Query psy3015
Match_columns 1791
No_of_seqs 624 out of 2973
Neff 5.6
Searched_HMMs 29240
Date Fri Aug 16 23:22:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3015.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/3015hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_A DNA-directed RNA polyme 100.0 2E-167 6E-172 1688.0 34.5 903 45-1406 509-1457(1752)
2 1twf_A B220, DNA-directed RNA 100.0 2E-158 8E-163 1601.1 49.3 908 45-1410 503-1455(1733)
3 3h0g_A DNA-directed RNA polyme 100.0 6.2E-97 2E-101 1000.6 3.2 559 988-1719 744-1325(1752)
4 1twf_A B220, DNA-directed RNA 100.0 1E-89 3.5E-94 931.6 12.3 559 988-1719 738-1319(1733)
5 4ayb_A DNA-directed RNA polyme 100.0 3.8E-84 1.3E-88 845.8 29.7 373 45-466 478-864 (880)
6 1hqm_D DNA-directed RNA polyme 100.0 6.2E-78 2.1E-82 793.3 8.7 302 45-464 501-866 (1265)
7 2a6h_D DNA-directed RNA polyme 100.0 5.1E-78 1.7E-82 790.6 7.0 310 45-464 761-1125(1524)
8 3lu0_D DNA-directed RNA polyme 100.0 8.6E-70 2.9E-74 702.9 18.8 281 45-437 482-812 (1407)
9 2a6h_D DNA-directed RNA polyme 100.0 4.5E-43 1.6E-47 461.2 8.2 372 988-1398 1015-1481(1524)
10 4ayb_C DNA-directed RNA polyme 100.0 1.1E-40 3.9E-45 405.0 15.6 356 957-1403 10-393 (395)
11 1hqm_D DNA-directed RNA polyme 100.0 5.9E-42 2E-46 452.4 4.4 364 988-1396 756-1220(1265)
12 3lu0_D DNA-directed RNA polyme 100.0 9.1E-39 3.1E-43 414.7 -3.2 96 988-1103 717-812 (1407)
13 4ayb_A DNA-directed RNA polyme 100.0 4.6E-37 1.6E-41 402.4 8.0 141 988-1132 720-860 (880)
14 4ayb_C DNA-directed RNA polyme 99.9 8.5E-29 2.9E-33 300.9 9.2 220 1391-1718 43-263 (395)
15 3qqc_A DNA-directed RNA polyme 98.9 1.1E-10 3.7E-15 142.7 -0.6 68 13-81 241-308 (436)
16 3qqc_A DNA-directed RNA polyme 88.1 0.11 3.7E-06 64.0 0.5 42 831-872 390-431 (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=1.6e-167 Score=1687.99 Aligned_cols=903 Identities=50% Similarity=0.824 Sum_probs=795.6
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccCCCCCCCceeCCCCcccHhhhhhhcC
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLII 111 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~~~lP~PaIlKP~~LWTGKQIfS~iL 111 (1791)
.||++++|+++|++++|+|++ .+.|+++++++||+||+..|++.+|+|||+||++|||||||||++|
T Consensus 509 ~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~lT~~~~f~~~~e~~~l~~~~~~~~~~~~~pai~kp~~~wtGkqifs~il 588 (1752)
T 3h0g_A 509 EITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVPDWDGILPPPVILKPKVLWTGKQILSLII 588 (1752)
T ss_dssp HTCCTTTTSEETTTTEESCCCCTHHHHHHHHHHSTTCEEETHHHHGGGGCSSSCCSSCCCCSBCSSSCEEETTHHHHTTS
T ss_pred HHhcCccceecCCCCCceeeecchhhhheeeeccccccCCHHHHHHHHHhhcccCCccCccceecCcCCCchhhHHhhhC
Confidence 689999999999999999998 3469999999999999999999999999999999999999999999
Q ss_pred CCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHH
Q psy3015 112 PGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVV 191 (1791)
Q Consensus 112 P~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~ 191 (1791)
|+++||..... ...+.+++|++|+|+||||++|++||++||++.+||||.||++||+++|+.|||++|+|+
T Consensus 589 p~~~~~~~~~~---------~~~~~~~~d~~v~i~~gell~g~l~K~~lg~~~~~li~~i~~~~G~~~~~~~ld~~~~l~ 659 (1752)
T 3h0g_A 589 PKGINLIRDDD---------KQSLSNPTDSGMLIENGEIIYGVVDKKTVGASQGGLVHTIWKEKGPEICKGFFNGIQRVV 659 (1752)
T ss_dssp CSSBCEECCCS---------SCCSSCTTTCSEEECBSCEEEECCSHHHHSSCTTCHHHHSSSSSCTTTHHHHHHHHHHHH
T ss_pred cCCCCceeccc---------cccCcCCCcCeEEEEcCeEEecccchHHhccCcccHHHHHHHHHCHHHHHHHHHHHHHHH
Confidence 99999965321 112567889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHH
Q psy3015 192 NNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAK 271 (1791)
Q Consensus 192 ~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 271 (1791)
++||+++||||||+|+++++++.+++.++|++|+
T Consensus 660 ~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~---------------------------------------------- 693 (1752)
T 3h0g_A 660 NYWLLHNGFSIGIGDTIADADTMKEVTRTVKEAR---------------------------------------------- 693 (1752)
T ss_dssp HHHHHHHCCCCCGGGGSCCSHHHHHHHHHHHTTT----------------------------------------------
T ss_pred HHHHHhcCceechhhcccCHHHHHHHHHHHHHHH----------------------------------------------
Confidence 9999999999999999999999888888888776
Q ss_pred HHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhccC
Q psy3015 272 EDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 351 (1791)
Q Consensus 272 ~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvGQ 351 (1791)
++|.+++++++.|.|+..||++++++||++|+++||++|+++++.+++++++.|++++|+.||||||.+||+||+|||||
T Consensus 694 ~~v~~~~~~~~~g~l~~~~g~~~~e~~e~~v~~~l~~~~~~~~~~~~~~l~~~N~~~~M~~SGakGs~~ni~Q~~~~~Gq 773 (1752)
T 3h0g_A 694 RQVAECIQDAQHNRLKPEPGMTLRESFEAKVSRILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQ 773 (1752)
T ss_dssp HHHHHHHTTTTTTCCCCCSSCCTTHHHHHHHHHHHHHHHHHHHHHHHTTSCSSCTTTHHHHHCSSCCHHHHHHHHTCCCC
T ss_pred HHHHHHHHHHHcCCCccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHhhhccccCHHHHHHHHhccCC
Confidence 46667788888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcc
Q psy3015 352 QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMES 431 (1791)
Q Consensus 352 Q~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LED 431 (1791)
|+++|+|||+||++||||||.++|++|+++|||+|||++||+|+|||||||||||||||||||||+||||||||||+|||
T Consensus 774 q~~~GkrIp~g~~~rtLP~f~k~d~~~~a~GfV~~sF~~GL~p~EfFfhtmggReGLiDTAvKTA~SGYLqRRLVk~leD 853 (1752)
T 3h0g_A 774 QIVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMED 853 (1752)
T ss_dssp CCSTTSSSCCCSTTSSSTTSCSSCCSTTTSSCCSSCTTTCCCHHHHHHHHHHHTTTTTHHHHTTTHHHHHHHHHHHHHTT
T ss_pred CccCCccCCCCCCCccCCCCCCCCCCcccCcchhhcccCCCCHHHHHHHhhhhhhhhhHhhhhcCcCchhHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeecCcEEecCCceEEEEecCCCCCcccccccccccccchhhhhhccccCCCCCCCccccchhhhhhhhcCCcccccc
Q psy3015 432 VMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTLRNVSSLRRVVNSKPLLIGC 511 (1791)
Q Consensus 432 l~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 511 (1791)
|+|+|||||||++|+||||+|||||+||+.+|.|+++++.+++..|+++|+++..+.. .+.
T Consensus 854 v~V~YDgTVRns~g~ivQF~YGeDGlD~~~~e~q~~~~~~~s~~~f~~~~~~~~~~~~-~~~------------------ 914 (1752)
T 3h0g_A 854 VMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEYQVFDSLRLSTKQFEKKYRIDLMEDR-SLS------------------ 914 (1752)
T ss_dssp CEEETTTEEECTTSCEEESSSSSSCBCGGGEEEEECTTTSCCHHHHTTTSCCCTTTTC-CGG------------------
T ss_pred eEEeeCCeeEcCCCcEEEEecCCCCcChHHhhccccccccCCHHHHHHHhcccccccc-ccc------------------
Confidence 9999999999999999999999999999999999999999999999888887543321 000
Q ss_pred ccchhhHHHHHHHHHHhccccchhHHHHHHHHHHhhhhhhhhhhcCCCCCccccccccchhhHHHHhhhhhhcccCCChh
Q psy3015 512 WKLTSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMR 591 (1791)
Q Consensus 512 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~mt~~~~~~~~~~~gi~~~~~~~~~~~~~~e~~~~i~~a~~~~~~~~~~ 591 (1791)
.+
T Consensus 915 ------------------------------------------------------------~~------------------ 916 (1752)
T 3h0g_A 915 ------------------------------------------------------------LY------------------ 916 (1752)
T ss_dssp ------------------------------------------------------------GT------------------
T ss_pred ------------------------------------------------------------HH------------------
Confidence 00
Q ss_pred hhHHHHHHHHHHHHHhhcccccccccccceeeeecCCCcccccccccccceeecChhhhhcccccCCchhhHhhhhccHH
Q psy3015 592 GYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERQLRRIFNED 671 (1791)
Q Consensus 592 ~ri~~~~~k~ie~V~~~yd~~vr~~vg~~~~~~~gE~g~~~~~ie~~~ip~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 671 (1791)
+ +
T Consensus 917 ----------------------------~--------------~------------------------------------ 918 (1752)
T 3h0g_A 917 ----------------------------M--------------E------------------------------------ 918 (1752)
T ss_dssp ----------------------------S--------------C------------------------------------
T ss_pred ----------------------------H--------------H------------------------------------
Confidence 0 0
Q ss_pred HHHHhhcCCCchhhhHHhhhcccchHHHHHhhhhhhHhhccCChHHHHHHHHHHHHHHHHHHHHHh-hccCCCcceeecc
Q psy3015 672 VLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMGSGDVISELEKEWEKLCEDREALRE-IFSSGESNVVLPC 750 (1791)
Q Consensus 672 ~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~~~~~e~~kL~~~~~~Lr~-i~~~~~~~~~l~~ 750 (1791)
..+..+.+++..+++||++|.+++..||+ ++..++.++.+|+
T Consensus 919 -------------------------------------~~l~~~~~~~~~l~~E~~~l~~dr~~lr~~i~~~~~~~~~lP~ 961 (1752)
T 3h0g_A 919 -------------------------------------NSIENDSSVQDLLDEEYTQLVADRELLCKFIFPKGDARWPLPV 961 (1752)
T ss_dssp -------------------------------------SCCTTSCSSTHHHHHHHHHHHHHHTTSSSSSSSCSCCEEEEES
T ss_pred -------------------------------------HHhccCHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccCCc
Confidence 00001112234566788999999998987 6777778889999
Q ss_pred hhHHHHHHHhhhhccCCcccccccceEEEeccCcccHHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccccccC
Q psy3015 751 NLMEVIFILQRWKLWGNENLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQ 830 (1791)
Q Consensus 751 N~~rii~~~~~~~~~~~~~~~~~~n~i~~IaAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~Gl~~~ 830 (1791)
|+.|+||++++ +|.+..|..
