Query psy13846
Match_columns 1423
No_of_seqs 469 out of 2805
Neff 6.6
Searched_HMMs 29240
Date Fri Aug 16 21:56:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13846.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/13846hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_A DNA-directed RNA polyme 100.0 6E-194 2E-198 1921.5 19.4 996 76-1399 13-1455(1752)
2 1twf_A B220, DNA-directed RNA 100.0 1E-182 3E-187 1816.8 48.8 991 76-1401 11-1451(1733)
3 1hqm_D DNA-directed RNA polyme 100.0 8E-136 3E-140 1323.0 3.2 520 78-670 4-853 (1265)
4 3lu0_D DNA-directed RNA polyme 100.0 7E-125 2E-129 1195.8 12.8 499 75-668 13-812 (1407)
5 2a6h_D DNA-directed RNA polyme 100.0 1E-124 4E-129 1212.1 0.5 292 341-670 696-1112(1524)
6 4ayb_A DNA-directed RNA polyme 100.0 2E-118 6E-123 1154.8 23.8 538 77-682 4-856 (880)
7 3h0g_A DNA-directed RNA polyme 100.0 8.4E-87 2.9E-91 890.7 -0.4 780 11-999 499-1391(1752)
8 1twf_A B220, DNA-directed RNA 100.0 4.6E-82 1.6E-86 846.5 -3.3 788 11-999 493-1385(1733)
9 4ayb_C DNA-directed RNA polyme 100.0 3.1E-64 1E-68 603.9 9.3 291 1099-1397 48-392 (395)
10 1hqm_D DNA-directed RNA polyme 100.0 1.4E-52 4.8E-57 545.1 -7.4 639 11-1046 491-1180(1265)
11 3qqc_A DNA-directed RNA polyme 100.0 5.8E-49 2E-53 468.6 12.2 248 63-344 52-302 (436)
12 2a6h_D DNA-directed RNA polyme 100.0 2.6E-50 8.9E-55 521.5 -3.3 632 10-1054 750-1445(1524)
13 3lu0_D DNA-directed RNA polyme 100.0 1.9E-47 6.4E-52 487.4 7.4 119 933-1053 1204-1329(1407)
14 4ayb_C DNA-directed RNA polyme 100.0 1.3E-40 4.4E-45 399.2 7.1 270 690-999 59-330 (395)
15 4ayb_A DNA-directed RNA polyme 100.0 1.9E-34 6.4E-39 372.8 -10.8 373 11-471 468-856 (880)
16 3qqc_A DNA-directed RNA polyme 95.6 0.0025 8.5E-08 76.5 0.9 68 1315-1384 359-431 (436)
No 1
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=6.3e-194 Score=1921.49 Aligned_cols=996 Identities=32% Similarity=0.544 Sum_probs=772.1
Q ss_pred ccceeeeEEEecCCHHHHhhcceeeeecCcccccCCC-CCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEcc
Q psy13846 76 KVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQ-RTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP 154 (1423)
Q Consensus 76 ~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~-g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~ 154 (1423)
..+|.+ |+|+++|||||+++||++|+++++| |.. |+|+.|||||||||+.++...|+|||++..+||||||||||+
T Consensus 13 ~~~i~~-i~Fg~~S~eeI~~~Sv~~I~~~~~~--d~~~~~P~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHFGHIELa 89 (1752)
T 3h0g_A 13 LRRVEE-VQFGILSPEEIRSMSVAKIEFPETM--DESGQRPRVGGLLDPRLGTIDRQFKCQTCGETMADCPGHFGHIELA 89 (1752)
T ss_dssp CCCCCC-BEECCCCHHHHHHHCCCCCCCTTCT--TCSSSSSCCSSSSSSSCCCSSSSCCCTTSCCSSSSCCCCCEECCCC
T ss_pred ceeeee-EEEecCCHHHHHHhCeeEEeccccc--ccccCCCCCCCCcCccccCCCCCCCCCCCCCCCCcCCCcceeeecc
Confidence 367889 9999999999999999999999999 666 799999999999999999999999999999999999999999
Q ss_pred CceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccC-----------
Q psy13846 155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVC----------- 223 (1423)
Q Consensus 155 ~PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C----------- 223 (1423)
+||||||||+++++||+|+|++ |++|++++++. .|.++++... .+.+++++++.|++++.|
T Consensus 90 ~PVfHpgF~~~I~kILr~vC~~--C~klll~~~~~-~f~~~lrlrd-----~k~r~~~V~~~ck~k~~Ce~~~~~~~~~~ 161 (1752)
T 3h0g_A 90 KPVFHIGFLSKIKKILECVCWN--CGKLKIDSSNP-KFNDTQRYRD-----PKNRLNAVWNVCKTKMVCDTGLSAGSDNF 161 (1752)
T ss_dssp SCBCCHHHHHHHHHHSSSSCTT--TCCCSCCSCSH-HHHHHHHSSC-----TTTTHHHHHHHHHHCCCCCSSTTCCSSCC
T ss_pred cceEeehhhHHHHHHHHHHHHH--hcccccccccH-HHHHHHHccC-----HHHHHHHHHHHhccccccCCCCcccccch
Confidence 9999999999999999999999 99999998765 4777655322 124567888888765556
Q ss_pred -----------CCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHH
Q psy13846 224 -----------PHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292 (1423)
Q Consensus 224 -----------~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~ 292 (1423)
++||+.||.|||+++ +++++ ++..+. ++ .+ ...+.|+|.+|+
T Consensus 162 ~~~~~~~~~~~~gCG~~qP~IRKegl-kl~~~-~k~~k~--~~----------------~~-------~~k~~LtP~eVl 214 (1752)
T 3h0g_A 162 DLSNPSANMGHGGCGAAQPTIRKDGL-RLWGS-WKRGKD--ES----------------DL-------PEKRLLSPLEVH 214 (1752)
T ss_dssp CSSCCCCCCSSCSSCCCCCCCEEETT-EEECC-BCCSSS--SC----------------BC-------SSCCCCCHHHHH
T ss_pred hcccccccccCCCcCCcCCcEEeecc-EEEEE-Eccccc--cc----------------cc-------ccceecCHHHHH
Confidence 479999999999984 77664 211110 00 00 124689999999
Q ss_pred HHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCC-C-------------------------------
Q psy13846 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK-S------------------------------- 340 (1423)
Q Consensus 293 eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~-~------------------------------- 340 (1423)
++|++||++|+.+|++++..+||+||||++|||||+|+||++.+|+. .
T Consensus 215 ~ifk~IsdeD~~lLGl~~~~~rPewmiL~vLPVpPp~vRPsv~ldg~~~~edDLt~~l~~II~~N~~Lk~~~~~gap~~~ 294 (1752)
T 3h0g_A 215 TIFTHISSEDLAHLGLNEQYARPDWMIITVLPVPPPSVRPSISVDGTSRGEDDLTHKLSDIIKANANVRRCEQEGAPAHI 294 (1752)
T ss_dssp HHHHHSCHHHHHHSSCCSSSCCGGGSSBSSCEECCGGGSCCCCCSSSCCCCCTTTTHHHHHHHHHHHHHGGGGCCSSSTT
T ss_pred HHHHhcCHHHHHHhCCCccCCChhheEeeccccCCCCccCceEcCCCccCCChHHHHHHHHHHHHHHHHHHHHhcchhHH
Confidence 99999999999999999999999999999999999999999998764 1
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 295 ~~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~rp~k~~~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~evGvP~ 374 (1752)
T 3h0g_A 295 VSEYEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPR 374 (1752)
T ss_dssp HHHHHHHHHHHHHHTTCTTCSSCCCCCSSSSCCCCCHHHHHTCSSSSSTTTTSSCCCSSEEEEEEEEETTSCTTBCBCCH
T ss_pred HHHHHHHHHHHHHHhhcCCCCCCccccccCCCCCcchHhhhhcccccccccccccccCCccceeecCCCCcccceeeChH
Confidence
Q ss_pred ---------------------------------------------------------------------CCeEEEEecCc
Q psy13846 341 ---------------------------------------------------------------------DNDVVLFNRQP 351 (1423)
Q Consensus 341 ---------------------------------------------------------------------~~d~Vl~nRqP 351 (1423)
+||+|||||||
T Consensus 375 ~~A~~Lt~Pe~vt~~ni~~l~~lv~nG~~~~pga~~v~~~~~~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~Vl~NRqP 454 (1752)
T 3h0g_A 375 SIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQP 454 (1752)
T ss_dssp HHHTSCCCCCBCCTTTHHHHHHHHHHCTTSSSCEEEEECTTCCBCCTTTTCSCCCCCCCSSCEEEECCCSCCEEEEECSS
T ss_pred HHHHhcCCCccccHHHHHHHHHHHHcCCccccCceeeecCCCcEeechhhchhhhhhcCcCcEEEeeeccCCeEEEecCc
Confidence 68999999999
Q ss_pred cccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccC
Q psy13846 352 SLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTP 431 (1423)
Q Consensus 352 sLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~ 431 (1423)
||||+|||||++|++|+|||||||++|+||||||||||||+|+||+++|||||+ +||.+.+|++||
T Consensus 455 tLHr~sima~~~~v~~gktirlh~~vC~~yNADFDGDeMnvHvPqs~eAraEa~--------------~Lm~~~~nilsP 520 (1752)
T 3h0g_A 455 SLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSEETRAEIQ--------------EITMVPKQIVSP 520 (1752)
T ss_dssp CCSGGGEEEEECCCCSSSSEEEEGGGSGGGTCCSSSCEEEEECCCSTTHHHHHH--------------HTCCTTTTSEET
T ss_pred ccchhhcccccceeecCceeeechhhCCCccCccccceeeeeccCCHHHHHHHH--------------HHhcCccceecC
Confidence 999999999999999999999999999999999999999999999999999999 999999999999
Q ss_pred CCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecc
Q psy13846 432 RNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL 511 (1423)
Q Consensus 432 ~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il 511 (1423)
++|+|+++++||+|+|+|.||.+|.|++++|++++++++. .+.+ .+|+|||+||.++|||||||+++|
T Consensus 521 ~~G~Pi~~~~QD~vlg~y~lT~~~~f~~~~e~~~l~~~~~----~~~~--------~~~~pai~kp~~~wtGkqifs~il 588 (1752)
T 3h0g_A 521 QSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVP----DWDG--------ILPPPVILKPKVLWTGKQILSLII 588 (1752)
T ss_dssp TTTEESCCCCTHHHHHHHHHHSTTCEEETHHHHGGGGCSS----SCCS--------SCCCCSBCSSSCEEETTHHHHTTS
T ss_pred CCCCceeeecchhhhheeeeccccccCCHHHHHHHHHhhc----ccCC--------ccCccceecCcCCCchhhHHhhhC
Confidence 9999999999999999999999999999999999998763 2332 689999999999999999999999
Q ss_pred cCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhh
Q psy13846 512 KPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRM 591 (1423)
Q Consensus 512 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l 591 (1423)
|++ +++..+.+ ....++++|+.|+|+|||+++|.+||+.+|+ +.+++||.+|++||++.|+.||++++++
T Consensus 589 p~~------~~~~~~~~---~~~~~~~~d~~v~i~~gell~g~l~K~~lg~-~~~~li~~i~~~~G~~~~~~~ld~~~~l 658 (1752)
T 3h0g_A 589 PKG------INLIRDDD---KQSLSNPTDSGMLIENGEIIYGVVDKKTVGA-SQGGLVHTIWKEKGPEICKGFFNGIQRV 658 (1752)
T ss_dssp CSS------BCEECCCS---SCCSSCTTTCSEEECBSCEEEECCSHHHHSS-CTTCHHHHSSSSSCTTTHHHHHHHHHHH
T ss_pred cCC------CCceeccc---cccCcCCCcCeEEEEcCeEEecccchHHhcc-CcccHHHHHHHHHCHHHHHHHHHHHHHH
Confidence 865 33433222 1224678899999999999999999999998 5699999999999999999999999999
Q ss_pred hhHHHhhcCcceecCCCCCCc-----------------------------------------------------------
Q psy13846 592 TSFYLMNRGFSIGIGDVTPGQ----------------------------------------------------------- 612 (1423)
Q Consensus 592 ~~~~L~~~GfsiGi~D~~~~~----------------------------------------------------------- 612 (1423)
+++||+.+|||||++|+++++
T Consensus 659 ~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~~v~~~~~~~~~g~l~~~~g~~~~e~~e~~v~~~l~~~~~~~~~~ 738 (1752)
T 3h0g_A 659 VNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMTLRESFEAKVSRILNQARDNAGRS 738 (1752)
T ss_dssp HHHHHHHHCCCCCGGGGSCCSHHHHHHHHHHHTTTHHHHHHHTTTTTTCCCCCSSCCTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhcCceechhhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999997655
Q ss_pred -----------------------------------------------------------------cccccccccCCCcee
Q psy13846 613 -----------------------------------------------------------------GFVQNSFFSGLTPTE 627 (1423)
Q Consensus 613 -----------------------------------------------------------------GfI~~sf~~GL~p~E 627 (1423)
|||.+||++||+|+|
T Consensus 739 ~~~~l~~~N~~~~M~~SGakGs~~ni~Q~~~~~Gqq~~~GkrIp~g~~~rtLP~f~k~d~~~~a~GfV~~sF~~GL~p~E 818 (1752)
T 3h0g_A 739 AEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQE 818 (1752)
T ss_dssp HHTTSCSSCTTTHHHHHCSSCCHHHHHHHHTCCCCCCSTTSSSCCCSTTSSSTTSCSSCCSTTTSSCCSSCTTTCCCHHH
T ss_pred HHHhcCCCCcHHHHhhhccccCHHHHHHHHhccCCCccCCccCCCCCCCccCCCCCCCCCCcccCcchhhcccCCCCHHH
Confidence 899999999999999
Q ss_pred eeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCccCCCcchheecCCCcccchh
Q psy13846 628 FFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCISGVSECIIMGLPMNVGTG 700 (1423)
Q Consensus 628 fffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~~~~~~~~~~~~~~~~g~~ 700 (1423)
||||||||||||+|||||||+||||||||||+||||+|+||+||||+ .||+|+.+.-..|.
T Consensus 819 fFfhtmggReGLiDTAvKTA~SGYLqRRLVk~leDv~V~YDgTVRns~g~ivQF~YGeDGlD~~~~e~------------ 886 (1752)
T 3h0g_A 819 FFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEY------------ 886 (1752)
T ss_dssp HHHHHHHHTTTTTHHHHTTTHHHHHHHHHHHHHTTCEEETTTEEECTTSCEEESSSSSSCBCGGGEEE------------
T ss_pred HHHHhhhhhhhhhHhhhhcCcCchhHHHHHHHHhheEEeeCCeeEcCCCcEEEEecCCCCcChHHhhc------------
Confidence 99999999999999999999999999999999999999999999998 48887554332221
Q ss_pred HHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCC
Q psy13846 701 LIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNIST 780 (1423)
Q Consensus 701 vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikT 780 (1423)
+...++.+++..|. +.|.+... ++ .++. .|++ +.+..
T Consensus 887 ------------q~~~~~~~s~~~f~---------~~~~~~~~----------~~-------~~~~--~~~~---~~l~~ 923 (1752)
T 3h0g_A 887 ------------QVFDSLRLSTKQFE---------KKYRIDLM----------ED-------RSLS--LYME---NSIEN 923 (1752)
T ss_dssp ------------EECTTTSCCHHHHT---------TTSCCCTT----------TT-------CCGG--GTSC---SCCTT
T ss_pred ------------cccccccCCHHHHH---------HHhccccc----------cc-------cccc--HHHH---HHhcc
Confidence 11122222221121 00000000 00 0000 0000 00000
Q ss_pred ceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCc
Q psy13846 781 PIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH 860 (1423)
Q Consensus 781 Piitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~ 860 (1423)
...+....+.|+.+..+.|-. |. .+++...+..+.+++|++|+. +...+.
T Consensus 924 ---~~~~~~~l~~E~~~l~~dr~~---lr------~~i~~~~~~~~~lP~N~~R~i------------~~~~~~------ 973 (1752)
T 3h0g_A 924 ---DSSVQDLLDEEYTQLVADREL---LC------KFIFPKGDARWPLPVNVQRII------------QNALQI------ 973 (1752)
T ss_dssp ---SCSSTHHHHHHHHHHHHHHTT---SS------SSSSSCSCCEEEEESCHHHHT------------TTTTTT------
T ss_pred ---CHHHHHHHHHHHHHHHHHHHH---HH------HHhhccccccccCCccHHHHH------------HHHHHh------
Confidence 001112224455544433310 11 112333444555666666541 000000
Q ss_pred ccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeeccccee
Q psy13846 861 LTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940 (1423)
Q Consensus 861 i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~ 940 (1423)
| .+|...
T Consensus 974 -------------------f------------------------------------------------------~~~~~~ 980 (1752)
T 3h0g_A 974 -------------------F------------------------------------------------------HLEAKK 980 (1752)
T ss_dssp -------------------S------------------------------------------------------CCCTTS
T ss_pred -------------------c------------------------------------------------------CCCcCc
Confidence 0 000000
Q ss_pred eccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHHHHHHHHhccCCCC
Q psy13846 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSD 1020 (1423)
Q Consensus 941 t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~~~~~~~~~~~~~~ 1020 (1423)
.| +... ..++..+++.++ ++...+ |. +
T Consensus 981 -~s-~l~p-----------~~~~~~v~~~~~---------------~l~~~~----g~---------------------d 1007 (1752)
T 3h0g_A 981 -PT-DLLP-----------SDIINGLNELIA---------------KLTIFR----GS---------------------D 1007 (1752)
T ss_dssp -CC-CCCH-----------HHHHHHHHHHHT---------------TCCCSC----CC---------------------S
T ss_pred -cC-CCCH-----------HHHHHHHHHHHH---------------hhhccc----CC---------------------c
Confidence 00 0000 011222222221 000001 10 0
Q ss_pred CCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhccccccCcccCCCCCChh
Q psy13846 1021 PSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSA 1100 (1423)
Q Consensus 1021 ~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1100 (1423)
.++.+ . . ..+...|...++.+ ++.+.+...++++++++ +
T Consensus 1008 -~l~~~-~--~-----------~na~~l~~~~lr~~--------------------l~~k~~~~~~~l~~~~~----~-- 1046 (1752)
T 3h0g_A 1008 -RITRD-V--Q-----------NNATLLFQILLRSK--------------------FAVKRVIMEYRLNKVAF----E-- 1046 (1752)
T ss_dssp -TTTTH-H--H-----------HTSSHHHHHHHTTS--------------------SSHHHHHHSSCCCHHHH----H--
T ss_pred -chhhh-h--h-----------hchHHHHHHHHHhh--------------------hhhhhhhhhcCcCHHHH----H--
Confidence 11100 0 0 01112233322222 12344556678999887 7
Q ss_pred HHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc-----------------------------------
Q psy13846 1101 CKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------------------- 1145 (1423)
Q Consensus 1101 ~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG----------------------------------- 1145 (1423)
||+++|+.+|.+|+|+||||||+|||||||||+||||||||||||
T Consensus 1047 ~~~~~~~~~y~~a~v~pGe~VG~iaAQSIgEp~TQMTLnTFHfAGvas~NVTlGVPRLkEIInask~ikTP~mtv~L~~~ 1126 (1752)
T 3h0g_A 1047 WIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKNIKTPSLTIYLMPW 1126 (1752)
T ss_dssp HHHHHHHHHHHTTBCCSSCCHHHHHHHHHHHHHHHHHHHTTSSCCCCCSSCCCSGGGHHHHHTTCSCCSCCCCEECCCSS
T ss_pred HHHHHHHHHHHHhccCcccchhhhhhcccCCchhhhhHHhhhhccccccccccCcccHHHHHhhhcCCCCCeEEEEecCc
Confidence 999999999999999999999999999999999999999999999
Q ss_pred ---------------------cccceeEEEEccCCcEE------------------------------EEEEchHHHHHh
Q psy13846 1146 ---------------------EVCEYIEEVFVPDDSFI------------------------------LIKLDMDRIRLL 1174 (1423)
Q Consensus 1146 ---------------------~i~~~i~~~~~~~~~~~------------------------------~i~l~~~~~~~~ 1174 (1423)
+|++.++++|+|+..+. .+++.+++.+++
T Consensus 1127 ~~~d~e~A~~v~~~ie~t~L~~v~~~~~i~~~p~~~~~~i~~d~~~v~~~~~~~~~~~~~~~~~~~~~~~rl~l~~~~~~ 1206 (1752)
T 3h0g_A 1127 IAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRLELDRAKML 1206 (1752)
T ss_dssp SCSSSTTTHHHHTTSSCCSSCSCCSCEEEECCCSTTCCCCSSSCSHHHHHHHTTCSSTTCSSCSCCCCEEEEECCTTSST
T ss_pred cccCHHHHHHHHHhhccEEHHHheeEEEEEEecCccceEEeecHHHHHHHhccchhhhhcccccccceeEEEEecHHHHH
Confidence 45667788888764433 344444444455
Q ss_pred cccCCHHHHHHHHHhccccCCceEE--ec----CcEEEEEeCCCC----c------hhhhHHHHHH-hccCCcEEcccCC
Q psy13846 1175 HLEVDIDSIRYCIERTRGISGHLTV--SG----HSFLILKPKDSS----K------SFNSKMYQMK-QLLPSVVIKGVQG 1237 (1423)
Q Consensus 1175 ~~~i~~~~i~~~i~~~k~~~~~~~~--~~----~~~i~i~~~~~~----~------~~~~~l~~l~-~~l~~~~v~Gi~~ 1237 (1423)
++++++++|..+|.+... .++.+ ++ +..+++++.... + .....|+.++ ..|++++|+||||
T Consensus 1207 ~~~l~~~~I~~~i~~~~~--~~~~v~~~d~~~~~~~i~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~l~~~~i~Gi~~ 1284 (1752)
T 3h0g_A 1207 DKKLSMSDVAGKIAESFE--RDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISLRGVPN 1284 (1752)
T ss_dssp TTTCCHHHHTTSGGGSST--TSCCEECCCTTCSSCEEEECCCCCSCCCCCSSCCCSCSCHHHHHHHHHHTTCCCSSCCTT
T ss_pred HcCCCHHHHHHHHHhhcc--CCeeEeecCCCccceeEEEEeccccccccccccccccHHHHHHHHHHhhccceEEecCCC
Confidence 667899999888754321 22222 11 224566553210 0 1224578887 4689999999999
Q ss_pred ccEEEEecccc---------cceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHHhhc
Q psy13846 1238 INRAVIHEEDV---------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMEN 1308 (1423)
Q Consensus 1238 i~r~~i~~~~~---------~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~ 1308 (1423)
|+||+|.+++. ...++|.|.|||+||+++|.+++||++||+||||+||+++|||||||++|++||+.||+.
