-+..++..+++.+++...|...+||+||+||||++++|+||+.||+.+|.++.+.+++.. ...++
T Consensus 420 Lt~~DIi~~i~~Li~l~~g~~~~DDiDHLgNrRvr~vGeLl~~qfr~~l~r~~r~i~~~~~~~~~~~~~~~~lin~~~i~ 499 (1342)
T 3lu0_C 420 LSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPIS 499 (1342)
T ss_dssp CCTTHHHHHHHHHHHHHHTSSCCCCSSSTTTSEEECHHHHHHHTHHHHHHHHHHHHTTHHHHCCSSCCSSTTTCCSSTTH
T ss_pred ecHHHHHHHHHHHHHHhhCCCCCcchhhhhcchhchHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCHHHHhccchHH
Confidence 445778888888888888888889999999999999999999999999999999998732 01122
Q ss_pred eccccceeecccC------ceeEee--------------cCccccc-ccCCCCCCCcccccC--CCCCeEEEecccccCC
Q psy4067 542 NLVSGWWFELKYG------NKIYIR--------------SPSRKLL-AAGFSGPHSGRVRLM--PEGPTILLNSCLRSGG 598 (1384)
Q Consensus 542 sl~~g~w~~~~~~------n~~~i~--------------t~~r~~~-a~Gvh~sh~GRicp~--pEgp~i~~~~~~~~~~ 598 (1384)
+.+...|+..... |..... |..+..+ ++.+|+||||||||+ ||||+|.+.
T Consensus 500 ~~~k~ffg~s~lSQ~lDqtNpLseltHkRRlsalGPGGLsr~~a~fevRdvH~thyGRiCPiETPEG~niGLI------- 572 (1342)
T 3lu0_C 500 AAVKEFFGSSQLSQFMVQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI------- 572 (1342)
T ss_dssp HHHTTTTTTCSSCEECCCSSHHHHHHHHSBEESCCSTTSCCSSCCTTTSSCCTTCSSSSCTTCCCSSSCSSSC-------
T ss_pred HHHHHHhCccccceeecCCCHHHHHhhhhcccccCCCCccccccCceecccCcccccccccccCCCCCceeee-------
Confidence 2222333322111 211111 2223333 466899999999999 999998442
Q ss_pred cchhhhHHHhhcccccccccccceeeccCCCCcccccccccceeeeEeeeccccccccccccccccCCCCCCCCCCCCCc
Q psy4067 599 KAQHEALYNAVQRHATKCCTLNFLFFLGGGGILPSIQRQTTCLLTLILFSLNGDGKRGARNSQQYCDCPDGYSSGCQPRP 678 (1384)
Q Consensus 599 ~~~~~~~~~~lk~~~~~~~~~~~~~fl~~g~i~~~~~~~~~~~l~~v~v~~~~~l~~~~r~~r~~~d~~~~~~~gr~~rP 678 (1384)
++.++++..+. .+.|++
T Consensus 573 -----------~sLA~~a~in~-----------------------------~Gfiet----------------------- 589 (1342)
T 3lu0_C 573 -----------NSLSVYAQTNE-----------------------------YGFLET----------------------- 589 (1342)
T ss_dssp -----------CBCCSSCCBCS-----------------------------SSCBCE-----------------------
T ss_pred -----------cchhheEEecc-----------------------------CCcccC-----------------------
Confidence 22222111111 133322
Q ss_pred ccccccccccccccccccccCcEEEeccCCCcceEEEeCCCCCC----------------------CccceeecccCccc
Q psy4067 679 TFLNMHQFLGFKRFDDFLYEGKIEYLDVNEGNDSHIAVSESGIR----------------------PGVTTHLEIAPFTL 736 (1384)
Q Consensus 679 l~~~~~~~~~~~~~~~~~~~~~~e~~~~~e~~~~~ia~~~~~~~----------------------~~~~th~ei~p~~~ 736 (1384)
++++..+-.-.+.|+||++.||+...||.....+. +..+||++++|.++
T Consensus 590 ---------Pyr~V~~g~v~~~i~yLsA~eE~~~~IAqan~~l~~~g~~~~~~v~~R~~~e~~~~~~~~v~~~dvsP~qi 660 (1342)
T 3lu0_C 590 ---------PYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQV 660 (1342)
T ss_dssp ---------EEEEEETTEEEEEEEEECTTTGGGSCBCCSSSCCSSSSCCSCSSEEEECSSCEEEECTTTCCEEESCTTTT
T ss_pred ---------CcEEEECCEEcCceeeCChHHhcCceEEecCcccCCCCcccCCeEEEEecCceEEeChHHCeeEecCHHHh
Confidence 22222222224569999999999999998765543 12689999999999
Q ss_pred ccccchhhhhhcccccCCCCCCCCCCCCCCccchhhhhhccccccccccccccccccceeeeccCCCceeeccccccccC
Q psy4067 737 LGVCAGIELLQYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITNF 816 (1384)
Q Consensus 737 l~v~a~~~~~~~~~~~~~~~lipf~~hNqspRn~yq~~m~kQ~~g~~~~~~~~R~D~~~~~l~~pQ~Piv~t~~~~~~~~ 816 (1384)
+||+|| ||||+|||+|+|++|||+|+|||+| |..|+.|||.|
T Consensus 661 vSvaas--------------lIPFLEhdDAnRaLMGsNMQRQAVP----------------Ll~~e~p~VgT-------- 702 (1342)
T 3lu0_C 661 VSVGAS--------------LIPFLEHDDANRALMGANMQRQAVP----------------TLRADKPLVGT-------- 702 (1342)
T ss_dssp SCHHHH--------------SCTTSTTBCHHHHHHHHHTTTTBCC----------------CSSCCCCSSBC--------
T ss_pred cchhhc--------------cCCCcccCCccccchhhhccccccc----------------cccCCCCeEec--------
Confidence 999999 9999999999999999999999999 99999999999
Q ss_pred CCCCCCccccCCCCccchhhcccccceeEEeecccceeeeccccccccc-------ccccccccccchhhcccccccccc
Q psy4067 817 HKLPAGKCQISPGGAEELTARESCHEVLKIISFSISVAVFDSVWLGDVK-------QGVHQLSEEKEPRLLRKFQYFDVR 889 (1384)
Q Consensus 817 ~~~p~G~n~~~~~g~e~~~~~~~~~~vva~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~d~~ 889 (1384)
|+|.++|+||+.+|+|.-++.+.|++.+.|.+.... .|+..|.
T Consensus 703 -------------G~E~~~a~dsg~~i~a~~~G~v~~vda~~I~Ir~~~~~~~~~~~~~~~y~----------------- 752 (1342)
T 3lu0_C 703 -------------GMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYN----------------- 752 (1342)
T ss_dssp -------------SCHHHHHHHTTTSCBCSSCBEECCCCSSBCCEEECSSSSSSSCCEEECCB-----------------
T ss_pred -------------ccchheeecCCceEEecCCCEEEEecCCeEEEEeCCCccccccCcceEEE-----------------
Confidence 999999999999999966666655555555554321 1122222
Q ss_pred hhhhhhhccccceeeccccCCCCccccCCCCCCCccchhhhcccccccceeeeccccceeeeeeeeeccCCceeeeeeE-
Q psy4067 890 TPYRLRRLLCWECVLYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTI- 968 (1384)
Q Consensus 890 ~~~~~~~~~~~~~~~~~k~s~s~glIPF~~HNqSPRntyq~~M~KQAiG~~~yN~~~RiDt~~~~L~ypQkPLV~T~~i- 968 (1384)
|+.|...||. .+|+|+|+|+++..