T Consensus 962 N~~R~i~~~~~---------------~f~~~~~~~--------------------------------------------- 981 (1752)
T 3h0g_A 962 NVQRIIQNALQ---------------IFHLEAKKP--------------------------------------------- 981 (1752)
T ss_dssp CHHHHTTTTTT---------------TSCCCTTSC---------------------------------------------
T ss_pred cHHHHHHHHHH---------------hcCCCcCcc---------------------------------------------
Confidence 99999998766 333322211
Q ss_pred CCcccccchhhhhhHHHHHHhhccCCCCCCCcccceecCCCCCCCcceeeeccccccccCCccccccccccCCCCccccC
Q psy3015 831 DTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGPAGMFFG 910 (1791)
Q Consensus 831 ~~S~L~~aSFE~T~d~L~~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~~~Ll~~~~k~k~~~~~~~~~~~~~~~~~~~~~ 910 (1791)
|.|.-..+ +.+|+| ++ +++
T Consensus 982 --s~l~p~~~------------------~~~v~~----------------~~---~~l---------------------- 1000 (1752)
T 3h0g_A 982 --TDLLPSDI------------------INGLNE----------------LI---AKL---------------------- 1000 (1752)
T ss_dssp --CCCCHHHH------------------HHHHHH----------------HH---TTC----------------------
T ss_pred --CCCCHHHH------------------HHHHHH----------------HH---Hhh----------------------
Confidence 11111111 113333 33 444
Q ss_pred CCCCCCCCCCCCCccccCccccccccCCCCcCCCCCCCCcccccCCcchhHHHHhcHHHHHHHHhHhhhhhHHHHhhccC
Q psy3015 911 SAATPSSMSPQMTPWAQSTPAYNALMSPGAAMTPGGPGFSPSVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRL 990 (1791)
Q Consensus 911 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Rs~L~sk~v~~~~rl 990 (1791)
++++|.|.|+++|++||++||++++|+.|++|+++++++|
T Consensus 1001 ----------------------------------------~~~~g~d~l~~~~~~na~~l~~~~lr~~l~~k~~~~~~~l 1040 (1752)
T 3h0g_A 1001 ----------------------------------------TIFRGSDRITRDVQNNATLLFQILLRSKFAVKRVIMEYRL 1040 (1752)
T ss_dssp ----------------------------------------CCSCCCSTTTTHHHHTSSHHHHHHHTTSSSHHHHHHSSCC
T ss_pred ----------------------------------------hcccCCcchhhhhhhchHHHHHHHHHhhhhhhhhhhhcCc
Confidence 4667899999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCCCCCCCCc
Q psy3015 991 SSEAFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDDYGPESRG 1048 (1791)
Q Consensus 991 n~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd~~PESrG 1048 (1791)
|+++|+|+++++..+|..+++.| |||+ || |++++||+|+|| |+|+
T Consensus 1041 ~~~~~~~~~~~~~~~y~~a~v~pGe~VG~iaAQSIgEp~TQMTLnTFHfAGvas~NVTlGVPR--LkEI----------- 1107 (1752)
T 3h0g_A 1041 NKVAFEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPR--LKEI----------- 1107 (1752)
T ss_dssp CHHHHHHHHHHHHHHHHTTBCCSSCCHHHHHHHHHHHHHHHHHHHTTSSCCCCCSSCCCSGGG--HHHH-----------
T ss_pred CHHHHHHHHHHHHHHHHHhccCcccchhhhhhcccCCchhhhhHHhhhhccccccccccCccc--HHHH-----------
Confidence 99999999999999999999999 8887 88 789999999999 9999
Q ss_pred ceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEECCCCCCcccccCcceeeeec
Q psy3015 1049 FVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYY 1122 (1791)
Q Consensus 1049 FV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Y 1122 (1791)
+|..++.+||++++|+ .+...++.|.+ .+++ +|.++++.++|.|||++.+|++.+|.++|+.||
T Consensus 1108 --Inask~ikTP~mtv~L--------~~~~~~d~e~A~~v~~~ie~t~L~~v~~~~~i~~~p~~~~~~i~~d~~~v~~~~ 1177 (1752)
T 3h0g_A 1108 --LNVAKNIKTPSLTIYL--------MPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFF 1177 (1752)
T ss_dssp --HTTCSCCSCCCCEECC--------CSSSCSSSTTTHHHHTTSSCCSSCSCCSCEEEECCCSTTCCCCSSSCSHHHHHH
T ss_pred --HhhhcCCCCCeEEEEe--------cCccccCHHHHHHHHHhhccEEHHHheeEEEEEEecCccceEEeecHHHHHHHh
Confidence 8999999999999999 45555566766 4554 677899999999999999999999999999999
Q ss_pred cCCCCC----CCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchh
Q psy3015 1123 EMPDFD----PTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEE 1198 (1791)
Q Consensus 1123 g~dg~D----~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~e 1198 (1791)
..++.| ....++|+++++||+.+|.++++++++|.++|.+.++.++.+++++++++++++++|+..+.+.... ++
T Consensus 1178 ~~~~~~~~~~~~~~~~~~~rl~l~~~~~~~~~l~~~~I~~~i~~~~~~~~~v~~~d~~~~~~~i~i~~~~~~~~~~~-~~ 1256 (1752)
T 3h0g_A 1178 AIPDEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVAGKIAESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAE-DD 1256 (1752)
T ss_dssp HTTCSSTTCSSCSCCCCEEEEECCTTSSTTTTCCHHHHTTSGGGSSTTSCCEECCCTTCSSCEEEECCCCCSCCCCC-SS
T ss_pred ccchhhhhcccccccceeEEEEecHHHHHHcCCCHHHHHHHHHhhccCCeeEeecCCCccceeEEEEeccccccccc-cc
Confidence 876655 4567899999999999999999999999999999998899998988888888888887543211100 00
Q ss_pred HHHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCC
Q psy3015 1199 DAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVD 1278 (1791)
Q Consensus 1199 e~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVD 1278 (1791)
+ ...+++.+|+.++..+|.+++|+||++|++++++ +.++.++..++.|....+|+|.|||+||.++|..++||
T Consensus 1257 ~--~~~~~~~~l~~l~~~~l~~~~i~Gi~~I~rv~i~-----~~~~~~~~~~g~~~~~~~~~l~teG~nL~~v~~~~gVD 1329 (1752)
T 3h0g_A 1257 D--NMIEEDVFLKTIEGHMLESISLRGVPNITRVYMM-----EHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVD 1329 (1752)
T ss_dssp C--CCSCSCHHHHHHHHHHTTCCCSSCCTTCCCCCEE-----EEEEEEECSSSCEEEEEEEEEECCSCCCSTTTSSSSCC
T ss_pred c--ccccHHHHHHHHHHhhccceEEecCCCccEEEEe-----cccceeecCCCcccccceEEEEecccCHHHHhCcCCCc
Confidence 0 1123456788888778999999999999999987 33455567777787778999999999999999999999
Q ss_pred cccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccchh
Q psy3015 1279 PVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFE 1358 (1791)
Q Consensus 1279 p~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSFE 1358 (1791)
++||+||||+||+++|||||||++|++|++.|+.++|++||+|||+||||+||++|++++||||||++++.|+|+|||||
T Consensus 1330 ~~rt~sNdI~ei~~vlGIEAAR~~Ii~Ei~~v~~~~G~~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~s~l~~aSFE 1409 (1752)
T 3h0g_A 1330 ATRTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFE 1409 (1752)
T ss_dssp TTTCCCSCHHHHHHHSCHHHHHHHHHHHHHTTSCSSSCCCCHHHHHHHHHHHTSSSSCCCCCTTSCSCCCSHHHHHHHHS
T ss_pred cccCeeCCHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccCCeEEeechhhhccCCCCHHHHhhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhccccccc
Q psy3015 1359 ETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCK 1406 (1791)
Q Consensus 1359 eTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~~~ 1406 (1791)
+|+++|++||++|+.|+|+||+|||||||++++|||+||+++++.+++
T Consensus 1410 ~T~~~L~~Aa~~g~~D~l~gvse~Ii~G~~~~~GTG~fdll~~~~~l~ 1457 (1752)
T 3h0g_A 1410 ETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTGAFDIYLDQDMLM 1457 (1752)
T ss_dssp CCTHHHHHHGGGTCCBCCCCSTTGGGTCSCCCSBTTSCEECCCHHHHH
T ss_pred HHHHHHHHHHHhcCcccccChhHHhhcCCCcCCccceEEEEeCHHHhc
Confidence 999999999999999999999999999999999999999999999887
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=2.3e-158 Score=1601.06 Aligned_cols=908 Identities=45% Similarity=0.757 Sum_probs=776.5
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccCCCCCCCceeCCCCcccHhhhhhhcC
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLII 111 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~~~lP~PaIlKP~~LWTGKQIfS~iL 111 (1791)
.||++++|+++|++++|+|++ .+.|+++++++|+++|+..|++.+|+|||+||++|||||||||++|
T Consensus 503 ~Lm~~~~nilsP~~G~Pi~~~~QD~v~g~y~lT~~~~f~~~~e~~~~~~~~~~~~~~~~~pai~kp~~~wtGkqifs~il 582 (1733)
T 1twf_A 503 QLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAI 582 (1733)
T ss_dssp HHTBGGGGSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHSTTCCSCCCCCSBCSSSCEEEHHHHHHHHS
T ss_pred HHhcCcccEEecCCCCeeEeeeccccccceeeecCcccCCHHHHHHHHHhhhhhcCccCCccccCcccCccHHHHHHHhC
Confidence 389999999999999999998 3469999999999999999999999999999999999999999999
Q ss_pred CCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHH
Q psy3015 112 PGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVV 191 (1791)
Q Consensus 112 P~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~ 191 (1791)
|+++|+.... +. ..|.+++|++|+|+||||++|++||++||++.+||||.||++||+++|+.|||++|+|+
T Consensus 583 p~~~~~~~~~---~~------~~~~~~~d~~v~i~~gel~~g~ldKk~lg~~~~~li~~i~~~~G~~~a~~~ld~l~~l~ 653 (1733)
T 1twf_A 583 PNGIHLQRFD---EG------TTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVV 653 (1733)
T ss_dssp CTTCCEEECC---TT------CCTTCTTCCSEEEETTEEEESCCCHHHHSSCTTSHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred CCCCceeecC---CC------cccCCcccceEEEeCCcEEEeecchHHhccChhHHHHHHHHHhCHHHHHHHHHHHHHHH
Confidence 9999996532 11 24677889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHH
Q psy3015 192 NNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAK 271 (1791)
Q Consensus 192 ~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 271 (1791)
++||+++||||||+|+++++++.++++++|++|+
T Consensus 654 ~~~l~~~GfSigi~D~~~~~~~~~~i~~~i~~a~---------------------------------------------- 687 (1733)
T 1twf_A 654 NFWLLHNGFSTGIGDTIADGPTMREITETIAEAK---------------------------------------------- 687 (1733)
T ss_dssp HHHHHTTCBCCCGGGGCCCHHHHHHHHHHHHHHH----------------------------------------------
T ss_pred HHHHHHcceEEehhhcCcCHHHHHHHHHHHHHHH----------------------------------------------
Confidence 9999999999999999999999888888888777
Q ss_pred HHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhccC
Q psy3015 272 EDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 351 (1791)
Q Consensus 272 ~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvGQ 351 (1791)
++|.+++++++.|.|+++||++.+++||++|+++|+++|+++++.+++++++.|++++|+.||||||.+|++||+|||||
T Consensus 688 ~~v~~~~~~~~~g~l~~~pg~~~~e~~e~~v~~il~~~~d~~~~~~~~~l~~~N~i~~Ma~SGAKGs~~Ni~Q~~~~~Gq 767 (1733)
T 1twf_A 688 KKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQ 767 (1733)
T ss_dssp HHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHTSSCCHHHHHHHHSCCEE
T ss_pred HHHHHHHHHHHhCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCeEEEeeccCcccHHhHHHHHhCcCC
Confidence 46667788889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcc
Q psy3015 352 QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMES 431 (1791)
Q Consensus 352 Q~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LED 431 (1791)
|+++|+|||+||++||||||.++|++|+|||||+|||++||+|+|||||||||||||||||||||+||||||||||+|||
T Consensus 768 q~~~Gkrip~g~~~RtLPhf~k~d~~p~s~GfI~ssF~~GLtp~EyFfh~mggReGLiDTAvKTA~SGYLqRRLVk~led 847 (1733)
T 1twf_A 768 QSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALED 847 (1733)
T ss_dssp CCBTTBSCCCCBTTBSSTTSCTTCCSTTTTTEECSCTTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred cccCCccCCCCCCCCCCCCCCCCCCCccccchhhhhhhcccchHHHhhhhhccccchhhhceecccCCcceeehhhhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeecCcEEecCCceEEEEecCCCCCcccccccccccccchhhhhhccccCCCCCCCccccchhhhhhhhcCCcccccc
Q psy3015 432 VMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTLRNVSSLRRVVNSKPLLIGC 511 (1791)
Q Consensus 432 l~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 511 (1791)
|+|+|||||||++|+||||+|||||+|++.+|.|+++++.++...|.+.|+++..+....+
T Consensus 848 v~V~yDgTVR~s~g~IvQF~YGeDGlD~~~~e~~~~~~~~~~~~~f~~~~~~~~~~~~~~l------------------- 908 (1733)
T 1twf_A 848 IMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTL------------------- 908 (1733)
T ss_dssp CEECTTSCEECTTCCEEESSGGGTTBCGGGEEEEECGGGSSCHHHHHHHHCCCTTCTTTSC-------------------
T ss_pred eEEEecCcEecCCCCEEEEEeccccCCcceeecccccccccCHHHHHHHhccccccccccC-------------------
Confidence 9999999999999999999999999999999999888777776666555544321110000
Q ss_pred ccchhhHHHHHHHHHHhccccchhHHHHHHHHHHhhhhhhhhhhcCCCCCccccccccchhhHHHHhhhhhhcccCCChh
Q psy3015 512 WKLTSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMR 591 (1791)
Q Consensus 512 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~mt~~~~~~~~~~~gi~~~~~~~~~~~~~~e~~~~i~~a~~~~~~~~~~ 591 (1791)
T Consensus 909 -------------------------------------------------------------------------------- 908 (1733)
T 1twf_A 909 -------------------------------------------------------------------------------- 908 (1733)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hhHHHHHHHHHHHHHhhcccccccccccceeeeecCCCcccccccccccceeecChhhhhcccccCCchhhHhhhhccHH
Q psy3015 592 GYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERQLRRIFNED 671 (1791)
Q Consensus 592 ~ri~~~~~k~ie~V~~~yd~~vr~~vg~~~~~~~gE~g~~~~~ie~~~ip~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 671 (1791)
... +. +
T Consensus 909 ------------------------------------------------------~~~------------------~~--~ 914 (1733)
T 1twf_A 909 ------------------------------------------------------DPS------------------LL--E 914 (1733)
T ss_dssp ------------------------------------------------------CTT------------------TB--T
T ss_pred ------------------------------------------------------CHH------------------HH--H
Confidence 000 00 0
Q ss_pred HHHHhhcCCCchhhhHHhhhcccchHHHHHhhhhhhHhhccCChHHHHHHHHHHHHHHHHHHHHHhhccCCCcceeecch
Q psy3015 672 VLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMGSGDVISELEKEWEKLCEDREALREIFSSGESNVVLPCN 751 (1791)
Q Consensus 672 ~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~~~~~e~~kL~~~~~~Lr~i~~~~~~~~~l~~N 751 (1791)
..+.+ ..+..++..++++|++|.+++..||+++..+..++.+|+|
T Consensus 915 ~~~~~-----------------------------------~~~~~~~~~l~~e~~~l~~~r~~lr~i~~~~~~~~~~P~n 959 (1733)
T 1twf_A 915 SGSEI-----------------------------------LGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVN 959 (1733)
T ss_dssp THHHH-----------------------------------TTCHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCEEEEESC
T ss_pred HHHHh-----------------------------------hccHHHHHHHHHHHHHHHHHHHHHHHhhccccccccCChh
Confidence 00000 1112233455667888888888899988877778889999
Q ss_pred hHHHHHHHhhhhccCCcccccccceEEEeccCcccHHHHHHHHhhcceeccchhhhhhhhhhcccceecceeccccccCC
Q psy3015 752 LMEVIFILQRWKLWGNENLRFLCKIIFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQD 831 (1791)
Q Consensus 752 ~~rii~~~~~~~~~~~~~~~~~~n~i~~IaAR~~Ii~Ei~~v~~~~GIsVd~RHi~LlaD~MT~~G~v~~itR~Gl~~~~ 831 (1791)
+.|++|++++ .|.+..|..
T Consensus 960 i~r~i~~~~~---------------~f~~~~~~~---------------------------------------------- 978 (1733)
T 1twf_A 960 IRRIIQNAQQ---------------TFHIDHTKP---------------------------------------------- 978 (1733)
T ss_dssp HHHHHHHHHH---------------HTTCCTTSC----------------------------------------------
T ss_pred HHHHHHHHHH---------------Hhccccccc----------------------------------------------
Confidence 9999998877 222222210
Q ss_pred CcccccchhhhhhHHHHHHhhccCCCCCCCcccceecCCCCCCCcceeeeccccccccCCccccccccccCCCCccccCC
Q psy3015 832 TGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGPAGMFFGS 911 (1791)
Q Consensus 832 ~S~L~~aSFE~T~d~L~~Aa~~g~~D~i~GVSe~II~G~~~~iGTg~~~Ll~~~~k~k~~~~~~~~~~~~~~~~~~~~~~ 911 (1791)
|.|.-.. -+.+|++ ++ +++
T Consensus 979 -s~l~p~~------------------~~~~v~~----------------~~---~~~----------------------- 997 (1733)
T 1twf_A 979 -SDLTIKD------------------IVLGVKD----------------LQ---ENL----------------------- 997 (1733)
T ss_dssp -BCCCHHH------------------HHHHHHH----------------HH---TTC-----------------------
T ss_pred -ccCCHHH------------------HHHHHHH----------------HH---Hhh-----------------------
Confidence 0000000 0112333 33 333
Q ss_pred CCCCCCCCCCCCccccCccccccccCCCCcCCCCCCCCcccccCCcchhHHHHhcHHHHHHHHhHhhhhhHHHHhhccCC
Q psy3015 912 AATPSSMSPQMTPWAQSTPAYNALMSPGAAMTPGGPGFSPSVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLS 991 (1791)
Q Consensus 912 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Rs~L~sk~v~~~~rln 991 (1791)
.++.|.|.++.++++||++||+|++|++|++|+++++++++
T Consensus 998 ---------------------------------------~~~~g~d~l~~~~~~n~~~l~~~~~rs~L~~k~~~~~~~l~ 1038 (1733)
T 1twf_A 998 ---------------------------------------LVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLT 1038 (1733)
T ss_dssp ---------------------------------------CSCCCCSHHHHHHHHHTTHHHHHHHHHHSCHHHHHHTSCCC
T ss_pred ---------------------------------------hcccCCcchhhhhhhchHHHHHHHhhhhhhhhhhhhhcCCC
Confidence 45678899999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhccceeccc--cccc---cc-----------------cCCcccCCCCcCccccccccCCCCCCCCcc
Q psy3015 992 SEAFEWLVGEIENRFQQAQVIA--CVGQ---QN-----------------VEGKRIPFGFRKRTLPHFIKDDYGPESRGF 1049 (1791)
Q Consensus 992 ~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs-----------------V~gKrI~~GfprRTLphf~kdd~~PESrGF 1049 (1791)
.++|+|+++++..+|..+++.| |||+ || |++++||+|+|| |.|+
T Consensus 1039 ~~~~~~~l~~i~~ky~~a~v~pGe~VG~iaAQSigEp~TQMTLnTFHfAGva~~NVTLGVPR--LkEI------------ 1104 (1733)
T 1twf_A 1039 KQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPR--LKEI------------ 1104 (1733)
T ss_dssp HHHHHHHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC----------CCSCCHHHH--HHHH------------
T ss_pred HHHHHHHHHHHHHHHHhccCCCCchhhhHhhhhcCCccccccccccccccccccCcccCcHH--HHHH------------
Confidence 9999999999999999999999 8887 87 899999999999 9999
Q ss_pred eeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHH-----HHHHHhcceEEEECCCCCCcccccCcceeeeecc
Q psy3015 1050 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLV-----FLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYE 1123 (1791)
Q Consensus 1050 V~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqR-----RLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg 1123 (1791)
+|..++.+||++++++ .+...++.+.+ .+++ +|.++++++.|.|||++.+|++.+|.++++.||.