T Consensus 1285 I~rv~i~~~~~~~~~~~g~~~~~~~~~l~teG~nL~~v~~~~gVD~~rt~sNdI~ei~~vlGIEAAR~~Ii~Ei~~v~~~ 1364 (1752)
T 3h0g_A 1285 ITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDATRTYSNSFVEILQILGIEATRSALLKELRNVIEF 1364 (1752)
T ss_dssp CCCCCEEEEEEEEECSSSCEEEEEEEEEECCSCCCSTTTSSSSCCTTTCCCSCHHHHHHHSCHHHHHHHHHHHHHTTSCS
T ss_pred ccEEEEecccceeecCCCcccccceEEEEecccCHHHHhCcCCCccccCeeCCHHHHHHHHhHHHHHHHHHHHHHHHHHh
Confidence 99999976431 124589999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecccccccc
Q psy13846 1309 HGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388 (1423)
Q Consensus 1309 ~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GT 1388 (1423)
||++||+|||+||||+||++|++++||||||+++++|||++||||+|+++|++||++|+.|+|+|||||||+|+++++||
T Consensus 1365 ~G~~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~s~l~~aSFE~T~~~L~~Aa~~g~~D~l~gvse~Ii~G~~~~~GT 1444 (1752)
T 3h0g_A 1365 DGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFEETVEILMDAAASGEKDDCKGISENIMLGQLAPMGT 1444 (1752)
T ss_dssp SSCCCCHHHHHHHHHHHTSSSSCCCCCTTSCSCCCSHHHHHHHHSCCTHHHHHHGGGTCCBCCCCSTTGGGTCSCCCSBT
T ss_pred cCCCCCHHHHHHHHHHhccCCeEEeechhhhccCCCCHHHHhhHHHHHHHHHHHHHhcCcccccChhHHhhcCCCcCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEEeecCCC
Q psy13846 1389 GLIKLLQAVPR 1399 (1423)
Q Consensus 1389 G~~~l~~~~~~ 1399 (1423)
|+|||+++.++
T Consensus 1445 G~fdll~~~~~ 1455 (1752)
T 3h0g_A 1445 GAFDIYLDQDM 1455 (1752)
T ss_dssp TSCEECCCHHH
T ss_pred ceEEEEeCHHH
Confidence 99999998554
No 2
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Probab=100.00 E-value=9.6e-183 Score=1816.76 Aligned_cols=991 Identities=31% Similarity=0.502 Sum_probs=765.1
Q ss_pred ccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccC
Q psy13846 76 KVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155 (1423)
Q Consensus 76 ~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~ 155 (1423)
..++.+ |+|+++||||||++||++|+++++|+ +.+.+|..|||+|||||+.++...|.|||....+||||||||||+.
T Consensus 11 ~~~i~~-I~f~l~SpeeIr~~Sv~eI~~pet~~-~~~~~P~~~GL~d~rlG~~~~~~~C~tCg~~~~~C~GHfGHIELa~ 88 (1733)
T 1twf_A 11 LRTVKE-VQFGLFSPEEVRAISVAKIRFPETMD-ETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAK 88 (1733)
T ss_dssp BCCCCE-EECCBCCHHHHHHTCCCCCCCSCCSC-TTSCCSCCSSSSCSSSCCCTTCCCSSSCCCCTTSCCCCCCCEEEEE
T ss_pred ccccce-EEEEeCCHHHHHHhCeeEEecccccc-cccCCCCcCCCcCcccCcccCCCEeCCCCCCCCcCCCccceeeccc
Confidence 467889 99999999999999999999999995 3455999999999999999999999999999999999999999999
Q ss_pred ceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccC------------
Q psy13846 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVC------------ 223 (1423)
Q Consensus 156 PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C------------ 223 (1423)
||||||||+.++++|+|+|++ |+++++++.+. .|.+.++... .+.+++++++.|++++.|
T Consensus 89 PV~HigF~k~i~kiLe~VC~~--Cskllld~~~~-~~~~~L~~~~-----pk~r~~~v~e~ck~k~~Ce~~~~~~~e~~~ 160 (1733)
T 1twf_A 89 PVFHVGFIAKIKKVCECVCMH--CGKLLLDEHNE-LMRQALAIKD-----SKKRFAAIWTLCKTKMVCETDVPSEDDPTQ 160 (1733)
T ss_dssp EEECGGGHHHHHHHHHHBCTT--TCCBSCCTTSH-HHHHHHTCCS-----HHHHHHHHHHHHTTCCBCCSEECCSSCTTS
T ss_pred ccccHHHHhhHHHHHHHHhHh--cceeeeccchH-HHHHHHHhcC-----HHHHHHHHHHHhcccccccccccchhcccc
Confidence 999999999999999999999 99999987765 4666554331 145567789998876666
Q ss_pred ----CCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccC
Q psy13846 224 ----PHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIP 299 (1423)
Q Consensus 224 ----~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~ 299 (1423)
.+||+.++.+||.++ ++.++ ++.... +. .. .....+.++|.+|+++|++|+
T Consensus 161 ~~~~~gCGa~qp~irk~gl-~l~~e-~k~~~~--~~--------------e~-------~~~~k~~Ltp~eV~eifk~I~ 215 (1733)
T 1twf_A 161 LVSRGGCGNTQPTIRKDGL-KLVGS-WKKDRA--TG--------------DA-------DEPELRVLSTEEILNIFKHIS 215 (1733)
T ss_dssp CEECCSCCCBCCCCEECSS-CEEEE-ECSSSS--CT--------------TS-------CSCEEEEECHHHHHHHHTTSC
T ss_pred ccccCCCCCccHHHHhcCC-ceEEe-eccccc--cc--------------cc-------chhhhccCCHHHHHHHHHhCC
Confidence 499999999999884 44432 211110 00 00 002356899999999999999
Q ss_pred CCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCC-C--------------------------------------
Q psy13846 300 LEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK-S-------------------------------------- 340 (1423)
Q Consensus 300 ~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~-~-------------------------------------- 340 (1423)
++|+.+|++++..+||+||||++|||||+|+||++.+++. .
T Consensus 216 deD~~lLgl~p~~~rPewmiLtvLPVpPp~vRPsv~ldg~~~~edDLT~~l~~II~~N~~Lk~~~~~gap~~ii~e~~~~ 295 (1733)
T 1twf_A 216 VKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESL 295 (1733)
T ss_dssp HHHHHHTTCBTTTBCGGGGEEEEECCCCTTTSCCCCCSSSCCCCCHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHH
T ss_pred HHHHHHhCCCccCCChheeeeeeeccCCCCccCceecCCCcccCCHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHH
Confidence 9999999999999999999999999999999999988763 1
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 296 LQ~~v~~~~dn~~~~~~~~~~~~~rp~k~i~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~L~~~evGvP~~~A~~Lt 375 (1733)
T 1twf_A 296 LQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLT 375 (1733)
T ss_dssp HHHHHHHHHCCCSSCCCCCSSCTTCCCCCSTTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEHHHHTTCE
T ss_pred HHHHHHHHhccCccCCCccccCCCccchhHHHHhccccchhhhcccccccCcccceEEeCCCCcccccccCcHHHHHhCC
Confidence
Q ss_pred --------------------------------------------------------------CCeEEEEecCcccccccc
Q psy13846 341 --------------------------------------------------------------DNDVVLFNRQPSLHKLSI 358 (1423)
Q Consensus 341 --------------------------------------------------------------~~d~Vl~nRqPsLHk~Si 358 (1423)
+||+|||||||||||+||
T Consensus 376 ~Pe~vt~~ni~~l~~lv~~g~~~~~ga~~~~~~~g~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~VllNRqPTLHr~si 455 (1733)
T 1twf_A 376 YPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSM 455 (1733)
T ss_dssp EEEECCTTTHHHHHHHHHHTTTSSSCEEEEECTTCCEEETTSCTTTTCCCCCTTCEEEEECCTTCEEEEECSSCCSGGGE
T ss_pred CCccccHHHHHHHHHHHHcCCccCCCceeEEcCCCcEEeccccchhhhhhcccCCEEEeeeccCCEEEEeCCCccccccc
Confidence 678999999999999999
Q ss_pred ceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCcccc
Q psy13846 359 MAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLI 438 (1423)
Q Consensus 359 mah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~ 438 (1423)
|||++|++|++||||||++|+||||||||||||+|+||+++|||||+ .||.+.+|++||++|+|++
T Consensus 456 ~a~~~~v~~~~tirlnp~vC~~yNADFDGDeMnvHvPqs~eAraEa~--------------~Lm~~~~nilsP~~G~Pi~ 521 (1733)
T 1twf_A 456 MAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELS--------------QLCAVPLQIVSPQSNKPCM 521 (1733)
T ss_dssp EEEEEEEESSSSEEECGGGHHHHTCCSSSCEEEEECCCSHHHHHHHH--------------HHTBGGGGSEETTTTEESC
T ss_pred eeEEEEEccCCeEEeChhhcCCCCccchhhhhhhhcCCCHHHHHHHH--------------HHhcCcccEEecCCCCeeE
Confidence 99999999999999999999999999999999999999999999999 9999999999999999999
Q ss_pred ccccceEEEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcc
Q psy13846 439 AATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCP 518 (1423)
Q Consensus 439 ~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~ 518 (1423)
+++||+|+|+|.||.+|.|++++|++++++++. .+.+ .+|+|+|+||.++|||||||+++||++
T Consensus 522 ~~~QD~v~g~y~lT~~~~f~~~~e~~~~~~~~~----~~~~--------~~~~pai~kp~~~wtGkqifs~ilp~~---- 585 (1733)
T 1twf_A 522 GIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVP----DWDG--------VIPTPAIIKPKPLWSGKQILSVAIPNG---- 585 (1733)
T ss_dssp CCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHST----TCCS--------CCCCCSBCSSSCEEEHHHHHHHHSCTT----
T ss_pred eeeccccccceeeecCcccCCHHHHHHHHHhhh----hhcC--------ccCCccccCcccCccHHHHHHHhCCCC----
Confidence 999999999999999999999999999998873 2333 578999999999999999999999875
Q ss_pred cccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhh
Q psy13846 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMN 598 (1423)
Q Consensus 519 ~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~ 598 (1423)
+++..+.. ...+.+..|+.|+|+|||+++|++||+.+|+ +.+++||.+|++||++.|+.||+++++++++|++.
T Consensus 586 --~~~~~~~~---~~~~~~~~d~~v~i~~gel~~g~ldKk~lg~-~~~~li~~i~~~~G~~~a~~~ld~l~~l~~~~l~~ 659 (1733)
T 1twf_A 586 --IHLQRFDE---GTTLLSPKDNGMLIIDGQIIFGVVEKKTVGS-SNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLH 659 (1733)
T ss_dssp --CCEEECCT---TCCTTCTTCCSEEEETTEEEESCCCHHHHSS-CTTSHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHT
T ss_pred --CceeecCC---CcccCCcccceEEEeCCcEEEeecchHHhcc-ChhHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHH
Confidence 33433221 1234567789999999999999999999998 56899999999999999999999999999999999
Q ss_pred cCcceecCCCCCCc------------------------------------------------------------------
Q psy13846 599 RGFSIGIGDVTPGQ------------------------------------------------------------------ 612 (1423)
Q Consensus 599 ~GfsiGi~D~~~~~------------------------------------------------------------------ 612 (1423)
+|||||++|+++++
T Consensus 660 ~GfSigi~D~~~~~~~~~~i~~~i~~a~~~v~~~~~~~~~g~l~~~pg~~~~e~~e~~v~~il~~~~d~~~~~~~~~l~~ 739 (1733)
T 1twf_A 660 NGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKD 739 (1733)
T ss_dssp TCBCCCGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSCT
T ss_pred cceEEehhhcCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 99999999997655
Q ss_pred ----------------------------------------------------------cccccccccCCCceeeeeeccc
Q psy13846 613 ----------------------------------------------------------GFVQNSFFSGLTPTEFFFHTMG 634 (1423)
Q Consensus 613 ----------------------------------------------------------GfI~~sf~~GL~p~Efffh~ma 634 (1423)
|||.+||++||+|+||||||||
T Consensus 740 ~N~i~~Ma~SGAKGs~~Ni~Q~~~~~Gqq~~~Gkrip~g~~~RtLPhf~k~d~~p~s~GfI~ssF~~GLtp~EyFfh~mg 819 (1733)
T 1twf_A 740 LNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMG 819 (1733)
T ss_dssp TCHHHHHHHHTSSCCHHHHHHHHSCCEECCBTTBSCCCCBTTBSSTTSCTTCCSTTTTTEECSCTTTCCCHHHHHHHHHH
T ss_pred CCCeEEEeeccCcccHHhHHHHHhCcCCcccCCccCCCCCCCCCCCCCCCCCCCccccchhhhhhhcccchHHHhhhhhc
Confidence 7899999999999999999999
Q ss_pred ccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc-------ccCCCccCCCcchheecCCCcccchhHHHHhhh
Q psy13846 635 GREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 707 (1423)
Q Consensus 635 GReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aq 707 (1423)
|||||||||||||+||||||||||+||||+|+||+||||+ .||+|+.+....+..
T Consensus 820 gReGLiDTAvKTA~SGYLqRRLVk~ledv~V~yDgTVR~s~g~IvQF~YGeDGlD~~~~e~~------------------ 881 (1733)
T 1twf_A 820 GREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQ------------------ 881 (1733)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTTCEECTTSCEECTTCCEEESSGGGTTBCGGGEEEE------------------
T ss_pred cccchhhhceecccCCcceeehhhhhcceEEEecCcEecCCCCEEEEEeccccCCcceeecc------------------
Confidence 9999999999999999999999999999999999999987 255543221100000
Q ss_pred cCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhHHHHhhhcCCCCceeeeec
Q psy13846 708 VPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYL 787 (1423)
Q Consensus 708 sige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L 787 (1423)
.| + +
T Consensus 882 ----------------~~----------------------------------------~--------------------~ 885 (1733)
T 1twf_A 882 ----------------SL----------------------------------------D--------------------T 885 (1733)
T ss_dssp ----------------EC----------------------------------------G--------------------G
T ss_pred ----------------cc----------------------------------------c--------------------c
Confidence 00 0 0
Q ss_pred ccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccc
Q psy13846 788 DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS 867 (1423)
Q Consensus 788 ~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~ 867 (1423)
....+..+.+..+... .++..
T Consensus 886 ~~~~~~~f~~~~~~~~-----------------~~~~~------------------------------------------ 906 (1733)
T 1twf_A 886 IGGSDAAFEKRYRVDL-----------------LNTDH------------------------------------------ 906 (1733)
T ss_dssp GSSCHHHHHHHHCCCT-----------------TCTTT------------------------------------------
T ss_pred cccCHHHHHHHhcccc-----------------ccccc------------------------------------------
Confidence 0000001110000000 00000
Q ss_pred cccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccccccceeecccceeeccCchH
Q psy13846 868 FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 947 (1423)
Q Consensus 868 ~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~ 947 (1423)
+ ..+ ++. +.
T Consensus 907 -~-l~~---------------------------~~~---------------------------------~~--------- 915 (1733)
T 1twf_A 907 -T-LDP---------------------------SLL---------------------------------ES--------- 915 (1733)
T ss_dssp -S-CCT---------------------------TTB---------------------------------TT---------
T ss_pred -c-CCH---------------------------HHH---------------------------------HH---------
Confidence 0 000 000 00
Q ss_pred HHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCCcchhhHHHHHHHHHhccC--CCCCCCCH
Q psy13846 948 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSS--RSDPSLSA 1025 (1423)
Q Consensus 948 eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~~~~~~~~~~~~~~~~~~~--~~~~~l~~ 1025 (1423)
....++-+..+..+-.|.....+ |.+ .|-..+ ..|.-. ...|+++.+++.+....... .....+.|
T Consensus 916 -~~~~~~~~~~~~~l~~e~~~l~~------~r~---~lr~i~-~~~~~~-~~~P~ni~r~i~~~~~~f~~~~~~~s~l~p 983 (1733)
T 1twf_A 916 -GSEILGDLKLQVLLDEEYKQLVK------DRK---FLREVF-VDGEAN-WPLPVNIRRIIQNAQQTFHIDHTKPSDLTI 983 (1733)
T ss_dssp -HHHHTTCHHHHHHHHHHHHHHHH------HHH---HHHHHT-TTCCCE-EEEESCHHHHHHHHHHHTTCCTTSCBCCCH
T ss_pred -HHHhhccHHHHHHHHHHHHHHHH------HHH---HHHHhh-cccccc-ccCChhHHHHHHHHHHHhcccccccccCCH
Confidence 00000000011111111111100 000 000000 011100 11588899988777665321 22345778
Q ss_pred HHHHHHhhhhcCcchh------h-----hhhhHHHHHHHHHHHHHhhhccccccccccCCchhhhhhhccccccCcccCC
Q psy13846 1026 QEILALSNETLDSKEF------L-----QDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRES 1094 (1423)
Q Consensus 1026 ~~~~~~~~~~l~~~~~------~-----~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1094 (1423)
..+.+.+++.+..... + ..+...|.-.+++++ +.+.+...++++++++
T Consensus 984 ~~~~~~v~~~~~~~~~~~g~d~l~~~~~~n~~~l~~~~~rs~L--------------------~~k~~~~~~~l~~~~~- 1042 (1733)
T 1twf_A 984 KDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRL--------------------ATRRVLQEYRLTKQAF- 1042 (1733)
T ss_dssp HHHHHHHHHHHTTCCSCCCCSHHHHHHHHHTTHHHHHHHHHHS--------------------CHHHHHHTSCCCHHHH-
T ss_pred HHHHHHHHHHHHhhhcccCCcchhhhhhhchHHHHHHHhhhhh--------------------hhhhhhhhcCCCHHHH-
Confidence 8888877776653210 0 011223433334332 2234445678898887
Q ss_pred CCCChhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc-----------------------------
Q psy13846 1095 NPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------------- 1145 (1423)
Q Consensus 1095 ~~~~~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG----------------------------- 1145 (1423)
+ +|+++|+.||.+|+|+||||||+|||||||||+||||||||||||
T Consensus 1043 ---~--~~l~~i~~ky~~a~v~pGe~VG~iaAQSigEp~TQMTLnTFHfAGva~~NVTLGVPRLkEIinask~ikTP~mt 1117 (1733)
T 1twf_A 1043 ---D--WVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLT 1117 (1733)
T ss_dssp ---H--HHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC----------CCSCCHHHHHHHHTTTCSSCSSCEEE
T ss_pred ---H--HHHHHHHHHHHhccCCCCchhhhHhhhhcCCccccccccccccccccccCcccCcHHHHHHHHhccCCCCCeEE
Confidence 7 999999999999999999999999999999999999999999999
Q ss_pred ---------------------------cccceeEEEEccCC-------------c-----------------EEEEEEch
Q psy13846 1146 ---------------------------EVCEYIEEVFVPDD-------------S-----------------FILIKLDM 1168 (1423)
Q Consensus 1146 ---------------------------~i~~~i~~~~~~~~-------------~-----------------~~~i~l~~ 1168 (1423)
+|++.++++|+|+. . .+.++|++
T Consensus 1118 v~L~~~~~~~~e~A~~v~~~ie~ttL~dv~~~i~i~~dp~~~~tvi~ed~~~~~~y~~i~~~d~~~~~~~~~~~~lrl~l 1197 (1733)
T 1twf_A 1118 VYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLEL 1197 (1733)
T ss_dssp EEBCSSSSSCHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHHTSSCC----------CCCSEEEEEEE
T ss_pred EEeCCcccccHHHHHHHHHhhceeEHHHhhheEEEEEccCccceeeecchhhhhhhhcccHHhhcchhhhcccceeEEEe
Confidence 45566777787761 0 13457778
Q ss_pred HHHHHhcccCCHHHHHHHHHhccccCCceEE--ecC----cEEEEEeCCCCc-------hhhhHHHHH-HhccCCcEEcc
Q psy13846 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTV--SGH----SFLILKPKDSSK-------SFNSKMYQM-KQLLPSVVIKG 1234 (1423)
Q Consensus 1169 ~~~~~~~~~i~~~~i~~~i~~~k~~~~~~~~--~~~----~~i~i~~~~~~~-------~~~~~l~~l-~~~l~~~~v~G 1234 (1423)
++.+++...+++++|..+|.+... .++.+ .++ ..++++.....+ .....++.+ ++.+.+++|+|
T Consensus 1198 ~~~~~~~~~l~~~~I~~~i~~~~~--~~~~~~~~d~~~~~~~~~i~~~~~~~~~~~~~~~~~~~l~~l~~~~l~~~~v~G 1275 (1733)
T 1twf_A 1198 DRAAMNDKDLTMGQVGERIKQTFK--NDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRG 1275 (1733)
T ss_dssp CHHHHHHTTCCHHHHHHHHHHHHG--GGEEEEECCTTSSSCEEEEEEC----------CCTTHHHHHHHHHHHHHCEEES
T ss_pred cHHHHHhcCCCHHHHHHHHHHhhC--CCcceecCCcccchhheeeeeccCccccccccchhHHHHHHHHHHhhhheEEec
Confidence 887787888999999998854211 12221 111 133444421110 001124444 77788999999
Q ss_pred cCCccEEEEec-------ccc--cceeeEEEEecCccHHHHhhcccccceecccccHHHHHHHhCHHHHHHHHHHHHHHH
Q psy13846 1235 VQGINRAVIHE-------EDV--EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 1305 (1423)
Q Consensus 1235 i~~i~r~~i~~-------~~~--~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v 1305 (1423)
+|||+||+|.+ ++. +..++|+|.|||+||.++|.+++||++||+||||+||+++|||||||++|++||++|
T Consensus 1276 i~~I~r~~i~~~~~~~~~~~g~~~~~~~~~L~teG~nL~~vl~~~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V 1355 (1733)
T 1twf_A 1276 VENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNV 1355 (1733)
T ss_dssp CTTCCCEEEEEEEEEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCTTTCBCSCHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred CCCccEEEEecccceeecCCCccccCcceEEEeecccHHHHhccCCcccccceeccHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 99999999863 111 235689999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeeccccc
Q psy13846 1306 MENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMN 1385 (1423)
Q Consensus 1306 ~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~ 1385 (1423)
|+.||++||+|||+||||+||++|.++|||||||+++++|||++||||+|+++|++||++|+.|+|+|||||||+|+++|
T Consensus 1356 ~~~~Gi~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~S~L~~aSFE~T~~~L~~Aa~~g~~D~l~gvsenII~G~~~~ 1435 (1733)
T 1twf_A 1356 IASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAP 1435 (1733)
T ss_dssp HHTTTCCCCHHHHHHHHHHTTTBSSCCCSSSCSSSCSSCCTTSSCCSSCSHHHHHHHHHHTCEECCCSHHHHHHTTCCCS
T ss_pred HhhcCccccchhhhhhhhhhccCceecccchhhhcccCCCchhhcchhhhHHHHHHHHhccCcCcccccccccccCCCCC
Confidence 99999999999999999999999999999999999989999999999999999999999999999999999999999999
Q ss_pred cccceEEEeecCCCCC
Q psy13846 1386 VGTGLIKLLQAVPRSE 1401 (1423)
Q Consensus 1386 ~GTG~~~l~~~~~~~~ 1401 (1423)
+|||+|||+++.+...