T Consensus 753 ------------------------L~kf~RSNq~-------------------------------Tc~~QrPiV~~G~~V 777 (1342)
T 3lu0_C 753 ------------------------LTKYTRSNQN-------------------------------TCINQMPCVSLGEPV 777 (1342)
T ss_dssp ------------------------CCCSCBCSSS-------------------------------CBCCCCBCCCSSCCB
T ss_pred ------------------------eccccccccc-------------------------------ccccccceeecCCEE
Confidence 6677777764 37999999999855
Q ss_pred ---ee------cccCCCCCCcceEEEEeeecccccccceeecccccccCCceeeEEecceeeeeecCCCccceeeCCccc
Q psy4067 969 ---RI------TNFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDRILGPLLE 1039 (1384)
Q Consensus 969 ---~~------~~~~elp~GqN~iVAvmsy~GYN~EDAIIiNkssidRG~~rs~~yr~~~~~i~~~~~~~~d~i~~p~~~ 1039 (1384)
++ ++.+|+|+|+|++||+|||.|||+|||||||++++++++|+|++++.|.++.+....+.++
T Consensus 778 ~~GdilADG~st~~GElaLG~N~lVAfMpW~GYNfEDAIlISErlV~eD~fTSIHIee~e~~aRdtklG~Ee-------- 849 (1342)
T 3lu0_C 778 ERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEE-------- 849 (1342)
T ss_dssp CTTCBCBCCSSCSSSSCCCSEECCEECCCCSSTTSSSEEEECTHHHHTTTSCEEEEEEEEEECCEETTEECC--------
T ss_pred ecCcEecccccccCCeeecccccEEEEecccCcccccchhhhhhhhhcCCceeEEEEEEeeeeeecCCCCce--------
Confidence 33 4889999999999999999999999999999999999999998887777666554443332
Q ss_pred cCCCC-Ccc---cccccCCCCcccCCceeecCceEEeeeccCccccccccCCCccccccccccccccccceEEEEecCcc
Q psy4067 1040 ADTRK-PVY---RHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEYKEVPVSYKGSVPSYLEKVLVSSNSE 1115 (1384)
Q Consensus 1040 ~~~~~-p~~---~~~~LDedGiv~~G~~V~~gDILIgKvsp~~~~~~~~~~~~e~k~~~~~~k~~~p~~vd~Vii~~~~~ 1115 (1384)
+|.+ |+. .+++||++|||++|++|++|||||||+||+.++ .++||+++++++|..+.....|.-
T Consensus 850 -iTrdIPnv~e~al~~LDe~GIv~iGa~V~~GDILVGKvtPkge~----~~tpEekLLraIFGeka~~vkDtS------- 917 (1342)
T 3lu0_C 850 -ITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGET----QLTPEEKLLRAIFGEKASDVKDSS------- 917 (1342)
T ss_dssp -CCSCCSSCCHHHHHSBCSSSCBCTTCCCCTTCEEECCCCBCCTT----TCCHHHHHGGGTSCSSSSSBCCCC-------
T ss_pred -ecccCCCCChHHHhcCCCCCCeecCcEECCCCEEEeccCCCCCC----cCChHHHHHHHHhcCcccccccCc-------
Confidence 2332 443 589999999999999999999999999999876 378999999998864433322211
Q ss_pred hhhhHHHhhhccccccccccccccCCCcceeeeEeecCCCCCCCCCCcCce-eeCCCCCCCcccc---------------
Q psy4067 1116 DAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDI-IMNPHGLKGCDRI--------------- 1179 (1384)
Q Consensus 1116 ~~~~vki~irq~R~p~IGDKfssRHGqKGVis~ilp~eDMPfte~Gi~pDI-IiNP~gvpsr~~i--------------- 1179 (1384)
+.-+||.+| ++.|+ +++-.+.......
T Consensus 918 --------------------L~vp~g~~G-----------------~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~ 960 (1342)
T 3lu0_C 918 --------------------LRVPNGVSG-----------------TVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL 960 (1342)
T ss_dssp --------------------EECCTTCCC-----------------EEEECCCCCCGGGCCCTHHHHHHHHHHHHHHHHH
T ss_pred --------------------EecCCCCcE-----------------EEEEEEEEecccccchhhhhHHHHHHHHHHHHhH
Confidence 112445444 33333 2221110000000
Q ss_pred -cce--------------------eee---ccc---c---cCCc----------------------cceeeEEE-Eec--
Q psy4067 1180 -TEY--------------------KEV---PVS---Y---KGSV----------------------PSYLEKVL-VSS-- 1204 (1384)
Q Consensus 1180 -~~~--------------------~e~---s~~---~---k~~e----------------------~~~vd~V~-i~~-- 1204 (1384)
.++ .+. .+. + .-.. ..+.+++. ++.
T Consensus 961 ~~~~~~l~~~~~~~l~~~l~~~g~t~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gd 1040 (1342)
T 3lu0_C 961 SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGD 1040 (1342)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTSCCHHHHTTSCGGGTTTCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCHHHHhhCCHHHhhccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCc
Confidence 000 000 000 0 0000 00000000 001
Q ss_pred --CCCCcEEEEEEEEeecCCCcCCcccccCCCceeEEEEeecCCCCCCCCCCcceEeeCCCCCCCccchhhhHHhhhhHH
Q psy4067 1205 --NSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAGKA 1282 (1384)
Q Consensus 1205 --~~~~~~~vkV~ir~~R~p~iGDKfsSRHGQKGvvg~i~~qeDMPft~dGi~PDIIiNPhg~PSRMTIGql~E~l~Gk~ 1282 (1384)
..+..++|||+||++|+|++|||||||||||||||+|+|+|||||++||++|||||||||||||||||||+||++|||
T Consensus 1041 ~l~~gv~k~VkV~ia~kRk~qvGDK~AgRHGnKGVis~I~p~EDMPf~~dG~~pDIIlNP~gvPSRMnIGqilE~~lG~a 1120 (1342)
T 3lu0_C 1041 DLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMA 1120 (1342)
T ss_dssp CCCSSSSCEEEEEEEEEECCCTTCEEECSSSCCEEECCCCCTTTSCEETTEEECSEECCGGGTTSSCBTHHHHHHHHHHG
T ss_pred ccCcCCceEEEEEEEEeccCCCCCCcccccCCCceEEEEecccCCCCCCCCCCCcEEeCCCCCCCccchhhhhHHhhhHH
Confidence 123578999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCe-----------------------------------------------------eeecc-CCCCCHHHHHHHHH
Q psy4067 1283 GLMEGNY-----------------------------------------------------KEGTA-FGGTKLVDVQEELI 1308 (1384)
Q Consensus 1283 ~~~~g~~-----------------------------------------------------~d~t~-F~~~~~~~i~~~L~ 1308 (1384)
|+..|.. ..+|| |+|.+.++|.+.|.
