Query 000249
Match_columns 1788
No_of_seqs 298 out of 1716
Neff 4.5
Searched_HMMs 29240
Date Tue Mar 26 16:42:32 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000249.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_28-31//hhsearch_pdb/000249hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 4b3f_X DNA-binding protein smu 1.0 1 1 337.3 27.2 366 1253-1788 2-384 (646)
2 2gk6_A Regulator of nonsense t 1.0 1 1 281.4 25.6 347 1247-1787 1-356 (624)
3 2xzl_A ATP-dependent helicase 1.0 1 1 276.4 27.8 352 1242-1787 174-534 (802)
4 2wjy_A Regulator of nonsense t 1.0 1 1 275.6 26.0 352 1242-1787 172-532 (800)
5 3e1s_A Exodeoxyribonuclease V, 1.0 1 1 95.7 9.2 66 1446-1575 187-252 (574)
6 3lfu_A DNA helicase II; SF1 he 1.0 1 1 94.8 8.8 26 1735-1781 552-577 (647)
7 1w36_D RECD, exodeoxyribonucle 1.0 1 1 89.4 8.8 67 1450-1576 151-217 (608)
8 3upu_A ATP-dependent DNA helic 1.0 1 1 87.9 9.2 71 1447-1575 24-94 (459)
9 3u4q_A ATP-dependent helicase/ 1.0 1 1 65.8 8.3 65 1448-1575 10-77 (1232)
10 3vkw_A Replicase large subunit 1.0 1 1 60.6 5.0 58 1469-1587 159-216 (446)
No 1
>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A
Probab=1.00 E-value=1 Score=337.27 Aligned_cols=366 Identities=24% Similarity=0.276 Sum_probs=231.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHCC--C-CCCCCCC----EEEEEEEEE-ECCEEEEEEEECCC---CCCCCCCC
Q ss_conf 896689996459999999999983221015--4-2224225----079995544-08749999961599---87444478
Q 000249 1253 QSPEQFVSIFRPLVLEEFKAQLHSSFLEMS--S-WEDMYYG----SLSVLSVER-VDDFHLVRFVHDDN---DSVTSKIF 1321 (1788)
Q Consensus 1253 sS~eEYi~tFePLLLEE~rAQL~sSleEis--s-~E~~~~g----~IsVlS~er-vDdF~lV~f~~~~~---d~lk~~~l 1321 (1788)
.+.++|++.|.+||..|..+++.+...... + .+....| .+.+.+... .++.+.++|..... ...+...|
T Consensus 2 ~~~~~~~~~~~~Ll~~E~~~e~~~~~~~~~~~~~~~~~~~G~~~~~l~~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~~~ 81 (646)
T 4b3f_X 2 AAVESFVTKQLDLLELERDAEVEERRSWQENISLKELQSRGVCLLKLQVSSQRTGLYGRLLVTFEPRRYGSAAALPSNSF 81 (646)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCHHHHGGGTSEEEEEEEEEEEECSSSCEEEEEEESCC---CCCCCCCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCEECCEEEEEEEECCCCEEEEEEEECCCCCCCCCCCCCC
T ss_conf 11899999999999999999999999998629999999679603264888889657985999998357788777866789
Q ss_pred CCCCEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCHHHHHHHHHHCCCCHHHHHCCCCCHHHHH
Q ss_conf 99969999823999999835799999985135788851999999831785102787532101430101320241489899
Q 000249 1322 SENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLRE 1401 (1788)
Q Consensus 1322 segDLVLLSke~P~~s~~~~h~LG~Ve~~e~d~~~~~~~I~IRi~l~n~s~rLnq~~~~L~~~S~w~l~KL~SLTTi~RE 1401 (1788)
..||+|+++...+.. ...+.|+|.+...+ .+.+++.... .....+.....|.+.++.|.+|+.|+