T Consensus 1436 ~GTG~FdLl~~~~~~~ 1451 (1733)
T 1twf_A 1436 IGTGAFDVMIDEESLV 1451 (1733)
T ss_dssp SGGGSSEEEECSCCC-
T ss_pred CCCccEEEEEchhhcc
Confidence 9999999999987643
No 3
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D
Probab=100.00 E-value=8.4e-136 Score=1323.00 Aligned_cols=520 Identities=22% Similarity=0.305 Sum_probs=356.8
Q ss_pred ceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCC-CCC--------------CCCCccCCCCCCCc
Q psy13846 78 FFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRM-GTN--------------QKEANCTTCGQNLS 142 (1423)
Q Consensus 78 ~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rL-G~~--------------~~~~~C~TCg~~~~ 142 (1423)
.+.+ |+|+++|||+|+++|+.+|++|++|+ +.+++|..+||+|+|| ||. ++...|.|||....
T Consensus 4 ~~~~-i~~gl~Spe~Ir~~S~geV~~pet~n-y~t~kP~~~GLfd~rifGp~k~~~C~Cgkyk~~~~~~~~C~~Cg~~~~ 81 (1265)
T 1hqm_D 4 EVRK-VRIALASPEKIRSWSYGEVEKPETIN-YRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVT 81 (1265)
T ss_dssp CBCC-CCCCCCCTTTHHHHTTTCCCCCCC--------------------------------------CCSCSSSSSSSSC
T ss_pred ccce-EEEecCCHHHHHHhhEEEEcchhhee-cCCCcccCCCCcCccccCCCccceecCCCccccCCCCCCCCCCCCccc
Confidence 4778 99999999999999999999999994 3699999999999999 775 37789999999999
Q ss_pred cc---CCccceEEccCceeEEeeeccH-----------HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHH
Q psy13846 143 DC---VGHFGYIDLPLPVFHIGYFRCV-----------INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKS 208 (1423)
Q Consensus 143 eC---pGHfGhIeL~~PV~h~gffd~v-----------~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~ 208 (1423)
+| |||||||+|+.||||+|||+.+ .+.|+|+|++ |+++++++.. .+..++.... .+.
T Consensus 82 ~~~vrrg~~GhIeLa~PV~Hi~y~k~~~s~l~~lL~~~~k~le~v~y~--~s~v~~~~~~--~l~~~l~~~~-----~~~ 152 (1265)
T 1hqm_D 82 RSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLFATELEQVLYF--NKYIVLDPKG--AVLDGVPVEK-----RQL 152 (1265)
T ss_dssp CSSSCCCSCCCCCCCSCCCSTTSTTHHHHTTTCTTTHHHHTTSSSCCC--CSCCCCSSSC--CCTTCCCCTT-----HHH
T ss_pred ccccccCccceEEecCceeeeeecccchHHHHHHhcCCHHhhccEeee--cceEeecCCc--hHhhhcCHHH-----HHH
Confidence 99 8999999999999999999974 5677778888 8888865430 0000111100 000
Q ss_pred HH----HHHHHHccCCccCCCCCCCCCceeecCcceehhhhhccccc-c-hhhHHHHHHHHhhhhhccChhhhhhhccCc
Q psy13846 209 LK----KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTK-K-KDAIVEDLLAEYNEAVKFNPEIEAHKKFGL 282 (1423)
Q Consensus 209 ~~----~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 282 (1423)
+. +++...+...+.| |....... + .+..++.+..... . -.+....+++..+-.. ...+.. ..
T Consensus 153 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~---~-~~~~~~~~~~~~~~~~G~~~~~~~l~~~~l~~-~~~~~~-----~~ 220 (1265)
T 1hqm_D 153 LTDXXXXXXXXXXXXXXXX--XXXXXXXX---X-XXXXXXXXXXXIDARMGAEAIQELLKELDLEK-LERELL-----EE 220 (1265)
T ss_dssp HTCCCCCCCCCCCCSSCCC--CCCCCTTS---C-CCCCCCCCCCCCCCCCSHHHHHHHHTHHHHCH-HHHHHH-----TT
T ss_pred Hhhhccccccccccccccc--cccccccc---c-cccccccchhhhhcccCchhHHHHHHhcCHHH-HHHHHH-----HH
Confidence 00 0000000001112 11111110 0 1111111110000 0 0011111111111000 000001 11
Q ss_pred cccCCHHHHHHHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCC----------------------
Q psy13846 283 IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS---------------------- 340 (1423)
Q Consensus 283 ~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~---------------------- 340 (1423)
.+..++....++|+++.. +-.+.++++||+||||++|||||+++||++.+++..
T Consensus 221 ~~~~~~~~~~~~~krl~~----~~~f~~~~~~Pewmil~~lPVpPp~~RP~v~l~gg~~~~~Dln~~~~~Ii~~N~~L~~ 296 (1265)
T 1hqm_D 221 MKHPSRARRAKARKRLEV----VRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKK 296 (1265)
T ss_dssp TCCSSHHHHHHHHHHHHH----HHHHHSSSCSSCCSCSSCCCCCSCC------------CCCGGGTHHHHTHHHHHHHHT
T ss_pred HhhccHHHHHHHhhhhhh----hhhhcccCCCcceEeeeccCCCCCcCccceecCCCceecChhHHHHHHHHHHHHHHHH
Confidence 222355666666666532 112344578999999999999999999999886631
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 297 ~~~~~ap~~ii~~~~~~LQ~~V~~l~Dn~~~g~~~~~~~~rp~lksl~~~LkGK~GrfR~NLmGKRVdfSaRSVI~pdP~ 376 (1265)
T 1hqm_D 297 LLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQ 376 (1265)
T ss_dssp SSSSCCCSTTTSTTTTTTGGGTTTTSSCCSSCCCSSCSSCCCCCCCSTTTSSSTTCTTTTTTSCCEETTCCCCBEEECCS
T ss_pred HHHcCCchhHHHHHHHHHHHHHHHHhCCCCCCCCccCCCCCccccchhhhcccchhhhhhhhcccccCcccceeEecCCC
Confidence
Q ss_pred -----------------------------------------------------------CCeEEEEecCcccccccccee
Q psy13846 341 -----------------------------------------------------------DNDVVLFNRQPSLHKLSIMAH 361 (1423)
Q Consensus 341 -----------------------------------------------------------~~d~Vl~nRqPsLHk~Simah 361 (1423)
+||+|||||||||||+|||||
T Consensus 377 L~i~evGvP~~~A~~L~~P~~~~~lv~~g~~~~i~~ak~~i~~~~~~~~~~~~v~~~v~~gd~VLlNRqPTLHr~sIma~ 456 (1265)
T 1hqm_D 377 LKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAF 456 (1265)
T ss_dssp SSSSBCCCBHHHHHHHHHHHHHHHHHHTTCSSCSHHHHHHHCSSSCCCHHHHTTTTTTTTTCCEECCCSSCCSGGGSCEE
T ss_pred cccccccChHHHHHHhCcHHHHHHHHHcCCcchhhhhhhhhhhccccCCccceeEEEeccCcEEEEecCcccccccccce
Confidence 789999999999999999999
Q ss_pred eeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccc
Q psy13846 362 RAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441 (1423)
Q Consensus 362 ~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~ 441 (1423)
+++++|++||||||++|+||||||||||||+|+|||++|||||+ .||.+.+|++||++|+|+++++
T Consensus 457 ~~~l~~~ktirlhp~vC~~yNADFDGDeMnvHvPqs~eA~aEa~--------------~Lm~~~~nilsP~~G~Pi~~~~ 522 (1265)
T 1hqm_D 457 QPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEAR--------------IQMLSAHNLLSPASGEPLAKPS 522 (1265)
T ss_dssp BCCCBSSSSEEECGGGHHHHCCCSSSCBCCCCCCCSTHHHHTTS--------------SSSBSSSSSSSCSSSSCSSCCC
T ss_pred eEEecCCCeEEechhhcCCcCCCcccceEEEecCCCHHHHHHHH--------------HHhCccccEecCCCCCeeEeee
Confidence 99999999999999999999999999999999999999999999 9999999999999999999999
Q ss_pred cceEEEEEeecccc--------cCCCHHHHHHHHHhhccCCccccceEe-eee------cc-ccCCce------------
Q psy13846 442 QDFITGGYLLTQKN--------AFFNRAQTMRIASTLIADTSDICGIIK-RFS------WR-SWNPVV------------ 493 (1423)
Q Consensus 442 qD~~~~~~~~t~~~--------~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~------~~-~l~~p~------------ 493 (1423)
||+++|+|.||.+| .|++++|++++++... .+.+..++ +.. |. .+++|+
T Consensus 523 QD~vlg~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~~---i~l~a~i~~~~~~~~~g~~k~~~t~P~k~I~~~~~g~~~ 599 (1265)
T 1hqm_D 523 RDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGE---VALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGLLD 599 (1265)
T ss_dssp TTHHHHHHHTTCCCCCCCCCCCCSSCCTHHHHHTTSSC---CSSCCCSSSCCSTTSSCCCCCTTTCSHHHHHHHHTTSSC
T ss_pred ccccceeEEeccccCCccCCCcccCCHHHHHHHHHCCC---CCCCCceEEecccccccccccccccccccccccccCccc
Confidence 99999999999999 7999999998654322 23333332 110 00 112121
Q ss_pred -------eecc--eeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEEeccccccccccccCCcCCCC
Q psy13846 494 -------FVRT--AVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGG 564 (1423)
Q Consensus 494 -------i~kp--~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~ 564 (1423)
.++| ...|+|||+|+.++|++.. . +. .+++-.+ +.|++||+.+|
T Consensus 600 ~q~~~~~~~k~~~~~t~~Gr~if~~~lp~~~~---------~---~~-----~p~~~~~-------~ngvldKk~lG--- 652 (1265)
T 1hqm_D 600 LQDTVTTRYLGRRLETNPGRILFARIVGEAVG---------D---EK-----VAQELIQ-------MDVPQEKNSLK--- 652 (1265)
T ss_dssp SSSCCCCEESSSEECCCHHHHHHHHHHHHHTT---------C---TT-----TTTTSSC-------CSSCCCSSHHH---
T ss_pred cccccceeccccceeccCCceEEeeecccccc---------c---cC-----CCCCCce-------EeeeecHHHHH---
Confidence 1244 6889999999999975422 0 00 1221111 45899999997
Q ss_pred CCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcC-cceecCCCCCCc-------------------------------
Q psy13846 565 KANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRG-FSIGIGDVTPGQ------------------------------- 612 (1423)
Q Consensus 565 ~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~G-fsiGi~D~~~~~------------------------------- 612 (1423)
+++|.+|++||++.|+.||+++++++++|++.+| ||+|++|+++.+
T Consensus 653 --~LI~~i~~~~G~~~a~~~ld~l~~l~~~~lt~~G~fSigi~D~~~~~~k~~~i~~a~~~v~~i~~~y~~g~lt~~e~~ 730 (1265)
T 1hqm_D 653 --DLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGIITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERY 730 (1265)
T ss_dssp --HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHTTCCCCSSSSCCCCSTTTTHHHHHHHHHHHHHTTTTSSSSCHHHHH
T ss_pred --HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhCCCceEeeccccCCHHHHHHHHHHHHHHHHHHHHHHcCCCcHHHHH
Confidence 6999999999999999999999999999999999 999999997544
Q ss_pred -----------------------------------------------------------------cccccccccCCCcee
Q psy13846 613 -----------------------------------------------------------------GFVQNSFFSGLTPTE 627 (1423)
Q Consensus 613 -----------------------------------------------------------------GfI~~sf~~GL~p~E 627 (1423)
+||.+||++||+|+|
T Consensus 731 ~~v~~~~~~~~d~~~~~~~~~l~~~~~~N~i~~Ma~SGAKGS~~ni~Ql~g~~G~ma~~~G~~i~~pI~ssF~eGLtp~E 810 (1265)
T 1hqm_D 731 DQVIQLWTETTEKVTQAVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLE 810 (1265)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHSCSSSCTTTTTTTSSSCCHHHHHHHSSCCCCCCCTTSCCCSCCCCCCBTTBCTTCT
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCCCcHHHHHHhcCCcCHHHHHHHHhhccccccCCCCccCcccccccccCCChHH
Confidence 789999999999999
Q ss_pred eeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccce
Q psy13846 628 FFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670 (1423)
Q Consensus 628 fffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~t 670 (1423)
||||||||||||+|||||||+||||||||||++||++|+||++
T Consensus 811 yFfhtmggReGLiDTAvKTA~SGYLqRRLVkv~qDv~V~~ddc 853 (1265)
T 1hqm_D 811 YFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADC 853 (1265)
T ss_dssp HHHHHHHHTTHHHHHTHHHHTSSSTHHHHHHHSCSCCCCSCCC
T ss_pred hheecccccccchhhhhhcccCCcceeeeeeecceEEEEECCC
Confidence 9999999999999999999999999999999999999999886
No 4
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*
Probab=100.00 E-value=6.9e-125 Score=1195.76 Aligned_cols=499 Identities=26% Similarity=0.370 Sum_probs=376.4
Q ss_pred cccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCC-CCC--------------CCCCccCCCCC
Q psy13846 75 RKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRM-GTN--------------QKEANCTTCGQ 139 (1423)
Q Consensus 75 ~~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rL-G~~--------------~~~~~C~TCg~ 139 (1423)
....+.. +++++.|||+|+++|+.||++|++++ +.+.+|..+||+++|+ ||. .+...|.+||-
T Consensus 13 ~~~~~~~-i~i~laSpe~I~~ws~GEV~kpetin-yrt~kPe~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~C~~Cgv 90 (1407)
T 3lu0_D 13 KTEEFDA-IKIALASPDMIRSWSFGEVKKPETIN-YRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGV 90 (1407)
T ss_dssp -CCCCCC-EEECCCCHHHHHHHBCSCCCSCCCCC-SSCCSCCSSSSSCTTTTCCSSSSCCSSCSCCSTTCSSSCCSSSCC
T ss_pred ccCccce-EEEEeCCHHHHHhhcCeEECCccccc-cCCCCCCCCCccchhhcCCCcCcEEeCccccccccCCCCCCCCCC
Confidence 3467888 99999999999999999999999996 6799999999999998 987 25678999999
Q ss_pred CCcccC---CccceEEccCceeEEeeeccH----HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHH
Q psy13846 140 NLSDCV---GHFGYIDLPLPVFHIGYFRCV----INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212 (1423)
Q Consensus 140 ~~~eCp---GHfGhIeL~~PV~h~gffd~v----~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~ 212 (1423)
...+|. .|||||+|+.||.|+|||+.+ ..+|.+.|+. |.++++-.... +..+....+.+.++..+
T Consensus 91 evt~~~vRr~rmGhI~La~PV~Hiwy~k~~ps~i~~lL~~~~k~--le~viy~~~~i------v~~~~~~~l~~~~~~~~ 162 (1407)
T 3lu0_D 91 EVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRD--IERVLYFESYV------VIEGGMTNLERQQILTE 162 (1407)
T ss_dssp CCCCTTHHHHCBCEEEEEEEECCTHHHHSSSCTTTTTTTSCSST--THHHHSSSCCC------EECCSSSCSCSSCCCCS
T ss_pred ccccCcchhhhcceeeecCceeEeeeccCCchHHHHHhCCCHHH--hhhheecceeE------eecCCCCccchhcccCH
Confidence 999998 999999999999999999987 7899999999 99888654321 11221111111111000
Q ss_pred HHHHccCCccCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHH
Q psy13846 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292 (1423)
Q Consensus 213 i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~ 292 (1423)
+.+.....|..- ....+.|. +.+.+.+.... -+...+.+.+++..... . . +..+.+.-.++.
T Consensus 163 --~~~~~~~~~~~~----~~~~~~Ga-eai~~lL~~~d--l~~~~~~l~~~~~~~~~---~----~--k~~~~~krl~~v 224 (1407)
T 3lu0_D 163 --EQYLDALEEFGD----EFDAKMGA-EAIQALLKSMD--LEQECEQLREELNETNS---E----T--KRKKLTKRIKLL 224 (1407)
T ss_dssp --TTCCCCCSSSCC----CCCEECSS-HHHHHHHHTCC--HHHHHHTHHHHHHHCCC---T----T--TTTTTTTSSTTH
T ss_pred --HHHHHHHHhhch----hhhccccH-HHHHHHHHhcC--HHHHHHHHHHHHHhccc---H----H--HHHHHHHHHHHH
Confidence 011111111110 11111110 11111110000 01111112122111000 0 0 000111111111
Q ss_pred HHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCC--------------------------------
Q psy13846 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS-------------------------------- 340 (1423)
Q Consensus 293 eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~-------------------------------- 340 (1423)
+ .+..+++||+||||++|||||+++||++.+++..
T Consensus 225 ~-------------~F~~s~~rPewmil~~lPVpPp~lRP~v~l~gg~~~~~DLn~ly~~II~~N~~Lk~~~~~~ap~~i 291 (1407)
T 3lu0_D 225 E-------------AFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDII 291 (1407)
T ss_dssp H-------------HHHSSSCCGGGSSEEEEECCCSTTSCCCBCSTTCBCCCTTTTTHHHHHHTTTTTGGGTSSCCCTTT
T ss_pred H-------------HHHhcCCCHHHhhhheeecCCCCCCCcEEeCCCccccCchHHHHHHHHHHHHHHHHHHHcCCcHHH
Confidence 1 2334678999999999999999999999987631
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 292 i~~~~~~LQ~~V~~l~Dn~~~g~~~~~~~~rplksl~qrLkGKeGrfR~NLmGKRVDfSaRSVIspdP~L~i~evGvP~~ 371 (1407)
T 3lu0_D 292 VRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKK 371 (1407)
T ss_dssp HHHHHHHHHHHHHHHHCSSSSCCCCBTTBCCCCCCTTHHHHTSSSTHHHHTTCCCCSSBCEEEEEECSSCCTTEEEEESH
T ss_pred HHHHHHHHHHHHHHhcCCCCCCCcccCCCCCcccchHHHhccccchhhcccccCCCCCcCceEEeCCCCccceeeeCCHH
Confidence
Q ss_pred ---------------------------------------------CCeEEEEecCccccccccceeeeEEecCCceeecc
Q psy13846 341 ---------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNE 375 (1423)
Q Consensus 341 ---------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~ 375 (1423)
+||+|||||||||||+|||||+++++|++|||+||
T Consensus 372 ~A~~L~~Pf~i~~L~~~g~~~~i~~ak~~v~~~~~~v~~vl~~vi~gd~VLlNRqPTLHr~sIma~~~~l~~~ktirlnp 451 (1407)
T 3lu0_D 372 MALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHP 451 (1407)
T ss_dssp HHHHHTCHHHHHHHTTSSSCSSTTTTTTTTTSSCSSHHHHHHTTTTSCCEEEEESSCCSGGGEEEEEEEEESSSSEEECT
T ss_pred HHHHhcchHHHHHHHHcCccccHHHHHHHHHhcCCchhhHHHHHhhceeeeecCCcccccccceeeeEEecCCceEEeCh
Confidence 78999999999999999999999999999999999
Q ss_pred CCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccc
Q psy13846 376 CVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN 455 (1423)
Q Consensus 376 ~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~ 455 (1423)
++|+||||||||||||+|+|||++|||||+ .||.+.+|++||++|+|+++++||+++|+|.||.+|
T Consensus 452 ~vC~~yNADFDGDeMnvHvPqs~eAraEa~--------------~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~lT~~~ 517 (1407)
T 3lu0_D 452 LVCAAYNADFDGDQMAVHVPLTLEAQLEAR--------------ALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDC 517 (1407)
T ss_dssp GGGGTTTCCSSSCEEEEECCCSSHHHHTTT--------------TSSBTTTCCSCSSSSSCSSCCCSHHHHHHHHHSCCC
T ss_pred hhcccccCCcccceeeeecCCCHHHHHHHH--------------HHHhCccccccCCCCCceeeecccchheeEEeeccc
Confidence 999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred c--------CCCHHHHHHHHHhhccCCccccceEeeeeccccCC------ceeecceeeeecceeeeecccCCCCccccc
Q psy13846 456 A--------FFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNP------VVFVRTAVIWTGKQIFSLILKPNRDCPVNA 521 (1423)
Q Consensus 456 ~--------~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~------p~i~kp~~~wtGKqi~s~il~~~~~~~~~~ 521 (1423)
. |.+.++++.++... .+..+.+++ +.++.+.+ |...++.+.|+|||+|+.+||++..