T Consensus 1121 a~~~G~~i~~~~~~~~~~~~~r~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~aTPvFdga~~~~i~~~L~ 1200 (1342)
T 3lu0_C 1121 AKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK 1200 (1342)
T ss_dssp GGTSSTHHHHTTTHHHHCTTTHHHHHHHTTTTCCCSSSCCTTTSCHHHHHHTTTTTSSCTTCBCCSSSSCCHHHHHHHTS
T ss_pred HHhcCchHHHHHHhhhhhHHHHHHHHHHhhcccccchhhhhcccchHHHHHHhhhhccCCcccCCCCCCCCHHHHHHHHH
Confidence 9987742 11676 99999999999999
Q ss_pred HcCCCCCCceEEeeCCCCcEEEeeEeEeeehhhccccccCccceeeccCCccccccCCCccccccCCCc
Q psy4067 1309 RHGYNYQGKDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTGRRWKLTFTP 1377 (1384)
Q Consensus 1309 ~~G~~~~Gke~lydG~TGe~l~~~IfiGp~YYqRLkHMV~DKiHaRsrGP~~~LTrQP~eGRsr~~~~~ 1377 (1384)
++||+++||++||||+|||+|+++||||++|||||+|||+|||||||+|||++|||||++||||+|||-
T Consensus 1201 ~aG~~~~Gk~~LydGrTGe~f~~~V~vG~~YylKL~HmVdDKiHaRs~GPysllTqQPl~Gkaq~GGqR 1269 (1342)
T 3lu0_C 1201 LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQR 1269 (1342)
T ss_dssp SSSSCSSSCBCCBCSSSCSBCSSCBCEECCEEEEBCCCGGGSCCCBSSCCBCSSSCCBCCCSSSCCCCC
T ss_pred HcCCCCCCCEEEEcCCCCCCcccceeeeehhHhhhhhccccceEEeccCCCcccccCCCCccccCCCee
Confidence 999999999999999999999999999999999999999999999999999999999999999999994
No 6
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=3e-72 Score=721.65 Aligned_cols=336 Identities=27% Similarity=0.387 Sum_probs=231.9
Q ss_pred cccCCcccccccccccccCCcccccccccccceEEEEEEEeeCCce-----------------eeeeeeeeccccceecc
Q psy4067 339 KEVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQR-----------------VVRSDLVIGRMPIMLQS 401 (1384)
Q Consensus 339 i~ig~Psv~e~~~~~R~i~P~EcRlrd~TYsa~i~V~v~~~~~~~~-----------------~~~~~V~IG~iPIMLrS 401 (1384)
+++|+|++.+.+...++++|+|||+||+||+|||+|+|+|+.++.. ...+.+.||+|||||||
T Consensus 82 i~v~kP~~~e~d~~~~~l~P~EcRlR~lTYsapl~Vdi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IG~iPIMlrS 161 (1210)
T 3h0g_B 82 IYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRS 161 (1210)
T ss_dssp EECCCCCCBCTTSCBCCCCTTTTTTTCCCCEEEEEEEEEC---------------------CCSSCCCEEEEEEECCSSS
T ss_pred EEEcCCceecCCCcccccCHHHHHhcCCccceeEEEEEEEEEcCccccccccccccccccccccccceEEEecCCEEeCC
Confidence 6799999998888889999999999999999999999999976521 23457999999999999
Q ss_pred ccccccCCccc-----------------ccccc-------------e--------------eeee----------E-EE-
Q psy4067 402 SKCVLRNKTEY-----------------TSSSR-------------R--------------ASTS----------S-VT- 425 (1384)
Q Consensus 402 ~~CvL~g~~~~-----------------is~~~-------------~--------------~s~t----------~-i~- 425 (1384)
+.|+|+|+++. +++++ + +... + ..
T Consensus 162 ~~C~L~g~s~~eL~~~gEcp~D~GGYFIING~EKVII~qerla~N~~iv~~~~~~~~~~~~a~irS~~~~~~~~~s~~~v 241 (1210)
T 3h0g_B 162 TFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQI 241 (1210)
T ss_dssp TTSSSSSCCHHHHHHTTCCTTCCCCCBCGGGSCBCCCBCBCCCCSCCCCCCCCCSSSCCCCCCCCCCCCSSSCCCCCCCC
T ss_pred CcccCCCCCHHHHHhcCCCCCCCCCEEEEeCEEEEEEechhhccceEEEEeecCCCCceEEEEEEEEecCCccceeEEEE
Confidence 99999999874 13332 1 0000 0 00
Q ss_pred --ec------c----------ccccch-------------hhhHHh-----------------h---------------c
Q psy4067 426 --MH------S----------QRTSPL-------------LSCKKL-----------------R---------------Q 442 (1384)
Q Consensus 426 --~~------~----------~~~~P~-------------~e~~~~-----------------~---------------~ 442 (1384)
.. + ...+|+ +-.+.+ . .
T Consensus 242 ~~~~~~~~~~~~~i~~~~~~~~~~IPi~ivlkALg~~sD~EI~~~I~~~~~d~~~~~~l~~slee~~~i~tq~~aL~yIG 321 (1210)
T 3h0g_B 242 KLMARNTENSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQDKDIALDYIG 321 (1210)
T ss_dssp CCCCCCTTSCSCCCCCCCTTSCSCCCSHHHHTTTTCCSTTHHHHHHCCSSCCHHHHHTHHHHHHTTSSCCSSHHHHHTTC
T ss_pred EEEeccccCCCceEEEEEeccccCCcHHHHHHHcCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHhhhcCCHHHHHHHHH
Confidence 00 0 011452 000000 0 0
Q ss_pred ccccc---ccCCChhhHHHHhhhccccccccccccchhhhHHHHHHHHHHHHhhcCCCCCCCCccccCcEeeehhhHHHH
Q psy4067 443 KRFQT---YKKTPVDDARDFLSSTCIAHIPVINMRFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGSLLSL 519 (1384)
Q Consensus 443 ~~~~~---~~~~~~~ea~e~L~~~~LpHv~v~~~~~~~Ka~yLg~MvRr~l~~~~~~~~~DDrD~ygNKRlelAG~Lls~ 519 (1384)
++|+. .+..+++.|+++|++++|||+++...+++.||+|||+|+||++++.+|.+.+|||||||||||+|||+||+.
T Consensus 322 ~r~~~~~~~~~~~~~~a~~iL~~~lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~l~G~Ll~~ 401 (1210)
T 3h0g_B 322 KRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLAS 401 (1210)
T ss_dssp CCSSSCCCCHHHHHHHHHHHHTTTSSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBCCHHHHHHH
T ss_pred HhccccCCCchhHHHHHHHHHHhhEEeCcCCCccchhHHHHHHHHHHHHHHHHhCCCCCCCCCccccCeEEecHHHHHHH
Confidence 23322 112245899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhc---------------------cccc-eeccccceeecccC-----------ceeEeecC---c
Q psy4067 520 MFEDVFKRFNSELKETN---------------------LSGV-VNLVSGWWFELKYG-----------NKIYIRSP---S 563 (1384)
Q Consensus 520 lFe~~fk~~~~~~k~~~---------------------~~~i-~sl~~g~w~~~~~~-----------n~~~i~t~---~ 563 (1384)
||+++|++|++++++.. ++++ ++|+||||++++.+ ++++..+. .
T Consensus 402 lfr~~~~~~~~~i~~~l~k~~~~~~~~~~~~~i~~~~It~~l~~~laTGNW~~~kk~~~~~sGvsqvl~R~n~~s~lShl 481 (1210)
T 3h0g_B 402 LFRMLFRKMTRDVYKYMQKCVETNREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHL 481 (1210)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTCCSCCCTTSSCSTTTSHHHHHHHSSSCSSTTSSCCSCCCCSCCBCCCSSHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCccCHHHhcchhhhHHHHHHHhhcCCcccccccccCcCCEEEEcccCCHHHHHHHH
Confidence 99999999999998732 1223 46999999987643 12111111 1
Q ss_pred cccc-----------ccCCCCCCCcccccC--CCCCeEEE--ec---ccccCCcc---hhhhHHHhhcccccc-----cc
Q psy4067 564 RKLL-----------AAGFSGPHSGRVRLM--PEGPTILL--NS---CLRSGGKA---QHEALYNAVQRHATK-----CC 617 (1384)
Q Consensus 564 r~~~-----------a~Gvh~sh~GRicp~--pEgp~i~~--~~---~~~~~~~~---~~~~~~~~lk~~~~~-----~~ 617 (1384)
|+.+ ++..|++|||++||+ |||+.|.+ ++ |..+++.+ +++.+..+ .-+.+. ..