T Consensus 1105 -inask~ikTP~mtv~L--------~~~~~~~~e~A~~v~~~ie~ttL~dv~~~i~i~~dp~~~~tvi~ed~~~~~~y~~ 1175 (1733)
T 1twf_A 1105 -LNVAKNMKTPSLTVYL--------EPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFS 1175 (1733)
T ss_dssp -TTTCSSCSSCEEEEEB--------CSSSSSCHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHHTSSC
T ss_pred -HHhccCCCCCeEEEEe--------CCcccccHHHHHHHHHhhceeEHHHhhheEEEEEccCccceeeecchhhhhhhhc
Confidence 8999999999999999 44444455656 4454 5778999999999999999999999999999988
Q ss_pred CCCC----CCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchhH
Q psy3015 1124 MPDF----DPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEED 1199 (1791)
Q Consensus 1124 ~dg~----D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~ee 1199 (1791)
.+.. |...+++|+++++||+.++.++++++++|.++|.+.++.++.++.++++++++++++|+...++.. ++
T Consensus 1176 i~~~d~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~I~~~i~~~~~~~~~~~~~d~~~~~~~~~i~~~~~~~~~----~~ 1251 (1733)
T 1twf_A 1176 LLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLD----AE 1251 (1733)
T ss_dssp C----------CCCSEEEEEEECHHHHHHTTCCHHHHHHHHHHHHGGGEEEEECCTTSSSCEEEEEEC------------
T ss_pred ccHHhhcchhhhcccceeEEEecHHHHHhcCCCHHHHHHHHHHhhCCCcceecCCcccchhheeeeeccCcccc----cc
Confidence 7532 456778999999999999999999999999999988887777777788888888888875532110 11
Q ss_pred HHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCCc
Q psy3015 1200 AVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDP 1279 (1791)
Q Consensus 1200 ~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVDp 1279 (1791)
...+++.++++++.+++.+++|+|+++|++++++. .++++.+.++.|....+|+|+|||+||.++|..++||+
T Consensus 1252 --~~~~~~~~l~~l~~~~l~~~~v~Gi~~I~r~~i~~-----~~~~~~~~~g~~~~~~~~~L~teG~nL~~vl~~~~VD~ 1324 (1733)
T 1twf_A 1252 --TEAEEDHMLKKIENTMLENITLRGVENIERVVMMK-----YDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDP 1324 (1733)
T ss_dssp ----CCTTHHHHHHHHHHHHHCEEESCTTCCCEEEEE-----EEEEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCT
T ss_pred --ccchhHHHHHHHHHHhhhheEEecCCCccEEEEec-----ccceeecCCCccccCcceEEEeecccHHHHhccCCccc
Confidence 11223457777877888899999999999999862 26777778777777789999999999999999999999
Q ss_pred ccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccccccccccchhh
Q psy3015 1280 VRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 1359 (1791)
Q Consensus 1280 ~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~S~L~raSFEe 1359 (1791)
+||+||||+||+++|||||||++|++|++.||.++|++||+|||+||||+||++|++++||||||++.+.|+|++||||+
T Consensus 1325 ~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~~~~~S~L~~aSFE~ 1404 (1733)
T 1twf_A 1325 TRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEE 1404 (1733)
T ss_dssp TTCBCSCHHHHHHHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTTBSSCCCSSSCSSSCSSCCTTSSCCSSC
T ss_pred ccceeccHHHHHHHhhHHHHHHHHHHHHHHHHhhcCccccchhhhhhhhhhccCceecccchhhhcccCCCchhhcchhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhccccccccccc
Q psy3015 1360 TVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIE 1410 (1791)
Q Consensus 1360 Tv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~~~~~~~~ 1410 (1791)
|+++|++||.+|+.|+|+||+||||+|+++++|||+||++++..+++.+.+
T Consensus 1405 T~~~L~~Aa~~g~~D~l~gvsenII~G~~~~~GTG~FdLl~~~~~~~~~~~ 1455 (1733)
T 1twf_A 1405 TVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMP 1455 (1733)
T ss_dssp SHHHHHHHHHHTCEECCCSHHHHHHTTCCCSSGGGSSEEEECSCCC-----
T ss_pred hHHHHHHHHhccCcCcccccccccccCCCCCCCCccEEEEEchhhcccccc
Confidence 999999999999999999999999999999999999999999988777553
No 3
>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=6.2e-97 Score=1000.62 Aligned_cols=559 Identities=33% Similarity=0.464 Sum_probs=436.7
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEee
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHA 1067 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhA 1067 (1791)
.+.|+..+|..+|++|+..|++|+.+|||||+|+|||||+||.+||||||.|+|++|+|||||+|||++||||+||||||
T Consensus 744 ~~~N~~~~M~~SGakGs~~ni~Q~~~~~Gqq~~~GkrIp~g~~~rtLP~f~k~d~~~~a~GfV~~sF~~GL~p~EfFfht 823 (1752)
T 3h0g_A 744 KDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQEFFFHA 823 (1752)
T ss_dssp CSSCTTTHHHHHCSSCCHHHHHHHHTCCCCCCSTTSSSCCCSTTSSSTTSCSSCCSTTTSSCCSSCTTTCCCHHHHHHHH
T ss_pred CCCCcHHHHhhhccccCHHHHHHHHhccCCCccCCccCCCCCCCccCCCCCCCCCCcccCcchhhcccCCCCHHHHHHHh
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcccceeeeeccccccc
Q psy3015 1068 MGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMT 1147 (1791)
Q Consensus 1068 MgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~wvlr~~Ld~~~m~ 1147 (1791)
|||||||+|||+|||++|||||||||+|||++|+||+ |||+++|+||||.||+||+|+.. ++.+.++..+++
T Consensus 824 mggReGLiDTAvKTA~SGYLqRRLVk~leDv~V~YDg----TVRns~g~ivQF~YGeDGlD~~~----~e~q~~~~~~~s 895 (1752)
T 3h0g_A 824 MAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDG----TVRNAMGDIIQFAYGEDGLDATL----VEYQVFDSLRLS 895 (1752)
T ss_dssp HHHTTTTTHHHHTTTHHHHHHHHHHHHHTTCEEETTT----EEECTTSCEEESSSSSSCBCGGG----EEEEECTTTSCC
T ss_pred hhhhhhhhHhhhhcCcCchhHHHHHHHHhheEEeeCC----eeEcCCCcEEEEecCCCCcChHH----hhccccccccCC
Confidence 9999999999999999999999999999999999999 78888999999999999999964 457788877777
Q ss_pred cccCCHHHHHHHHhhccCCCcccccCCcccccceEEEEEecCccccccchhHHHHhhhhhhhHHHHhhcccccceecccc
Q psy3015 1148 DKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIE 1227 (1791)
Q Consensus 1148 dk~l~~~~I~~~I~~~~~~dl~~i~~d~n~~~l~~riri~~~~~~~~~~~ee~~~~~~dr~~Lr~i~~~il~~~~LkGi~ 1227 (1791)
+..|. +.|+.++.... ....++.. .+..+.+.+..+++|+.++.++|.+||... +
T Consensus 896 ~~~f~---------~~~~~~~~~~~--~~~~~~~~--~l~~~~~~~~~l~~E~~~l~~dr~~lr~~i---~--------- 950 (1752)
T 3h0g_A 896 TKQFE---------KKYRIDLMEDR--SLSLYMEN--SIENDSSVQDLLDEEYTQLVADRELLCKFI---F--------- 950 (1752)
T ss_dssp HHHHT---------TTSCCCTTTTC--CGGGTSCS--CCTTSCSSTHHHHHHHHHHHHHHTTSSSSS---S---------
T ss_pred HHHHH---------HHhcccccccc--cccHHHHH--HhccCHHHHHHHHHHHHHHHHHHHHHHHHh---h---------
Confidence 76553 55554432110 00001000 112223334456788888888888777531 1
Q ss_pred ccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCCcccccchhHHHHHHhhhHHHHHHHHHHHH
Q psy3015 1228 AIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEM 1307 (1791)
Q Consensus 1228 ~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El 1307 (1791)
..++-.+.+|+ |+.|+|++++..|+... ...++++|..+ |+++++.+.+.+
T Consensus 951 ~~~~~~~~lP~--N~~R~i~~~~~~f~~~~--------------~~~s~l~p~~~-------------~~~v~~~~~~l~ 1001 (1752)
T 3h0g_A 951 PKGDARWPLPV--NVQRIIQNALQIFHLEA--------------KKPTDLLPSDI-------------INGLNELIAKLT 1001 (1752)
T ss_dssp SCSCCEEEEES--CHHHHTTTTTTTSCCCT--------------TSCCCCCHHHH-------------HHHHHHHHTTCC
T ss_pred ccccccccCCc--cHHHHHHHHHHhcCCCc--------------CccCCCCHHHH-------------HHHHHHHHHhhh
Confidence 12344566777 99999999998886421 23456777644 555554442211
Q ss_pred HHHhhhcCeeecccchhhhhhcccccCccccccccccccccc-ccccccchhhhHHHHHHHhhccCCCCCCccccceecc
Q psy3015 1308 NTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDT-GALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMG 1386 (1791)
Q Consensus 1308 ~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~~-S~L~raSFEeTv~iL~~AA~~ge~D~lkgVsenIi~G 1386 (1791)
...|. | .+++ .++.+ ..|+++.+.+++. .+.+.
T Consensus 1002 ----~~~g~-----------d---------~l~~---~~~~na~~l~~~~lr~~l~-------------~k~~~------ 1035 (1752)
T 3h0g_A 1002 ----IFRGS-----------D---------RITR---DVQNNATLLFQILLRSKFA-------------VKRVI------ 1035 (1752)
T ss_dssp ----CSCCC-----------S---------TTTT---HHHHTSSHHHHHHHTTSSS-------------HHHHH------
T ss_pred ----cccCC-----------c---------chhh---hhhhchHHHHHHHHHhhhh-------------hhhhh------
Confidence 11121 1 1111 12222 2344433333220 01111
Q ss_pred ccccCCcchhhhhcccccccccccccCCCCcchhh-hhhccCCCCCCCCCCCCCCCcceeeeeeeccccceecccchhHH
Q psy3015 1387 QLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGP-AGMFFGSAATPSSIPGPPAWYPIHIAISLLSRFTTVICIYTLKT 1465 (1791)
Q Consensus 1387 q~~~lGTGaFd~lLge~~~~~~~~~~v~pGEmVG~-aAQSIGEPa~~~~~TQmT~lnTFH~aGVs~~~~t~~lGvprlke 1465 (1791)
+..++...+|+|++++++.++.++. |+||||||+ ||||||||+ |||| |||||||||+++||| ||||||||
T Consensus 1036 ~~~~l~~~~~~~~~~~~~~~y~~a~-v~pGe~VG~iaAQSIgEp~-----TQMT-LnTFHfAGvas~NVT--lGVPRLkE 1106 (1752)
T 3h0g_A 1036 MEYRLNKVAFEWIMGEVEARFQQAV-VSPGEMVGTLAAQSIGEPA-----TQMT-LNTFHYAGVSSKNVT--LGVPRLKE 1106 (1752)
T ss_dssp HSSCCCHHHHHHHHHHHHHHHHTTB-CCSSCCHHHHHHHHHHHHH-----HHHH-HHTTSSCCCCCSSCC--CSGGGHHH
T ss_pred hhcCcCHHHHHHHHHHHHHHHHHhc-cCcccchhhhhhcccCCch-----hhhh-HHhhhhccccccccc--cCcccHHH
Confidence 3457888899999999999999999 999999999 799999999 9999 999999999999998 99999999
Q ss_pred HhhccCCCCCCCCCccceeEEEEeeccccCCccccCCCCCchhhHhhHhHHHHHhhccccccchhhhcceeEEEEcCCCC
Q psy3015 1466 FLEMKDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQ 1545 (1791)
Q Consensus 1466 i~nv~~~~k~~~~~~~~~~~t~~~~~I~~~pk~~~~P~~~~~~~~~vq~~~~~~~~~~~~~~~l~~vt~~t~i~ydpd~~ 1545 (1791)
|||++|++|||+ +|+||.+ ..++ +.+.|+.++..++ +|+|++|+..++||||||+.
T Consensus 1107 IInask~ikTP~-------mtv~L~~------~~~~---d~e~A~~v~~~ie--------~t~L~~v~~~~~i~~~p~~~ 1162 (1752)
T 3h0g_A 1107 ILNVAKNIKTPS-------LTIYLMP------WIAA---NMDLAKNVQTQIE--------HTTLSTVTSATEIHYDPDPQ 1162 (1752)
T ss_dssp HHTTCSCCSCCC-------CEECCCS------SSCS---SSTTTHHHHTTSS--------CCSSCSCCSCEEEECCCSTT
T ss_pred HHhhhcCCCCCe-------EEEEecC------cccc---CHHHHHHHHHhhc--------cEEHHHheeEEEEEEecCcc
Confidence 999999999997 8999983 2322 4566777777776 79999999999999999999
Q ss_pred CCcccccHHHHHHhhcCCCCC----CCCCCcceEEEEeccccccccccCHHHHHhhhhcCCCCCCCCCCCCchhhhHHHH
Q psy3015 1546 NTVIPEDQEFVNVYYEMPDFD----PTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEA 1621 (1791)
Q Consensus 1546 ~tvi~eD~~~v~~~~~~pd~~----~~~~spwllr~~ldr~~m~dk~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~ 1621 (1791)
+|+|++|++||+.||++||++ ++++++|+|||+|||++|++|+|+|++|++
T Consensus 1163 ~~~i~~d~~~v~~~~~~~~~~~~~~~~~~~~~~~rl~l~~~~~~~~~l~~~~I~~------------------------- 1217 (1752)
T 3h0g_A 1163 DTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVAG------------------------- 1217 (1752)
T ss_dssp CCCCSSSCSHHHHHHHTTCSSTTCSSCSCCCCEEEEECCTTSSTTTTCCHHHHTT-------------------------
T ss_pred ceEEeecHHHHHHHhccchhhhhcccccccceeEEEEecHHHHHHcCCCHHHHHH-------------------------
Confidence 999999999999999999975 567999999999999999999999999997
Q ss_pred HHHHHhcccCCCceeeecCCcccceEEEEEEecCCCCccc-----hhh-hhhhc----cccceeeccccccceeEeeccc
Q psy3015 1622 ISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQ-----DEE-DAVDK----MEDDMFLRCIEETDRSFVKVDF 1691 (1791)
Q Consensus 1622 ~~~~i~~~f~~~l~~i~~ddna~~lv~r~r~~~~~~~~~~-----~~~-~~~~~----~~~~~~lr~~~~~~~~~~~~~~ 1691 (1791)
+|.+.|++|++|+++|||+++++||||+.++++.+++ .++ ..+++ +..++.||||++|+||||+.+.