T Consensus 518 ~~~~~~~~~F~~~~ev~~al~~g---~v~l~a~i~-vr~~~~~~~~~g~~~~~~~~~~tt~Gr~ifs~ilP~~~~----- 588 (1407)
T 3lu0_D 518 VNAKGEGMVLTGPKEAERLYRSG---LASLHARVK-VRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLP----- 588 (1407)
T ss_dssp CCSCCSCCCCSSCSHHHHHHHHS---SSSSSSCSS-SSCCCCSCSHHHHHHHTTTSCCSSSHHHHHHHHGGGSSC-----
T ss_pred ccccCCcceeCCHHHHHHHHHcC---CCCCCCeeE-EecCccccCcCCcccccceeeecCCccccHHhhCCCCCC-----
Confidence 6 66788877765432 124444442 00101000 1123456789999999999986421
Q ss_pred ceeecccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCc
Q psy13846 522 NLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGF 601 (1423)
Q Consensus 522 ~~~~~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~Gf 601 (1423)
.+++.|.++|+.+| ++|+.+|++||.+.|..||++++++..+|++.+||
T Consensus 589 --------------------------~~~ing~l~KK~lg-----~LI~~i~~~~G~~~t~~flD~lk~Lgf~~at~~Gf 637 (1407)
T 3lu0_D 589 --------------------------YSIVNQALGKKAIS-----KMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGA 637 (1407)
T ss_dssp --------------------------CTTTTTCCSSSTTT-----THHHHHHHHSCSHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred --------------------------ceeeecccchhhHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCe
Confidence 12567899999986 69999999999999999999999999999999999
Q ss_pred ceecCCCCCCc---------------------------------------------------------------------
Q psy13846 602 SIGIGDVTPGQ--------------------------------------------------------------------- 612 (1423)
Q Consensus 602 siGi~D~~~~~--------------------------------------------------------------------- 612 (1423)
|+|++|+++.+
T Consensus 638 SIgI~D~~ip~~K~~iI~~A~~eV~ei~~~y~~G~lt~~er~~kVi~iw~~a~e~v~~~m~~~l~~~~~~d~~G~~~~l~ 717 (1407)
T 3lu0_D 638 SVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQV 717 (1407)
T ss_dssp CCCSTTSCCCTTHHHHHHHHHTHHHHHHHHHHHTSCCSSTTTTTHHHHHHTHHHHHHHHHHTTHHHH------------C
T ss_pred EEeeccCccChHHHHHHHHHHHHHHHHHHHHHcCCCccchHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccC
Confidence 99999996433
Q ss_pred ---------------------------------------cccccccccCCCceeeeeecccccccchhcccccCCCCcch
Q psy13846 613 ---------------------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQ 653 (1423)
Q Consensus 613 ---------------------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlq 653 (1423)
++|.+||++||+|.|||||||||||||+|||||||+|||||
T Consensus 718 ~~N~i~mMa~SGARGS~~qI~QLaGmrGlmakpdG~iie~PI~ssFreGLtp~EyFfst~GaRKGL~DTALKTAdSGYLT 797 (1407)
T 3lu0_D 718 SFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLT 797 (1407)
T ss_dssp SCCHHHHHHHSSSSCCTTHHHHHSSCCCCCBCSSSCBCSSCCCCCSSSCCCHHHHHHHHHHHHHHHHHTTTTTTCTTTTT
T ss_pred CCCChheeeeccccCCHHHHHHHHHhcCCccCCCCCCcchhhhcccccCCCHHHhhhhcccchhhhhhhhhhcccchhHH
Confidence 67889999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhhhccc
Q psy13846 654 RRLVKSLEDLCVQYD 668 (1423)
Q Consensus 654 RrLvk~ledl~v~yD 668 (1423)
|||||++||++|.++
T Consensus 798 RRLVdv~QDviV~e~ 812 (1407)
T 3lu0_D 798 RRLVDVAQDLVVTED 812 (1407)
T ss_dssp HHHHTTSTTCCBCCC
T ss_pred HHHHHhhcceEEEec
Confidence 999999999998864
No 5
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Probab=100.00 E-value=1.2e-124 Score=1212.11 Aligned_cols=292 Identities=28% Similarity=0.419 Sum_probs=239.0
Q ss_pred CCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhh
Q psy13846 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKV 420 (1423)
Q Consensus 341 ~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~ 420 (1423)
+||+|||||||||||+|||||+++++|++||||||++|+||||||||||||+|+|||++|||||+ .
T Consensus 696 dgd~VLlNRqPTLHRlSIqAf~~kl~~gkTiRLhplVC~pyNADFDGDEMnvHvPqS~eAraEA~--------------~ 761 (1524)
T 2a6h_D 696 HGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEAR--------------I 761 (1524)
T ss_dssp TTCCEEEECSSCCSGGGEEEEEEEEESSSCEEECSGGGTTTTCCTTTCEEEEECCCSHHHHHHHH--------------H
T ss_pred cCceEEEccCCcccccccceeEEEEcCCccceeChhhcCCccCCcccceeeEecCCCHHHHHHHH--------------H
Confidence 68999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred hhccccccccCCCCccccccccceEEEEEeecccc--------cCCCHHHHHHHHHhhccCCccccceEe-eee-c----
Q psy13846 421 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN--------AFFNRAQTMRIASTLIADTSDICGIIK-RFS-W---- 486 (1423)
Q Consensus 421 l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~--------~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~-~---- 486 (1423)
||.+.+|++||++|+|+++++||+++|+|.||.++ .|++.++++.+.+.-.. +.+.+++ ++. |
T Consensus 762 LM~~~~nilsP~~G~Pi~~~~QD~vlG~y~LT~~~~~~~~~g~~F~~~~e~~~ay~~~~~---~l~~~i~v~~~~~~~~~ 838 (1524)
T 2a6h_D 762 QMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEV---ALNAPIKVAGRETSVGR 838 (1524)
T ss_dssp HSBTTTCCBCSSSSSBSSCCCHHHHHHHHHHHCCCCCCCCSCCCTTSCHHHHHHHHHHHH---TTSSCSSCCCSSCCHHH
T ss_pred HhCCccceecCCCCCeeeeecccchhhheecccccccccCCCceeCCHHHHHHHHhcCCc---CcCCceEEecccccccc
Confidence 99999999999999999999999999999999984 78899998876543211 2222221 100 0
Q ss_pred --cccCCce--eecceeeeecceeeeec----ccCCCCcccccceeecccc-ccc------CcccccCCcEEEecccccc
Q psy13846 487 --RSWNPVV--FVRTAVIWTGKQIFSLI----LKPNRDCPVNANLKTKGRA-YTA------NEEFCHRDSYVILRNSELL 551 (1423)
Q Consensus 487 --~~l~~p~--i~kp~~~wtGKqi~s~i----l~~~~~~~~~~~~~~~~~~-~~~------~~~~~~~d~~v~i~~~ell 551 (1423)
..+|||+ |+|| |||||+++.+ ++.+. .....++. +.. .....|++- ..+
T Consensus 839 ~~~~~p~P~~aIlKp---wtGKQi~~~~~~~~I~~~~------~~tt~Gr~ifn~~lp~~l~~~~~P~d~-------~~i 902 (1524)
T 2a6h_D 839 LKYVFANPDEALLAV---AHGIVDLQDVVTVRYMGKR------LETSPGRILFARIVAEAVEDEKVAWEL-------IQL 902 (1524)
T ss_dssp HHCEESSHHHHHHHH---HTTSSCTTSCCEEECSSCE------ECCCHHHHHHHHHHHHHSSCHHHHHHT-------CCT
T ss_pred cccccCCchhhhcCC---CCCccccccccccceecce------eecccchhhHHHHhhhhcccccCCCcc-------cce
Confidence 0234554 7787 9999998842 11100 00001110 000 000012111 123
Q ss_pred ccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCc-------------------
Q psy13846 552 AGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ------------------- 612 (1423)
Q Consensus 552 ~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~------------------- 612 (1423)
.|++||+.+| +++|.+|++||++.|+.||+++++++++|++.+|||||++|+++++
T Consensus 903 nGvLdKk~LG-----~LI~~i~~~yG~~~t~~fLD~lk~Lg~~~lt~~GfSIGI~Dlii~~~K~eiI~eA~~~v~~i~~~ 977 (1524)
T 2a6h_D 903 DVPQEKNSLK-----DLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQA 977 (1524)
T ss_dssp TSCCCHHHHH-----HHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHTCCCCSTTSCCCTTHHHHHHHHHHHHHHHHHH
T ss_pred eceecHHHHH-----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeehhhccCCHHHHHHHHHHHHHHHHHHHH
Confidence 5899999997 5999999999999999999999999999999999999999998764
Q ss_pred -----------------------------------------------------------------------------ccc
Q psy13846 613 -----------------------------------------------------------------------------GFV 615 (1423)
Q Consensus 613 -----------------------------------------------------------------------------GfI 615 (1423)
.+|
T Consensus 978 y~~G~lt~~Er~~~Vi~iw~~a~d~v~~~~~~~L~~~~~~N~i~~Ma~SGAKGS~~NI~Ql~gmrGqma~p~GkiIp~PI 1057 (1524)
T 2a6h_D 978 YEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPV 1057 (1524)
T ss_dssp HHTTCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHSSSSCCHHHHHHHTSCCCCCBCSSSCBCSSCC
T ss_pred HHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCHHHHHHhcCCcCHHHHHHHHhhccccccCCCCCccccc
Confidence 369
Q ss_pred ccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccce
Q psy13846 616 QNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670 (1423)
Q Consensus 616 ~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~t 670 (1423)
.+||++||+|+|||||||||||||+|||||||+||||||||||++||++|.||.+
T Consensus 1058 ~ssF~eGLtp~EyFfhtmGgReGLvDTAvKTAdSGYLqRRLVkv~qDviVr~dDc 1112 (1524)
T 2a6h_D 1058 RSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADC 1112 (1524)
T ss_dssp CCCSSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCSCC
T ss_pred ccccccCCChHHhheecccccCCccccceeeccCCcceeeeeeecceeEEEeCCC
Confidence 9999999999999999999999999999999999999999999999999999876
No 6
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Probab=100.00 E-value=1.7e-118 Score=1154.76 Aligned_cols=538 Identities=38% Similarity=0.657 Sum_probs=469.8
Q ss_pred cceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCc
Q psy13846 77 VFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156 (1423)
Q Consensus 77 ~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~P 156 (1423)
.+|.+ |+||++||||||++||++|++|++| |.+|+|++|||+|||||+.++...|+|||....+||||||||+|+.|
T Consensus 4 k~i~~-I~f~l~SpeeIr~~S~~eV~~p~t~--n~~g~p~~ggl~D~~lG~~~~~~~C~tCg~~~~~c~ghfGhIeLa~P 80 (880)
T 4ayb_A 4 KNIKG-IKFGILSPDEIRKMSVTAIITPDVY--DEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFGHIELVRP 80 (880)
T ss_dssp EEEEE-EEEECCCHHHHHHHTCSCBCCSCCC--BSSSSSBCSSSSCGGGCCCSSSCCCTTTCCCGGGCCCCCEEEEEEEE
T ss_pred ceece-EEEEeCCHHHHHHhcceEEeCcceE--CCCCCccCCCCCChhhCCCCCCCCCCCCCCCCCCCCCCCeeeccccc
Confidence 56889 9999999999999999999999999 67999999999999999999999999999999999999999999999
Q ss_pred eeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCch-hHHHHHHHHHHHHHHccCCccCCCCCCCCCceee
Q psy13846 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPAL-SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK 235 (1423)
Q Consensus 157 V~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~-~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk 235 (1423)
||||+||+.+.++|+++|++ |+++++.+++...|......... .....+.+...+.+.+.+.+.|++||+.++.+++
T Consensus 81 V~h~~f~~~i~~lL~~~c~~--C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~cg~~~~~i~~ 158 (880)
T 4ayb_A 81 VIHVGFVKHVYEFLKATCRR--CGRVKISEDEIEKYSRIYNAIKKRWPSAARRLTEYVKKTAMKAQVCPHCGEKQFKIKL 158 (880)
T ss_dssp EECGGGTTHHHHHHHTSCTT--SSCCCSSCCHHHHHHHHHHHHGGGCHHHHHHHHHHHHHHHTTCSSCTTTTCCCCCCEE
T ss_pred ccchhHHHHHHHHHhCcccc--ccCCcCCHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHhcccccchhccchhhhhhh
Confidence 99999999999999999999 99999998887766554322111 1122344555566677888999999999998887
Q ss_pred cCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCCcccccccccCCCCC
Q psy13846 236 CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315 (1423)
Q Consensus 236 ~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~d~~lL~m~~~~arP 315 (1423)
.....+..+. + .....++|.+++++|++|+++|+.+++++++++||
T Consensus 159 ~~~~~~~~~~---------------------------------~-~~~~~l~~~~~~~~l~~i~~~~~~~l~~~~~~~~P 204 (880)
T 4ayb_A 159 EKPYNFYEER---------------------------------K-EGVAKLTPSDIRERLEKVPESDVEILGYDPTTSRP 204 (880)
T ss_dssp EETTEEEEEE---------------------------------T-TEEEECCHHHHHHHHTTCCHHHHHHTTCCTTTCCS
T ss_pred cCcCCHHHHH---------------------------------H-HHHHhcCHHHHHHHHHHhHHHHHHHhCCCCcCCCc
Confidence 6433322110 0 12346899999999999999999999999999999
Q ss_pred cceEEEEecCCCCCCCCcEEcCCCC-------------------------------------------------------
Q psy13846 316 SDLILTRLLVPPNCIRPSVISDLKS------------------------------------------------------- 340 (1423)
Q Consensus 316 e~liLt~lpVPP~~vRPsv~~g~~~------------------------------------------------------- 340 (1423)
+||||++|||||+++||++.+++..
T Consensus 205 ewmil~~lPV~Pp~~RP~v~l~~g~~~~~dl~~~~~~ii~~N~~lk~~~~~~ap~~i~~~~~~~LQ~~V~~l~dn~~~g~ 284 (880)
T 4ayb_A 205 EWMILTVLPVPPITIRPSIMIESGIRAEDDLTHKLVDIVRINERLKESIDAGAPQLIIEDLWDLLQYHVATYFDNEIPGL 284 (880)
T ss_dssp GGGEEEEEEECCSSSSCC-----CCCCCCSSHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHCSCCSSS
T ss_pred hheEEeeeeCCCCCCCchhhcCCcccccchHHHHHHHHHHhhhhhhhhhhcCCchhHHHHHHHHHHHHHHHHHhccCCCC
Confidence 9999999999999999999887642
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 341 -------------------------------------------------------------------------------- 340 (1423)
Q Consensus 341 -------------------------------------------------------------------------------- 340 (1423)
T Consensus 285 ~~~~~~~~rp~ksl~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~e~GvP~~~A~~Lt~Pe~vt~~N~~~l~~~ 364 (880)
T 4ayb_A 285 PPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGVPEIIARTLTVPERITPWNIEKLRQF 364 (880)
T ss_dssp CCCCCTTSCCCCCHHHHHHSSSSTHHHHTSSEECSSEEEEEEEECTTSCSSEEEECHHHHTTSEEEEECCTTTHHHHHHH
T ss_pred CccCCCCCCcccchhhhhcccchhhhhcccceeecccCceeeeCCCCccccccCCcHHHHHhCCCCeEEcHHHHHHHHHH
Confidence
Q ss_pred ------------------------------------------------CCeEEEEecCccccccccceeeeEEecCCcee
Q psy13846 341 ------------------------------------------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFR 372 (1423)
Q Consensus 341 ------------------------------------------------~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir 372 (1423)
+||+|||||||||||+|||||+++++|++|||
T Consensus 365 v~ng~~~~pga~~~i~~~~~~~~l~~~~~~~~~~~~l~~g~~V~rhl~dgd~VLlNRqPTLHr~si~a~~~~l~~gktir 444 (880)
T 4ayb_A 365 VINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFR 444 (880)
T ss_dssp HHHTTSSSSCEEEEECSSCCEEEGGGCSSCTTHHHHCCTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEECSSSSEE
T ss_pred HHcCCccccchhhhhhccceEEEeecchhhhHHHHhccccceEeeeeecCcEEEecCCCcccccceeeeeeecccCceee
Confidence 78999999999999999999999999999999
Q ss_pred eccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeec
Q psy13846 373 FNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLT 452 (1423)
Q Consensus 373 ~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t 452 (1423)
+||++|+||||||||||||+|+|||++|||||+ .||.+.+|++||++|+|+++++||+++|+|.||
T Consensus 445 lhp~vC~~yNADFDGDeMnvHvPqS~eA~aEa~--------------~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~lT 510 (880)
T 4ayb_A 445 LNLLVCPPYNADFDGDEMNLHVPQSEEAIAEAK--------------EIMLVHKNIITPRYGGPIIGAAQDYISGAYLLT 510 (880)
T ss_dssp ECGGGHHHHTCCSSSCEEEEECCCSHHHHHHHH--------------HHSBSGGGCBCSSSSSBCSCCCSHHHHHHHHHT
T ss_pred eccccccccccCcccceeEEeccCCHHHHHHHH--------------HHHhChhccccCCCCCccccccccHHHHhHHhh
Confidence 999999999999999999999999999999999 999999999999999999999999999999999
Q ss_pred ccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeeccccccc
Q psy13846 453 QKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTA 532 (1423)
Q Consensus 453 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~ 532 (1423)
.+|.|+++.+++++++... + ++ .+++|+|.+|.++|||||+|++++|++.......+....++..
T Consensus 511 ~~~~~~~~~~~~~~~~~~~-----~--~~------~~~~p~i~~~~~~~tgkqi~s~~lp~~~~~~~~~~~~~~~~~~-- 575 (880)
T 4ayb_A 511 VKTTLLTKEEAQQILGVAD-----V--KI------DLGEPAILAPREYYTGKQVVSAFLPKDFNFHGQANVSSGPRLC-- 575 (880)
T ss_dssp SSSCEECHHHHHHHHTTSC-----C--CC------CCCSCSEESSSEEEEHHHHHHTTSCTTCCEEEECTTCSGGGCC--
T ss_pred cCcccCCHHHHhhhhcccc-----e--ec------ccCccceecceeEeccceEEEEEecccccccceeEeecCCccc--
Confidence 9999999999999876543 1 12 7899999999999999999999998764322222222222211
Q ss_pred CcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCCCCCCc
Q psy13846 533 NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612 (1423)
Q Consensus 533 ~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D~~~~~ 612 (1423)
..+.++.|..|+|+||++++|.+||+.+|++..++++|.+|++||+..|..||+++++++++|++.+|||+|++|+++++
T Consensus 576 ~~~~~~~~~~v~i~~g~l~~g~ldk~~lg~~~~~~li~~i~~~~G~~~t~~~ld~l~~lg~~~lt~~GfSigi~Di~i~~ 655 (880)
T 4ayb_A 576 KNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIRFVELQGFTMRLEDVSLGD 655 (880)
T ss_dssp SSSCCTTSCEEEEETTEEEECCCSTTTSSTTCTTSHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHCCCCCGGGGCCCH
T ss_pred cCccCCCcceEEEeCceeeeeeecchhhcccccceeeehhhhhcccHHHHHHHHHHHHHHHHHHHhcCCcccccccccch
Confidence 23457788999999999999999999999866789999999999999999999999999999999999999999997543
Q ss_pred --------------------------------------------------------------------------------
Q psy13846 613 -------------------------------------------------------------------------------- 612 (1423)
Q Consensus 613 -------------------------------------------------------------------------------- 612 (1423)
T Consensus 656 ~~~~~i~~~i~~a~~~v~~i~~~~~~g~l~~~~g~~~~e~~e~~v~~~l~~~~~~~~~~~~~~l~~~N~i~mMa~SGARG 735 (880)
T 4ayb_A 656 DVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARG 735 (880)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTSSC
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHhhcCccC
Confidence
Q ss_pred --------------------------------------------cccccccccCCCceeeeeecccccccchhcccccCC
Q psy13846 613 --------------------------------------------GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAE 648 (1423)
Q Consensus 613 --------------------------------------------GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~ 648 (1423)
|||.+||++||+|+|||||||||||||+|||||||+
T Consensus 736 S~~ni~Qlagm~Gqq~~~G~RIprg~~~rtLP~f~~~d~~p~a~GfI~ssF~eGLtp~EyF~ht~ggRkGL~DTAlKTA~ 815 (880)
T 4ayb_A 736 SVLNITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQ 815 (880)
T ss_dssp CSTTHHHHHTCCEECBSSSSBSCCSBTTBSSTTSCTTCCSTTTTSEECSCTTTCCCHHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred CHHHHHHHHhcccccccCCccCcCCCccCCCCCCCCCCCCcccCCeEhhcccCCCCHHHHHHhhhhhhhhHHhcchhhch
Confidence 789999999999999999999999999999999999
Q ss_pred CCcchHHHHHHHhhhhhcccceeecc-------ccCCCccC
Q psy13846 649 TGYMQRRLVKSLEDLCVQYDMSFDAA-------FYGQTDCI 682 (1423)
Q Consensus 649 sGYlqRrLvk~ledl~v~yD~tVR~s-------~yG~~~~~ 682 (1423)
||||||||||++|||+|+||+|||++ .||+|+.+
T Consensus 816 SGYLtRRLVdv~qDv~V~yDgTVR~~~g~ivqf~YGeDgld 856 (880)
T 4ayb_A 816 SGYMQRRLINALSDLRAEYDGTVRSLYGEVIQVAYGDDGVF 856 (880)
T ss_dssp HHHHHHHHHHHHTTEEECTTSCEEETTTEEEESSTTTTCBC
T ss_pred hhHHHHHHHHHHcCEEEecCCCccCCCCcEEEEecCCcccc
Confidence 99999999999999999999999987 37777543
No 7
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=8.4e-87 Score=890.75 Aligned_cols=780 Identities=20% Similarity=0.255 Sum_probs=522.3
Q ss_pred hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCH
Q psy13846 11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKE 90 (1423)
Q Consensus 11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~ 90 (1423)
.-+||||||++||+|++||+||++|+||||++||+|+|+|+||+||+|++++|++++++|+... ...+.. |
T Consensus 499 qs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~lT~~~~f~~~~e~~~l~~~~~~~-~~~~~~--------p 569 (1752)
T 3h0g_A 499 QSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVPDW-DGILPP--------P 569 (1752)
T ss_dssp CSTTHHHHHHHTCCTTTTSEETTTTEESCCCCTHHHHHHHHHHSTTCEEETHHHHGGGGCSSSC-CSSCCC--------C
T ss_pred CCHHHHHHHHHHhcCccceecCCCCCceeeecchhhhheeeeccccccCCHHHHHHHHHhhccc-CCccCc--------c
Confidence 4479999999999999999999999999999999999999999999999999999999985211 111111 1
Q ss_pred HHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEeeeccHH---
Q psy13846 91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVI--- 167 (1423)
Q Consensus 91 eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v~--- 167 (1423)
. -+....+| +||++.+-++++.++...+.. |. ..+|-+.+++.+....+..|.+++..