T Consensus 82 ~~Gd~v~~~~~~~~~---~~~~~g~v~~~~~~------~i~v~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~r~ 146 (646)
T 4b3f_X 82 TSGDIVGLYDAANEG---SQLATGILTRVTQK------SVTVAFDESH------DFQLSLDRENSYRLLKLANDVTYRRL 146 (646)
T ss_dssp CTTCEEEEEETTTTS---CCCEEEEEEEEETT------EEEEECC-------------CCCSSCCEEEEEECCHHHHHHH
T ss_pred CCCCEEEEEECCCCC---CCEEEEEEEEEECC------EEEEEECCCC------CCCCCCCCCCCEEEEEECCCHHHHHH
T ss_conf 989989999668998---71489999999499------9999988865------33335578984799980660689999
Q ss_pred HHHHCCCCCCC------CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCEEE
Q ss_conf 98404398899------600004998888887787434224213678785018999899999999804999867776167
Q 000249 1402 FHALSSLKSIP------LLPIILNPVNVSRGYNESRELDLGKLSQLQQILKTSFNESQLQAISVAIGLSSSWKKDCELSL 1475 (1788)
Q Consensus 1402 y~AL~sL~~lP------L~~~ILsP~~~~~~~~~s~~v~~~~ip~L~~~Lk~~LNeSQleAI~aALs~~~~~~~~~gIsL 1475 (1788)
+.||..+...+ +.+.|+...++.+... ... ..+++.+||++|.+||..+|... +++|
T Consensus 147 ~~al~~l~~~~~~~~~~l~~~l~~~~~p~~~~~-~~~---------~~~~~~~LN~~Q~~AV~~al~~~-------~~~l 209 (646)
T 4b3f_X 147 KKALIALKKYHSGPASSLIEVLFGRSAPSPASE-IHP---------LTFFNTCLDTSQKEAVLFALSQK-------ELAI 209 (646)
T ss_dssp HHHHHHHHTCCSSTTHHHHHHHTTSSCCCCCCC-CCC---------CCCSSTTCCHHHHHHHHHHHHCS-------SEEE
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCC-CCC---------CCCCCCCCCHHHHHHHHHHHCCC-------CCEE
T ss_conf 999998521246725779998749999997655-576---------53257888999999999996589-------9659
Q ss_pred EECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 86789998245799999999960389975455575655578876651479997888899985311221011245444468
Q 000249 1476 IQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSVR 1555 (1788)
Q Consensus 1476 IQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~avar~W~~~alarql~~d~~~~~~s~~~~~k 1555 (1788)
||||||||||+||+.+|..++.. +
T Consensus 210 I~GPPGTGKT~ti~~~I~~l~~~--------------------------------------------------------~ 233 (646)
T 4b3f_X 210 IHGPPGTGKTTTVVEIILQAVKQ--------------------------------------------------------G 233 (646)
T ss_dssp EECCTTSCHHHHHHHHHHHHHHT--------------------------------------------------------T
T ss_pred EECCCCCCHHHHHHHHHHHHHHC--------------------------------------------------------C
T ss_conf 98899988899999999999848--------------------------------------------------------9
Q ss_pred CEEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 71999907558999999998825976899986689488983455546888543178999999898520369975200122
Q 000249 1556 ARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKTVHPNSLPFFIDTLVDHRLAEERMHLTDPKNEFCTR 1635 (1788)
Q Consensus 1556 ~RILVCAPSNAAVDEIV~RLlk~GI~d~dGk~ykP~IVRIG~~~aihs~vl~vsLD~LV~qrL~~e~~~~~d~k~~~~~e 1635 (1788)
.+||||||||.||||+++||...| .+++|+|+..++++.+..+++|..+... + ....