T Consensus 482 Rrv~~p~~~~~K~~~~R~Lhpt~WG~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~pI~~~l~~~-gme~le~~~~~~~ 560 (1210)
T 3h0g_B 482 RRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEW-GLETLEDYNPSAS 560 (1210)
T ss_dssp TBBCCSCCSSCCSSSSSSCCGGGTTTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSSHHHHHHHSS-SCCCCSCCCSSSS
T ss_pred HhccCchhhccccccccccChhhheeeccccCCCCCcccccccccceeeeECCCCcHHHHHHHHHh-CCcchhhcCcccC
Confidence 2222 455699999999999 99997544 33 44555533 44433322 112221 12
Q ss_pred cccceeeccCCCCcccccccccceee-----------eEeeeccccccccccccccccCCCCCCCCCCCCCcccccccc
Q psy4067 618 TLNFLFFLGGGGILPSIQRQTTCLLT-----------LILFSLNGDGKRGARNSQQYCDCPDGYSSGCQPRPTFLNMHQ 685 (1384)
Q Consensus 618 ~~~~~~fl~~g~i~~~~~~~~~~~l~-----------~v~v~~~~~l~~~~r~~r~~~d~~~~~~~gr~~rPl~~~~~~ 685 (1384)
+..+.+||+ | .|-..++.+..+.. ..+|++.+++++ |++++|+| +||.+||+|++..+
T Consensus 561 ~~~tkVfvN-G-~wVGvh~dp~~Lv~~lR~lRR~g~Is~eVSIvrdir~--rE~~IfTD------aGRv~RPLfvVen~ 629 (1210)
T 3h0g_B 561 PNATKVFVN-G-VWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIRE--KELRLFTD------AGRICRPLFIVDNN 629 (1210)
T ss_dssp SSSCCCCST-T-CCCCCCSCHHHHHHHHHHHHTTTSSCTTCCCCCCTTT--CCCCCCCS------SCCBCCEEEECCCS
T ss_pred CCceEEEEC-C-EEEEEeCCHHHHHHHHHHHhhcCCCCCceEEEecCCC--CeEEEecC------CCcccceEEEEccC
Confidence 455668885 3 33333333332222 237888888876 89999999 99999999987754
No 7
>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=100.00 E-value=4.4e-69 Score=687.46 Aligned_cols=231 Identities=12% Similarity=0.088 Sum_probs=173.2
Q ss_pred EEEEEE-ecceeeEeccchhe----eccccccccchHHHHhhhccccc-----------cceecccccccccccccccce
Q psy4067 32 YIFFLL-EGLQAILFLPLFKQ----VDFGDSKVVSLRELLSHVTYQKR-----------LYRLTVQPNWLGTVKAVHGTY 95 (1384)
Q Consensus 32 ~~~~~~-~~~~~~~~~~~~~~----~~~~~~~~~sd~~~~~~i~~~~~-----------~~~~~~~~~~~~~~~~~~g~~ 95 (1384)
++-|.. ..-.+.+-++. +. |+|||||+ ||+||+++|++|.. +.+++.||.+|+++- +||+-
T Consensus 171 ~l~~~~d~~~~i~vri~r-~kIPi~ilLrALG~-sD~eIl~~~~~~~~~~~tl~~d~~~~~~~~eAl~~i~~~l-r~g~~ 247 (1119)
T 2a6h_C 171 WIDLEVEPNGVVSMKVNK-RKFPLVLLLRVLGY-DQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFTLL-RPGDP 247 (1119)
T ss_dssp CEEEEEETTTEEEEESSS-SEECHHHHHHHHTC-CHHHHHHHHHSSCTTHHHHSSCHHHHTCHHHHHHHHHHHS-SSCCC
T ss_pred eEEEEEcCCCEEEEEEeC-cceeHHHHHHHHCC-CHHHHHHHHccCHHHHHHHHhhhcccCCHHHHHHHHHHHh-cCCCC
Confidence 555554 44456677888 55 89999999 99999999998864 346889999999884 47731
Q ss_pred eeeeccccccCCCCHHHHHHHHHHHHHHHhcCccccccCh-----------h------h-------HHHHHHHHHHHHHh
Q psy4067 96 LTMVTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDS-----------F------D-------YFINVEIKKLMQAN 151 (1384)
Q Consensus 96 ~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~kgl~~~hi~~-----------~------~-------~f~~~~i~~~~~~~ 151 (1384)
.+.| .+.+...+. |+..+-.-++|++. . + ..+.+|+++++.+.
T Consensus 248 ---~~~e-----~a~~~l~~~-----ff~~~rydl~~vGr~~ln~kl~l~~~~~~~~~~~~~~l~~~di~~mi~~Ll~l~ 314 (1119)
T 2a6h_C 248 ---PKRD-----KAVAYVYGL-----IADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALT 314 (1119)
T ss_dssp ---SCCS-----SHHHHHTSS-----SSSSCCSCTTTSSHHHHHTTSCSCCSTTTTCCCSSSCCCCTTHHHHHHHHHHHH
T ss_pred ---CcHH-----HHHHHHHHh-----hCCcccccchhcchhhhhhhhccCCccccccccccccccHHHHHHHHHHHHHhh
Confidence 1112 122222111 10000001223321 1 1 12567999999998
Q ss_pred cCcC---CCCChhhhhhHHhhhhcchhhh-----------c----ccccccccccccccchhhHHHHHHHHHHhCCcccc
Q psy4067 152 ANIY---SDVDPLFYLKYLDIHVGIADKI-----------I----PKIKAAQFDIVNHMRQDTITNALTAAIQTGNWTIR 213 (1384)
Q Consensus 152 ~~~~---~d~~d~f~~k~~d~~~~~~~k~-----------~----~~~~~~~~~~~~~~~~~~IT~~l~~alsTGNW~~~ 213 (1384)
.+.. .||.|||+|||+++.|..++.. + .+...+.+++..+++++.||++|+++|+|||
T Consensus 315 ~G~~~~~~DD~DhlgNkRv~~~GeLl~~~fr~~l~r~~~~i~~~~~~~~~~~~~~~~~i~~~~It~~lk~ff~tg~---- 390 (1119)
T 2a6h_C 315 AGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQ---- 390 (1119)
T ss_dssp TSCSSCCCCCTTSTTTEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHSCSSCCSSTTTCCSHHHHHHHHHHHHTCS----
T ss_pred cCCCCCCCcCcchhhceEehhhhHHHHHHHHHHHHHHHHHHHHHhhhhcccccchHHhhccchhHHHHHHHhhccC----
Confidence 8765 4888999999999988543311 1 1112346777788899999999999999986
Q ss_pred cccccccceeeeecccchhhcccccccccc----cccccccccCCCcCCCCCcccccCCCCCCCccccchhhcccccccc
Q psy4067 214 RFKMERQGVTQVLSRLSYISGLGMMTRINS----QFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHIT 289 (1384)
Q Consensus 214 ~~~~~r~GvsQvL~Rln~ls~lshlrRv~s----~~~~~~K~~~pR~LhpsqwG~iCP~eTPEG~~cGLVKnLAl~a~It 289 (1384)
|||+|+|+||+|+|||+||+|+ ++++++|.++||+||||||||+||+|||||+|||||||||+||+|+
T Consensus 391 --------lSQ~Ldq~N~ls~LsH~RRisslgpggl~re~k~~~vRdlHpShwGriCPiETPEG~ncGLVknLAl~a~I~ 462 (1119)
T 2a6h_C 391 --------LSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVD 462 (1119)
T ss_dssp --------SEEECCCSSTHHHHHHHHEEESSSSSSSCCSSCCHHHHSCCGGGTTTBCSSCSCSSSSCSSEEEBCSSCEEC
T ss_pred --------ccccccccchHhhhhhhheecccCCCccccccccCcccccCHhhCcccCCCcCCCCCcccchhhhhhheeec
Confidence 5899999999999999999999 5999999999999999999999999999999999999999999998
Q ss_pred c
Q psy4067 290 T 290 (1384)
Q Consensus 290 ~ 290 (1384)
.