T Consensus 570 a--------i~kp~~~w----tGkqifs~ilp~~~~~~~~~~----~~---~~~~~~d~~v~i~~gell~g~l~K~~lg~ 630 (1752)
T 3h0g_A 570 V--------ILKPKVLW----TGKQILSLIIPKGINLIRDDD----KQ---SLSNPTDSGMLIENGEIIYGVVDKKTVGA 630 (1752)
T ss_dssp S--------BCSSSCEE----ETTHHHHTTSCSSBCEECCCS----SC---CSSCTTTCSEEECBSCEEEECCSHHHHSS
T ss_pred c--------eecCcCCC----chhhHHhhhCcCCCCceeccc----cc---cCcCCCcCeEEEEcCeEEecccchHHhcc
Confidence 1 12334678 899999999988776554321 21 24566789999999999999998541
Q ss_pred ---HHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehhh
Q psy13846 168 ---NILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHE 244 (1423)
Q Consensus 168 ---~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e 244 (1423)
.|++.++.. ++.++...|++++++....++.+.+|+.++.|...... ..+...+
T Consensus 631 ~~~~li~~i~~~-------~G~~~~~~~ld~~~~l~~~~l~~~GfSigi~D~~~~~~----------------~~~~~~~ 687 (1752)
T 3h0g_A 631 SQGGLVHTIWKE-------KGPEICKGFFNGIQRVVNYWLLHNGFSIGIGDTIADAD----------------TMKEVTR 687 (1752)
T ss_dssp CTTCHHHHSSSS-------SCTTTHHHHHHHHHHHHHHHHHHHCCCCCGGGGSCCSH----------------HHHHHHH
T ss_pred CcccHHHHHHHH-------HCHHHHHHHHHHHHHHHHHHHHhcCceechhhcccCHH----------------HHHHHHH
Confidence 345555555 78888999999999888888888888888877642110 0000111
Q ss_pred hhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHh--------------------hccCCCccc
Q psy13846 245 KYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLF--------------------EAIPLEDIP 304 (1423)
Q Consensus 245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiL--------------------e~I~~~d~~ 304 (1423)
.+ ++..+.++++.+.|+. +.++..++..+++.| +.+. .+++
T Consensus 688 ~i----~~a~~~v~~~~~~~~~--------------g~l~~~~g~~~~e~~e~~v~~~l~~~~~~~~~~~~~~l~-~~N~ 748 (1752)
T 3h0g_A 688 TV----KEARRQVAECIQDAQH--------------NRLKPEPGMTLRESFEAKVSRILNQARDNAGRSAEHSLK-DSNN 748 (1752)
T ss_dssp HH----HTTTHHHHHHHTTTTT--------------TCCCCCSSCCTTHHHHHHHHHHHHHHHHHHHHHHHTTSC-SSCT
T ss_pred HH----HHHHHHHHHHHHHHHc--------------CCCccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCc
Confidence 11 1111222233322221 111222211111111 2232 3578
Q ss_pred ccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCC
Q psy13846 305 LLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNAD 384 (1423)
Q Consensus 305 lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nad 384 (1423)
++.|..+|+|+++.+++||. +|++||.+.|.+++.++ +.|.||| |.+.+.+|...+
T Consensus 749 ~~~M~~SGakGs~~ni~Q~~---~~~Gqq~~~GkrIp~g~-----------------~~rtLP~----f~k~d~~~~a~G 804 (1752)
T 3h0g_A 749 VKQMVAAGSKGSFINISQMS---ACVGQQIVEGKRIPFGF-----------------KYRTLPH----FPKDDDSPESRG 804 (1752)
T ss_dssp TTHHHHHCSSCCHHHHHHHH---TCCCCCCSTTSSSCCCS-----------------TTSSSTT----SCSSCCSTTTSS
T ss_pred HHHHhhhccccCHHHHHHHH---hccCCCccCCccCCCCC-----------------CCccCCC----CCCCCCCcccCc
Confidence 89999999999999999999 99999999999988888 8899999 999999999999
Q ss_pred CcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHH
Q psy13846 385 FDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 464 (1423)
Q Consensus 385 Fdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~ 464 (1423)
|+-+++..+|.+.| ||||+||||||+++||++|+.|||.+|+|+..+|| |.+.||+|+||+.+++.||.
T Consensus 805 fV~~sF~~GL~p~E----------fFfhtmggReGLiDTAvKTA~SGYLqRRLVk~leD-v~V~YDgTVRns~g~ivQF~ 873 (1752)
T 3h0g_A 805 FIENSYLRGLTPQE----------FFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMED-VMVRYDGTVRNAMGDIIQFA 873 (1752)
T ss_dssp CCSSCTTTCCCHHH----------HHHHHHHHTTTTTHHHHTTTHHHHHHHHHHHHHTT-CEEETTTEEECTTSCEEESS
T ss_pred chhhcccCCCCHHH----------HHHHhhhhhhhhhHhhhhcCcCchhHHHHHHHHhh-eEEeeCCeeEcCCCcEEEEe
Confidence 99999999999666 99999999999999999999999999999999999 99999999999999999999
Q ss_pred HHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEEE
Q psy13846 465 RIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVI 544 (1423)
Q Consensus 465 ~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~ 544 (1423)
|+.++++. ..++.+ -+..+-..+ ..+ .+.|.- +. .+...
T Consensus 874 YGeDGlD~--~~~e~q-------------------------~~~~~~~s~------~~f---~~~~~~--~~-~~~~~-- 912 (1752)
T 3h0g_A 874 YGEDGLDA--TLVEYQ-------------------------VFDSLRLST------KQF---EKKYRI--DL-MEDRS-- 912 (1752)
T ss_dssp SSSSCBCG--GGEEEE-------------------------ECTTTSCCH------HHH---TTTSCC--CT-TTTCC--
T ss_pred cCCCCcCh--HHhhcc-------------------------ccccccCCH------HHH---HHHhcc--cc-ccccc--
Confidence 98887742 122211 000000000 000 000000 00 00000
Q ss_pred eccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHH---------------HhhhhhhHHHhhcCcceecCCCC
Q psy13846 545 LRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMW---------------RLSRMTSFYLMNRGFSIGIGDVT 609 (1423)
Q Consensus 545 i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~---------------~l~~l~~~~L~~~GfsiGi~D~~ 609 (1423)
+ .-.+.+...++.....++..-|+..-. ...++. +++|+.... ...|.+ +
T Consensus 913 ~------~~~~~~~l~~~~~~~~~l~~E~~~l~~--dr~~lr~~i~~~~~~~~~lP~N~~R~i~~~--~~~f~~--~--- 977 (1752)
T 3h0g_A 913 L------SLYMENSIENDSSVQDLLDEEYTQLVA--DRELLCKFIFPKGDARWPLPVNVQRIIQNA--LQIFHL--E--- 977 (1752)
T ss_dssp G------GGTSCSCCTTSCSSTHHHHHHHHHHHH--HHTTSSSSSSSCSCCEEEEESCHHHHTTTT--TTTSCC--C---
T ss_pred c------cHHHHHHhccCHHHHHHHHHHHHHHHH--HHHHHHHHhhccccccccCCccHHHHHHHH--HHhcCC--C---
Confidence 0 000001122221111222222221100 000000 011111000 011111 0
Q ss_pred CCccccccccccCCCceeee------ee---cccccccchhcccccCCCCcchHHHHHHH-----h--hhhhcccceeec
Q psy13846 610 PGQGFVQNSFFSGLTPTEFF------FH---TMGGREGLVDTAVKTAETGYMQRRLVKSL-----E--DLCVQYDMSFDA 673 (1423)
Q Consensus 610 ~~~GfI~~sf~~GL~p~Eff------fh---~maGReGLiDTAvKTa~sGYlqRrLvk~l-----e--dl~v~yD~tVR~ 673 (1423)
.+=.+.|+|.+++ +. ..-|-..|...|-+.|. .|.+.+ . .+...|-.|-..
T Consensus 978 -------~~~~s~l~p~~~~~~v~~~~~~l~~~~g~d~l~~~~~~na~------~l~~~~lr~~l~~k~~~~~~~l~~~~ 1044 (1752)
T 3h0g_A 978 -------AKKPTDLLPSDIINGLNELIAKLTIFRGSDRITRDVQNNAT------LLFQILLRSKFAVKRVIMEYRLNKVA 1044 (1752)
T ss_dssp -------TTSCCCCCHHHHHHHHHHHHTTCCCSCCCSTTTTHHHHTSS------HHHHHHHTTSSSHHHHHHSSCCCHHH
T ss_pred -------cCccCCCCHHHHHHHHHHHHHhhhcccCCcchhhhhhhchH------HHHHHHHHhhhhhhhhhhhcCcCHHH
Confidence 0011223332211 00 00011111100110000 011110 0 000001000000
Q ss_pred cccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeeccc
Q psy13846 674 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELW 753 (1423)
Q Consensus 674 s~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~ 753 (1423)
- ++.-+..+..|.++.++||++||++||||||||+||||| +||||||| +++|+||
T Consensus 1045 ~-----~~~~~~~~~~y~~a~v~pGe~VG~iaAQSIgEp~TQMTL----nTFHfAGv-------------as~NVTl--- 1099 (1752)
T 3h0g_A 1045 F-----EWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTL----NTFHYAGV-------------SSKNVTL--- 1099 (1752)
T ss_dssp H-----HHHHHHHHHHHHTTBCCSSCCHHHHHHHHHHHHHHHHHH----HTTSSCCC-------------CCSSCCC---
T ss_pred H-----HHHHHHHHHHHHHhccCcccchhhhhhcccCCchhhhhH----Hhhhhccc-------------ccccccc---
Confidence 0 000011123357899999999999999999999999999 99999999 8999999
Q ss_pred CCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCC--hHHHHHHHhhhhcccchhhhhhhheeeecCCCcceee---
Q psy13846 754 NPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILI--- 828 (1423)
Q Consensus 754 ~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~--~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i--- 828 (1423)
|||||||||||||+||||+|+++|.++. +.+.|+.++++||+++|+||+++++++|+++..+..+
T Consensus 1100 ----------GVPRLkEIInask~ikTP~mtv~L~~~~~~d~e~A~~v~~~ie~t~L~~v~~~~~i~~~p~~~~~~i~~d 1169 (1752)
T 3h0g_A 1100 ----------GVPRLKEILNVAKNIKTPSLTIYLMPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEED 1169 (1752)
T ss_dssp ----------SGGGHHHHHTTCSCCSCCCCEECCCSSSCSSSTTTHHHHTTSSCCSSCSCCSCEEEECCCSTTCCCCSSS
T ss_pred ----------CcccHHHHHhhhcCCCCCeEEEEecCccccCHHHHHHHHHhhccEEHHHheeEEEEEEecCccceEEeec
Confidence 9999999999999999999999999884 7899999999999999999999999999887544444
Q ss_pred ---------------------------ehhhhHHHhhccccchhhhhHHhhhcccccCcccccc----cccccccCCCCc
Q psy13846 829 ---------------------------KLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSG----HSFLILKPKDSS 877 (1423)
Q Consensus 829 ---------------------------~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~----~~~~~~~~~~~~ 877 (1423)
++.+++.++++++++++.|...|.+.+..+..+.... ...+.++.....
T Consensus 1170 ~~~v~~~~~~~~~~~~~~~~~~~~~~~rl~l~~~~~~~~~l~~~~I~~~i~~~~~~~~~v~~~d~~~~~~~i~i~~~~~~ 1249 (1752)
T 3h0g_A 1170 KDFVEAFFAIPDEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVAGKIAESFERDLFTIWSEDNADKLIIRCRIIRDD 1249 (1752)
T ss_dssp CSHHHHHHHTTCSSTTCSSCSCCCCEEEEECCTTSSTTTTCCHHHHTTSGGGSSTTSCCEECCCTTCSSCEEEECCCCCS
T ss_pred HHHHHHHhccchhhhhcccccccceeEEEEecHHHHHHcCCCHHHHHHHHHhhccCCeeEeecCCCccceeEEEEecccc
Confidence 4444455556667778888888866543222222211 112223221110
Q ss_pred ----c------ccchhhhhhh-hcCCceEEccccccceeeeecccc-----cc----eeEEeeeccCccccccceeeccc
Q psy13846 878 ----K------SFNSKMYQMK-QLLPSVVIKGVQGINRAVIHEEDV-----EG----VTKYKLLVEGDNLRDVMATYGVK 937 (1423)
Q Consensus 878 ----~------~~~~~l~~l~-~~l~~v~IkGi~~I~r~~i~~~~~-----~~----~~~~~l~~eG~nL~~vl~~~gvD 937 (1423)
+ .....++.++ ..+++++|+|++||+|++|++++. +| ..+|.|.|||+||+++|.++|||
T Consensus 1250 ~~~~~~~~~~~~~~~~l~~l~~~~l~~~~i~Gi~~I~rv~i~~~~~~~~~~~g~~~~~~~~~l~teG~nL~~v~~~~gVD 1329 (1752)
T 3h0g_A 1250 DRKAEDDDNMIEEDVFLKTIEGHMLESISLRGVPNITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVD 1329 (1752)
T ss_dssp CCCCCSSCCCSCSCHHHHHHHHHHTTCCCSSCCTTCCCCCEEEEEEEEECSSSCEEEEEEEEEECCSCCCSTTTSSSSCC
T ss_pred ccccccccccccHHHHHHHHHHhhccceEEecCCCccEEEEecccceeecCCCcccccceEEEEecccCHHHHhCcCCCc
Confidence 0 1112356666 468999999999999999976542 22 46899999999999999999999
Q ss_pred ceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 938 ~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
+.+|+||||+||+++|||||||++|++||+.||+.||++||+|||+||||+||++|++++++
T Consensus 1330 ~~rt~sNdI~ei~~vlGIEAAR~~Ii~Ei~~v~~~~G~~Vd~RHl~LlaD~MT~~G~~~~it 1391 (1752)
T 3h0g_A 1330 ATRTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAIT 1391 (1752)
T ss_dssp TTTCCCSCHHHHHHHSCHHHHHHHHHHHHHTTSCSSSCCCCHHHHHHHHHHHTSSSSCCCCC
T ss_pred cccCeeCCHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccCCeEEeec
Confidence 99999999999999999999999999999999999999999999999999999999999975
No 8
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Probab=100.00 E-value=4.6e-82 Score=846.45 Aligned_cols=788 Identities=20% Similarity=0.234 Sum_probs=505.1
Q ss_pred hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcc-cccceeeeEEEecCC
Q psy13846 11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG-RKVFFRGLIEGTVTK 89 (1423)
Q Consensus 11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~-~~~~i~~~i~F~~~S 89 (1423)
.-+||||||++||++++||+||++|+||||++||+|+|+|+||++|+|++++|++++++|+-.. +....+.
T Consensus 493 qs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~v~g~y~lT~~~~f~~~~e~~~~~~~~~~~~~~~~~pa-------- 564 (1733)
T 1twf_A 493 QSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPA-------- 564 (1733)
T ss_dssp CSHHHHHHHHHHTBGGGGSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHSTTCCSCCCCCS--------
T ss_pred CCHHHHHHHHHHhcCcccEEecCCCCeeEeeeccccccceeeecCcccCCHHHHHHHHHhhhhhcCccCCcc--------
Confidence 4589999999999999999999999999999999999999999999999999999999986211 1111122
Q ss_pred HHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEeeeccH---
Q psy13846 90 EDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCV--- 166 (1423)
Q Consensus 90 ~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v--- 166 (1423)
-+....+| +|+++.+-++++.++...+...+ ..|+..++++.+..+.+..|.+++-
T Consensus 565 ----------i~kp~~~w----tGkqifs~ilp~~~~~~~~~~~~-------~~~~~~d~~v~i~~gel~~g~ldKk~lg 623 (1733)
T 1twf_A 565 ----------IIKPKPLW----SGKQILSVAIPNGIHLQRFDEGT-------TLLSPKDNGMLIIDGQIIFGVVEKKTVG 623 (1733)
T ss_dssp ----------BCSSSCEE----EHHHHHHHHSCTTCCEEECCTTC-------CTTCTTCCSEEEETTEEEESCCCHHHHS
T ss_pred ----------ccCcccCc----cHHHHHHHhCCCCCceeecCCCc-------ccCCcccceEEEeCCcEEEeecchHHhc
Confidence 12334678 89999999998766554322111 2344468999999999999999944
Q ss_pred ---HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehh
Q psy13846 167 ---INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISH 243 (1423)
Q Consensus 167 ---~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~ 243 (1423)
..|+..++.. ++.+....|++++++....++.+.+|+.++.|..... ...
T Consensus 624 ~~~~~li~~i~~~-------~G~~~a~~~ld~l~~l~~~~l~~~GfSigi~D~~~~~--------------------~~~ 676 (1733)
T 1twf_A 624 SSNGGLIHVVTRE-------KGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADG--------------------PTM 676 (1733)
T ss_dssp SCTTSHHHHHHHH-------HCHHHHHHHHHHHHHHHHHHHHTTCBCCCGGGGCCCH--------------------HHH
T ss_pred cChhHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHHcceEEehhhcCcCH--------------------HHH
Confidence 1344444444 7888888999999887777777777777776653111 010
Q ss_pred hhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHh--------------------hccCCCcc
Q psy13846 244 EKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLF--------------------EAIPLEDI 303 (1423)
Q Consensus 244 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiL--------------------e~I~~~d~ 303 (1423)
+.+.+..++....+.++.+.|.. +.++.+++.+..+.| +.+. .++
T Consensus 677 ~~i~~~i~~a~~~v~~~~~~~~~--------------g~l~~~pg~~~~e~~e~~v~~il~~~~d~~~~~~~~~l~-~~N 741 (1733)
T 1twf_A 677 REITETIAEAKKKVLDVTKEAQA--------------NLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLK-DLN 741 (1733)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH--------------TCCCCCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSC-TTC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh--------------CCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-cCC
Confidence 11111111112223333333332 222222222222222 1232 357
Q ss_pred cccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccC
Q psy13846 304 PLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNA 383 (1423)
Q Consensus 304 ~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~na 383 (1423)
+++.|..+|+|+++.+++||. +|+++|...|.+++.+| +.|.||| |.+.+.+|...