T Consensus 1218 ---~i~~~~~~~~~v~~~d~~~~~~~i~i~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~l~~~~i~Gi~~I~rv~i~~~~ 1294 (1752)
T 3h0g_A 1218 ---KIAESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISLRGVPNITRVYMMEHK 1294 (1752)
T ss_dssp ---SGGGSSTTSCCEECCCTTCSSCEEEECCCCCSCCCCCSSCCCSCSCHHHHHHHHHHTTCCCSSCCTTCCCCCEEEEE
T ss_pred ---HHHhhccCCeeEeecCCCccceeEEEEeccccccccccccccccHHHHHHHHHHhhccceEEecCCCccEEEEeccc
Confidence 6778899999999999999999999999865321111 111 12333 3457889999999999998742
Q ss_pred C-------CccccccEEEEEecccccccHHHHHhh
Q psy3015 1692 V-------EPKDLVEWKTLLKQMHSDFCLAQIIKC 1719 (1791)
Q Consensus 1692 ~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1719 (1791)
. ++....||.++| ||++|+++|++
T Consensus 1295 ~~~~~~~g~~~~~~~~~l~t----eG~nL~~v~~~ 1325 (1752)
T 3h0g_A 1295 IVRQIEDGTFERADEWVLET----DGINLTEAMTV 1325 (1752)
T ss_dssp EEEECSSSCEEEEEEEEEEC----CSCCCSTTTSS
T ss_pred ceeecCCCcccccceEEEEe----cccCHHHHhCc
Confidence 1 122245899999 99999999976
No 4
>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=1e-89 Score=931.61 Aligned_cols=559 Identities=33% Similarity=0.467 Sum_probs=401.2
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEee
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHA 1067 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhA 1067 (1791)
.+.|+..+|..+|++|+..|++|+.+|||||+++|||||+||.+||||||.|+|++|+|||||+|||++||||+||||||
T Consensus 738 ~~~N~i~~Ma~SGAKGs~~Ni~Q~~~~~Gqq~~~Gkrip~g~~~RtLPhf~k~d~~p~s~GfI~ssF~~GLtp~EyFfh~ 817 (1733)
T 1twf_A 738 KDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHA 817 (1733)
T ss_dssp CTTCHHHHHHHHTSSCCHHHHHHHHSCCEECCBTTBSCCCCBTTBSSTTSCTTCCSTTTTTEECSCTTTCCCHHHHHHHH
T ss_pred ccCCCeEEEeeccCcccHHhHHHHHhCcCCcccCCccCCCCCCCCCCCCCCCCCCCccccchhhhhhhcccchHHHhhhh
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcccceeeeeccccccc
Q psy3015 1068 MGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMT 1147 (1791)
Q Consensus 1068 MgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~wvlr~~Ld~~~m~ 1147 (1791)
|||||||+|||+|||++|||||||||+|||++|+||+ |||+++|+||||.||+||+|+. |+..+.++..++.
T Consensus 818 mggReGLiDTAvKTA~SGYLqRRLVk~ledv~V~yDg----TVR~s~g~IvQF~YGeDGlD~~----~~e~~~~~~~~~~ 889 (1733)
T 1twf_A 818 MGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDN----TTRNSLGNVIQFIYGEDGMDAA----HIEKQSLDTIGGS 889 (1733)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCEECTTS----CEECTTCCEEESSGGGTTBCGG----GEEEEECGGGSSC
T ss_pred hccccchhhhceecccCCcceeehhhhhcceEEEecC----cEecCCCCEEEEEeccccCCcc----eeecccccccccC
Confidence 9999999999999999999999999999999999998 7778899999999999999996 4455666655554
Q ss_pred cccCCHHHHHHHHhhccCCCccc---ccCCcccccceEEEEEecCccccccchhHHHHhhhhhhhHHHHhhcccccceec
Q psy3015 1148 DKKLTMEAISEKINAGFGDDLNC---IFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1224 (1791)
Q Consensus 1148 dk~l~~~~I~~~I~~~~~~dl~~---i~~d~n~~~l~~riri~~~~~~~~~~~ee~~~~~~dr~~Lr~i~~~il~~~~Lk 1224 (1791)
+..| .+.|..+... .+..+..+ ..-. +..+.+.....++++.++.++|.++|.+...
T Consensus 890 ~~~f---------~~~~~~~~~~~~~~l~~~~~~-~~~~--~~~~~~~~~~l~~e~~~l~~~r~~lr~i~~~-------- 949 (1733)
T 1twf_A 890 DAAF---------EKRYRVDLLNTDHTLDPSLLE-SGSE--ILGDLKLQVLLDEEYKQLVKDRKFLREVFVD-------- 949 (1733)
T ss_dssp HHHH---------HHHHCCCTTCTTTSCCTTTBT-THHH--HTTCHHHHHHHHHHHHHHHHHHHHHHHHTTT--------
T ss_pred HHHH---------HHHhccccccccccCCHHHHH-HHHH--hhccHHHHHHHHHHHHHHHHHHHHHHHhhcc--------
Confidence 4432 2233322110 00000000 0000 0001011112245566666777777765321
Q ss_pred cccccceEEEeccccCCCceEEEccCCcccccceEEEeecccchhcccccCCCCcccccchhHHHHHHhhhHHHHHHHHH
Q psy3015 1225 GIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVE 1304 (1791)
Q Consensus 1225 Gi~~I~kv~i~lp~~~n~~RiI~na~~~f~~~~e~~L~teG~nL~~vl~~~dVDp~rt~sNdI~eI~~vlGIEAaR~~li 1304 (1791)
+...+.+|+ |+.|+||+++..|+... ...++++|.++ +++++..+.
T Consensus 950 -----~~~~~~~P~--ni~r~i~~~~~~f~~~~--------------~~~s~l~p~~~-------------~~~v~~~~~ 995 (1733)
T 1twf_A 950 -----GEANWPLPV--NIRRIIQNAQQTFHIDH--------------TKPSDLTIKDI-------------VLGVKDLQE 995 (1733)
T ss_dssp -----CCCEEEEES--CHHHHHHHHHHHTTCCT--------------TSCBCCCHHHH-------------HHHHHHHHT
T ss_pred -----ccccccCCh--hHHHHHHHHHHHhcccc--------------cccccCCHHHH-------------HHHHHHHHH
Confidence 112344666 88999999988776421 22355666533 344333322
Q ss_pred HHHHHHhhhcCeeecccchhhhhhcccccCcccccccccccccc-cccccccchhhhHHHHHHHhhccCCCCCCccccce
Q psy3015 1305 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQD-TGALMRCSFEETVDVLMDAAAHAEADPMRGVSENI 1383 (1791)
Q Consensus 1305 ~El~~V~~~~Gi~Vn~RHL~LLaD~MT~~G~l~~itR~Gi~rq~-~S~L~raSFEeTv~iL~~AA~~ge~D~lkgVsenI 1383 (1791)
+. ....|. .+....++. ...|+++.+++++.. +.+.
T Consensus 996 ~~----~~~~g~-----------------------d~l~~~~~~n~~~l~~~~~rs~L~~-------------k~~~--- 1032 (1733)
T 1twf_A 996 NL----LVLRGK-----------------------NEIIQNAQRDAVTLFCCLLRSRLAT-------------RRVL--- 1032 (1733)
T ss_dssp TC----CSCCCC-----------------------SHHHHHHHHHTTHHHHHHHHHHSCH-------------HHHH---
T ss_pred hh----hcccCC-----------------------cchhhhhhhchHHHHHHHhhhhhhh-------------hhhh---
Confidence 11 111121 000011111 122334333332210 1111
Q ss_pred eccccccCCcchhhhhcccccccccccccCCCCcchhh-hhhccCCCCCCCCCCCCCCCcceeeeeeeccccceecccch
Q psy3015 1384 IMGQLPRMGTGCFDLLLDAEKCKDGIEIPLATGMMGGP-AGMFFGSAATPSSIPGPPAWYPIHIAISLLSRFTTVICIYT 1462 (1791)
Q Consensus 1384 i~Gq~~~lGTGaFd~lLge~~~~~~~~~~v~pGEmVG~-aAQSIGEPa~~~~~TQmT~lnTFH~aGVs~~~~t~~lGvpr 1462 (1791)
+..++...+|+|++++.+.++.++. |+||||||+ ||||||||+ |||| |||||||||+++||| |||||
T Consensus 1033 ---~~~~l~~~~~~~~l~~i~~ky~~a~-v~pGe~VG~iaAQSigEp~-----TQMT-LnTFHfAGva~~NVT--LGVPR 1100 (1733)
T 1twf_A 1033 ---QEYRLTKQAFDWVLSNIEAQFLRSV-VHPGEMVGVLAAQSIGEPA-----TQMT-LNTFHFAGVASKKVT--SGVPR 1100 (1733)
T ss_dssp ---HTSCCCHHHHHHHHHHHHHHHHHHB-CCTTCCHHHHHHHHHHHHH-----TTCC-C----------CCSC--CHHHH
T ss_pred ---hhcCCCHHHHHHHHHHHHHHHHhcc-CCCCchhhhHhhhhcCCcc-----cccc-ccccccccccccCcc--cCcHH
Confidence 2246777899999999999999988 999999999 799999999 9999 999999999999997 99999
Q ss_pred hHHHhhccCCCCCCCCCccceeEEEEeeccccCCccccCCCCCchhhHhhHhHHHHHhhccccccchhhhcceeEEEEcC
Q psy3015 1463 LKTFLEMKDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDP 1542 (1791)
Q Consensus 1463 lkei~nv~~~~k~~~~~~~~~~~t~~~~~I~~~pk~~~~P~~~~~~~~~vq~~~~~~~~~~~~~~~l~~vt~~t~i~ydp 1542 (1791)
|+||||+++++|||+ +||+|.+ ..++ +.+.|+.++..++ +|+|++|+.+++|+|||
T Consensus 1101 LkEIinask~ikTP~-------mtv~L~~------~~~~---~~e~A~~v~~~ie--------~ttL~dv~~~i~i~~dp 1156 (1733)
T 1twf_A 1101 LKEILNVAKNMKTPS-------LTVYLEP------GHAA---DQEQAKLIRSAIE--------HTTLKSVTIASEIYYDP 1156 (1733)
T ss_dssp HHHHTTTCSSCSSCE-------EEEEBCS------SSSS---CHHHHHHHHHHHS--------CEEGGGTEEEEEEEECC
T ss_pred HHHHHHhccCCCCCe-------EEEEeCC------cccc---cHHHHHHHHHhhc--------eeEHHHhhheEEEEEcc
Confidence 999999988888987 9999983 2222 4566777777776 79999999999999999
Q ss_pred CCCCCcccccHHHHHHhhcCCCC----CCCCCCcceEEEEeccccccccccCHHHHHhhhhcCCCCCCCCCCCCchhhhH
Q psy3015 1543 DPQNTVIPEDQEFVNVYYEMPDF----DPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLT 1618 (1791)
Q Consensus 1543 d~~~tvi~eD~~~v~~~~~~pd~----~~~~~spwllr~~ldr~~m~dk~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~ 1618 (1791)
|+.+|||+||++||+.||++|++ +.+++++|+|||+|||++|++++|+|++|++
T Consensus 1157 ~~~~tvi~ed~~~~~~y~~i~~~d~~~~~~~~~~~~lrl~l~~~~~~~~~l~~~~I~~---------------------- 1214 (1733)
T 1twf_A 1157 DPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGE---------------------- 1214 (1733)
T ss_dssp CSSSCSSGGGHHHHHTSSCC----------CCCSEEEEEEECHHHHHHTTCCHHHHHH----------------------
T ss_pred CccceeeecchhhhhhhhcccHHhhcchhhhcccceeEEEecHHHHHhcCCCHHHHHH----------------------
Confidence 99999999999999999999954 5678999999999999999999999999997
Q ss_pred HHHHHHHHhcccCCCceeeecCCcccceEEEEEEecCCCCcc--c-hhhhhhh----ccccceeeccccccceeEeecc-
Q psy3015 1619 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKM--Q-DEEDAVD----KMEDDMFLRCIEETDRSFVKVD- 1690 (1791)
Q Consensus 1619 ~~~~~~~i~~~f~~~l~~i~~ddna~~lv~r~r~~~~~~~~~--~-~~~~~~~----~~~~~~~lr~~~~~~~~~~~~~- 1690 (1791)
+|.+.|++|+.|+++||||+++++|+|+...++.++ . +++..++ ++..++.|+||++|+||+|+..
T Consensus 1215 ------~i~~~~~~~~~~~~~d~~~~~~~~~i~~~~~~~~~~~~~~~~~~~l~~l~~~~l~~~~v~Gi~~I~r~~i~~~~ 1288 (1733)
T 1twf_A 1215 ------RIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYD 1288 (1733)
T ss_dssp ------HHHHHHGGGEEEEECCTTSSSCEEEEEEC----------CCTTHHHHHHHHHHHHHCEEESCTTCCCEEEEEEE
T ss_pred ------HHHHhhCCCcceecCCcccchhheeeeeccCccccccccchhHHHHHHHHHHhhhheEEecCCCccEEEEeccc
Confidence 556668899999999999999999999987542110 0 0111122 2234577999999999999741
Q ss_pred -----c-CCccccccEEEEEecccccccHHHHHhh
Q psy3015 1691 -----F-VEPKDLVEWKTLLKQMHSDFCLAQIIKC 1719 (1791)
Q Consensus 1691 -----~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1719 (1791)
. -.+++..+|++.| ||++|+++++.