T Consensus 463 ~ 463 (1119)
T 2a6h_C 463 E 463 (1119)
T ss_dssp S
T ss_pred c
Confidence 4
No 8
>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=100.00 E-value=1.9e-64 Score=655.97 Aligned_cols=335 Identities=28% Similarity=0.379 Sum_probs=219.6
Q ss_pred cccCCcccccccccccccCCcccccccccccceEEEEE--EEeeCCce----e-------e------eeeeeecccccee
Q psy4067 339 KEVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDI--EYTRGSQR----V-------V------RSDLVIGRMPIML 399 (1384)
Q Consensus 339 i~ig~Psv~e~~~~~R~i~P~EcRlrd~TYsa~i~V~v--~~~~~~~~----~-------~------~~~V~IG~iPIML 399 (1384)
+++++|++.+.+...++++|+|||+||+||+|||||++ +++++++. . . +++|+||+|||||
T Consensus 95 i~l~~P~~~e~~~~~~~l~P~EcRlR~lTYsapl~v~v~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~v~iG~iPIMl 174 (1224)
T 1twf_B 95 IYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIML 174 (1224)
T ss_dssp CEEEEEEECCSSSCCEECCHHHHHHTTCCCEEEEECCEECCCCC-------------------------CCEEEEEECCT
T ss_pred EEEeCCceeccCCccccCCHHHHhhcCCccceeEEEEEEEEEEeCCcccccccccccccccccccccceeeEeCCCCeEe
Confidence 67899999888777889999999999999999999999 66655432 1 1 4579999999999
Q ss_pred ccccccccCCccc-----------------ccccce-------------------------eeeeEEE------------
Q psy4067 400 QSSKCVLRNKTEY-----------------TSSSRR-------------------------ASTSSVT------------ 425 (1384)
Q Consensus 400 rS~~CvL~g~~~~-----------------is~~~~-------------------------~s~t~i~------------ 425 (1384)
||+.|+|+|+++. +|++++ +..++++
T Consensus 175 rS~~C~L~~~s~~el~~~gEcp~D~GGYFIING~ERVIv~Qe~~s~N~i~~~~~~~~~~~~~~~~irsv~~~~~~~~~~~ 254 (1224)
T 1twf_B 175 RSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTL 254 (1224)
T ss_dssp TSTTSGGGTCCHHHHHHTTCCTTCCCCSEEETTEEEEECEEEEECSSCCEEEECCTTSSEEEEEEEECCCSSSCCCCCEE
T ss_pred ccCcccCCCCCHHHHHhhccCccCCCCEEEEeCcEEEEEEeeeccCCeEEEEeccCCCcceEEEEEEEEeccCCcceeEE
Confidence 9999999999884 133321 0111111
Q ss_pred --e--c-----c----------ccccchh------------h-hHHhh-----------------c--------------
Q psy4067 426 --M--H-----S----------QRTSPLL------------S-CKKLR-----------------Q-------------- 442 (1384)
Q Consensus 426 --~--~-----~----------~~~~P~~------------e-~~~~~-----------------~-------------- 442 (1384)
. . . ...+|+. | .+.+. .
T Consensus 255 ~l~~~~~~~~~~~~i~vr~~~~k~~IPi~illkALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~e~~~~~t~~~AL~yI 334 (1224)
T 1twf_B 255 QVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFI 334 (1224)
T ss_dssp EEEEESCSSCSSCCEEEECTTCSSCEEHHHHHHHTTCCSHHHHHHHHCCCTTCHHHHHHHHHHHHHTTTCCSHHHHHHHH
T ss_pred EEEEeccccCCCCEEEEEEecccccccHHHHHHHhcCCCHHHHHHHhcccCCcHHHHHHHHHHHHHhhhcCCHHHHHHHH
Confidence 0 1 0 1114520 0 00000 0
Q ss_pred -cc-ccc--ccCCChhhHHHHhhhccccccccccccchhhhHHHHHHHHHHHHhhcCCCCCCCCccccCcEeeehhhHHH
Q psy4067 443 -KR-FQT--YKKTPVDDARDFLSSTCIAHIPVINMRFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGSLLS 518 (1384)
Q Consensus 443 -~~-~~~--~~~~~~~ea~e~L~~~~LpHv~v~~~~~~~Ka~yLg~MvRr~l~~~~~~~~~DDrD~ygNKRlelAG~Lls 518 (1384)
++ +.. .+..+++.|+++|++.+||||+....+...|++|||+|+|+++++.+|...+|||||||||||+|||+||+
T Consensus 335 g~r~~~~g~~~~~~~~~a~~iL~~~~l~Hvg~~~~~~~~K~~~L~~mi~kLl~~~~g~~~~DD~DhlgnkRv~l~G~Ll~ 414 (1224)
T 1twf_B 335 GRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLA 414 (1224)
T ss_dssp HHTTSCTTSCHHHHHHHHHHHHHHTSSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEECHHHHHH
T ss_pred HHhhccCCCCCccHHHHHHHHHHhhcccccCCCccccccHHHHHHHHHHHHHHHhcCCCCCCCCccccccEEehhhHHHH
Confidence 11 111 01123578999999999999999877779999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhc---------------------cccc-eeccccceeecccC-----------ceeEeecC---
Q psy4067 519 LMFEDVFKRFNSELKETN---------------------LSGV-VNLVSGWWFELKYG-----------NKIYIRSP--- 562 (1384)
Q Consensus 519 ~lFe~~fk~~~~~~k~~~---------------------~~~i-~sl~~g~w~~~~~~-----------n~~~i~t~--- 562 (1384)
.||+++|++|++++++.. ++++ ++|+||||++++.+ ++++..+.
T Consensus 415 ~lfr~~~~r~~~~i~~~l~~~~~~~~~~~~~~~i~~~~It~~lk~~~aTGNw~~~k~~~~~~sGvSQvldr~n~ls~LSH 494 (1224)
T 1twf_B 415 QLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSH 494 (1224)
T ss_dssp HHHHHHHHHHHHHHHHHHHSCCC--------CCCCTHHHHHHHHHHHHHCCCC---------CCCEEECCCSSHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhcccchhhcchhheeeccccccccccccccceeEeecccchhhhhhh
Confidence 999999999999998733 1223 35889999987653 22222221
Q ss_pred ccccc-----------ccCCCCCCCcccccC--CCCCeEEE--ec---ccccCCcc---hhhhHHHhhcccccc-----c
Q psy4067 563 SRKLL-----------AAGFSGPHSGRVRLM--PEGPTILL--NS---CLRSGGKA---QHEALYNAVQRHATK-----C 616 (1384)
Q Consensus 563 ~r~~~-----------a~Gvh~sh~GRicp~--pEgp~i~~--~~---~~~~~~~~---~~~~~~~~lk~~~~~-----~ 616 (1384)
+|+.+ ++.+|+||||||||+ ||||+|.+ ++ |..+++.+ +++.+... .-+.+. .