T Consensus 742 ~i~~Ma~SGAKGs~~Ni~Q~~---~~~Gqq~~~Gkrip~g~-----------------~~RtLPh----f~k~d~~p~s~ 797 (1733)
T 1twf_A 742 NVKQMVMAGSKGSFINIAQMS---ACVGQQSVEGKRIAFGF-----------------VDRTLPH----FSKDDYSPESK 797 (1733)
T ss_dssp HHHHHHHHTSSCCHHHHHHHH---SCCEECCBTTBSCCCCB-----------------TTBSSTT----SCTTCCSTTTT
T ss_pred CeEEEeeccCcccHHhHHHHH---hCcCCcccCCccCCCCC-----------------CCCCCCC----CCCCCCCcccc
Confidence 888999999999999999999 99999999888888888 8999999 99999999999
Q ss_pred CCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHH
Q psy13846 384 DFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQT 463 (1423)
Q Consensus 384 dFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~ 463 (1423)
+|.-+.+..+|.+.| ||||+||||||+++++++|+.|||.+|+|+..+|| +.+.||+|+||+.+++.||
T Consensus 798 GfI~ssF~~GLtp~E----------yFfh~mggReGLiDTAvKTA~SGYLqRRLVk~led-v~V~yDgTVR~s~g~IvQF 866 (1733)
T 1twf_A 798 GFVENSYLRGLTPQE----------FFFHAMGGREGLIDTAVKTAETGYIQRRLVKALED-IMVHYDNTTRNSLGNVIQF 866 (1733)
T ss_dssp TEECSCTTTCCCHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CEECTTSCEECTTCCEEES
T ss_pred chhhhhhhcccchHH----------HhhhhhccccchhhhceecccCCcceeehhhhhcc-eEEEecCcEecCCCCEEEE
Confidence 999999999999666 99999999999999999999999999999999999 9999999999999999999
Q ss_pred HHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeecccccccCcccccCCcEE
Q psy13846 464 MRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYV 543 (1423)
Q Consensus 464 ~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~v 543 (1423)
.|+.++++.. ..+. |-+..+-..+ ..+ .+.|.- .. .++..+
T Consensus 867 ~YGeDGlD~~--~~e~-------------------------~~~~~~~~~~------~~f---~~~~~~--~~-~~~~~~ 907 (1733)
T 1twf_A 867 IYGEDGMDAA--HIEK-------------------------QSLDTIGGSD------AAF---EKRYRV--DL-LNTDHT 907 (1733)
T ss_dssp SGGGTTBCGG--GEEE-------------------------EECGGGSSCH------HHH---HHHHCC--CT-TCTTTS
T ss_pred EeccccCCcc--eeec-------------------------ccccccccCH------HHH---HHHhcc--cc-cccccc
Confidence 9988876421 1110 0010000000 000 000000 00 000000
Q ss_pred Eeccccccccccc--cCCcCCCCCCchHHHHHHHhCHHHH-HHHHHHhhhhhhHHHhhcCcceecCCC-----CC--Ccc
Q psy13846 544 ILRNSELLAGSMD--KSTLGSGGKANVFYILLRDFGEDVA-VTAMWRLSRMTSFYLMNRGFSIGIGDV-----TP--GQG 613 (1423)
Q Consensus 544 ~i~~~ell~g~ld--K~~~g~~~~~~li~~i~~~~G~~~a-~~~l~~l~~l~~~~L~~~GfsiGi~D~-----~~--~~G 613 (1423)
+-..+.+ +...++ ..+...+.++|..-.. ..++.. +...|-..-...+ +. ..-
T Consensus 908 ------l~~~~~~~~~~~~~~---~~~~~~l~~e~~~l~~~r~~lr~--------i~~~~~~~~~~P~ni~r~i~~~~~~ 970 (1733)
T 1twf_A 908 ------LDPSLLESGSEILGD---LKLQVLLDEEYKQLVKDRKFLRE--------VFVDGEANWPLPVNIRRIIQNAQQT 970 (1733)
T ss_dssp ------CCTTTBTTHHHHTTC---HHHHHHHHHHHHHHHHHHHHHHH--------HTTTCCCEEEEESCHHHHHHHHHHH
T ss_pred ------CCHHHHHHHHHhhcc---HHHHHHHHHHHHHHHHHHHHHHH--------hhccccccccCChhHHHHHHHHHHH
Confidence 0000000 011111 1122222222210000 011110 0011110000000 00 000
Q ss_pred c-cccccccCCCceeeeeecccccccchhccc-ccCC---CCcch-------HHHHHH-Hhh--hhhcccceeeccccCC
Q psy13846 614 F-VQNSFFSGLTPTEFFFHTMGGREGLVDTAV-KTAE---TGYMQ-------RRLVKS-LED--LCVQYDMSFDAAFYGQ 678 (1423)
Q Consensus 614 f-I~~sf~~GL~p~Efffh~maGReGLiDTAv-KTa~---sGYlq-------RrLvk~-led--l~v~yD~tVR~s~yG~ 678 (1423)
| +..+..+.|+|.+++-. =|+ +.+..+ +... +-+.| ++++.. |.. +...|..+-.. +
T Consensus 971 f~~~~~~~s~l~p~~~~~~---v~~-~~~~~~~~~g~d~l~~~~~~n~~~l~~~~~rs~L~~k~~~~~~~l~~~~--~-- 1042 (1733)
T 1twf_A 971 FHIDHTKPSDLTIKDIVLG---VKD-LQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQA--F-- 1042 (1733)
T ss_dssp TTCCTTSCBCCCHHHHHHH---HHH-HHTTCCSCCCCSHHHHHHHHHTTHHHHHHHHHHSCHHHHHHTSCCCHHH--H--
T ss_pred hcccccccccCCHHHHHHH---HHH-HHHhhhcccCCcchhhhhhhchHHHHHHHhhhhhhhhhhhhhcCCCHHH--H--
Confidence 0 00011123333322100 000 000000 0000 00111 111110 000 00011001000 0
Q ss_pred CccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCC
Q psy13846 679 TDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDY 758 (1423)
Q Consensus 679 ~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~ 758 (1423)
+..-+..+..|.+++++|||+||++||||||||+||||| +||||||+ |++|+||
T Consensus 1043 -~~~l~~i~~ky~~a~v~pGe~VG~iaAQSigEp~TQMTL----nTFHfAGv-------------a~~NVTL-------- 1096 (1733)
T 1twf_A 1043 -DWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTL----NTFHFAGV-------------ASKKVTS-------- 1096 (1733)
T ss_dssp -HHHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC---------------------------CCSCC--------
T ss_pred -HHHHHHHHHHHHhccCCCCchhhhHhhhhcCCccccccc----cccccccc-------------cccCccc--------
Confidence 000000112356789999999999999999999999999 99999999 8999999
Q ss_pred ccCCCCchhhHHHHhhhcCCCCceeeeecccCC--hHHHHHHHhhhhcccchhhhhhhheeeecCCC-------------
Q psy13846 759 KLSQDGVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVPDD------------- 823 (1423)
Q Consensus 759 ~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~--~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~------------- 823 (1423)
|||||+|||||||+||||+|+++|.++. +.+.|+.++++||+++|+||+++++++|+++.
T Consensus 1097 -----GVPRLkEIinask~ikTP~mtv~L~~~~~~~~e~A~~v~~~ie~ttL~dv~~~i~i~~dp~~~~tvi~ed~~~~~ 1171 (1733)
T 1twf_A 1097 -----GVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQ 1171 (1733)
T ss_dssp -----HHHHHHHHTTTCSSCSSCEEEEEBCSSSSSCHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHH
T ss_pred -----CcHHHHHHHHhccCCCCCeEEEEeCCcccccHHHHHHHHHhhceeEHHHhhheEEEEEccCccceeeecchhhhh
Confidence 9999999999999999999999999874 78999999999999999999999999887761
Q ss_pred c-----------------ceeeehhhhHHHhhccccchhhhhHHhhhcccccCcccccccc----c--ccccCCCC--c-
Q psy13846 824 S-----------------FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS----F--LILKPKDS--S- 877 (1423)
Q Consensus 824 ~-----------------~~~i~ld~~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~----~--~~~~~~~~--~- 877 (1423)
. .+.+++++++.+++.++++++.|...|.+..+....+...+++ . +.+..... +
T Consensus 1172 ~y~~i~~~d~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~I~~~i~~~~~~~~~~~~~d~~~~~~~~~i~~~~~~~~~~~ 1251 (1733)
T 1twf_A 1172 LHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAE 1251 (1733)
T ss_dssp TSSCC----------CCCSEEEEEEECHHHHHHTTCCHHHHHHHHHHHHGGGEEEEECCTTSSSCEEEEEEC--------
T ss_pred hhhcccHHhhcchhhhcccceeEEEecHHHHHhcCCCHHHHHHHHHHhhCCCcceecCCcccchhheeeeeccCcccccc
Confidence 1 2356777888888888888888888886543211111111110 1 11111000 0
Q ss_pred -cc-cchhhhhh-hhcCCceEEccccccceeeeecc-------cc--cceeEEeeeccCccccccceeecccceeeccCc
Q psy13846 878 -KS-FNSKMYQM-KQLLPSVVIKGVQGINRAVIHEE-------DV--EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNN 945 (1423)
Q Consensus 878 -~~-~~~~l~~l-~~~l~~v~IkGi~~I~r~~i~~~-------~~--~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~ 945 (1423)
+. ....+..+ .+.+++++|+|+++|+|++|.+. +. +...+|+|.|+|+||+++|.+++||+.+|+|||
T Consensus 1252 ~~~~~~~~l~~l~~~~l~~~~v~Gi~~I~r~~i~~~~~~~~~~~g~~~~~~~~~L~teG~nL~~vl~~~~VD~~rt~SNd 1331 (1733)
T 1twf_A 1252 TEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNS 1331 (1733)
T ss_dssp --CCTTHHHHHHHHHHHHHCEEESCTTCCCEEEEEEEEEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCTTTCBCSC
T ss_pred ccchhHHHHHHHHHHhhhheEEecCCCccEEEEecccceeecCCCccccCcceEEEeecccHHHHhccCCcccccceecc
Confidence 00 00013334 66778999999999999998631 11 134689999999999999999999999999999
Q ss_pred hHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 946 TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 946 i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
|+||+++|||||||++|++|++.||+.||++||+|||+||||+||++|++++++
T Consensus 1332 I~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHl~LlaD~MT~~G~~~~it 1385 (1733)
T 1twf_A 1332 FIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVT 1385 (1733)
T ss_dssp HHHHHHHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTTBSSCCCSS
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHhhcCccccchhhhhhhhhhccCceecccc
Confidence 999999999999999999999999999999999999999999999999999985
No 9
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Probab=100.00 E-value=3.1e-64 Score=603.86 Aligned_cols=291 Identities=36% Similarity=0.560 Sum_probs=232.1
Q ss_pred hhHHHHHHHHHhhhccCCCCcchhhhhhcccCCcccccccccccccc--------------cccce--------eE----
Q psy13846 1099 SACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEY--------IE---- 1152 (1423)
Q Consensus 1099 ~~~~~~~~~~~y~~s~v~PGeaVG~iAAQSIGEP~TQmTLnTFH~AG--------------~i~~~--------i~---- 1152 (1423)
|.++.+.|..||.|++|+||||||+|||||||||+|||||||||+|| |+.+. +.
T Consensus 48 ~~~~~~~~~~~y~r~lv~pGEAVGiIAAQSIGEPgTQlTLrTFH~gGva~~nvT~GlPRl~Ei~~a~k~~~tp~~~i~l~ 127 (395)
T 4ayb_C 48 IDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIYLT 127 (395)
T ss_dssp HHHHHHHHHHHHHHTBCCTTCCHHHHHHHHHHHHHHTCC-------------CCCSHHHHHHHHTCCSSCSSCEEEECCT
T ss_pred HHHHHHHHHHHHHHhcCCCCchHhHHHHhhcCCchhhhccccceeeeecceeeecCccceEEecccccCCCCCceEEEec
Confidence 34999999999999999999999999999999999999999999999 11110 00
Q ss_pred ----------------------------EEEccCCcEEEEEEchHHHHHhcccCCHHHHHHHHHhccccCCceEEecCcE
Q psy13846 1153 ----------------------------EVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF 1204 (1423)
Q Consensus 1153 ----------------------------~~~~~~~~~~~i~l~~~~~~~~~~~i~~~~i~~~i~~~k~~~~~~~~~~~~~ 1204 (1423)
....+....+.+.++...++ ...++++++..++.+++.....+..++...
T Consensus 128 ~~~~~~~e~~~~~~~~ie~~~~~~~~~~~~i~~~~~~~~~~~d~~~~~--~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 205 (395)
T 4ayb_C 128 DEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLK--DKGVTVDDVKKAINRLKLGEFVIDESEGNT 205 (395)
T ss_dssp TTGGGCHHHHHHHHHHHHCCCHHHHEEEEEEETTTTEEEEEECGGGGB--TTBCHHHHHHHHHHHSCCSSEEEEECSSEE
T ss_pred ccccccHHHHHhhccceeEEEccceeeeeEEeecccceeeehhhhhhh--hcCccHHHHHHHHhhhccCcEEEecccCcE
Confidence 01122233344555554433 346788899988877654222222333344
Q ss_pred EEEEeCCCCchhhhHHHHHHhccCCcEEcccCCccEEEEecccccceeeEEEEecCccHHHHhhcccccceecccccHHH
Q psy13846 1205 LILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284 (1423)
Q Consensus 1205 i~i~~~~~~~~~~~~l~~l~~~l~~~~v~Gi~~i~r~~i~~~~~~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~ 1284 (1423)
+.+.+... +....|..+++.+.++.|+|++||.|+.+.+. .++|.+.|+|.|+.++|..+++|+++++||||++
T Consensus 206 ~~~~~~~~--~~v~~l~~~~~~~~~~~i~gi~gi~r~~~~~~----~~~~~~~t~g~~l~~~~~~~~vd~~~~~sn~i~e 279 (395)
T 4ayb_C 206 LNISFANI--DSIAALFKLRDKILNTKIKGIKGIKRAIVQKK----GDEYIILTDGSNLSGVLSVKGVDIAKVETNNIRE 279 (395)
T ss_dssp EEEECCSS--CCCCCTHHHHHHHHHHCCCSSSSCCEEEEEEE----TTEEEEEEESCCHHHHTTSTTCCTTTCEESCTTH
T ss_pred EEeecCCC--chHHHHHHHHhhccccEEecccceeEEEEecc----CCEEEEEecCCCceeeeEeecccccccccCcchh
Confidence 55554321 11223444555666789999999999998754 3589999999999999999999999999999999
Q ss_pred HHHHhCHHHHHHHHHHHHHHHhhcCCccccCCchhhhhccccceeEEEeeecccccccccchhhhccchhhHHHHHhhcc
Q psy13846 1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAF 1364 (1423)
Q Consensus 1285 i~~~lGIEAar~~ii~Ei~~v~~~~Gi~v~~rHl~LiaD~Mt~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~ 1364 (1423)
|+++|||||||++|++|+++||..||++||+|||+||||+||++|.+.+++|+|++.+++|||++||||+|+++|++||+
T Consensus 280 I~~vlGiEAar~~iv~Ei~~V~~~~Gv~In~rHi~li~d~Mt~~G~~~~igr~g~s~~t~S~LsaASFqeTt~vLteAAi 359 (395)
T 4ayb_C 280 IEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAA 359 (395)
T ss_dssp HHHHHCHHHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHGGGSCCCSSSSSHHHHCSCHHHHHHHSCTHHHHHHHHH
T ss_pred hhhhhhHHHHHHHHHHhHHHHHhccCceechHHhhhhhhhhhccceEeccCcccccCCCCCHHHHhcChhHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999888999999999999999999999
Q ss_pred cCCcccccccccceeeccccccccceEEEeecC
Q psy13846 1365 YGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397 (1423)
Q Consensus 1365 ~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~ 1397 (1423)
+|++|+|+|+|||||+|+++|+|||+|+|+++.
T Consensus 360 ~Gk~D~L~GlkENVIvGklipaGTG~f~l~~~p 392 (395)
T 4ayb_C 360 RGDVEEFKGVVENIIIGHPIKLGTGMVELTMRP 392 (395)
T ss_dssp TTCBCCCCSHHHHHHHTCCCSSGGGTCEEEECS
T ss_pred cCCCCCCCChHHHeecCCCCCCCcCceEEEecc
Confidence 999999999999999999999999999999874
No 10
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D
Probab=100.00 E-value=1.4e-52 Score=545.12 Aligned_cols=639 Identities=16% Similarity=0.149 Sum_probs=362.3
Q ss_pred hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCC--------cccCHHHHHHHHHHhhcccccceeee
Q psy13846 11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN--------AFFNRAQTMRIASTLIAGRKVFFRGL 82 (1423)
Q Consensus 11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~--------~~~~~~~~~~~~~~~~~~~~~~i~~~ 82 (1423)
.-+||||||++||++++||+||++|+|+||++||+++|+|+||++| +|++++|++++++. + ...++..
T Consensus 491 qs~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~---~-~i~l~a~ 566 (1265)
T 1hqm_D 491 LSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYER---G-EVALNAP 566 (1265)
T ss_dssp CSTHHHHTTSSSSBSSSSSSSCSSSSCSSCCCTTHHHHHHHTTCCCCCCCCCCCCSSCCTHHHHHTTS---S-CCSSCCC
T ss_pred CCHHHHHHHHHHhCccccEecCCCCCeeEeeeccccceeEEeccccCCccCCCcccCCHHHHHHHHHC---C-CCCCCCc
Confidence 4579999999999999999999999999999999999999999999 79999999987652 2 1111110
Q ss_pred EEE-----------ecCC-HH-HHh-----hc---ceeeee-c---CcccccCCCCCCcCCccccCCCCCCCCCCccCCC
Q psy13846 83 IEG-----------TVTK-ED-RVQ-----QQ---SHIQIV-S---KNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTC 137 (1423)
Q Consensus 83 i~F-----------~~~S-~e-eIr-----kl---Sv~eIt-~---~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TC 137 (1423)
+.. ..++ |+ .|. ++ .+..+. . -.+| +|+++.+-++++.+.
T Consensus 567 i~~~~~~~~~g~~k~~~t~P~k~I~~~~~g~~~~q~~~~~~~k~~~~~t~----~Gr~if~~~lp~~~~----------- 631 (1265)
T 1hqm_D 567 IVVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQDTVTTRYLGRRLETN----PGRILFARIVGEAVG----------- 631 (1265)
T ss_dssp SSSCCSTTSSCCCCCTTTCSHHHHHHHHTTSSCSSSCCCCEESSSEECCC----HHHHHHHHHHHHHTT-----------
T ss_pred eEEecccccccccccccccccccccccccCccccccccceeccccceecc----CCceEEeeecccccc-----------
Confidence 000 0111 11 111 00 000000 0 1233 455555544433332
Q ss_pred CCCCcccCCccceEEccCceeEEeeecc--HHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHH-HHHHHH
Q psy13846 138 GQNLSDCVGHFGYIDLPLPVFHIGYFRC--VINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKS-LKKKIL 214 (1423)
Q Consensus 138 g~~~~eCpGHfGhIeL~~PV~h~gffd~--v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~-~~~~i~ 214 (1423)
...+|..++++ + |.+++ +..|+..+... ++.+....|++++++....++.+.+ |+.++.
T Consensus 632 ---~~~~p~~~~~~-------n-gvldKk~lG~LI~~i~~~-------~G~~~a~~~ld~l~~l~~~~lt~~G~fSigi~ 693 (1265)
T 1hqm_D 632 ---DEKVAQELIQM-------D-VPQEKNSLKDLVYQAFLR-------LGMEKTARLLDALKYYGFTLSTTSGIITIGID 693 (1265)
T ss_dssp ---CTTTTTTSSCC-------S-SCCCSSHHHHHHHHHHHH-------SCHHHHHHHHHHHHHHHHHHHHHTTCCCCSSS
T ss_pred ---ccCCCCCCceE-------e-eeecHHHHHHHHHHHHHH-------HCHHHHHHHHHHHHHHHHHHHHhCCCceEeec
Confidence 01234444431 1 44553 23455554444 7888899999999988777777777 777766
Q ss_pred HHccCCccCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChh----hhhhhccCccccCCHHH
Q psy13846 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE----IEAHKKFGLIQTLNPLE 290 (1423)
Q Consensus 215 ~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~L~p~~ 290 (1423)
|...... |....+.. +..+++..+.|..-.-...+ +-.... . ....-+..
T Consensus 694 D~~~~~~-------------k~~~i~~a-----------~~~v~~i~~~y~~g~lt~~e~~~~v~~~~~-~-~~d~~~~~ 747 (1265)
T 1hqm_D 694 DAVIPEE-------------KQRYLEEA-----------DRKLRQIEQAYEMGFLTDRERYDQVIQLWT-E-TTEKVTQA 747 (1265)
T ss_dssp SCCCCST-------------TTTHHHHH-----------HHHHHHHHTTTTSSSSCHHHHHHHHHHHHH-H-HHHHHHHH
T ss_pred cccCCHH-------------HHHHHHHH-----------HHHHHHHHHHHHcCCCcHHHHHHHHHHHHH-H-HHHHHHHH
Confidence 6532110 00111111 11111111111100000000 000000 0 00001233
Q ss_pred HHHHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCc
Q psy13846 291 VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRT 370 (1423)
Q Consensus 291 V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~t 370 (1423)
+.+.|..- ..+++++.|..+|||+++.+++||. +|+++++..++++ ++
T Consensus 748 ~~~~l~~~-~~~N~i~~Ma~SGAKGS~~ni~Ql~---g~~G~ma~~~G~~-------------------------i~--- 795 (1265)
T 1hqm_D 748 VFNNFEEN-YPFNPLYVMAQSGARGNPQQIRQLC---GMRGLMQKPSGET-------------------------FE--- 795 (1265)
T ss_dssp HHHHHHHS-CSSSCTTTTTTTSSSCCHHHHHHHS---SCCCCCCCTTSCC-------------------------CS---
T ss_pred HHHHhccc-CCCCcHHHHHHhcCCcCHHHHHHHH---hhccccccCCCCc-------------------------cC---
Confidence 44444422 2357899999999999999999999 9999876443331 11
Q ss_pred eeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEe
Q psy13846 371 FRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYL 450 (1423)
Q Consensus 371 ir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~ 450 (1423)
.|.-+++..+|.+.| ||||+||||||++|||.+|+.|||.+|+|+...|| +++.|+
T Consensus 796 -------------~pI~ssF~eGLtp~E----------yFfhtmggReGLiDTAvKTA~SGYLqRRLVkv~qD-v~V~~d 851 (1265)
T 1hqm_D 796 -------------VPVRSSFREGLTVLE----------YFISSHGARKGGADTALRTADSGYLTRKLVDVAHE-IVVREA 851 (1265)
T ss_dssp -------------CCCCCCBTTBCTTCT----------HHHHHHHHTTHHHHHTHHHHTSSSTHHHHHHHSCS-CCCCSC
T ss_pred -------------cccccccccCCChHH----------hheecccccccchhhhhhcccCCcceeeeeeecce-EEEEEC
Confidence 247778889999776 99999999999999999999999999999999999 666655
Q ss_pred ecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceeeccccc
Q psy13846 451 LTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAY 530 (1423)
Q Consensus 451 ~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~~~~~~ 530 (1423)
-+.-+ .+ + .+..+. .|+.+.+..+.... .+. .+.+
T Consensus 852 dc~t~----------------------dG-i--------~v~~~~------~~~~i~~~~~~~~~------~L~--~ri~ 886 (1265)
T 1hqm_D 852 DCGTT----------------------KY-I--------SVPLFQ------MDEVTRTLRLRKRS------DIE--SGLY 886 (1265)
T ss_dssp CCCCC----------------------CC-E--------ECCSEE------CCSTTCCCEECCTT------TTH--HHHT
T ss_pred CCCCC----------------------CC-E--------EEEEee------cCceeechhhhhhh------HHH--HHHH
Confidence 54210 00 0 011110 02111111110000 000 0000
Q ss_pred ccCcccccCCcE---EEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceecCC
Q psy13846 531 TANEEFCHRDSY---VILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607 (1423)
Q Consensus 531 ~~~~~~~~~d~~---v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi~D 607 (1423)
+... ..+.. +--..++++ . ..+..+ ...++ ... |+..