T Consensus 234 ~~ILv~a~TN~AvD~i~erL~~~~----------~~ilRlG~~~r~~~~~~~~~l~~~~~~~---------~----~~~~ 290 (646)
T 4b3f_X 234 LKVLCCAPSNIAVDNLVERLALCK----------QRILRLGHPARLLESIQQHSLDAVLARS---------D----SAQI 290 (646)
T ss_dssp CCEEEEESSHHHHHHHHHHHHHTT----------CCEEECSCCSSCCHHHHTTBHHHHHTTT---------T----CSST
T ss_pred CEEEEECCCHHHHHHHHHHHHHCC----------CCEEEECCHHHHHHHHHHHHHHHHHHHC---------H----HHHH
T ss_conf 829999185188879999998627----------7658823656520255430188898504---------1----7889
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 15899999999989999998640246899999886421112488766566999999999999999999999899999877
Q 000249 1636 SSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQEKK 1715 (1788)
Q Consensus 1636 ~s~Lr~kLekL~~ei~~~ea~R~~~~~g~~~~k~~l~~~~~kg~~~gls~~eL~~kL~kL~eqrrqL~~eL~~~~~~ekk 1715 (1788)
...++.+++.+.. ... . ..+...+ . .+..++..
T Consensus 291 ~~~~~~~~~~~~~------------~~~-----~-~~~~~~~---~-------------------~~~~~~~~------- 323 (646)
T 4b3f_X 291 VADIRKDIDQVFV------------KNK-----K-TQDKREK---S-------------------NFRNEIKL------- 323 (646)
T ss_dssp HHHHHHHHTTSST------------TTT-----C-------C---C-------------------SSHHHHHH-------
T ss_pred HHHHHHHHHHHHH------------HHH-----H-HHHHHHH---H-------------------HHHHHHHH-------
T ss_conf 9999988899998------------634-----3-2237888---7-------------------77889999-------
Q ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCC
Q ss_conf 9999999999999988505959998177887775334444446765699998999999999268421002479
Q 000249 1716 SYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHEL 1788 (1788)
Q Consensus 1716 ~~rele~~Rrkir~~IL~eAdIVCSTLSGSGsell~~c~et~aaakf~~l~~~~~FDtVIIDEAAQAvElStL 1788 (1788)
..++++..++....++|.+|+|||+|++++++..... ......||+||||||+|++|+++|
T Consensus 324 l~~~l~~~~~~~~~~~l~~~~vv~~t~~~a~~~~~~~------------~~~~~~Fd~vIIDEAsQ~~e~~~l 384 (646)
T 4b3f_X 324 LRKELKEREEAAMLESLTSANVVLATNTGASADGPLK------------LLPESYFDVVVIDECAQALEASCW 384 (646)
T ss_dssp HHHHHHHHHHHHHHHHHHHCSEEEEETTTTCSSSGGG------------GSCTTCCSEEEETTGGGSCHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHH------------HHHHCCCCEEEECCCCCCCHHHHH
T ss_conf 9999988888888988763354222201222335887------------643126888997175444557887
No 2
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A
Probab=1.00 E-value=1 Score=281.41 Aligned_cols=347 Identities=22% Similarity=0.257 Sum_probs=212.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCCCCE
Q ss_conf 46854589668999645999999999998322101542224225079995544087499999615998744447899969
Q 000249 1247 EVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSSWEDMYYGSLSVLSVERVDDFHLVRFVHDDNDSVTSKIFSENDL 1326 (1788)
Q Consensus 1247 kVP~TFsS~eEYi~tFePLLLEE~rAQL~sSleEiss~E~~~~g~IsVlS~ervDdF~lV~f~~~~~d~lk~~~lsegDL 1326 (1788)
+|+.+|.|..+|+++|.|||..|.+++... .+.. .. ..+.+......++.+.+.|..+.. .....+..||+
T Consensus 1 ~~~~~~~~~~~y~~~~~~ll~~E~~~~~~~--~~~~-~~----~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~Gd~ 71 (624)
T 2gk6_A 1 PLGSRYEDAYQYQNIFGPLVKLEADYDKKL--KESQ-TQ----DNITVRWDLGLNKKRIAYFTLPKT--DSDMRLMQGDE 71 (624)
T ss_dssp --CCCCSSHHHHHHHHHHHHHHHHHHHHHH--HHHT-CE----EEECEEEEECTTSCEEEEEECC---------CCTTCE
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH--HHHH-HC----CCCEEEEEECCCCCEEEEEEECCC--CCCCCCCCCCE
T ss_conf 967765999999999999999999997888--7654-04----582587663478816999970643--35796899998
Q ss_pred EEEEECCCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCHHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHHHC
Q ss_conf 99982399999983579999998513578885199999983178510278753210143010132024148989998404
Q 000249 1327 VLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLREFHALS 1406 (1788)
Q Consensus 1327 VLLSke~P~~s~~~~h~LG~Ve~~e~d~~~~~~~I~IRi~l~n~s~rLnq~~~~L~~~S~w~l~KL~SLTTi~REy~AL~ 1406 (1788)
|+++...+.. ....+.|.|.+...+. ...+.+.+.... .. +. .....+.+.++.+.+|+.|++.||.