T Consensus 1289 ~~~~~~~g~~~~~~~~~L~t----eG~nL~~vl~~ 1319 (1733)
T 1twf_A 1289 RKVPSPTGEYVKEPEWVLET----DGVNLSEVMTV 1319 (1733)
T ss_dssp EEEECTTSSEEEEEEEEEEE----ESCCHHHHTTS
T ss_pred ceeecCCCccccCcceEEEe----ecccHHHHhcc
Confidence 0 1234467999999 99999999864
No 5
>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=3.8e-84 Score=845.82 Aligned_cols=373 Identities=36% Similarity=0.560 Sum_probs=342.4
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cCccccHhHHHHHHhcCCccCCCCCCCceeCCCCcccHhhhhhhcC
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HGSARNQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLII 111 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~Gs~~~rddlmqLlm~~~~~~~~lP~PaIlKP~~LWTGKQIfS~iL 111 (1791)
.||++++|+++|++++|++++ .+.|+++++++|++++ ..+...+|+|||+||+++||||||||++|
T Consensus 478 ~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~lT~~~~~~~~~~~~~~~~~-~~~~~~~~~p~i~~~~~~~tgkqi~s~~l 556 (880)
T 4ayb_A 478 EIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQILGV-ADVKIDLGEPAILAPREYYTGKQVVSAFL 556 (880)
T ss_dssp HHSBSGGGCBCSSSSSBCSCCCSHHHHHHHHHTSSSCEECHHHHHHHHTT-SCCCCCCCSCSEESSSEEEEHHHHHHTTS
T ss_pred HHHhChhccccCCCCCccccccccHHHHhHHhhcCcccCCHHHHhhhhcc-cceecccCccceecceeEeccceEEEEEe
Confidence 489999999999999999998 3458999999999864 56778899999999999999999999999
Q ss_pred CCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCC-ccHHHHHHHHhCHHHHHHHHHHHHHH
Q psy3015 112 PGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSS-GSLLHICFLELGHEVCGRFYGNIQTV 190 (1791)
Q Consensus 112 P~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~-~gLih~i~~~yG~~~a~~fL~~lqrL 190 (1791)
|+++++......... ....+.+.++.|++|+|+||+|++|++||+++|++. ++|+|.+|++||+++|..|||++++|
T Consensus 557 p~~~~~~~~~~~~~~--~~~~~~~~~~~~~~v~i~~g~l~~g~ldk~~lg~~~~~~li~~i~~~~G~~~t~~~ld~l~~l 634 (880)
T 4ayb_A 557 PKDFNFHGQANVSSG--PRLCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRV 634 (880)
T ss_dssp CTTCCEEEECTTCSG--GGCCSSSCCTTSCEEEEETTEEEECCCSTTTSSTTCTTSHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred cccccccceeEeecC--CccccCccCCCcceEEEeCceeeeeeecchhhcccccceeeehhhhhcccHHHHHHHHHHHHH
Confidence 998888543221111 011223456889999999999999999999999764 78999999999999999999999999
Q ss_pred HHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHH
Q psy3015 191 VNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKA 270 (1791)
Q Consensus 191 ~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 270 (1791)
+++|++.+|||||++|+++++++.+++.+.+++|+
T Consensus 635 g~~~lt~~GfSigi~Di~i~~~~~~~i~~~i~~a~--------------------------------------------- 669 (880)
T 4ayb_A 635 FIRFVELQGFTMRLEDVSLGDDVKKEIYNEIDRAK--------------------------------------------- 669 (880)
T ss_dssp HHHHHHHHCCCCCGGGGCCCHHHHHHHHHHHHHHH---------------------------------------------
T ss_pred HHHHHHhcCCcccccccccchhhHHHHHHHHHHHH---------------------------------------------
Confidence 99999999999999999999998888777777666
Q ss_pred HHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCChHHHHhhcCCCcchhhHHHHHhhcc
Q psy3015 271 KEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVG 350 (1791)
Q Consensus 271 ~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~~~N~l~~Mv~sGSKGS~iNisQi~acvG 350 (1791)
.+|.+++++++.|.++..+|++.++++|++++.+|+++++.+++.+.+++++.|++++|+.||||||.+|++||+||||
T Consensus 670 -~~v~~i~~~~~~g~l~~~~g~~~~e~~e~~v~~~l~~~~~~~~~~~~~~l~~~N~i~mMa~SGARGS~~ni~Qlagm~G 748 (880)
T 4ayb_A 670 -VEVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLG 748 (880)
T ss_dssp -HHHHHHHHHHHTTCCCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTSSCCSTTHHHHHTCCE
T ss_pred -HHHHHHHHHHHcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHhhcCccCCHHHHHHHHhccc
Confidence 4666778888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhc
Q psy3015 351 QQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAME 430 (1791)
Q Consensus 351 QQ~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LE 430 (1791)
||+++|+|||+||.+||||||.++|.+|+|+|||.|||++||+|+|||||||||||||+|||||||+||||||||||+||
T Consensus 749 qq~~~G~RIprg~~~rtLP~f~~~d~~p~a~GfI~ssF~eGLtp~EyF~ht~ggRkGL~DTAlKTA~SGYLtRRLVdv~q 828 (880)
T 4ayb_A 749 QQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALS 828 (880)
T ss_dssp ECBSSSSBSCCSBTTBSSTTSCTTCCSTTTTSEECSCTTTCCCHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHT
T ss_pred ccccCCccCcCCCccCCCCCCCCCCCCcccCCeEhhcccCCCCHHHHHHhhhhhhhhHHhcchhhchhhHHHHHHHHHHc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEeecCcEEecCCceEEEEecCCCCCcccccccc
Q psy3015 431 SVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQR 466 (1791)
Q Consensus 431 Dl~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~~~ 466 (1791)
||+|+|||||||++|+||||.|||||+||.+.+.++
T Consensus 829 Dv~V~yDgTVR~~~g~ivqf~YGeDgldp~~~~~~~ 864 (880)
T 4ayb_A 829 DLRAEYDGTVRSLYGEVIQVAYGDDGVFPMYSAHGK 864 (880)
T ss_dssp TEEECTTSCEEETTTEEEESSTTTTCBCTTTSBTTB
T ss_pred CEEEecCCCccCCCCcEEEEecCCcccceeecccCC
Confidence 999999999999999999999999999998876644
No 6
>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=6.2e-78 Score=793.34 Aligned_cols=302 Identities=21% Similarity=0.223 Sum_probs=249.3
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------cC--------ccccHhHHHHHHhcC--CccC-CCCCC---------
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------HG--------SARNQEQMMNILMFL--PIWD-GKMPQ--------- 91 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~G--------s~~~rddlmqLlm~~--~~~~-~~lP~--------- 91 (1791)
.+|++++|+++|++++|++++ .. .|+++++++++++.. +... ..+.+
T Consensus 501 ~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~~i~l~a~i~~~~~~~~~g~~k 580 (1265)
T 1hqm_D 501 IQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLK 580 (1265)
T ss_dssp SSSBSSSSSSSCSSSSCSSCCCTTHHHHHHHTTCCCCCCCCCCCCSSCCTHHHHHTTSSCCSSCCCSSSCCSTTSSCCCC
T ss_pred HHhCccccEecCCCCCeeEeeeccccceeEEeccccCCccCCCcccCCHHHHHHHHHCCCCCCCCceEEecccccccccc
Confidence 799999999999999999998 11 489999999987641 1000 01111
Q ss_pred -----Cc-------------------eeCC--CCcccHhhhhhhcCCCCccccccCCCCCCCCCCCCCCCCCCCCCeEEE
Q psy3015 92 -----PC-------------------ILKP--KPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVV 145 (1791)
Q Consensus 92 -----Pa-------------------IlKP--~~LWTGKQIfS~iLP~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI 145 (1791)
|+ .+|| ..+|||||+||++||++++ +..+| +|-. +
T Consensus 581 ~~~t~P~k~I~~~~~g~~~~q~~~~~~~k~~~~~t~~Gr~if~~~lp~~~~----~~~~p-------------~~~~--~ 641 (1265)
T 1hqm_D 581 FVFANPDEALLAVAHGLLDLQDTVTTRYLGRRLETNPGRILFARIVGEAVG----DEKVA-------------QELI--Q 641 (1265)
T ss_dssp CTTTCSHHHHHHHHTTSSCSSSCCCCEESSSEECCCHHHHHHHHHHHHHTT----CTTTT-------------TTSS--C
T ss_pred cccccccccccccccCccccccccceeccccceeccCCceEEeeecccccc----ccCCC-------------CCCc--e
Confidence 11 1244 5789999999999987555 11112 1111 1
Q ss_pred EcCeEEEEeeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcC-cccccCCcccChhhHHHHHHHHHHH
Q psy3015 146 EHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVVNNWLLLEG-HSIGIGDTIADPQTYLEIQMAIKKA 224 (1791)
Q Consensus 146 ~nGeLl~G~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~~~~L~~~G-FSiGi~D~i~~~~t~~~i~~~i~~a 224 (1791)
++|++||+++| +|||.+|++||+++|..|||++++|+++|++++| ||||++|++++++. .++|++|
T Consensus 642 -----~ngvldKk~lG----~LI~~i~~~~G~~~a~~~ld~l~~l~~~~lt~~G~fSigi~D~~~~~~k----~~~i~~a 708 (1265)
T 1hqm_D 642 -----MDVPQEKNSLK----DLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGIITIGIDDAVIPEEK----QRYLEEA 708 (1265)
T ss_dssp -----CSSCCCSSHHH----HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHTTCCCCSSSSCCCCSTT----TTHHHHH
T ss_pred -----EeeeecHHHHH----HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhCCCceEeeccccCCHHH----HHHHHHH
Confidence 34899999997 5999999999999999999999999999999999 99999999999862 4556555
Q ss_pred HHHHHHHHHHHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHH
Q psy3015 225 KEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNR 304 (1791)
Q Consensus 225 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~ 304 (1791)
+ ++|.+++++++.|.+ .+++++++|..
T Consensus 709 ~----------------------------------------------~~v~~i~~~y~~g~l-------t~~e~~~~v~~ 735 (1265)
T 1hqm_D 709 D----------------------------------------------RKLRQIEQAYEMGFL-------TDRERYDQVIQ 735 (1265)
T ss_dssp H----------------------------------------------HHHHHHHTTTTSSSS-------CHHHHHHHHHH
T ss_pred H----------------------------------------------HHHHHHHHHHHcCCC-------cHHHHHHHHHH
Confidence 5 455556666655543 36778999999
Q ss_pred HHHHHHhhhhhhhhhccC---CCChHHHHhhcCCCcchhhHHHHHhhccCcc-cCCceeccCCccCCCCCCCCCCCCCcc
Q psy3015 305 ILNDARDKTGGSAKKSLT---EYNNLKAMVVAGSKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTLPHFIKDDYGPES 380 (1791)
Q Consensus 305 iLn~~rd~~g~~~~~~l~---~~N~l~~Mv~sGSKGS~iNisQi~acvGQQ~-veGkRIp~gf~~RtLPhF~~~d~~p~s 380 (1791)
+|+++++.+++.+++++. +.|++++|+.||||||.+|++||+||+|||. .+|++++
T Consensus 736 ~~~~~~d~~~~~~~~~l~~~~~~N~i~~Ma~SGAKGS~~ni~Ql~g~~G~ma~~~G~~i~-------------------- 795 (1265)
T 1hqm_D 736 LWTETTEKVTQAVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFE-------------------- 795 (1265)
T ss_dssp HHHHHHHHHHHHHHHHHHHSCSSSCTTTTTTTSSSCCHHHHHHHSSCCCCCCCTTSCCCS--------------------
T ss_pred HHHHHHHHHHHHHHHHhcccCCCCcHHHHHHhcCCcCHHHHHHHHhhccccccCCCCccC--------------------
Confidence 999999999999999998 8999999999999999999999999999995 6666542
Q ss_pred cceeccccccCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcceEEeecCcEEecCCceEEEEecCCCCCcc
Q psy3015 381 RGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGE 460 (1791)
Q Consensus 381 rGFV~nSfl~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LEDl~V~YDgTVRns~G~IVQF~YGeDGlD~~ 460 (1791)
++|.|||++||+|+|||||||||||||||||||||+||||||||||+|||++|.||++ ||+||+|+.
T Consensus 796 -~pI~ssF~eGLtp~EyFfhtmggReGLiDTAvKTA~SGYLqRRLVkv~qDv~V~~ddc------------~t~dGi~v~ 862 (1265)
T 1hqm_D 796 -VPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADC------------GTTKYISVP 862 (1265)
T ss_dssp -CCCCCCBTTBCTTCTHHHHHHHHTTHHHHHTHHHHTSSSTHHHHHHHSCSCCCCSCCC------------CCCCCEECC
T ss_pred -cccccccccCCChHHhheecccccccchhhhhhcccCCcceeeeeeecceEEEEECCC------------CCCCCEEEE
Confidence 4699999999999999999999999999999999999999999999999999999986 599999998
Q ss_pred cccc
Q psy3015 461 AVEH 464 (1791)
Q Consensus 461 ~~e~ 464 (1791)
.++.
T Consensus 863 ~~~~ 866 (1265)
T 1hqm_D 863 LFQM 866 (1265)
T ss_dssp SEEC
T ss_pred Eeec
Confidence 8876
No 7
>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=5.1e-78 Score=790.63 Aligned_cols=310 Identities=20% Similarity=0.233 Sum_probs=243.8
Q ss_pred ceEEeeccCCCCCCCCCeEEe-------------c--------CccccHhHHHHHHhc----------C--CccC-----
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-------------H--------GSARNQEQMMNILMF----------L--PIWD----- 86 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-------------~--------Gs~~~rddlmqLlm~----------~--~~~~----- 86 (1791)
.+|++++|+++|++++|++++ . ..|.++++++++++. + +.|+
T Consensus 761 ~LM~~~~nilsP~~G~Pi~~~~QD~vlG~y~LT~~~~~~~~~g~~F~~~~e~~~ay~~~~~~l~~~i~v~~~~~~~~~~~ 840 (1524)
T 2a6h_D 761 IQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLK 840 (1524)
T ss_dssp HHSBTTTCCBCSSSSSBSSCCCHHHHHHHHHHHCCCCCCCCSCCCTTSCHHHHHHHHHHHHTTSSCSSCCCSSCCHHHHH
T ss_pred HHhCCccceecCCCCCeeeeecccchhhheecccccccccCCCceeCCHHHHHHHHhcCCcCcCCceEEecccccccccc
Confidence 479999999999999999998 1 147889999987642 1 1121
Q ss_pred CCCCCC--ceeCCCCcccHhhhhhhc----CCCCcccccc-------CCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEE
Q psy3015 87 GKMPQP--CILKPKPLWTGKQVFSLI----IPGNVNMTRT-------HSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMG 153 (1791)
Q Consensus 87 ~~lP~P--aIlKP~~LWTGKQIfS~i----LP~~inl~~~-------~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G 153 (1791)
+.+|+| ||+|| |||||+++.+ ++. ++..+ +...|.... .+..|+|- ..++|
T Consensus 841 ~~~p~P~~aIlKp---wtGKQi~~~~~~~~I~~--~~~~tt~Gr~ifn~~lp~~l~----~~~~P~d~-------~~inG 904 (1524)
T 2a6h_D 841 YVFANPDEALLAV---AHGIVDLQDVVTVRYMG--KRLETSPGRILFARIVAEAVE----DEKVAWEL-------IQLDV 904 (1524)
T ss_dssp CEESSHHHHHHHH---HTTSSCTTSCCEEECSS--CEECCCHHHHHHHHHHHHHSS----CHHHHHHT-------CCTTS
T ss_pred cccCCchhhhcCC---CCCccccccccccceec--ceeecccchhhHHHHhhhhcc----cccCCCcc-------cceec
Confidence 233555 48988 8888888742 111 11000 000000000 00001110 11248
Q ss_pred eeccccccCCCccHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHH
Q psy3015 154 ILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQ 233 (1791)
Q Consensus 154 ~ldKk~vG~s~~gLih~i~~~yG~~~a~~fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~ 233 (1791)
++||+++| +|||.||++||+++|..|||++++|+++|++++||||||+|++++++ +.++|++|+
T Consensus 905 vLdKk~LG----~LI~~i~~~yG~~~t~~fLD~lk~Lg~~~lt~~GfSIGI~Dlii~~~----K~eiI~eA~-------- 968 (1524)
T 2a6h_D 905 PQEKNSLK----DLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEE----KKQYLEEAD-------- 968 (1524)
T ss_dssp CCCHHHHH----HHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHTCCCCSTTSCCCTT----HHHHHHHHH--------
T ss_pred eecHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCceeehhhccCCHH----HHHHHHHHH--------
Confidence 99999997 59999999999999999999999999999999999999999999986 456666665
Q ss_pred HHhcCCCCCCCCcccccCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhh
Q psy3015 234 KAHNMDLEPTPGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKT 313 (1791)
Q Consensus 234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~ 313 (1791)
++|.+++++++.|.+ ..+.+++++..+|+++++.+
T Consensus 969 --------------------------------------~~v~~i~~~y~~G~l-------t~~Er~~~Vi~iw~~a~d~v 1003 (1524)
T 2a6h_D 969 --------------------------------------RKLLQIEQAYEMGFL-------TDRERYDQILQLWTETTEKV 1003 (1524)
T ss_dssp --------------------------------------HHHHHHHHHHHTTCS-------CHHHHHHHHHHHHHHHHHHH
T ss_pred --------------------------------------HHHHHHHHHHHcCCC-------CHHHHHHHHHHHHHHHHHHH
Confidence 456666777777654 24557889999999999999
Q ss_pred hhhhhhccC---CCChHHHHhhcCCCcchhhHHHHHhhccCc-ccCCceeccCCccCCCCCCCCCCCCCcccceeccccc
Q psy3015 314 GGSAKKSLT---EYNNLKAMVVAGSKGSNINISQVIACVGQQ-NVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYL 389 (1791)
Q Consensus 314 g~~~~~~l~---~~N~l~~Mv~sGSKGS~iNisQi~acvGQQ-~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl 389 (1791)
++.+++++. +.|++++|+.||||||.+|++||+||+||| +.+|++||. | |.|||+
T Consensus 1004 ~~~~~~~L~~~~~~N~i~~Ma~SGAKGS~~NI~Ql~gmrGqma~p~GkiIp~-------P--------------I~ssF~ 1062 (1524)
T 2a6h_D 1004 TQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEV-------P--------------VRSSFR 1062 (1524)
T ss_dssp HHHHHHHHHHTCTTCHHHHHHHSSSSCCHHHHHHHTSCCCCCBCSSSCBCSS-------C--------------CCCCSS
T ss_pred HHHHHHhhcccCCCCCHHHHHHhcCCcCHHHHHHHHhhccccccCCCCCccc-------c--------------cccccc
Confidence 999999998 899999999999999999999999999996 578888762 2 999999
Q ss_pred cCCChhhhhhhcccCcccchhcccccCCcchhHHHHHHhhcceEEeecCcEEecCCceEEEEecCCCCCcccccc
Q psy3015 390 AGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEH 464 (1791)
Q Consensus 390 ~GL~P~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LEDl~V~YDgTVRns~G~IVQF~YGeDGlD~~~~e~ 464 (1791)
+||+|+|||||||||||||||||||||+||||||||||+|||++|.||++ +|+||+|+..+..