T Consensus 887 --gr~~-~~~i~~~~~~p~~~~~i--------~---~~~~~i-----------------~~~~i-----~~~----gi~~ 926 (1265)
T 1hqm_D 887 --GRVL-AREVEALGRRLEEGRYL--------S---LEDVHF-----------------LIKAA-----EAG----EVRE 926 (1265)
T ss_dssp --TCEE-SSCEEETTEEECSSCBC--------C---TTHHHH-----------------HHHHH-----HTT----SCSS
T ss_pred --hhhh-hhcccccccCCCCccEE--------e---cCcchh-----------------hHHHH-----HHc----CCCE
Confidence 0000 00000 000001110 0 000111 00011 001 1110
Q ss_pred CCCCccccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeeccccCCCccCCCcch
Q psy13846 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSE 687 (1423)
Q Consensus 608 ~~~~~GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s~yG~~~~~~~~~~ 687 (1423)
+.. | ++-|-++ -..|=..|||.+
T Consensus 927 v~i-------------------------R------s~ltc~s------------------~~gvc~~CYgr~-------- 949 (1265)
T 1hqm_D 927 VPV-------------------------R------SPLTCQT------------------RYGVCQKCYGYD-------- 949 (1265)
T ss_dssp CEE-------------------------E------CGGGCSC------------------TTSCCSSSSCSC--------
T ss_pred EEe-------------------------e------cCcCHHH------------------HHHHHHHHhhhh--------
Confidence 000 0 0001111 001112267776
Q ss_pred heecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCcccccccccccccccc-ccceeecccCCCCCccCCCCch
Q psy13846 688 CIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTA-SVKVTLELWNPGDYKLSQDGVP 766 (1423)
Q Consensus 688 ~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~a-s~~itl~~~~~g~~~~~~~GvP 766 (1423)
++.+.+++||+|||++||||||||+||+|| +|||++|+ | +++||| |+|
T Consensus 950 -La~~~lV~~GEaVGiIAAQSIGEPGTQlTL----rTFH~gGv-------------as~~dIT~-------------GLP 998 (1265)
T 1hqm_D 950 -LSMARPVSIGEAVGVVAAESIGEPGTQLTM----RTFHTGGV-------------AVGTDITQ-------------GLP 998 (1265)
T ss_dssp -SSSSSCCCTTCCHHHHHHHHHHGGGTTSCC----CC---------------------CCTTSS-------------HHH
T ss_pred -hccCCEeccCceeeeeeccccCCCCceeee----EEEEEcce-------------eccccccc-------------Cch
Confidence 456789999999999999999999999999 99999999 7 489999 999
Q ss_pred hhHHHHhhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhh
Q psy13846 767 RIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDS 846 (1423)
Q Consensus 767 RlkEIinaSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~ 846 (1423)
|++||++|++ ||||.|.+++..... +++ ..+...+.+.
T Consensus 999 Rv~El~eArk-pk~p~i~a~~~g~v~---------------~~~---------~~~~~~i~i~----------------- 1036 (1265)
T 1hqm_D 999 RVIELFEARR-PKAKAVISEIDGVVR---------------IEE---------GEDRLSVFVE----------------- 1036 (1265)
T ss_dssp HHHHHHHCCC-CSSCBCCCSSSCBCC---------------CCC---------CSSCCCCCCB-----------------
T ss_pred hHHHHHhhcC-CCCceEEEeccceEE---------------Eee---------cCCccEEEEE-----------------
Confidence 9999999876 999999887754211 000 0000000000
Q ss_pred hhHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCcc
Q psy13846 847 IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 926 (1423)
Q Consensus 847 I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~n 926 (1423)
.......+ -++...++.+++.+. . ..|
T Consensus 1037 --------------------------~~g~~~~~-----------------~ip~~~~l~v~~g~~--v------~~g-- 1063 (1265)
T 1hqm_D 1037 --------------------------SEGFSKEY-----------------KLPKDARLLVKDGDY--V------EAG-- 1063 (1265)
T ss_dssp --------------------------CSSCCCCC-----------------CCSSCCCCCCCSCCS--S------TTC--
T ss_pred --------------------------ECCcEEEE-----------------EcCCceEEEEecCCE--E------ecC--
Confidence 00000000 012223333332111 0 011
Q ss_pred ccccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------
Q psy13846 927 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG------- 999 (1423)
Q Consensus 927 L~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~------- 999 (1423)
+.....+||++||++++||||+|..|++|++++++.||++||.|||+||||+||++++|...|
T Consensus 1064 ----------~~lteG~~~~~eil~v~Giea~~~~lv~EIq~vyr~QGv~I~dkHievivrqM~~kv~i~~~g~t~~l~G 1133 (1265)
T 1hqm_D 1064 ----------QPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSPLLEG 1133 (1265)
T ss_dssp ----------SCCCCSBSHHHHHHHTTHHHHHHHHHHHHHHHHHHTTSCCCCSSTHHHHHHHHTTEECBSSCCSSCCSCC
T ss_pred ----------ceeeccCccHHHHHHHhhHHHHHHHHHHHHHHHHHHcCccccHHHHHHHHHHHhcceEEecCCCcCCCCC
Confidence 122233589999999999999999999999999999999999999999999999999998644
Q ss_pred cchhhHHHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhh
Q psy13846 1000 TPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTS 1046 (1423)
Q Consensus 1000 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~ 1046 (1423)
..|+..++.+.+++....+.+|+.....+++++++.|++++|+++||
T Consensus 1134 e~v~~~~~~~~n~~~~~~g~~~~~~~~~llGITkasl~t~SflsaAS 1180 (1265)
T 1hqm_D 1134 QVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALSTKSWLSAAS 1180 (1265)
T ss_dssp CEEGGGTTTTTTTTTTC---CCCCBCCCCCCTHHHHTSCSCHHHHTT
T ss_pred ceecHHHHHHHHHHHHhcCCCcceeeeeeecceecccccCChhhccc
Confidence 56777777777766666666777777778899999999999998877
No 11
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus}
Probab=100.00 E-value=5.8e-49 Score=468.60 Aligned_cols=248 Identities=31% Similarity=0.535 Sum_probs=200.2
Q ss_pred HHHHHHHHhh-cccccceeeeEEEecCCHHHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCC
Q psy13846 63 QTMRIASTLI-AGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNL 141 (1423)
Q Consensus 63 ~~~~~~~~~~-~~~~~~i~~~i~F~~~S~eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~ 141 (1423)
.+|+|..|+. .....+|.+ |+||++|||||+++||++|+++++| |.+|+|+.|||||||||++++...|+|||++.
T Consensus 52 ~smnI~~rl~~~d~~~~i~~-i~F~~~s~eeI~~~Sv~~I~~~~~~--d~~~~P~~gGl~D~rlG~~~~~~~C~TCg~~~ 128 (436)
T 3qqc_A 52 KAMVIRPKLNLSEGGKVIGS-IEFGILSPQEIRKMSAVEVTVPDTY--DDDGYPIEGGVMDKRMGVIDPGLRCETCGGRA 128 (436)
T ss_dssp HHTTBCCEEEEEC--CEEEE-EECCBCCHHHHHHTEEEECCBCCCC--C----CCCSBSSCSSSCCCSSCCCCSSSCCCS
T ss_pred HhCCeeceeecccccceeee-eeeccCCHHHHHHhCCeEEeccccc--CCCCCccCCCccCccccCCCCCCCCCCCCCCC
Confidence 3445555544 223478899 9999999999999999999999999 77899999999999999999999999999999
Q ss_pred cccCCccceEEccCceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCc
Q psy13846 142 SDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVS 221 (1423)
Q Consensus 142 ~eCpGHfGhIeL~~PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k 221 (1423)
.+||||||||+|+.||||||||+++++||+|+|++ |+++++++++...|.++++++......++.+.+.+++.|++.+
T Consensus 129 ~~CpGHfGhIeL~~PVfh~gF~~~I~kILr~vC~~--C~klll~~~~~~~f~~~lr~~~~~~~~~k~~~~~i~~~~k~~~ 206 (436)
T 3qqc_A 129 GECPGHFGHIELARPVIHVGFAKTIYRILESTCRE--CGRIKLTDEEIEEYMKKIELARNRRSEFNEIIKEIHKKAKERM 206 (436)
T ss_dssp SSCCCCEEEEEEEEEEECGGGHHHHHHHHHHSCST--TCCCSSCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHTCC
T ss_pred CcCCCCceeEeechHHHHHHHHHHHHHHHHHHHHH--hcccccccccHHHHHHHHHhhhhccccHHHHHHHHHHHcccCC
Confidence 99999999999999999999999999999999999 9999999988888999888765555567888999999999999
Q ss_pred cCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhhhhhccCccccCCHHHHHHHhhccCCC
Q psy13846 222 VCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLE 301 (1423)
Q Consensus 222 ~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~p~~V~eiLe~I~~~ 301 (1423)
+|++||+.||.||+++.... .+ .. + +++ + . ...+.|+|.+|+++|++|+++
T Consensus 207 ~C~gCG~~qp~Ir~e~~~~~-~~---~~-~--~~~------------------~---~-~~k~~LtP~~vl~ifk~Isde 257 (436)
T 3qqc_A 207 VCPHCGAPQYPIKFEKPTIY-WE---IR-K--DEQ------------------G---N-EYRHRLMPTEVRDWLEKIPDK 257 (436)
T ss_dssp SCC-------CCCBCSSSCE-EE---EC-C--C------------------------C-CCEEEECHHHHHHHHHHSCTT
T ss_pred cCcccCCcCceEEEecceee-ee---cc-c--ccc------------------c---c-ccccccCHHHHHHHHHhCCHH
Confidence 99999999999999874221 11 00 0 000 0 0 235689999999999999999
Q ss_pred cccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCC--CCCeE
Q psy13846 302 DIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK--SDNDV 344 (1423)
Q Consensus 302 d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~--~~~d~ 344 (1423)
|+.+||++++.+||+||||++|||||+++||++.+++. .++|.
T Consensus 258 D~~lLGl~~~~~rPewmIlt~LPVpPp~vRPsv~~~~g~~~edDL 302 (436)
T 3qqc_A 258 DLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDL 302 (436)
T ss_dssp TGGGSSCCTTTCCGGGGEEEEEEECCGGGSCCBCC---CCBCCHH
T ss_pred HHHHhcccccCCCcceeEeeccccCCCcCcccEEeCCCcCCCChH
Confidence 99999999999999999999999999999999998643 45565
No 12
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Probab=100.00 E-value=2.6e-50 Score=521.45 Aligned_cols=632 Identities=16% Similarity=0.133 Sum_probs=368.5
Q ss_pred hhHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccC--------CcccCHHHHHHHHHHh-hc-ccccce
Q psy13846 10 TLYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQK--------NAFFNRAQTMRIASTL-IA-GRKVFF 79 (1423)
Q Consensus 10 ~~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~--------~~~~~~~~~~~~~~~~-~~-~~~~~i 79 (1423)
-.-+||||||++||++++||+||++|+|+||.+||+++|+|+||++ ++|+++++++++++.- +. .....+
T Consensus 750 PqS~eAraEA~~LM~~~~nilsP~~G~Pi~~~~QD~vlG~y~LT~~~~~~~~~g~~F~~~~e~~~ay~~~~~~l~~~i~v 829 (1524)
T 2a6h_D 750 PLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKV 829 (1524)
T ss_dssp CCSHHHHHHHHHHSBTTTCCBCSSSSSBSSCCCHHHHHHHHHHHCCCCCCCCSCCCTTSCHHHHHHHHHHHHTTSSCSSC
T ss_pred CCCHHHHHHHHHHhCCccceecCCCCCeeeeecccchhhheecccccccccCCCceeCCHHHHHHHHhcCCcCcCCceEE
Confidence 3458999999999999999999999999999999999999999998 4899999999876521 10 111111
Q ss_pred --eeeE-----EEecCCHHH-HhhcceeeeecCcccccCCCCCCcCC----------------------ccccCCCCCCC
Q psy13846 80 --RGLI-----EGTVTKEDR-VQQQSHIQIVSKNLYCQDPQRTPIPH----------------------GLLDRRMGTNQ 129 (1423)
Q Consensus 80 --~~~i-----~F~~~S~ee-IrklSv~eIt~~~~y~~D~~g~P~~g----------------------GLlD~rLG~~~ 129 (1423)
+. | .+.+..|.+ |.+- | +|+++.+ .+++..++
T Consensus 830 ~~~~-~~~~~~~~~~p~P~~aIlKp----------w----tGKQi~~~~~~~~I~~~~~~tt~Gr~ifn~~lp~~l~--- 891 (1524)
T 2a6h_D 830 AGRE-TSVGRLKYVFANPDEALLAV----------A----HGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVE--- 891 (1524)
T ss_dssp CCSS-CCHHHHHCEESSHHHHHHHH----------H----TTSSCTTSCCEEECSSCEECCCHHHHHHHHHHHHHSS---
T ss_pred eccc-ccccccccccCCchhhhcCC----------C----CCccccccccccceecceeecccchhhHHHHhhhhcc---
Confidence 11 1 111223332 2210 3 3333322 22211111
Q ss_pred CCCccCCCCCCCcccCCccceEEccCceeEEeeeccHHHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHH
Q psy13846 130 KEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209 (1423)
Q Consensus 130 ~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~ 209 (1423)
...+|..++++ + |.++ ++-|..+... |++. ++.+....|++++++....++.+.+|
T Consensus 892 -----------~~~~P~d~~~i-------n-GvLd--Kk~LG~LI~~--i~~~-yG~~~t~~fLD~lk~Lg~~~lt~~Gf 947 (1524)
T 2a6h_D 892 -----------DEKVAWELIQL-------D-VPQE--KNSLKDLVYQ--AFLR-LGMEKTARLLDALKYYGFTFSTTSGI 947 (1524)
T ss_dssp -----------CHHHHHHTCCT-------T-SCCC--HHHHHHHHHH--HHHH-TCHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred -----------cccCCCcccce-------e-ceec--HHHHHHHHHH--HHHH-hCHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 11224333332 1 5566 4444444444 4443 78888999999999888888888888
Q ss_pred HHHHHHHccCCccCCCCCCCCCceeecCcceehhhhhcccccchhhHHHHHHHHhhhhhccChhhh----hhhccCcccc
Q psy13846 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIE----AHKKFGLIQT 285 (1423)
Q Consensus 210 ~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~ 285 (1423)
+.++.|...... |. +++. + ....+++..+.|+.-.-...+.. ...+ ... .
T Consensus 948 SIGI~Dlii~~~-------------K~---eiI~----e----A~~~v~~i~~~y~~G~lt~~Er~~~Vi~iw~-~a~-d 1001 (1524)
T 2a6h_D 948 TIGIDDAVIPEE-------------KK---QYLE----E----ADRKLLQIEQAYEMGFLTDRERYDQILQLWT-ETT-E 1001 (1524)
T ss_dssp CCCSTTSCCCTT-------------HH---HHHH----H----HHHHHHHHHHHHHTTCSCHHHHHHHHHHHHH-HHH-H
T ss_pred eeehhhccCCHH-------------HH---HHHH----H----HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH-HHH-H
Confidence 888877642110 00 1111 0 11112222222221000000000 0000 000 0
Q ss_pred CCHHHHHHHhhccCCCcccccccccCCCCCcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEE
Q psy13846 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKV 365 (1423)
Q Consensus 286 L~p~~V~eiLe~I~~~d~~lL~m~~~~arPe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~ 365 (1423)
.-+..+.+.|..- ..+++++.|..+|||+++.+++||. +|++++....++ +
T Consensus 1002 ~v~~~~~~~L~~~-~~~N~i~~Ma~SGAKGS~~NI~Ql~---gmrGqma~p~Gk-------------------------i 1052 (1524)
T 2a6h_D 1002 KVTQAVFKNFEEN-YPFNPLYVMAQSGARGNPQQIRQLC---GLRGLMQKPSGE-------------------------T 1052 (1524)
T ss_dssp HHHHHHHHHHHHT-CTTCHHHHHHHSSSSCCHHHHHHHT---SCCCCCBCSSSC-------------------------B
T ss_pred HHHHHHHHhhccc-CCCCCHHHHHHhcCCcCHHHHHHHH---hhccccccCCCC-------------------------C
Confidence 0122333344322 2357889999999999999999999 999986533222 1
Q ss_pred ecCCceeeccCCCCcccCCCcccccccccCCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceE
Q psy13846 366 LPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFI 445 (1423)
Q Consensus 366 ~~~~tir~~~~~~~~~nadFdgd~m~~~~p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~ 445 (1423)
+| + +.-+++..+|.+.| ||||+||||+|+++|+.+|+.|||.+|+|+...|| +
T Consensus 1053 Ip-----~-----------PI~ssF~eGLtp~E----------yFfhtmGgReGLvDTAvKTAdSGYLqRRLVkv~qD-v 1105 (1524)
T 2a6h_D 1053 FE-----V-----------PVRSSFREGLTVLE----------YFISSHGARKGGADTALRTADSGYLTRKLVDVTHE-I 1105 (1524)
T ss_dssp CS-----S-----------CCCCCSSSCCCSHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-C
T ss_pred cc-----c-----------ccccccccCCChHH----------hheecccccCCccccceeeccCCcceeeeeeecce-e
Confidence 11 1 16677888999776 99999999999999999999999999999999999 5
Q ss_pred EEEEeecccccCCCHHHHHHHHHhhccCCccccceEeeeeccccCCceeecceeeeecceeeeecccCCCCcccccceee
Q psy13846 446 TGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKT 525 (1423)
Q Consensus 446 ~~~~~~t~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~p~i~kp~~~wtGKqi~s~il~~~~~~~~~~~~~~ 525 (1423)
++.|+-+. . ..+ + .+..+ -.|+.
T Consensus 1106 iVr~dDcg-----------------t-----~dG-i--------~v~~~------~~g~~-------------------- 1128 (1524)
T 2a6h_D 1106 VVREADCG-----------------T-----TNY-I--------SVPLF------QPDEV-------------------- 1128 (1524)
T ss_dssp CBCCSCCC-----------------C-----CCC-E--------EEESB------CSCSS--------------------
T ss_pred EEEeCCCC-----------------C-----CCC-e--------EEEEe------ecCCc--------------------
Confidence 44443331 0 000 0 00000 00000
Q ss_pred cccccccCcccccCCcEEEeccccccccccccCCcCCCCCCchHHHHHHHhCHHHHHHHHHHhhhhhhHHHhhcCcceec
Q psy13846 526 KGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGI 605 (1423)
Q Consensus 526 ~~~~~~~~~~~~~~d~~v~i~~~ell~g~ldK~~~g~~~~~~li~~i~~~~G~~~a~~~l~~l~~l~~~~L~~~GfsiGi 605 (1423)
+ +.++ ..++..+.. ++.-++ -.
T Consensus 1129 --------------~------------~~~~---------~~~i~~l~~---------------ri~gR~--------~~ 1150 (1524)
T 2a6h_D 1129 --------------T------------RSLR---------LRKRADIEA---------------GLYGRV--------LA 1150 (1524)
T ss_dssp --------------S------------SCCC---------BCCHHHHHH---------------HHTTCB--------BS
T ss_pred --------------c------------ccch---------hHHHHHHHH---------------HHhccc--------ch
Confidence 0 0000 001111111 111111 11
Q ss_pred CCCCCCccccccccccCCCceeeeeecccccccchhcccccCCCCcchHHHHHHHhhhhhcccceeecc-----------
Q psy13846 606 GDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA----------- 674 (1423)
Q Consensus 606 ~D~~~~~GfI~~sf~~GL~p~Efffh~maGReGLiDTAvKTa~sGYlqRrLvk~ledl~v~yD~tVR~s----------- 674 (1423)
.|+. +.+..|. .| .+.-...-|+ +++.+....+. ...||+.