T Consensus 72 v~l~~~~~~~--~~~~~~g~v~~~~~~~---~~~v~v~~~~~~-~~------~~-~~~~~~~~~~~~~~~~~~r~~~al~ 138 (624)
T 2gk6_A 72 ICLRYKGDLA--PLWKGIGHVIKVPDNY---GDEIAIELRSSV-GA------PV-EVTHNFQVDFVWKSTSFDRMQSALK 138 (624)
T ss_dssp EEEEECSSSS--CCCEEEEEEEECSCSS---CSEEEEEESCCT-TC------CC-SCCSSEEEEECCCCHHHHHHHHHHH
T ss_pred EEEEECCCCC--CCCEEEEEEEEECCCC---CCEEEEEECCCC-CC------CC-CCCCCEEEEEEECCCHHHHHHHHHH
T ss_conf 9999788888--8747899999964778---878999982688-88------63-3566558999957726999999999
Q ss_pred CCCCC-----C-CCCCCCCCCCCCCCCCCCCCCCCCCHHH-HHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEECC
Q ss_conf 39889-----9-6000049988888877874342242136-787850189998999999998049998677761678678
Q 000249 1407 SLKSI-----P-LLPIILNPVNVSRGYNESRELDLGKLSQ-LQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGP 1479 (1788)
Q Consensus 1407 sL~~l-----P-L~~~ILsP~~~~~~~~~s~~v~~~~ip~-L~~~Lk~~LNeSQleAI~aALs~~~~~~~~~gIsLIQGP 1479 (1788)
.+... + +...++....+...... .+|. +.......+|++|.+||..++.. +++|||||
T Consensus 139 ~~~~~~~~~~~~~~~~ll~~~~~~~~~~~-------~~~~~~~~~~~~~ln~~Q~~av~~~l~~--------~~~li~Gp 203 (624)
T 2gk6_A 139 TFAVDETSVSGYIYHKLLGHEVEDVIIKC-------QLPKRFTAQGLPDLNHSQVYAVKTVLQR--------PLSLIQGP 203 (624)
T ss_dssp HHHHCTTSBCSHHHHHHTTCCCCCCCCCC-------CCCSCCSCTTSCCCCHHHHHHHHHHHTC--------SEEEEECC
T ss_pred HHHHCCCCCHHHHHHHHCCCCCCCCCCCC-------CCCCCCCCCCCCCCCHHHHHHHHHHHCC--------CCEEEECC
T ss_conf 98760455127789986188876421245-------6752125445678999999999999628--------97699899
Q ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEE
Q ss_conf 99982457999999999603899754555756555788766514799978888999853112210112454444687199
Q 000249 1480 PGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSVRARVL 1559 (1788)
Q Consensus 1480 PGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~avar~W~~~alarql~~d~~~~~~s~~~~~k~RIL 1559 (1788)
||||||+|+..++..++.. .+.+||
T Consensus 204 pGTGKT~~~~~~i~~l~~~-------------------------------------------------------~~~~il 228 (624)
T 2gk6_A 204 PGTGKTVTSATIVYHLARQ-------------------------------------------------------GNGPVL 228 (624)
T ss_dssp TTSCHHHHHHHHHHHHHTS-------------------------------------------------------SSCCEE
T ss_pred CCCCHHHHHHHHHHHHHHC-------------------------------------------------------CCCEEE
T ss_conf 9987899999999999974-------------------------------------------------------898099
Q ss_pred EEECCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCC--CCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCH
Q ss_conf 99075589999999988259768999866894889834555--4688854317899999989852036997520012215
Q 000249 1560 ICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKT--VHPNSLPFFIDTLVDHRLAEERMHLTDPKNEFCTRSS 1637 (1788)
Q Consensus 1560 VCAPSNAAVDEIV~RLlk~GI~d~dGk~ykP~IVRIG~~~a--ihs~vl~vsLD~LV~qrL~~e~~~~~d~k~~~~~e~s 1637 (1788)
||||||.|+|++..|+.+.|+ +++|+|...+ +...+..++++.++.. .+. .