T Consensus 1063 eGLtp~EyFfhtmGgReGLvDTAvKTAdSGYLqRRLVkv~qDviVr~dDc------------gt~dGi~v~~~~~ 1125 (1524)
T 2a6h_D 1063 EGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADC------------GTTNYISVPLFQP 1125 (1524)
T ss_dssp SCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCSCC------------CCCCCEEEESBCS
T ss_pred cCCChHHhheecccccCCccccceeeccCCcceeeeeeecceeEEEeCCC------------CCCCCeEEEEeec
Confidence 99999999999999999999999999999999999999999999999987 3888888876543
No 8
>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=8.6e-70 Score=702.89 Aligned_cols=281 Identities=22% Similarity=0.327 Sum_probs=229.2
Q ss_pred ceEEeeccCCCCCCCCCeEEe-----cC----------------ccccHhHHHHHHhc--CC---ccCCCCCC-------
Q psy3015 45 DWMLVTVLPVPPLSVRPAVVM-----HG----------------SARNQEQMMNILMF--LP---IWDGKMPQ------- 91 (1791)
Q Consensus 45 ~~mlv~~~iVsP~~~rP~~~i-----~G----------------s~~~rddlmqLlm~--~~---~~~~~lP~------- 91 (1791)
.+|++++|+++|++++|++++ .| .|.+.+++++++.. +. .+...+|.
T Consensus 482 ~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~lT~~~~~~~~~~~~F~~~~ev~~al~~g~v~l~a~i~vr~~~~~~~~~g 561 (1407)
T 3lu0_D 482 ALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANG 561 (1407)
T ss_dssp TSSBTTTCCSCSSSSSCSSCCCSHHHHHHHHHSCCCCCSCCSCCCCSSCSHHHHHHHHSSSSSSSCSSSSCCCCSCSHHH
T ss_pred HHHhCccccccCCCCCceeeecccchheeEEeecccccccCCcceeCCHHHHHHHHHcCCCCCCCeeEEecCccccCcCC
Confidence 689999999999999999998 11 16678899887642 11 01112222
Q ss_pred --CceeCCCCcccHhhhhhhcCCCCccccccCCCCCCCCCCCCCCCCCCCCCeEEEEcCeEEEEeeccccccCCCccHHH
Q psy3015 92 --PCILKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLH 169 (1791)
Q Consensus 92 --PaIlKP~~LWTGKQIfS~iLP~~inl~~~~~~~~~~~~~~~~~~~~~~d~~ViI~nGeLl~G~ldKk~vG~s~~gLih 169 (1791)
|...|+.++||||||||++||+++++ ++++|++||+++| +|||
T Consensus 562 ~~~~~~~~~~tt~Gr~ifs~ilP~~~~~-------------------------------~~ing~l~KK~lg----~LI~ 606 (1407)
T 3lu0_D 562 ELVAKTSLKDTTVGRAILWMIVPKGLPY-------------------------------SIVNQALGKKAIS----KMLN 606 (1407)
T ss_dssp HHHHTTTSCCSSSHHHHHHHHGGGSSCC-------------------------------TTTTTCCSSSTTT----THHH
T ss_pred cccccceeeecCCccccHHhhCCCCCCc-------------------------------eeeecccchhhHH----HHHH
Confidence 11235678999999999999987655 1345899999997 6999
Q ss_pred HHHHHhCHHHHHHHHHHHHHHHHHHHHhcCcccccCCcccChhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccc
Q psy3015 170 ICFLELGHEVCGRFYGNIQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIG 249 (1791)
Q Consensus 170 ~i~~~yG~~~a~~fL~~lqrL~~~~L~~~GFSiGi~D~i~~~~t~~~i~~~i~~ak~~~~~~~~~~~~~~~~~~~~~~~~ 249 (1791)
.+|++||++.|..|||++++|+++|++.+|||||++|+++|++. .++|++|+
T Consensus 607 ~i~~~~G~~~t~~flD~lk~Lgf~~at~~GfSIgI~D~~ip~~K----~~iI~~A~------------------------ 658 (1407)
T 3lu0_D 607 TCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKK----HEIISEAE------------------------ 658 (1407)
T ss_dssp HHHHHSCSHHHHHHHHHHHHHHHHHHHHHTCCCCSTTSCCCTTH----HHHHHHHH------------------------
T ss_pred HHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEEeeccCccChHH----HHHHHHHH------------------------
Confidence 99999999999999999999999999999999999999988764 45566555
Q ss_pred cCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhhhccC-------
Q psy3015 250 IGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLT------- 322 (1791)
Q Consensus 250 ~~~~~~~~~~~~~~~~~~~~~~~~v~~~i~~~~~~~L~~~pg~~~~~~fE~~vn~iLn~~rd~~g~~~~~~l~------- 322 (1791)
++|.+++++++.|.|+..+ .+++|..+|+++++.+++.+++++.
T Consensus 659 ----------------------~eV~ei~~~y~~G~lt~~e-------r~~kVi~iw~~a~e~v~~~m~~~l~~~~~~d~ 709 (1407)
T 3lu0_D 659 ----------------------AEVAEIQEQFQSGLVTAGE-------RYNKVIDIWAAANDRVSKAMMDNLQTETVINR 709 (1407)
T ss_dssp ----------------------THHHHHHHHHHHTSCCSST-------TTTTHHHHHHTHHHHHHHHHHTTHHHH-----
T ss_pred ----------------------HHHHHHHHHHHcCCCccch-------HHHHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 5667777788888776543 3567888888888888777776653
Q ss_pred --------CCChHHHHhhcCCCcchhhHHHHHhhccCcccCCceeccCCccCCCCCCCCCCCCCcccceeccccccCCCh
Q psy3015 323 --------EYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTP 394 (1791)
Q Consensus 323 --------~~N~l~~Mv~sGSKGS~iNisQi~acvGQQ~veGkRIp~gf~~RtLPhF~~~d~~p~srGFV~nSfl~GL~P 394 (1791)
+.|++++|+.||||||.+||+||+||+|||.....+ +. ..+|.|||++||+|
T Consensus 710 ~G~~~~l~~~N~i~mMa~SGARGS~~qI~QLaGmrGlmakpdG~-------------------ii-e~PI~ssFreGLtp 769 (1407)
T 3lu0_D 710 DGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGS-------------------II-ETPITANFREGLNV 769 (1407)
T ss_dssp -------CSCCHHHHHHHSSSSCCTTHHHHHSSCCCCCBCSSSC-------------------BC-SSCCCCCSSSCCCH
T ss_pred cccccccCCCCChheeeeccccCCHHHHHHHHHhcCCccCCCCC-------------------Cc-chhhhcccccCCCH
Confidence 579999999999999999999999999999742221 22 23577999999999
Q ss_pred hhhhhhcccCcccchhcccccCCcchhHHHHHHhhcceEEeec
Q psy3015 395 SEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVHYD 437 (1791)
Q Consensus 395 ~EfFFHaMaGREGLIDTAVKTaeTGYlQRrLvK~LEDl~V~YD 437 (1791)
+|||||||||||||+|||||||+||||||||||+|||++|.++
T Consensus 770 ~EyFfst~GaRKGL~DTALKTAdSGYLTRRLVdv~QDviV~e~ 812 (1407)
T 3lu0_D 770 LQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED 812 (1407)
T ss_dssp HHHHHHHHHHHHHHHHTTTTTTCTTTTTHHHHTTSTTCCBCCC
T ss_pred HHhhhhcccchhhhhhhhhhcccchhHHHHHHHhhcceEEEec
Confidence 9999999999999999999999999999999999999999754
No 9
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Probab=100.00 E-value=4.5e-43 Score=461.25 Aligned_cols=372 Identities=20% Similarity=0.262 Sum_probs=222.7
Q ss_pred ccCCHHHHHHHHHHHhhhccceecccccccc-ccCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEe
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQ-NVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFH 1066 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~Q-sV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffh 1066 (1791)
++.|+..+|..+|++||..|++|+.+|+||| .++|++|| +| |.|||++||||+|||||
T Consensus 1015 ~~~N~i~~Ma~SGAKGS~~NI~Ql~gmrGqma~p~GkiIp-------~P--------------I~ssF~eGLtp~EyFfh 1073 (1524)
T 2a6h_D 1015 YPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFE-------VP--------------VRSSFREGLTVLEYFIS 1073 (1524)
T ss_dssp CTTCHHHHHHHSSSSCCHHHHHHHTSCCCCCBCSSSCBCS-------SC--------------CCCCSSSCCCSHHHHHH
T ss_pred CCCCCHHHHHHhcCCcCHHHHHHHHhhccccccCCCCCcc-------cc--------------cccccccCCChHHhhee
Confidence 3799999999999999999999999999995 59999998 34 68999999999999999
Q ss_pred ecCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeee-eccCC-C-CCCCCcccc----eeee
Q psy3015 1067 AMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNV-YYEMP-D-FDPTRISPW----LLRI 1139 (1791)
Q Consensus 1067 AMgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf-~Yg~d-g-~D~~~~~~w----vlr~ 1139 (1791)
||||||||+|||+|||++|||||||||++||++|.||.+. .+||-.+.. .++.+ + ++...+++. +.|.
T Consensus 1074 tmGgReGLvDTAvKTAdSGYLqRRLVkv~qDviVr~dDcg-----t~dGi~v~~~~~g~~~~~~~~~~i~~l~~ri~gR~ 1148 (1524)
T 2a6h_D 1074 SHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCG-----TTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRV 1148 (1524)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCSCCC-----CCCCEEEESBCSCSSSSCCCBCCHHHHHHHHTTCB
T ss_pred cccccCCccccceeeccCCcceeeeeeecceeEEEeCCCC-----CCCCeEEEEeecCCccccchhHHHHHHHHHHhccc
Confidence 9999999999999999999999999999999999999742 334544432 23321 1 010000000 0000
Q ss_pred e--------ccc---cccccccCCHHHHHHHHhhccCCC-ccc--ccCCcccccceEEE--E------EecCccc----c
Q psy3015 1140 E--------LDR---KRMTDKKLTMEAISEKINAGFGDD-LNC--IFNDDNAEKLVLRI--R------IMNSDDS----K 1193 (1791)
Q Consensus 1140 ~--------Ld~---~~m~dk~l~~~~I~~~I~~~~~~d-l~~--i~~d~n~~~l~~ri--r------i~~~~~~----~ 1193 (1791)
. +|. +.+..++-.+ .++++.+. +.+ +.+ .+.......+|..+ + +....+. .
T Consensus 1149 ~~~di~~~~~~p~~~e~i~~~~~~I--~~~~i~~~-gi~~v~iRS~ltC~s~~gvc~~CYgr~La~~~~v~~GeaVGiia 1225 (1524)
T 2a6h_D 1149 LAREVEVLGVRLEEGRYLSMDDVHL--LIKAAEAG-EIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVA 1225 (1524)
T ss_dssp BSSCEECSSCEECTTCBCCTTTTTH--HHHHHHHT-SCSEEEECCGGGCCCSSCBCHHHHCSCSSSSSSCCTTCCHHHHH
T ss_pred chhhhhhhccCCCcCcEEeCCCCee--hHHHHHHc-CCCcccccccccHHHHHHHHHHHhccccccCCccccccceeehh
Confidence 0 110 0111111111 22222211 000 000 00000000000000 0 0000000 0
Q ss_pred ccchhHHHHhhhhhhhHHHHhhccc-ccceeccccccceEE-----------------EeccccCCCceEEEccCCcccc
Q psy3015 1194 MQDEEDAVDKMEDDMFLRCIEANML-SDMTLQGIEAIGKVY-----------------MHLPQTDSKKRIIITESGEFKA 1255 (1791)
Q Consensus 1194 ~~~~ee~~~~~~dr~~Lr~i~~~il-~~~~LkGi~~I~kv~-----------------i~lp~~~n~~RiI~na~~~f~~ 1255 (1791)
.+...|--.++.-++|=- .... ..=...|+|++.+++ +.+...++..+++..... .