T Consensus 495 ~RRi~~~~~r~~k~~~~R~LHpshwG~iCPiETPEG~~cGLVknLAl~a~Is~g~~~~pi~~~l~~~-G~~~l~e~~~~~ 573 (1224)
T 1twf_B 495 LRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEW-GMEPLEDYVPHQ 573 (1224)
T ss_dssp HTEEECCC------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCHHHHHHHHHT-TCEEGGGCCGGG
T ss_pred hhcccccccccccccccccccCccceeecCCCCCCCcccchhhhHHhhCcccCCCCHHHHHHHHHHc-CCcceeeccccc
Confidence 13332 455799999999999 99997543 43 33444432 33333322 111111 1
Q ss_pred ccccceeeccCCCCccccccccccee-----------eeEeeeccccccccccccccccCCCCCCCCCCCCCccccccc
Q psy4067 617 CTLNFLFFLGGGGILPSIQRQTTCLL-----------TLILFSLNGDGKRGARNSQQYCDCPDGYSSGCQPRPTFLNMH 684 (1384)
Q Consensus 617 ~~~~~~~fl~~g~i~~~~~~~~~~~l-----------~~v~v~~~~~l~~~~r~~r~~~d~~~~~~~gr~~rPl~~~~~ 684 (1384)
.++.+.+||++- +.+ .+..+..+. -.-+|++..+++. +++++|+| +||.+||+|++..
T Consensus 574 ~~~~~kVfvnG~-~vG-~~~~p~~lv~~lr~lRR~g~i~~evsiv~d~r~--~ei~I~TD------~GRv~RPl~vV~~ 642 (1224)
T 1twf_B 574 SPDATRVFVNGV-WHG-VHRNPARLMETLRTLRRKGDINPEVSMIRDIRE--KELKIFTD------AGRVYRPLFIVED 642 (1224)
T ss_dssp CTTCEEEEETTE-EEE-EESCHHHHHHHHHHHHHHTSSCTTCEEEEETTT--TEEEEECC------SCCEEEEEEEEEC
T ss_pred CCCceEEEECCE-EEE-EeCCHHHHHHHHHHHHhccCCCCeEEEEEeccc--CeEEEecc------CceeeeeEEEecC
Confidence 134566776632 222 121111111 1125667777765 78999999 9999999997654
No 9
>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=100.00 E-value=4.4e-59 Score=608.11 Aligned_cols=486 Identities=23% Similarity=0.337 Sum_probs=307.6
Q ss_pred cccCCcccccccccccccCCcccccccccccceEEEEEEEeeCCceeeeeeeeeccccceeccccccccCCccc------
Q psy4067 339 KEVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDLVIGRMPIMLQSSKCVLRNKTEY------ 412 (1384)
Q Consensus 339 i~ig~Psv~e~~~~~R~i~P~EcRlrd~TYsa~i~V~v~~~~~~~~~~~~~V~IG~iPIMLrS~~CvL~g~~~~------ 412 (1384)
+++|+|.+.+.+...++++|+|||+||+||+|||+|++.++.++..+.+++|+||+||||++|+.|+|+|+++.
T Consensus 66 ~~l~~P~~~e~d~~~~~l~P~EcR~r~~TYsapl~v~v~~~~~~~~~~~~~v~lG~iPiM~~S~~C~L~~~s~~el~~~g 145 (1131)
T 4ayb_B 66 IRIGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAEPEEVYIGDLPIMLKSAIDPISQYTLDKLIEIG 145 (1131)
T ss_dssp EEECCSEEEETTTEEEECCHHHHHHHTCCCEEEEEEEEEEEETTEECCCEEEEEEEEECCTTSTTSGGGGCCHHHHHHHT
T ss_pred EEEeCCeeecCCCCcCccCHHHHHhcCCCccceEEEEEEEEECCcEEEEEEEEEEECCEEeCCCcccCCCCCHHHHHhcC
Confidence 56899999988888889999999999999999999999999999888889999999999999999999998874
Q ss_pred -----------ccccce-------------------------eeeeEEEecccc-----------------------ccc
Q psy4067 413 -----------TSSSRR-------------------------ASTSSVTMHSQR-----------------------TSP 433 (1384)
Q Consensus 413 -----------is~~~~-------------------------~s~t~i~~~~~~-----------------------~~P 433 (1384)
+|++++ ++.+++...+.| .+|
T Consensus 146 Ec~~D~GGyFIING~ERVIv~Q~~~spn~~~~~~~~~~~~~~~~a~ii~~~~~~~~~~~i~~~~~~~~~v~~~~~~~~iP 225 (1131)
T 4ayb_B 146 EDPKDPGGYFIVNGSERVIVTQEDLAPNRVLVDTGKTGSNITHTAKIISSTAGYRVPVTIERLKDGTFHVSFPAVPGKIP 225 (1131)
T ss_dssp CCTTCCCCCEEETTEEEEECEEEEECCSSCEEEECCTTCSEEEEEECEEECSSCEEECCEEEETTTCCEECCSSSCCCEE
T ss_pred CCcCCCCcEEEeCCEEEEEEEeeccCCCeEEEEeccCCCcEEEEEEEEECCCCceeeEEEEEeCCCEEEEEEcCcCceee
Confidence 133331 112222222211 134
Q ss_pred h---hhh-------HH---h---------------hc--------------ccccc--ccCCChhhHHHHhhhccccccc
Q psy4067 434 L---LSC-------KK---L---------------RQ--------------KRFQT--YKKTPVDDARDFLSSTCIAHIP 469 (1384)
Q Consensus 434 ~---~e~-------~~---~---------------~~--------------~~~~~--~~~~~~~ea~e~L~~~~LpHv~ 469 (1384)
+ ..| ++ . .. +++.. .+....+.|+++|++++|||++
T Consensus 226 i~illrALG~~sD~eI~~~i~~~~~~~~~l~~~~~~~~~i~~~~~al~~i~~r~~~~~~~~~~~~~a~~il~~~~l~hl~ 305 (1131)
T 4ayb_B 226 FVILMRALGILTDRDIVYAVSLDPEIQNELFPSLEQASSIANVDDALDFIGSRVAIGQKRENRIEKAQQIIDKYFLPHLG 305 (1131)
T ss_dssp HHHHHHHHTCCSHHHHHHHHCSCHHHHTTTHHHHHHHTTTCCSSHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTSSTTSC
T ss_pred HHHHHHHhCCcchhhHHHHhcccHHHHHHHHHHHHHhcccccHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHhhccccc
Confidence 2 000 00 0 00 11111 1112357899999999999999
Q ss_pred cccccchhhhHHHHHHHHHHHHhhcCCCCCCCCccccCcEeeehhhHHHHHHHHHHHHHHHHHHhhc-------------
Q psy4067 470 VINMRFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKETN------------- 536 (1384)
Q Consensus 470 v~~~~~~~Ka~yLg~MvRr~l~~~~~~~~~DDrD~ygNKRlelAG~Lls~lFe~~fk~~~~~~k~~~------------- 536 (1384)
....+++.|++||++|+|+++.+..|...+||+|||||||++++|+||+.||++.|++|.+++|+..