T Consensus 229 v~a~tn~A~~~l~~~l~~~~~----------~~~R~~~~~r~~~~~~~~~~tl~~~~~~---------~~~-------~- 281 (624)
T 2gk6_A 229 VCAPSNIAVDQLTEKIHQTGL----------KVVRLCAKSREAIDSPVSFLALHNQIRN---------MDS-------M- 281 (624)
T ss_dssp EEESSHHHHHHHHHHHHTTTC----------CEEECCCTGGGSCCCTTTTTBHHHHHTS---------CSS-------C-
T ss_pred EEECCHHHHHHHHHHHHHCCC----------EEEEECCCCCHHHCCCHHHHHHHHHHHH---------CCC-------H-
T ss_conf 992718999999999986197----------5896053220111130456659999980---------523-------6-
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999999998999999864024689999988642111248876656699999999999999999999989999987799
Q 000249 1638 TLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQEKKSY 1717 (1788)
Q Consensus 1638 ~Lr~kLekL~~ei~~~ea~R~~~~~g~~~~k~~l~~~~~kg~~~gls~~eL~~kL~kL~eqrrqL~~eL~~~~~~ekk~~ 1717 (1788)
.++.++.. .+ + ..+.++... .
T Consensus 282 ---~~l~~l~~-------~~----~----------------~~~~~~~~~-----------------------------~ 302 (624)
T 2gk6_A 282 ---PELQKLQQ-------LK----D----------------ETGELSSAD-----------------------------E 302 (624)
T ss_dssp ---HHHHHHHT-------TC----C--------------------CCHHH-----------------------------H
T ss_pred ---HHHHHHHH-------HH----H----------------HHCCCCHHH-----------------------------H
T ss_conf ---99999999-------98----7----------------642137778-----------------------------9
Q ss_pred HHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf 9999999999998850595999817788777533444444676569999899999999926842100247
Q 000249 1718 EETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHE 1787 (1788)
Q Consensus 1718 rele~~Rrkir~~IL~eAdIVCSTLSGSGsell~~c~et~aaakf~~l~~~~~FDtVIIDEAAQAvElSt 1787 (1788)
+..+..++.+...+|++++|||+|++++++..+. ...||+||||||+|+.|+++
T Consensus 303 ~~~~~~~~~~~~~~l~~~~vI~~T~~~~~~~~l~----------------~~~fd~viIDEAsQ~~e~~~ 356 (624)
T 2gk6_A 303 KRYRALKRTAERELLMNADVICCTCVGAGDPRLA----------------KMQFRSILIDESTQATEPEC 356 (624)
T ss_dssp HHHHHHHHHHHHHHHHTCSEEEEETGGGGCGGGT----------------TCCCSEEEETTGGGSCHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCEEEECCHHHCCHHHH----------------CCCCCEEEEECCCCCCCHHH
T ss_conf 9999999988999871499999927011514664----------------67988799963014675899
No 3
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}
Probab=1.00 E-value=1 Score=276.38 Aligned_cols=352 Identities=25% Similarity=0.271 Sum_probs=216.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCEEEEEEEECCCCCCCCCCC
Q ss_conf 26566468545896689996459999999999983221015422242250799955440874999996159987444478
Q 000249 1242 HCKLKEVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSSWEDMYYGSLSVLSVERVDDFHLVRFVHDDNDSVTSKIF 1321 (1788)
Q Consensus 1242 ~~~LkkVP~TFsS~eEYi~tFePLLLEE~rAQL~sSleEiss~E~~~~g~IsVlS~ervDdF~lV~f~~~~~d~lk~~~l 1321 (1788)
..++.+||.+|.|..+|.++|.||+..|.+++... .+..... .+.+......++.+.+.|..+... .....+