T Consensus 1226 AQSIGEPgTQlTlrTFH~---gGv~~~~dIt~GlPRv~El~eARkpk~~aiI~ei~G~V~i~~~~~~r~i~i~~~~---~ 1299 (1524)
T 2a6h_D 1226 AQSIGEPGTQLTMRTFHT---GGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEG---F 1299 (1524)
T ss_dssp HHHHHSGGGTCCCC--------------CCCCSHHHHHHHHTTCCCSSBCCBCSSCEEEEECCCSSCEEEEEECSS---C
T ss_pred hhccCCCcccccceeeee---ccccccccccccCcchhhheecccCCCcceEEEeceEEEEeecCCceEEEEEcCC---c
Confidence 000000001111111100 0000 000113444432211 001111112223322211 0
Q ss_pred cceEEEeecccchhcccccCCCCc---ccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhhcccc
Q psy3015 1256 IADWLLETDGTSLMKVLSERDVDP---VRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTA 1332 (1791)
Q Consensus 1256 ~~e~~L~teG~nL~~vl~~~dVDp---~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD~MT~ 1332 (1791)
..+|.+. .+..+ .+-.-+.+.. -.--++|++|+++++||||+|++|++|++.||..||++||+|||++|+|+||+
T Consensus 1300 ~~~~~ip-~~~~l-~V~~gd~v~~g~~lteG~~~~~dil~v~Giea~~~~iv~Eiq~Vyr~QGv~I~dKHIevIvrqM~~ 1377 (1524)
T 2a6h_D 1300 SKEYKLP-KEARL-LVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMK 1377 (1524)
T ss_dssp EEEEEEC-TTCCC-CCCTTSEECTTCBSSSSBCCHHHHHHHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTS
T ss_pred eeEEecC-CceEE-EEecCCeeecCeEEecCCCCchhheeecCHHHHHHHHHHHHHHHHHhcCcccchhHHHHHHHHHhc
Confidence 1122210 11000 0000001111 11125899999999999999999999999999999999999999999999965
Q ss_pred ----------------------------------------cCcccccccccccccccccccccchhhhHHHHHHHhhccC
Q psy3015 1333 ----------------------------------------KGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAE 1372 (1791)
Q Consensus 1333 ----------------------------------------~G~l~~itR~Gi~rq~~S~L~raSFEeTv~iL~~AA~~ge 1372 (1791)
++.++||||++++ ..|+|++||||+|.++|.+||++|+
T Consensus 1378 kv~i~~~Gdt~~l~Ge~v~~~~~~~~n~~~~~~g~~~a~~~~~llGITkasL~--t~SfLsaASFqeTtrvLt~AAi~Gk 1455 (1524)
T 2a6h_D 1378 YVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALS--TKSWLSAASFQNTTHVLTEAAIAGK 1455 (1524)
T ss_dssp EEEEEECSSSCSSCEEEHHHHHHHHHHHHTTSCSCCCCEEEECCCCHHHHHHS--CSCHHHHHHSSCHHHHHHHHHHTTE
T ss_pred eeEEecCCCccCCCCceeeHHHHHHHHHHHHHcCCCcceeeeeeeeeeecccc--cCChhhhcChHHHHHHHHHHHhcCC
Confidence 3567899999997 6799999999999999999999999
Q ss_pred CCCCCccccceeccccccCCcchhhh
Q psy3015 1373 ADPMRGVSENIIMGQLPRMGTGCFDL 1398 (1791)
Q Consensus 1373 ~D~lkgVsenIi~Gq~~~lGTGaFd~ 1398 (1791)
.|+|+|++||||+|+++|+|||.|++
T Consensus 1456 ~D~L~GlkENVIiG~lIPaGTG~~~~ 1481 (1524)
T 2a6h_D 1456 KDELIGLKENVILGRLIPAGTGSDFV 1481 (1524)
T ss_dssp EEECCSHHHHHHTTCCCSSSTTCTTT
T ss_pred CCCCCCcHHHeeecCCccCCcCchhh
Confidence 99999999999999999999998876
No 10
>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=1.1e-40 Score=404.98 Aligned_cols=356 Identities=25% Similarity=0.376 Sum_probs=278.4
Q ss_pred cchhHHHHhcHHHHHHHHhHhhhhhHHHHhhccCCHHHHHHHHHHHhhhccceeccc--cccc---cc------------
Q psy3015 957 DQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQVIA--CVGQ---QN------------ 1019 (1791)
Q Consensus 957 ~~~~~~~~~~~~~~~~~~~Rs~L~sk~v~~~~rln~~a~~~i~gei~~~~~~sqv~~--mvG~---Qs------------ 1019 (1791)
+.+-++..+++..++...+...|..+...+.+.+++..++|+.|.+...|..+++.| +||. ||
T Consensus 10 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~lv~pGEAVGiIAAQSIGEPgTQlTLrT 89 (395)
T 4ayb_C 10 KSYLEEKVKQASNILPQKIVEDLKNLISNKEVLVTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRT 89 (395)
T ss_dssp HHHHHHHHHHHHTTSCSHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHTBCCTTCCHHHHHHHHHHHHHHTCC---
T ss_pred chhHHHHHHhhcccccHHHHHHHHHHhccceeecCHHHHHHHHHHHHHHHHHhcCCCCchHhHHHHhhcCCchhhhcccc
Confidence 334445555566566566667778887888889999999999999999999999999 7777 88
Q ss_pred -----cCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEeecCCCCccchhhhccchhH-HHHHHHH-
Q psy3015 1020 -----VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETV-NVLVFLF- 1092 (1791)
Q Consensus 1020 -----V~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhAMgGREGLiDTAvKTAEtG-YIqRRLv- 1092 (1791)
|++++||.|+|| |.|+ .|..+..+||+..++. .|...++.+.+ .+.+++.
T Consensus 90 FH~gGva~~nvT~GlPR--l~Ei-------------~~a~k~~~tp~~~i~l--------~~~~~~~~e~~~~~~~~ie~ 146 (395)
T 4ayb_C 90 FHFAGIRELNVTLGLPR--LIEI-------------VDAKKVPSTPMMTIYL--------TDEYKHDKEKALEVARKLEY 146 (395)
T ss_dssp ----------CCCSHHH--HHHH-------------HTCCSSCSSCEEEECC--------TTTGGGCHHHHHHHHHHHHC
T ss_pred ceeeeecceeeecCccc--eEEe-------------cccccCCCCCceEEEe--------cccccccHHHHHhhccceeE
Confidence 888999999999 9999 7899999999999998 56665666665 4455443
Q ss_pred ----HHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcccceeeeeccccccccccCCHHHHHHHHhhccCCCc
Q psy3015 1093 ----QVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDL 1168 (1791)
Q Consensus 1093 ----k~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~wvlr~~Ld~~~m~dk~l~~~~I~~~I~~~~~~dl 1168 (1791)
+......+.| .+|....++|.+.+.+++++++++...+.+....+.
T Consensus 147 ~~~~~~~~~~~i~~------------------------------~~~~~~~~~d~~~~~~~~~~~~~i~~~~~~~~~~~~ 196 (395)
T 4ayb_C 147 TKIENVVSSTSIDI------------------------------ASMSIILQLDNEMLKDKGVTVDDVKKAINRLKLGEF 196 (395)
T ss_dssp CCHHHHEEEEEEET------------------------------TTTEEEEEECGGGGBTTBCHHHHHHHHHHHSCCSSE
T ss_pred EEccceeeeeEEee------------------------------cccceeeehhhhhhhhcCccHHHHHHHHhhhccCcE
Confidence 2222222211 256667788999999999999999998876554433
Q ss_pred ccccCCcccccceEEEEEecCccccccchhHHHHhhhhhhhHHHHhhcccccceeccccccceEEEeccccCCCceEEEc
Q psy3015 1169 NCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIIT 1248 (1791)
Q Consensus 1169 ~~i~~d~n~~~l~~riri~~~~~~~~~~~ee~~~~~~dr~~Lr~i~~~il~~~~LkGi~~I~kv~i~lp~~~n~~RiI~n 1248 (1791)
.+...+. ..+++.....+.... +.+ +|. .+.+..|+|++++.++.+..
T Consensus 197 ~~~~~~~----~~~~~~~~~~~~v~~--------l~~----~~~----~~~~~~i~gi~gi~r~~~~~------------ 244 (395)
T 4ayb_C 197 VIDESEG----NTLNISFANIDSIAA--------LFK----LRD----KILNTKIKGIKGIKRAIVQK------------ 244 (395)
T ss_dssp EEEECSS----EEEEEECCSSCCCCC--------THH----HHH----HHHHHCCCSSSSCCEEEEEE------------
T ss_pred EEecccC----cEEEeecCCCchHHH--------HHH----HHh----hccccEEecccceeEEEEec------------
Confidence 2222211 112222111111100 000 111 12246789999999886641
Q ss_pred cCCcccccceEEEeecccchhcccccCCCCcccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhhhh
Q psy3015 1249 ESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCD 1328 (1791)
Q Consensus 1249 a~~~f~~~~e~~L~teG~nL~~vl~~~dVDp~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LLaD 1328 (1791)
...+|++.|+|.|+.+++..+++|+.++.|||+++|+++|||||+|++|++|++.||..+|++||+|||+||||
T Consensus 245 ------~~~~~~~~t~g~~l~~~~~~~~vd~~~~~sn~i~eI~~vlGiEAar~~iv~Ei~~V~~~~Gv~In~rHi~li~d 318 (395)
T 4ayb_C 245 ------KGDEYIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVAD 318 (395)
T ss_dssp ------ETTEEEEEEESCCHHHHTTSTTCCTTTCEESCTTHHHHHHCHHHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHH
T ss_pred ------cCCEEEEEecCCCceeeeEeecccccccccCcchhhhhhhhHHHHHHHHHHhHHHHHhccCceechHHhhhhhh
Confidence 12479999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCcccccccccccccccccccccchhhhHHHHHHHhhccCCCCCCccccceeccccccCCcchhhhhcccc
Q psy3015 1329 VMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAE 1403 (1791)
Q Consensus 1329 ~MT~~G~l~~itR~Gi~rq~~S~L~raSFEeTv~iL~~AA~~ge~D~lkgVsenIi~Gq~~~lGTGaFd~lLge~ 1403 (1791)
+||++|.+++++|+|++.+..|+|++||||+|.++|.+||++|+.|+|+|++||||+|+++|+|||+||++++..
T Consensus 319 ~Mt~~G~~~~igr~g~s~~t~S~LsaASFqeTt~vLteAAi~Gk~D~L~GlkENVIvGklipaGTG~f~l~~~p~ 393 (395)
T 4ayb_C 319 VMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTMRPI 393 (395)
T ss_dssp HHHGGGSCCCSSSSSHHHHCSCHHHHHHHSCTHHHHHHHHHTTCBCCCCSHHHHHHHTCCCSSGGGTCEEEECSC
T ss_pred hhhccceEeccCcccccCCCCCHHHHhcChhHHHHHHHHHhcCCCCCCCChHHHeecCCCCCCCcCceEEEeccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999988753
No 11
>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=5.9e-42 Score=452.43 Aligned_cols=364 Identities=20% Similarity=0.254 Sum_probs=220.7
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccccc-cCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEe
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQN-VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFH 1066 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~Qs-V~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffh 1066 (1791)
++.|+..+|..+|++||..|++|+.+|+|||+ ++|++++ ++|.|||++||||+|||||
T Consensus 756 ~~~N~i~~Ma~SGAKGS~~ni~Ql~g~~G~ma~~~G~~i~---------------------~pI~ssF~eGLtp~EyFfh 814 (1265)
T 1hqm_D 756 YPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFE---------------------VPVRSSFREGLTVLEYFIS 814 (1265)
T ss_dssp CSSSCTTTTTTTSSSCCHHHHHHHSSCCCCCCCTTSCCCS---------------------CCCCCCBTTBCTTCTHHHH
T ss_pred CCCCcHHHHHHhcCCcCHHHHHHHHhhccccccCCCCccC---------------------cccccccccCCChHHhhee
Confidence 37999999999999999999999999999985 7887664 3478999999999999999
Q ss_pred ecCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCcccceee--------
Q psy3015 1067 AMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLR-------- 1138 (1791)
Q Consensus 1067 AMgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~~~wvlr-------- 1138 (1791)
||||||||+|||+|||++|||||||||++||++|.||++. .+||-.++...+ . ..+++|..+
T Consensus 815 tmggReGLiDTAvKTA~SGYLqRRLVkv~qDv~V~~ddc~-----t~dGi~v~~~~~-~----~~i~~~~~~~~~~L~~r 884 (1265)
T 1hqm_D 815 SHGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADCG-----TTKYISVPLFQM-D----EVTRTLRLRKRSDIESG 884 (1265)
T ss_dssp HHHHTTHHHHHTHHHHTSSSTHHHHHHHSCSCCCCSCCCC-----CCCCEECCSEEC-C----STTCCCEECCTTTTHHH
T ss_pred cccccccchhhhhhcccCCcceeeeeeecceEEEEECCCC-----CCCCEEEEEeec-C----ceeechhhhhhhHHHHH
Confidence 9999999999999999999999999999999999999732 334444433332 1 111222211
Q ss_pred ----ee--------cccc---ccccccCCHHHHHHHHhhccCCC-ccc--ccCCcccccceEEEE--------Ee-cCcc
Q psy3015 1139 ----IE--------LDRK---RMTDKKLTMEAISEKINAGFGDD-LNC--IFNDDNAEKLVLRIR--------IM-NSDD 1191 (1791)
Q Consensus 1139 ----~~--------Ld~~---~m~dk~l~~~~I~~~I~~~~~~d-l~~--i~~d~n~~~l~~rir--------i~-~~~~ 1191 (1791)
.. +|.. .+..++-.+ ++++|.+ ++.+ +.+ .+.......++-.+- +. ..+.
T Consensus 885 i~gr~~~~~i~~~~~~p~~~~~i~~~~~~i--~~~~i~~-~gi~~v~iRs~ltc~s~~gvc~~CYgr~La~~~lV~~GEa 961 (1265)
T 1hqm_D 885 LYGRVLAREVEALGRRLEEGRYLSLEDVHF--LIKAAEA-GEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEA 961 (1265)
T ss_dssp HTTCEESSCEEETTEEECSSCBCCTTHHHH--HHHHHHT-TSCSSCEEECGGGCSCTTSCCSSSSCSCSSSSSCCCTTCC
T ss_pred HHhhhhhhcccccccCCCCccEEecCcchh--hHHHHHH-cCCCEEEeecCcCHHHHHHHHHHHhhhhhccCCEeccCce
Confidence 00 1100 000000001 2333322 1111 000 000000000000000 00 0000
Q ss_pred c---cccchhHHHHhhhhhhhHHHHhhccc--ccceeccccccceEEE-ecccc----------------CCCceEEEcc
Q psy3015 1192 S---KMQDEEDAVDKMEDDMFLRCIEANML--SDMTLQGIEAIGKVYM-HLPQT----------------DSKKRIIITE 1249 (1791)
Q Consensus 1192 ~---~~~~~ee~~~~~~dr~~Lr~i~~~il--~~~~LkGi~~I~kv~i-~lp~~----------------~n~~RiI~na 1249 (1791)
. ..+...|--.++.-|+|=- .... .++ ..|+|++.+.+- +-|.+ +...+++...