T Consensus 306 ~~~~~~~~K~~~L~~mi~~Ll~l~~g~~~~DD~Dhl~NkRvr~vGeLl~~~fr~~l~r~~r~ir~~~~~~~~~~~~~~~~ 385 (1131)
T 4ayb_B 306 TSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALK 385 (1131)
T ss_dssp SSTTSHHHHHHHHHHHHHHHHHHHHTSSCCCCTTSGGGEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTCSCCCHH
T ss_pred ccccchhHHHHHHHHHHHHHHHHHcCCCCCCCCcchhcceecchhHHHHHHHHHHHHHHHHHhhhhcccchhcccccchh
Confidence 9999999999999999999999999999999999999999999999999999999999999997522
Q ss_pred --c------ccc-eeccccceeecccC--------ceeEeecCc----------cccc-ccCCCCCCCcccccC--CCCC
Q psy4067 537 --L------SGV-VNLVSGWWFELKYG--------NKIYIRSPS----------RKLL-AAGFSGPHSGRVRLM--PEGP 586 (1384)
Q Consensus 537 --~------~~i-~sl~~g~w~~~~~~--------n~~~i~t~~----------r~~~-a~Gvh~sh~GRicp~--pEgp 586 (1384)
+ +++ ..|+||||..+..+ |.....|.+ |+.+ ++.+|+|||||+||+ ||||
T Consensus 386 ~li~~~~it~~i~~~~aTGn~~~~~sglSQ~mdq~NpLs~lsH~RRlsagl~rera~~evRdlHpShyGriCPIETPEG~ 465 (1131)
T 4ayb_B 386 ALVRPDIVTERIRHALATGNWVGGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGP 465 (1131)
T ss_dssp HHCCTHHHHHHHHHHHHTTBCSSSCBCCEEECCCSSHHHHHHHHTEEEECSCSSSCCHHHHSCCGGGTTTBCSSCCCSST
T ss_pred hhcCCchhhhhhHHHHhhcccccCCCceEEEeccCCHHHHHHhhhhhcCCcccccccccccccCHhhccccccccCCCCc
Confidence 1 112 24789999877655 211111111 3333 466899999999999 9999
Q ss_pred eEEEecccccCC---cchhhhHHHhhcccccccccccceeeccCCCCcccccccccceeeeEeeeccccccccccccccc
Q psy4067 587 TILLNSCLRSGG---KAQHEALYNAVQRHATKCCTLNFLFFLGGGGILPSIQRQTTCLLTLILFSLNGDGKRGARNSQQY 663 (1384)
Q Consensus 587 ~i~~~~~~~~~~---~~~~~~~~~~lk~~~~~~~~~~~~~fl~~g~i~~~~~~~~~~~l~~v~v~~~~~l~~~~r~~r~~ 663 (1384)
+|.+..+|+.-. ..+.+.++..+-.+ + ++ +.+...+...
T Consensus 466 niGLI~sLA~~a~I~~g~~e~~i~~~l~~-~--------------g~----------------~~~e~~~~~~------- 507 (1131)
T 4ayb_B 466 NSGLVKNLALMAQIAVGINEKIVEKTLYE-M--------------GV----------------VPVEEVIRRV------- 507 (1131)
T ss_dssp TBTTEEEBBSSCEECCCCCHHHHHHHHHH-T--------------TC----------------EEHHHHHHTT-------
T ss_pred cccccccceeeEEEecCCCCcceeeehhh-c--------------Cc----------------eeeeeeehhh-------
Confidence 875544333211 11112221111000 0 00 0000000000
Q ss_pred cCCCCCCCCCCCCCcccccccccccccccccccccCcEEEeccCCCcceEEEeCCCC--CCC-ccceeecccCccccccc
Q psy4067 664 CDCPDGYSSGCQPRPTFLNMHQFLGFKRFDDFLYEGKIEYLDVNEGNDSHIAVSESG--IRP-GVTTHLEIAPFTLLGVC 740 (1384)
Q Consensus 664 ~d~~~~~~~gr~~rPl~~~~~~~~~~~~~~~~~~~~~~e~~~~~e~~~~~ia~~~~~--~~~-~~~th~ei~p~~~l~v~ 740 (1384)
. ++.. .......+....-+|.+ ++..... +.. .........+...+||.
T Consensus 508 ~-------~~~~---------~~~~~~~~~~v~lng~~------------vg~~~~~~~~~~~~~~~~~~~~i~~~vsi~ 559 (1131)
T 4ayb_B 508 T-------EGGE---------DQNEYLKWSKVILNGRL------------VGYYRDGEELAKKIRERRRKGEISDEVNVG 559 (1131)
T ss_dssp T-------TC--------------CCCCCCEEEETTEE------------EEECSCHHHHHHHHHHHHHHTSSCTTCEEE
T ss_pred c-------cccc---------ccchhhhhcceeecCce------------EEEeccchhhhhhhhhhhccCccCceEEEe
Confidence 0 0000 00000011111112221 1111100 000 00011123344567888
Q ss_pred chhhhhhcccccCCCCCCCCCCCCCCccchhhhhhccccccccccccccccccceeeeccCCCceeeccccccccCCCCC
Q psy4067 741 AGIELLQYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITNFHKLP 820 (1384)
Q Consensus 741 a~~~~~~~~~~~~~~~lipf~~hNqspRn~yq~~m~kQ~~g~~~~~~~~R~D~~~~~l~~pQ~Piv~t~~~~~~~~~~~p 820 (1384)
+. ++||.+|.... +.++|+.|++. +..++.|+|.+...+.+..+...
T Consensus 560 ~~--------------~~~~~~~~~i~---~d~~r~~rpv~----------------~~~~~~p~v~~~~~~~~~~g~~~ 606 (1131)
T 4ayb_B 560 HI--------------VTDFINEVHVN---CDSGRVRRPLI----------------IVSNGNPLVTREDIEKLDSGSIT 606 (1131)
T ss_dssp EE--------------CTTTCCEEEEE---CCTTCEEEEEE----------------EBSSSSBSCCHHHHHHHHTTTCC
T ss_pred ec--------------cccccceeeee---cCCcccccceE----------------EeecccccccHHHHHHHhcCChh
Confidence 88 99999886543 67777777765 67788999998666555433221
Q ss_pred CCccccCCCCccchhhcccccceeEEeecccceeeecccccccccccccccccccchhhcccccccccchhhhhhhcccc
Q psy4067 821 AGKCQISPGGAEELTARESCHEVLKIISFSISVAVFDSVWLGDVKQGVHQLSEEKEPRLLRKFQYFDVRTPYRLRRLLCW 900 (1384)
Q Consensus 821 ~G~n~~~~~g~e~~~~~~~~~~vva~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~ 900 (1384)
. .+++-.+-+|..-|.+..++.||+-... ... .....++.+...