T Consensus 174 ~~~~~~v~~~y~~~~~Y~~~~~~ll~lE~~~~~~~--~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ 245 (802)
T 2xzl_A 174 QEAIPPLLLRYQDAYEYQRSYGPLIKLEADYDKQL--KESQALE-----HISVSWSLALNNRHLASFTLSTFE-SNELKV 245 (802)
T ss_dssp ----CCCCSSCSSHHHHHHHHHHHHHHHHHHHHHH--HCCC--C-----CBCEEEEECTTSCEEEEEC----------CC
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH--HHHHHCC-----CCEEEEECCCCCEEEEEEEECCCC-CCCCCC
T ss_conf 55646666556999999999989999999762234--6676444-----826754406798389999806645-578989
Q ss_pred CCCCEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCHHHHHHHHHHCCCCHHHHHCCCCCHHHHH
Q ss_conf 99969999823999999835799999985135788851999999831785102787532101430101320241489899
Q 000249 1322 SENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLRE 1401 (1788)
Q Consensus 1322 segDLVLLSke~P~~s~~~~h~LG~Ve~~e~d~~~~~~~I~IRi~l~n~s~rLnq~~~~L~~~S~w~l~KL~SLTTi~RE 1401 (1788)
..||.|+++...+.. ......|.|.+..... ...+.+++......... .....+.+.++.+.+|+.|+
T Consensus 246 ~~GD~v~l~~~~~~~--~~~~~~g~V~~v~~~~---~~~v~v~~~~~~~~~p~-------~~~~~~~v~~~~~~~~~~r~ 313 (802)
T 2xzl_A 246 AIGDEMILWYSGMQH--PDWEGRGYIVRLPNSF---QDTFTLELKPSKTPPPT-------HLTTGFTAEFIWKGTSYDRM 313 (802)
T ss_dssp CTTCEEEEEECSSSS--SCEEEEEEEEECCC------CCEEEEECCCSSCCCT-------TCCSSEEEEECCCCHHHHHH
T ss_pred CCCCEEEEEECCCCC--CCEEEEEEEEEECCCC---CCEEEEEEECCCCCCCC-------CCCCCEEEEEEECCCHHHHH
T ss_conf 999989999789888--9515789999987888---87899999678889960-------02777489997568618999
Q ss_pred HHHHCCCCC--CC----CCCCCCCCCCCCCCCCCCCCCCCCCHHH-HHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCEE
Q ss_conf 984043988--99----6000049988888877874342242136-7878501899989999999980499986777616
Q 000249 1402 FHALSSLKS--IP----LLPIILNPVNVSRGYNESRELDLGKLSQ-LQQILKTSFNESQLQAISVAIGLSSSWKKDCELS 1474 (1788)
Q Consensus 1402 y~AL~sL~~--lP----L~~~ILsP~~~~~~~~~s~~v~~~~ip~-L~~~Lk~~LNeSQleAI~aALs~~~~~~~~~gIs 1474 (1788)
+.||..+.. .. +.+.++....+...... .+|. +.......||++|.+||..++.. +++
T Consensus 314 ~~AL~~~~~~~~~~~~~l~~~ll~~~~~~~~~~~-------~lp~~~~~~~~~~Ln~~Q~~Av~~~l~~--------~~~ 378 (802)
T 2xzl_A 314 QDALKKFAIDKKSISGYLYYKILGHQVVDISFDV-------PLPKEFSIPNFAQLNSSQSNAVSHVLQR--------PLS 378 (802)
T ss_dssp HHHHHHHHHCTTSBCHHHHHHHHTCCCCCCCCCC-------CCCSCCSCTTSCCCCHHHHHHHHHHTTC--------SEE
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCC-------CCCCCCCCCCCCCCCHHHHHHHHHHHCC--------CCE
T ss_conf 9999998751334036788876077656543465-------6851115434556899999999998639--------977
Q ss_pred EEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 78678999824579999999996038997545557565557887665147999788889998531122101124544446
Q 000249 1475 LIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSV 1554 (1788)
Q Consensus 1475 LIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~avar~W~~~alarql~~d~~~~~~s~~~~~ 1554 (1788)
|||||||||||+||+.++..++.. .