T Consensus 1151 ~di~----------~~~~~p~-------~~-------e~i~~~~~~I---~~~~i~~~gi~-~v~iRS~ltC~s~~gvc~ 1202 (1524)
T 2a6h_D 1151 REVE----------VLGVRLE-------EG-------RYLSMDDVHL---LIKAAEAGEIQ-EVPVRSPLTCQTRYGVCQ 1202 (1524)
T ss_dssp SCEE----------CSSCEEC-------TT-------CBCCTTTTTH---HHHHHHHTSCS-EEEECCGGGCCCSSCBCH
T ss_pred hhhh----------hhccCCC-------cC-------cEEeCCCCee---hHHHHHHcCCC-cccccccccHHHHHHHHH
Confidence 1110 0011110 00 0000111133 33333332221 1344532
Q ss_pred -ccCCCccCCCcchheecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCcccccccccccccccc-ccceeecc
Q psy13846 675 -FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTA-SVKVTLEL 752 (1423)
Q Consensus 675 -~yG~~~~~~~~~~~~~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~a-s~~itl~~ 752 (1423)
|||.+ ++.+.+++||+|||++||||||||+||+|| +|||++|+ + +++|||
T Consensus 1203 ~CYgr~---------La~~~~v~~GeaVGiiaAQSIGEPgTQlTl----rTFH~gGv-------------~~~~dIt~-- 1254 (1524)
T 2a6h_D 1203 KCYGYD---------LSMARPVSIGEAVGIVAAQSIGEPGTQLTM----RTFHTGGV-------------AGAADITQ-- 1254 (1524)
T ss_dssp HHHCSC---------SSSSSSCCTTCCHHHHHHHHHHSGGGTCCC----C------------------------CCCC--
T ss_pred HHhccc---------cccCCccccccceeehhhhccCCCcccccc----eeeeeccc-------------cccccccc--
Confidence 47765 456789999999999999999999999999 99999998 6 689999
Q ss_pred cCCCCCccCCCCchhhHHHHhhhcCCCCceeeeecccCChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhh
Q psy13846 753 WNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDM 832 (1423)
Q Consensus 753 ~~~g~~~~~~~GvPRlkEIinaSk~ikTPiitv~L~~~~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~ 832 (1423)
|+||++||++|++...+++++- . ..+++ +++ ..+.
T Consensus 1255 -----------GlPRv~El~eARkpk~~aiI~e-i------------~G~V~---i~~---------~~~~--------- 1289 (1524)
T 2a6h_D 1255 -----------GLPRVIELFEARRPKAKAVISE-I------------DGVVR---IEE---------TEEK--------- 1289 (1524)
T ss_dssp -----------SHHHHHHHHTTCCCSSBCCBCS-S------------CEEEE---ECC---------CSSC---------
T ss_pred -----------cCcchhhheecccCCCcceEEE-e------------ceEEE---Eee---------cCCc---------
Confidence 9999999999998888877541 1 11110 000 0000
Q ss_pred hHHHhhccccchhhhhHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccc
Q psy13846 833 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDV 912 (1423)
Q Consensus 833 ~r~~~~~l~i~~~~I~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~ 912 (1423)
..+.+.+.+.. .--.+|..+++.+++.+.
T Consensus 1290 ----------------------------------r~i~i~~~~~~-----------------~~~~ip~~~~l~V~~gd~ 1318 (1524)
T 2a6h_D 1290 ----------------------------------LSVFVESEGFS-----------------KEYKLPKEARLLVKDGDY 1318 (1524)
T ss_dssp ----------------------------------EEEEEECSSCE-----------------EEEEECTTCCCCCCTTSE
T ss_pred ----------------------------------eEEEEEcCCce-----------------eEEecCCceEEEEecCCe
Confidence 00111111000 001234444444433211
Q ss_pred cceeEEeeeccCccccccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccc
Q psy13846 913 EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 992 (1423)
Q Consensus 913 ~~~~~~~l~~eG~nL~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~ 992 (1423)
...+...++ .+||++||++++||||||++|++|+++||+.||++||.|||+||||+||++
T Consensus 1319 --v~~g~~lte------------------G~~~~~dil~v~Giea~~~~iv~Eiq~Vyr~QGv~I~dKHIevIvrqM~~k 1378 (1524)
T 2a6h_D 1319 --VEAGQPLTR------------------GAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKY 1378 (1524)
T ss_dssp --ECTTCBSSS------------------SBCCHHHHHHHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTSE
T ss_pred --eecCeEEec------------------CCCCchhheeecCHHHHHHHHHHHHHHHHHhcCcccchhHHHHHHHHHhce
Confidence 011122233 358999999999999999999999999999999999999999999999999
Q ss_pred cccccCC-------cchhhHHHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHHH
Q psy13846 993 GEVLGNG-------TPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIK 1054 (1423)
Q Consensus 993 G~i~g~~-------~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~ 1054 (1423)
++|...| ..|+..++.+.+.+...++..|+.....+++++++.|++++|+++|| |.+..+
T Consensus 1379 v~i~~~Gdt~~l~Ge~v~~~~~~~~n~~~~~~g~~~a~~~~~llGITkasL~t~SfLsaAS--FqeTtr 1445 (1524)
T 2a6h_D 1379 VEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAAS--FQNTTH 1445 (1524)
T ss_dssp EEEEECSSSCSSCEEEHHHHHHHHHHHHTTSCSCCCCEEEECCCCHHHHHHSCSCHHHHHH--SSCHHH
T ss_pred eEEecCCCccCCCCceeeHHHHHHHHHHHHHcCCCcceeeeeeeeeeecccccCChhhhcC--hHHHHH
Confidence 9998755 56788889999988888888888888888999999999999998776 544433
No 13
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*
Probab=100.00 E-value=1.9e-47 Score=487.44 Aligned_cols=119 Identities=16% Similarity=0.256 Sum_probs=104.7
Q ss_pred eecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC-------cchhhH
Q psy13846 933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG-------TPVELK 1005 (1423)
Q Consensus 933 ~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~-------~~~~~~ 1005 (1423)
+...|...-.+.|++||++++||||+|++|++|+++|++.||++||+|||++++++||++++|...| ..|+..
T Consensus 1204 v~~G~~l~~G~~~p~dil~v~Giea~~~ylv~Evq~VYr~QGV~IndKHIEvIvrqM~~kv~I~d~Gdt~fl~Ge~vd~~ 1283 (1407)
T 3lu0_D 1204 VERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYS 1283 (1407)
T ss_dssp CCTTCCCSSSCCCHHHHHHHSCHHHHHHHTTTTTHHHHHHHTCCCCSHHHHTTTGGGTSBCEESSCSSSCSCCCCBSHHH
T ss_pred EcCCCCccCCCCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHHHhCceEEeeCCCcccCCcceecHH
Confidence 3334666667889999999999999999999999999999999999999999999999999998755 568888
Q ss_pred HHHHHHHHhccCCCCCCCCHHHHHHHhhhhcCcchhhhhhhHHHHHHH
Q psy13846 1006 RLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDI 1053 (1423)
Q Consensus 1006 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~ 1053 (1423)
++.+.+.+...++..|+...+.+++++++.|++++|+++|| |++..
T Consensus 1284 ~~~~~N~~~~~~g~~pa~~~p~llGITkasl~t~SflSaAS--FQeTt 1329 (1407)
T 3lu0_D 1284 RVKIANRELEANGKVGATYSRDLLGITKASLATESFISAAS--FQETT 1329 (1407)
T ss_dssp HHHHHHHHTTSSSCCCCCEECCCCCTTTTTTSCSCTTTGGG--SSCHH
T ss_pred HHHHHHHHHHHcCCCCceeeeeeeceeeccccCCCchhhcc--hhhHH
Confidence 99999999888888888887778899999999999998877 54443
No 14
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Probab=100.00 E-value=1.3e-40 Score=399.21 Aligned_cols=270 Identities=30% Similarity=0.438 Sum_probs=204.6
Q ss_pred ecCCCcccchhHHHHhhhcCCCCCCccccccCCCCcccCccccccccccccccccccceeecccCCCCCccCCCCchhhH
Q psy13846 690 IMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIK 769 (1423)
Q Consensus 690 ~~~~~~~~g~~vg~i~aqsige~~tq~tL~~~~~tFh~agv~~~~~~~~~~~~~as~~itl~~~~~g~~~~~~~GvPRlk 769 (1423)
|.+++++||||||.+||||||||+||||| +|||+||+ |++|+|| |+||++
T Consensus 59 y~r~lv~pGEAVGiIAAQSIGEPgTQlTL----rTFH~gGv-------------a~~nvT~-------------GlPRl~ 108 (395)
T 4ayb_C 59 YSEGLIAPGEAIGIVAAQSVGEPGTQMTL----RTFHFAGI-------------RELNVTL-------------GLPRLI 108 (395)
T ss_dssp HHHTBCCTTCCHHHHHHHHHHHHHHTCC------------------------------CCC-------------SHHHHH
T ss_pred HHHhcCCCCchHhHHHHhhcCCchhhhcc----ccceeeee-------------cceeeec-------------CccceE
Confidence 56778999999999999999999999999 99999999 8999999 999999
Q ss_pred HHHhhhcCCCCceeeeecccC--ChHHHHHHHhhhhcccchhhhhhhheeeecCCCcceeeehhhhHHHhhccccchhhh
Q psy13846 770 EIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI 847 (1423)
Q Consensus 770 EIinaSk~ikTPiitv~L~~~--~~~e~a~~v~~rie~~~l~dii~~i~~~~~~~~~~~~i~ld~~r~~~~~l~i~~~~I 847 (1423)
||+||+|+++||.++++|.++ .+.+.++.++.+++++++.+++...+..+ ....+.+.+|... +....++.+.+
T Consensus 109 Ei~~a~k~~~tp~~~i~l~~~~~~~~e~~~~~~~~ie~~~~~~~~~~~~i~~--~~~~~~~~~d~~~--~~~~~~~~~~i 184 (395)
T 4ayb_C 109 EIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDI--ASMSIILQLDNEM--LKDKGVTVDDV 184 (395)
T ss_dssp HHHTCCSSCSSCEEEECCTTTGGGCHHHHHHHHHHHHCCCHHHHEEEEEEET--TTTEEEEEECGGG--GBTTBCHHHHH
T ss_pred EecccccCCCCCceEEEecccccccHHHHHhhccceeEEEccceeeeeEEee--cccceeeehhhhh--hhhcCccHHHH
Confidence 999999999999999999876 46789999999999999999987655433 2233344444433 34566777888
Q ss_pred hHHhhhcccccCcccccccccccccCCCCccccchhhhhhhhcCCceEEccccccceeeeecccccceeEEeeeccCccc
Q psy13846 848 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927 (1423)
Q Consensus 848 ~~~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~v~IkGi~~I~r~~i~~~~~~~~~~~~l~~eG~nL 927 (1423)
...+.+.+.....+.......+.+...... -...++.+.+.+.+..|+|++||.|+.+.... ++|.+.++|+|+
T Consensus 185 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~v~~l~~~~~~~~~~~i~gi~gi~r~~~~~~~----~~~~~~t~g~~l 258 (395)
T 4ayb_C 185 KKAINRLKLGEFVIDESEGNTLNISFANID--SIAALFKLRDKILNTKIKGIKGIKRAIVQKKG----DEYIILTDGSNL 258 (395)
T ss_dssp HHHHHHSCCSSEEEEECSSEEEEEECCSSC--CCCCTHHHHHHHHHHCCCSSSSCCEEEEEEET----TEEEEEEESCCH
T ss_pred HHHHhhhccCcEEEecccCcEEEeecCCCc--hHHHHHHHHhhccccEEecccceeEEEEeccC----CEEEEEecCCCc
Confidence 888876543222111111111111111100 01124455666667889999999999887543 479999999999
Q ss_pred cccceeecccceeeccCchHHHHHHhchHHHHHHHHHHHHHHHHhcCccccCCchhhHhhhhccccccccCC
Q psy13846 928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999 (1423)
Q Consensus 928 ~~vl~~~gvD~~~t~SN~i~eV~~~LGIEAAR~~Ii~Ei~~v~e~~Gi~Id~RHi~LLAD~MT~~G~i~g~~ 999 (1423)
.+++.++++|..++.|||++||+++|||||||++|++|++++|..||++||+|||+|+||+||++|++.+.+
T Consensus 259 ~~~~~~~~vd~~~~~sn~i~eI~~vlGiEAar~~iv~Ei~~V~~~~Gv~In~rHi~li~d~Mt~~G~~~~ig 330 (395)
T 4ayb_C 259 SGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIG 330 (395)
T ss_dssp HHHTTSTTCCTTTCEESCTTHHHHHHCHHHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHGGGSCCCSS
T ss_pred eeeeEeecccccccccCcchhhhhhhhHHHHHHHHHHhHHHHHhccCceechHHhhhhhhhhhccceEeccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999865
No 15
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Probab=99.97 E-value=1.9e-34 Score=372.83 Aligned_cols=373 Identities=16% Similarity=0.171 Sum_probs=264.4
Q ss_pred hHHHhHHHHHHHhccCCccccCCCCCceEeeehhhhhheeecccCCcccCHHHHHHHHHHhhcccccceeeeEEEecCCH
Q psy13846 11 LYYATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKE 90 (1423)
Q Consensus 11 ~~~earae~~~l~~v~~~i~sp~~~~p~~g~~qd~~~g~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~F~~~S~ 90 (1423)
.-+||||||++||++++||+||++|+||||.+||+++|+|+||.+|+|++++++++++++ +.....+.. |
T Consensus 468 qS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~lT~~~~~~~~~~~~~~~~~--~~~~~~~~~--------p 537 (880)
T 4ayb_A 468 QSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQILGV--ADVKIDLGE--------P 537 (880)
T ss_dssp CSHHHHHHHHHHSBSGGGCBCSSSSSBCSCCCSHHHHHHHHHTSSSCEECHHHHHHHHTT--SCCCCCCCS--------C
T ss_pred CCHHHHHHHHHHHhChhccccCCCCCccccccccHHHHhHHhhcCcccCCHHHHhhhhcc--cceecccCc--------c
Confidence 458999999999999999999999999999999999999999999999999999999874 111111111 0
Q ss_pred HHHhhcceeeeecCcccccCCCCCCcCCccccCCCCCCCCCCccCCCCCCCcccCCccceEEccCceeEEeeeccH----
Q psy13846 91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCV---- 166 (1423)
Q Consensus 91 eeIrklSv~eIt~~~~y~~D~~g~P~~gGLlD~rLG~~~~~~~C~TCg~~~~eCpGHfGhIeL~~PV~h~gffd~v---- 166 (1423)
. -+....+| +|+++.+.++++.+....+............+-+.+.+++.+....+-.|.|++-
T Consensus 538 ~--------i~~~~~~~----tgkqi~s~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~~g~l~~g~ldk~~lg~ 605 (880)
T 4ayb_A 538 A--------ILAPREYY----TGKQVVSAFLPKDFNFHGQANVSSGPRLCKNEDCPHDSYVVIKNGILLEGVFDKKAIGN 605 (880)
T ss_dssp S--------EESSSEEE----EHHHHHHTTSCTTCCEEEECTTCSGGGCCSSSCCTTSCEEEEETTEEEECCCSTTTSST
T ss_pred c--------eecceeEe----ccceEEEEEecccccccceeEeecCCccccCccCCCcceEEEeCceeeeeeecchhhcc
Confidence 0 11234456 7888887777665543322222222222222333356788899999999988753
Q ss_pred ---HHHhhhccccccccccccChhhHHHHHHHhcCCchhHHHHHHHHHHHHHHccCCccCCCCCCCCCceeecCcceehh
Q psy13846 167 ---INILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISH 243 (1423)
Q Consensus 167 ---~~iL~~iC~~~~C~~ll~~~~~~~~~~~kl~~~~~~~~~~~~~~~~i~~~~kk~k~C~~Cg~~~~~irk~~~~ki~~ 243 (1423)
..|++.+... ++.+....|++++++....++.+.+++.++.|.... ....
T Consensus 606 ~~~~~li~~i~~~-------~G~~~t~~~ld~l~~lg~~~lt~~GfSigi~Di~i~--------------------~~~~ 658 (880)
T 4ayb_A 606 QQPESILHWLIKE-------YSDEYGKWLMDNLFRVFIRFVELQGFTMRLEDVSLG--------------------DDVK 658 (880)
T ss_dssp TCTTSHHHHHHHT-------SCHHHHHHHHHHHHHHHHHHHHHHCCCCCGGGGCCC--------------------HHHH
T ss_pred cccceeeehhhhh-------cccHHHHHHHHHHHHHHHHHHHhcCCcccccccccc--------------------hhhH
Confidence 2456665555 788888899999988777777777777776665210 0000
Q ss_pred hhhcccccchhhHHHHHHHHhhhhhccC-------hhhhhhhccCccccCC--HHHHHHHhhccCCCcccccccccCCCC
Q psy13846 244 EKYKNRTKKKDAIVEDLLAEYNEAVKFN-------PEIEAHKKFGLIQTLN--PLEVLQLFEAIPLEDIPLLLMNAELSK 314 (1423)
Q Consensus 244 e~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~L~--p~~V~eiLe~I~~~d~~lL~m~~~~ar 314 (1423)
+.+.+..++....+++..+.|+...-.. .+.+... .+.++ -.++-+....--+.+++++.|+.+|||
T Consensus 659 ~~i~~~i~~a~~~v~~i~~~~~~g~l~~~~g~~~~e~~e~~v----~~~l~~~~~~~~~~~~~~l~~~N~i~mMa~SGAR 734 (880)
T 4ayb_A 659 KEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYI----LDTLDKLRSTAGDIASKYLDPFNFAYVMARTGAR 734 (880)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTCCCCCSSSCHHHHHHHHH----HHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTSS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHH----HHHHHHHHHHHHHHHHhhCCCCCCHHHHhhcCcc
Confidence 0000001111222333334443211000 0000000 00000 011111222222345788899999999
Q ss_pred CcceEEEEecCCCCCCCCcEEcCCCCCCeEEEEecCccccccccceeeeEEecCCceeeccCCCCcccCCCccccccccc
Q psy13846 315 PSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHL 394 (1423)
Q Consensus 315 Pe~liLt~lpVPP~~vRPsv~~g~~~~~d~Vl~nRqPsLHk~Simah~~~~~~~~tir~~~~~~~~~nadFdgd~m~~~~ 394 (1423)
++..+++||. .|++||...|.+++.++ ..|+||| |.+...+|...+|.-+.+..+|
T Consensus 735 GS~~ni~Qla---gm~Gqq~~~G~RIprg~-----------------~~rtLP~----f~~~d~~p~a~GfI~ssF~eGL 790 (880)
T 4ayb_A 735 GSVLNITQMA---AMLGQQSVRGERIKRGY-----------------MTRTLPH----FKPYDISPEARGFIYSSFRTGL 790 (880)
T ss_dssp CCSTTHHHHH---TCCEECBSSSSBSCCSB-----------------TTBSSTT----SCTTCCSTTTTSEECSCTTTCC
T ss_pred CCHHHHHHHH---hcccccccCCccCcCCC-----------------ccCCCCC----CCCCCCCcccCCeEhhcccCCC
Confidence 9999999999 99999999999998888 7899999 9999999999999999999999
Q ss_pred CCCHHHHhcccccchhhhhhhhhhhhhhccccccccCCCCccccccccceEEEEEeecccccCCCHHHHHHHHHhhc
Q psy13846 395 PQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 471 (1423)
Q Consensus 395 p~~~~araE~~~~~~~~~~~~~r~~~l~~~~~~~~s~~~~~~~~~~~qD~~~~~~~~t~~~~~~~~~~~~~l~~~~~ 471 (1423)
.+.| ||||+||||+|++|||.+|+.|||.+|+|+...|| |.+.|++|+||+.+++.||.|+.++++
T Consensus 791 tp~E----------yF~ht~ggRkGL~DTAlKTA~SGYLtRRLVdv~qD-v~V~yDgTVR~~~g~ivqf~YGeDgld 856 (880)
T 4ayb_A 791 KPTE----------LFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSD-LRAEYDGTVRSLYGEVIQVAYGDDGVF 856 (880)
T ss_dssp CHHH----------HHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTT-EEECTTSCEEETTTEEEESSTTTTCBC
T ss_pred CHHH----------HHHhhhhhhhhHHhcchhhchhhHHHHHHHHHHcC-EEEecCCCccCCCCcEEEEecCCcccc
Confidence 9666 99999999999999999999999999999999999 888999999999999999999877764
No 16
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus}
Probab=95.63 E-value=0.0025 Score=76.53 Aligned_cols=68 Identities=34% Similarity=0.404 Sum_probs=36.4
Q ss_pred CCchhhhhcccc-----ceeEEEeeecccccccccchhhhccchhhHHHHHhhcccCCcccccccccceeecccc
Q psy13846 1315 FRHPMLVADLMT-----SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384 (1423)
Q Consensus 1315 ~rHl~LiaD~Mt-----~~G~~~~i~r~g~~~~~~S~l~~aSFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~ 1384 (1423)
-|-+.=|+|... |+|.++| =|--.+. ++|+|.+|+||.+.+||.+|+.+|++|+++||.|+|++|+.-
T Consensus 359 ~rp~ksi~~rLkGKeGRfR~NL~G-KRVdy~~-~~s~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 431 (436)
T 3qqc_A 359 GRPLKTLAQRLKGKEGRFRGNLSG-GAGSGAG-SGSVLARAAFEITVQHLFEAAEKGEVDNLNGVIENVLIGQKH 431 (436)
T ss_dssp SCBCCCHHHHHCC-----------------------------CCCCHHHHHHHHHHTCEEECCSSCCTTSCC---
T ss_pred CCCccchHhhhccccceecCcCCC-CCCCccc-chhHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhhhcccc
Confidence 444555556555 4455555 3555543 679999999999999999999999999999999999999853
Done!