T Consensus 607 ~-~~~~~~g~veyvd~~e~~~~~ia~~~~~----------------~~~------------~~th~ei~p~~i------- 650 (1131)
T 4ayb_B 607 F-DDLVRQGKIEYLDAEEEENAYVALEPSD----------------LTP------------EHTHLEIWSPAI------- 650 (1131)
T ss_dssp H-HHHHHTTSEEEEEHHHHTTCCEESSGGG----------------CCT------------TCSEECSCGGGG-------
T ss_pred H-HHHhhCCceeeeeccccceeEEEeeccc----------------ccc------------cccceeeccccc-------
Confidence 0 0111112245555555555555511000 000 011111111111
Q ss_pred ceeeccccCCCCccccCCCCCCCccchhhhcccccccceeeeccccceeeeeeeeeccCCceeeee
Q psy4067 901 ECVLYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESK 966 (1384)
Q Consensus 901 ~~~~~~k~s~s~glIPF~~HNqSPRntyq~~M~KQAiG~~~yN~~~RiDt~~~~L~ypQkPLV~T~ 966 (1384)
-++.+++|||++|||||||+|||+|+|||||.+.+|+..|.|+..|.++|||+|||+|+
T Consensus 651 -------l~v~a~lipf~~~NqspRn~yq~~m~KQa~G~~~~~~~~r~D~~~~~l~ypQ~PlV~t~ 709 (1131)
T 4ayb_B 651 -------LGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTR 709 (1131)
T ss_dssp -------SBTTGGGCSSGGGSCHHHHHHHHHHGGGBCSCCCGGGGTCCCSEEEEESSCCCCSSBCH
T ss_pred -------cccccceecccccCccchheeccccccccCCceeecceeeeccccceeecCCccccccc
Confidence 14778999999999999999999999999999999999999999999999999999886
No 10
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C*
Probab=100.00 E-value=1e-54 Score=550.04 Aligned_cols=142 Identities=17% Similarity=0.224 Sum_probs=116.9
Q ss_pred hHHHHHHHHHHHHHhcCcCC-CCChhhhhhHHhhhhcchhhh-----------ccc----ccccccccccccchhhHHHH
Q psy4067 137 DYFINVEIKKLMQANANIYS-DVDPLFYLKYLDIHVGIADKI-----------IPK----IKAAQFDIVNHMRQDTITNA 200 (1384)
Q Consensus 137 ~~f~~~~i~~~~~~~~~~~~-d~~d~f~~k~~d~~~~~~~k~-----------~~~----~~~~~~~~~~~~~~~~IT~~ 200 (1384)
...+-.+++.++++..+... ||-||++|||+...|..++.+ +.. .....+.....+.++.||++
T Consensus 422 ~~DIi~~i~~Li~l~~g~~~~DDiDHLgNrRvr~vGeLl~~qfr~~l~r~~r~i~~~~~~~~~~~~~~~~lin~~~i~~~ 501 (1342)
T 3lu0_C 422 KDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAA 501 (1342)
T ss_dssp TTHHHHHHHHHHHHHHTSSCCCCSSSTTTSEEECHHHHHHHTHHHHHHHHHHHHTTHHHHCCSSCCSSTTTCCSSTTHHH
T ss_pred HHHHHHHHHHHHHHhhCCCCCcchhhhhcchhchHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCHHHHhccchHHHH
Confidence 35666788999988766544 777999999999988544422 111 11234555667888899999
Q ss_pred HHHHHHhCCcccccccccccceeeeecccchhhcccccccccc----cccccccccCCCcCCCCCcccccCCCCCCCccc
Q psy4067 201 LTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINS----QFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEAC 276 (1384)
Q Consensus 201 l~~alsTGNW~~~~~~~~r~GvsQvL~Rln~ls~lshlrRv~s----~~~~~~K~~~pR~LhpsqwG~iCP~eTPEG~~c 276 (1384)
++++| .++||||+|||+||||+|+|+||+++ +++++++.+++|++||||||||||+|||||+||
T Consensus 502 ~k~ff------------g~s~lSQ~lDqtNpLseltHkRRlsalGPGGLsr~~a~fevRdvH~thyGRiCPiETPEG~ni 569 (1342)
T 3lu0_C 502 VKEFF------------GSSQLSQFMVQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 569 (1342)
T ss_dssp HTTTT------------TTCSSCEECCCSSHHHHHHHHSBEESCCSTTSCCSSCCTTTSSCCTTCSSSSCTTCCCSSSCS
T ss_pred HHHHh------------CccccceeecCCCHHHHHhhhhcccccCCCCccccccCceecccCcccccccccccCCCCCce
Confidence 98875 25899999999999999999999963 567999999999999999999999999999999
Q ss_pred cchhhccccccccc
Q psy4067 277 GLVKNLALMTHITT 290 (1384)
Q Consensus 277 GLVKnLAl~a~It~ 290 (1384)
|||+|||++|+|+.
T Consensus 570 GLI~sLA~~a~in~ 583 (1342)
T 3lu0_C 570 GLINSLSVYAQTNE 583 (1342)
T ss_dssp SSCCBCCSSCCBCS
T ss_pred eeecchhheEEecc
Confidence 99999999999985
No 11
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus}
Probab=99.38 E-value=2.9e-13 Score=144.07 Aligned_cols=58 Identities=21% Similarity=0.522 Sum_probs=51.9
Q ss_pred cCCcccccccccccceEEEEEEEeeCCc-eeeeeeeeeccccceeccccccccCCcccc
Q psy4067 356 TTPHECRLRDLTYSAPITVDIEYTRGSQ-RVVRSDLVIGRMPIMLQSSKCVLRNKTEYT 413 (1384)
Q Consensus 356 i~P~EcRlrd~TYsa~i~V~v~~~~~~~-~~~~~~V~IG~iPIMLrS~~CvL~g~~~~i 413 (1384)
++|+|||+||+||+||+||+++++.++. .+.++.|+||+||||+..+.+++||..+.+
T Consensus 63 ~~p~Ecr~r~lTYsapl~v~v~l~~~~~~~i~~~~v~iG~iPlMt~gGyFIING~ERVI 121 (188)
T 3mlq_A 63 FSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVI 121 (188)
T ss_dssp SCHHHHHHTTCCCEEEEEEEEEEEETTTCCEEEEEEEEEEEECCCTTSCEEETTEEEEC
T ss_pred CCHHHHHhcCCCcceeEEEEEEEEECCCceEEEEEEEEcccCEECCCCEEEECCEEEEE
Confidence 7899999999999999999999997654 466789999999999999999999976654
No 12
>3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory protein, transcription; 3.00A {Escherichia coli}
Probab=98.75 E-value=3e-09 Score=114.95 Aligned_cols=72 Identities=28% Similarity=0.362 Sum_probs=51.9
Q ss_pred eeeecCCCccceeeCCccccCCCC-Cc---ccccccCCCCcccCCceeecCceEEeeeccCccccccccCCCcccccccc
Q psy4067 1021 VLKQYPNQTHDRILGPLLEADTRK-PV---YRHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEYKEVPVS 1096 (1384)
Q Consensus 1021 ~i~~~~~~~~d~i~~p~~~~~~~~-p~---~~~~~LDedGiv~~G~~V~~gDILIgKvsp~~~~~~~~~~~~e~k~~~~~ 1096 (1384)
|+++|....+++..|++ .+|.+ |+ ..+++||++|||++|++|++|||||||+||+.++ ..+||+++++++
T Consensus 3 HIeeyei~~r~tk~G~E--eIT~dIPnv~e~~l~~LDe~GIV~iGs~V~~GDILVGKvTPk~~~----~~tpEekLL~aI 76 (228)
T 3tbi_B 3 HIQELACVSRDTKLGPE--EITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGET----QLTPEEKLLRAI 76 (228)
T ss_dssp EEEEEEEEEEEETTEEC--EESSCCSSCCHHHHHTBCTTSBBCTTCCCBTTCEEECEEEECCGG----GCCHHHHHHHHH
T ss_pred cEEEEEEEEEEcCCCCe--EEecCCCCccHHHHhcCCCCCCeecCCEECCCCEEEeccCCCCCC----CCChHHHHHHHH
Confidence 44444444444444442 22332 44 3589999999999999999999999999998875 368888887776
Q ss_pred cc
Q psy4067 1097 YK 1098 (1384)
Q Consensus 1097 ~k 1098 (1384)
|.
T Consensus 77 fg 78 (228)
T 3tbi_B 77 FG 78 (228)
T ss_dssp HC
T ss_pred hC
Confidence 64
Done!