T Consensus 962 VGiIAAQSIGEPGTQlTLrTFH~---gGvas~~dI-T~GLPRv~El~eArkpk~p~i~a~~~g~v~~~~~~~~~~i~i~~ 1037 (1265)
T 1hqm_D 962 VGVVAAESIGEPGTQLTMRTFHT---GGVAVGTDI-TQGLPRVIELFEARRPKAKAVISEIDGVVRIEEGEDRLSVFVES 1037 (1265)
T ss_dssp HHHHHHHHHHGGGTTSCCCC-----------CCTT-SSHHHHHHHHHHCCCCSSCBCCCSSSCBCCCCCCSSCCCCCCBC
T ss_pred eeeeeccccCCCCceeeeEEEEE---cceeccccc-ccCchhHHHHHhhcCCCCceEEEeccceEEEeecCCccEEEEEE
Confidence 0 0000111111121111100 0000 011 245555543210 00110 0011111111
Q ss_pred CCcccccceEEEeecccchhcccccCCCC---cccccchhHHHHHHhhhHHHHHHHHHHHHHHHhhhcCeeecccchhhh
Q psy3015 1250 SGEFKAIADWLLETDGTSLMKVLSERDVD---PVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALL 1326 (1791)
Q Consensus 1250 ~~~f~~~~e~~L~teG~nL~~vl~~~dVD---p~rt~sNdI~eI~~vlGIEAaR~~li~El~~V~~~~Gi~Vn~RHL~LL 1326 (1791)
.+. ..+|.+. .+..+ .+..-+.+. ...-.+++++|+++++||||+|.+|++|++.||..||+.||+|||++|
T Consensus 1038 ~g~---~~~~~ip-~~~~l-~v~~g~~v~~g~~lteG~~~~~eil~v~Giea~~~~lv~EIq~vyr~QGv~I~dkHievi 1112 (1265)
T 1hqm_D 1038 EGF---SKEYKLP-KDARL-LVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIV 1112 (1265)
T ss_dssp SSC---CCCCCCS-SCCCC-CCCSCCSSTTCSCCCCSBSHHHHHHHTTHHHHHHHHHHHHHHHHHHTTSCCCCSSTHHHH
T ss_pred CCc---EEEEEcC-CceEE-EEecCCEEecCceeeccCccHHHHHHHhhHHHHHHHHHHHHHHHHHHcCccccHHHHHHH
Confidence 110 0111110 00000 000001111 112236899999999999999999999999999999999999999999
Q ss_pred hhcccc----------------------------------------cCcccccccccccccccccccccchhhhHHHHHH
Q psy3015 1327 CDVMTA----------------------------------------KGHLMAITRHGINRQDTGALMRCSFEETVDVLMD 1366 (1791)
Q Consensus 1327 aD~MT~----------------------------------------~G~l~~itR~Gi~rq~~S~L~raSFEeTv~iL~~ 1366 (1791)
+|+||+ ++.++||||++++ ..|+|++||||+|.++|.+
T Consensus 1113 vrqM~~kv~i~~~g~t~~l~Ge~v~~~~~~~~n~~~~~~g~~~~~~~~~llGITkasl~--t~SflsaASFqeTt~vL~~ 1190 (1265)
T 1hqm_D 1113 VRQMLKYVEVTDPGDSPLLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALS--TKSWLSAASFQNTTHVLTE 1190 (1265)
T ss_dssp HHHHTTEECBSSCCSSCCSCCCEEGGGTTTTTTTTTTC---CCCCBCCCCCCTHHHHTS--CSCHHHHTTSTTHHHHHHH
T ss_pred HHHHhcceEEecCCCcCCCCCceecHHHHHHHHHHHHhcCCCcceeeeeeecceecccc--cCChhhccchHHHHHHHHH
Confidence 999965 4567899999997 5799999999999999999
Q ss_pred HhhccCCCCCCccccceeccccccCCcchh
Q psy3015 1367 AAAHAEADPMRGVSENIIMGQLPRMGTGCF 1396 (1791)
Q Consensus 1367 AA~~ge~D~lkgVsenIi~Gq~~~lGTGaF 1396 (1791)
||++|+.|+|+|++||||+|+++|+|||..
T Consensus 1191 AAi~gk~D~L~GlkEnVIiG~lipaGTG~~ 1220 (1265)
T 1hqm_D 1191 AAIAGKKDELIGLKENVILGRLIPAGTGSD 1220 (1265)
T ss_dssp HHHSCCCCTTCSSHHHHHHTCCCSSGGGCT
T ss_pred HHHcCCCCcCCCcHHheeeCCcccCCcCch
Confidence 999999999999999999999999999953
No 12
>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=9.1e-39 Score=414.75 Aligned_cols=96 Identities=23% Similarity=0.223 Sum_probs=84.7
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEee
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHA 1067 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhA 1067 (1791)
.++|+..+|..+|++||..|++|+.+|||||+.. -| .+.++ +|.|||++||||+||||||
T Consensus 717 ~~~N~i~mMa~SGARGS~~qI~QLaGmrGlmakp-----dG--------------~iie~-PI~ssFreGLtp~EyFfst 776 (1407)
T 3lu0_D 717 VSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKP-----DG--------------SIIET-PITANFREGLNVLQYFIST 776 (1407)
T ss_dssp CSCCHHHHHHHSSSSCCTTHHHHHSSCCCCCBCS-----SS--------------CBCSS-CCCCCSSSCCCHHHHHHHH
T ss_pred CCCCChheeeeccccCCHHHHHHHHHhcCCccCC-----CC--------------CCcch-hhhcccccCCCHHHhhhhc
Confidence 4689999999999999999999999999998632 12 22222 3569999999999999999
Q ss_pred cCCCCccchhhhccchhHHHHHHHHHHhcceEEEEC
Q psy3015 1068 MGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYD 1103 (1791)
Q Consensus 1068 MgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YD 1103 (1791)
|||||||+|||+|||+||||||||||++||++|.++
T Consensus 777 ~GaRKGL~DTALKTAdSGYLTRRLVdv~QDviV~e~ 812 (1407)
T 3lu0_D 777 HGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED 812 (1407)
T ss_dssp HHHHHHHHHTTTTTTCTTTTTHHHHTTSTTCCBCCC
T ss_pred ccchhhhhhhhhhcccchhHHHHHHHhhcceEEEec
Confidence 999999999999999999999999999999987766
No 13
>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=4.6e-37 Score=402.44 Aligned_cols=141 Identities=37% Similarity=0.524 Sum_probs=137.1
Q ss_pred ccCCHHHHHHHHHHHhhhccceeccccccccccCCcccCCCCcCccccccccCCCCCCCCcceeeccccCCCcceEEEee
Q psy3015 988 YRLSSEAFEWLVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHA 1067 (1791)
Q Consensus 988 ~rln~~a~~~i~gei~~~~~~sqv~~mvG~QsV~gKrI~~GfprRTLphf~kdd~~PESrGFV~Nsf~~GLTPsEfffhA 1067 (1791)
.+.|+..+|..+|++||..|++|+++|+|||+++|+|||.||-.||||||.++|++|||+|||.|||++||||+||||||
T Consensus 720 ~~~N~i~mMa~SGARGS~~ni~Qlagm~Gqq~~~G~RIprg~~~rtLP~f~~~d~~p~a~GfI~ssF~eGLtp~EyF~ht 799 (880)
T 4ayb_A 720 DPFNFAYVMARTGARGSVLNITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHA 799 (880)
T ss_dssp CTTSHHHHHHHHTSSCCSTTHHHHHTCCEECBSSSSBSCCSBTTBSSTTSCTTCCSTTTTSEECSCTTTCCCHHHHHHHH
T ss_pred CCCCCHHHHhhcCccCCHHHHHHHHhcccccccCCccCcCCCccCCCCCCCCCCCCcccCCeEhhcccCCCCHHHHHHhh
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCccchhhhccchhHHHHHHHHHHhcceEEEECCCCCCcccccCcceeeeeccCCCCCCCCc
Q psy3015 1068 MGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRI 1132 (1791)
Q Consensus 1068 MgGREGLiDTAvKTAEtGYIqRRLvk~~Edv~V~YDgtvrnTVr~~d~~iVQf~Yg~dg~D~~~~ 1132 (1791)
|||||||+|||+|||++|||||||||++||+.|.||| |||+++|++|||.||+||+||...
T Consensus 800 ~ggRkGL~DTAlKTA~SGYLtRRLVdv~qDv~V~yDg----TVR~~~g~ivqf~YGeDgldp~~~ 860 (880)
T 4ayb_A 800 AGGREGLVDTAVRTSQSGYMQRRLINALSDLRAEYDG----TVRSLYGEVIQVAYGDDGVFPMYS 860 (880)
T ss_dssp HHHHHHHHHHHHTHHHHHHHHHHHHHHHTTEEECTTS----CEEETTTEEEESSTTTTCBCTTTS
T ss_pred hhhhhhHHhcchhhchhhHHHHHHHHHHcCEEEecCC----CccCCCCcEEEEecCCcccceeec
Confidence 9999999999999999999999999999999999998 777788999999999999999653
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=99.95 E-value=8.5e-29 Score=300.89 Aligned_cols=220 Identities=17% Similarity=0.160 Sum_probs=155.5
Q ss_pred CCcchhhhhcccccccccccccCCCCcchhh-hhhccCCCCCCCCCCCCCCCcceeeeeeeccccceecccchhHHHhhc
Q psy3015 1391 MGTGCFDLLLDAEKCKDGIEIPLATGMMGGP-AGMFFGSAATPSSIPGPPAWYPIHIAISLLSRFTTVICIYTLKTFLEM 1469 (1791)
Q Consensus 1391 lGTGaFd~lLge~~~~~~~~~~v~pGEmVG~-aAQSIGEPa~~~~~TQmT~lnTFH~aGVs~~~~t~~lGvprlkei~nv 1469 (1791)
+....|+++++....++.+++ |+||||||+ ||||||||| |||| |||||||||+++|+| +|||||+||+|+
T Consensus 43 ~~~~~~~~~~~~~~~~y~r~l-v~pGEAVGiIAAQSIGEPg-----TQlT-LrTFH~gGva~~nvT--~GlPRl~Ei~~a 113 (395)
T 4ayb_C 43 VTRDEIDKIFDLAIKEYSEGL-IAPGEAIGIVAAQSVGEPG-----TQMT-LRTFHFAGIRELNVT--LGLPRLIEIVDA 113 (395)
T ss_dssp CCHHHHHHHHHHHHHHHHHTB-CCTTCCHHHHHHHHHHHHH-----HTCC--------------CC--CSHHHHHHHHTC
T ss_pred cCHHHHHHHHHHHHHHHHHhc-CCCCchHhHHHHhhcCCch-----hhhc-cccceeeeecceeee--cCccceEEeccc
Confidence 444689999999999999988 999999999 899999999 9999 999999999999887 999999999999
Q ss_pred cCCCCCCCCCccceeEEEEeeccccCCccccCCCCCchhhHhhHhHHHHHhhccccccchhhhcceeEEEEcCCCCCCcc
Q psy3015 1470 KDFKKPPQKGFGLLTLTLMVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYYDPDPQNTVI 1549 (1791)
Q Consensus 1470 ~~~~k~~~~~~~~~~~t~~~~~I~~~pk~~~~P~~~~~~~~~vq~~~~~~~~~~~~~~~l~~vt~~t~i~ydpd~~~tvi 1549 (1791)
++++++|+ +++++.. .... +.+.+..+...++ ++++.+++..++|.|
T Consensus 114 ~k~~~tp~-------~~i~l~~------~~~~---~~e~~~~~~~~ie--------~~~~~~~~~~~~i~~--------- 160 (395)
T 4ayb_C 114 KKVPSTPM-------MTIYLTD------EYKH---DKEKALEVARKLE--------YTKIENVVSSTSIDI--------- 160 (395)
T ss_dssp CSSCSSCE-------EEECCTT------TGGG---CHHHHHHHHHHHH--------CCCHHHHEEEEEEET---------
T ss_pred ccCCCCCc-------eEEEecc------cccc---cHHHHHhhcccee--------EEEccceeeeeEEee---------
Confidence 99999996 8888773 1221 3455555555555 789999999888754
Q ss_pred cccHHHHHHhhcCCCCCCCCCCcceEEEEeccccccccccCHHHHHhhhhcCCCCCCCCCCCCchhhhHHHHHHHHHhcc
Q psy3015 1550 PEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINAG 1629 (1791)
Q Consensus 1550 ~eD~~~v~~~~~~pd~~~~~~spwllr~~ldr~~m~dk~l~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ 1629 (1791)
++|..++++|++.+.+++++++++.. .+...
T Consensus 161 ---------------------~~~~~~~~~d~~~~~~~~~~~~~i~~----------------------------~~~~~ 191 (395)
T 4ayb_C 161 ---------------------ASMSIILQLDNEMLKDKGVTVDDVKK----------------------------AINRL 191 (395)
T ss_dssp ---------------------TTTEEEEEECGGGGBTTBCHHHHHHH----------------------------HHHHS
T ss_pred ---------------------cccceeeehhhhhhhhcCccHHHHHH----------------------------HHhhh
Confidence 35888999999999999999999887 44445
Q ss_pred cCCCceeeecCCcccceEEEEEEecCCCCccchhhhhhhccccceeeccccccceeEeecccCCccccccEEEEEecccc
Q psy3015 1630 FGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEETDRSFVKVDFVEPKDLVEWKTLLKQMHS 1709 (1791)
Q Consensus 1630 f~~~l~~i~~ddna~~lv~r~r~~~~~~~~~~~~~~~~~~~~~~~~lr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1709 (1791)
...+..+..++.| .++++..+.+.-..- ..+.+.-....+++++++.|+++.. ...+|.+++ +
T Consensus 192 ~~~~~~~~~~~~~----~~~~~~~~~~~v~~l---~~~~~~~~~~~i~gi~gi~r~~~~~------~~~~~~~~t----~ 254 (395)
T 4ayb_C 192 KLGEFVIDESEGN----TLNISFANIDSIAAL---FKLRDKILNTKIKGIKGIKRAIVQK------KGDEYIILT----D 254 (395)
T ss_dssp CCSSEEEEECSSE----EEEEECCSSCCCCCT---HHHHHHHHHHCCCSSSSCCEEEEEE------ETTEEEEEE----E
T ss_pred ccCcEEEecccCc----EEEeecCCCchHHHH---HHHHhhccccEEecccceeEEEEec------cCCEEEEEe----c
Confidence 5567666655544 444544332211110 0011111235799999999999876 346899999 9
Q ss_pred cccHHHHHh
Q psy3015 1710 DFCLAQIIK 1718 (1791)
Q Consensus 1710 ~~~~~~~~~ 1718 (1791)
|.+|.+++.
T Consensus 255 g~~l~~~~~ 263 (395)
T 4ayb_C 255 GSNLSGVLS 263 (395)
T ss_dssp SCCHHHHTT
T ss_pred CCCceeeeE
Confidence 999999875
No 15
>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=98.91 E-value=1.1e-10 Score=142.68 Aligned_cols=68 Identities=34% Similarity=0.752 Sum_probs=61.7
Q ss_pred ccccceeeeeecccCChhhHhhhCCCCCCCCcceEEeeccCCCCCCCCCeEEecCccccHhHHHHHHhc
Q psy3015 13 HVSNTSVYAWYVVPYPYEESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQEQMMNILMF 81 (1791)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~d~~~lg~~~~~~~p~~mlv~~~iVsP~~~rP~~~i~Gs~~~rddlmqLlm~ 81 (1791)
-++|++||++|+ +||+|||++||||++++||+||+++++||||++.||++.++|..+++||+..++..
T Consensus 241 ~LtP~~vl~ifk-~IsdeD~~lLGl~~~~~rPewmIlt~LPVpPp~vRPsv~~~~g~~~edDLT~kl~~ 308 (436)
T 3qqc_A 241 RLMPTEVRDWLE-KIPDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDLTHKLVD 308 (436)
T ss_dssp EECHHHHHHHHH-HSCTTTGGGSSCCTTTCCGGGGEEEEEEECCGGGSCCBCC---CCBCCHHHHHHHH
T ss_pred ccCHHHHHHHHH-hCCHHHHHHhcccccCCCcceeEeeccccCCCcCcccEEeCCCcCCCChHHHHHHH
Confidence 489999999999 99999999999999999999999999999999999999998878899999888764
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=88.08 E-value=0.11 Score=64.01 Aligned_cols=42 Identities=40% Similarity=0.612 Sum_probs=29.8
Q ss_pred CCcccccchhhhhhHHHHHHhhccCCCCCCCcccceecCCCC
Q psy3015 831 DTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLP 872 (1791)
Q Consensus 831 ~~S~L~~aSFE~T~d~L~~Aa~~g~~D~i~GVSe~II~G~~~ 872 (1791)
+.|||..|+||.+..||++|+.+|+.|.+.||-|+|++|+.-
T Consensus 390 ~~s~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 431 (436)
T 3qqc_A 390 SGSVLARAAFEITVQHLFEAAEKGEVDNLNGVIENVLIGQKH 431 (436)
T ss_dssp ---------CCCCHHHHHHHHHHTCEEECCSSCCTTSCC---
T ss_pred chhHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhhhcccc
Confidence 679999999999999999999999999999999999999853
Done!