T Consensus 379 lI~GppGTGKT~~i~~~i~~l~~~-------------------------------------------------------~ 403 (802)
T 2xzl_A 379 LIQGPPGTGKTVTSATIVYHLSKI-------------------------------------------------------H 403 (802)
T ss_dssp EEECSTTSSHHHHHHHHHHHHHHH-------------------------------------------------------H
T ss_pred EEECCCCCCHHHHHHHHHHHHHHC-------------------------------------------------------C
T ss_conf 998789977899999999999867-------------------------------------------------------9
Q ss_pred CCEEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCC--CCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 8719999075589999999988259768999866894889834555--46888543178999999898520369975200
Q 000249 1555 RARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKT--VHPNSLPFFIDTLVDHRLAEERMHLTDPKNEF 1632 (1788)
Q Consensus 1555 k~RILVCAPSNAAVDEIV~RLlk~GI~d~dGk~ykP~IVRIG~~~a--ihs~vl~vsLD~LV~qrL~~e~~~~~d~k~~~ 1632 (1788)
+.+||||||||.|+|++.+||.+.|+ +++|+|...+ +...+..++++.++... ..
T Consensus 404 ~~~ILv~a~tn~A~d~l~~rL~~~g~----------~ilR~g~~~r~~i~~~~~~~tl~~~~~~~----------~~--- 460 (802)
T 2xzl_A 404 KDRILVCAPSNVAVDHLAAKLRDLGL----------KVVRLTAKSREDVESSVSNLALHNLVGRG----------AK--- 460 (802)
T ss_dssp CCCEEEEESSHHHHHHHHHHHHHTTC----------CEEECCCGGGTTSCCTTGGGBHHHHHHTT----------CC---
T ss_pred CCEEEEECCCHHHHHHHHHHHHHHCC----------CEEEECCCCHHHHCCHHHHHHHHHHHHHH----------CH---
T ss_conf 97299984857999999999986275----------07862223222103156564299999851----------68---
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 12215899999999989999998640246899999886421112488766566999999999999999999999899999
Q 000249 1633 CTRSSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQ 1712 (1788)
Q Consensus 1633 ~~e~s~Lr~kLekL~~ei~~~ea~R~~~~~g~~~~k~~l~~~~~kg~~~gls~~eL~~kL~kL~eqrrqL~~eL~~~~~~ 1712 (1788)
. .+.++..... . . ++++..+.
T Consensus 461 ----~----~l~~l~~~~~---~------~------------------~~ls~~~~------------------------ 481 (802)
T 2xzl_A 461 ----G----ELKNLLKLKD---E------V------------------GELSASDT------------------------ 481 (802)
T ss_dssp ----T----HHHHHHHHHH---H------H------------------SCCCHHHH------------------------
T ss_pred ----H----HHHHHHHHHH---H------H------------------CCCCHHHH------------------------
T ss_conf ----9----9999999988---6------4------------------45788899------------------------
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf 877999999999999998850595999817788777533444444676569999899999999926842100247
Q 000249 1713 EKKSYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHE 1787 (1788)
Q Consensus 1713 ekk~~rele~~Rrkir~~IL~eAdIVCSTLSGSGsell~~c~et~aaakf~~l~~~~~FDtVIIDEAAQAvElSt 1787 (1788)
+..+..+++....+|+.++|||+|++++++..+ .. .||.||||||+|+.|+++
T Consensus 482 -----~~~~~~~~~~~~~~l~~a~VI~~T~~~~~~~~L----------------~~-~fd~viIDEA~q~~e~~~ 534 (802)
T 2xzl_A 482 -----KRFVKLVRKTEAEILNKADVVCCTCVGAGDKRL----------------DT-KFRTVLIDESTQASEPEC 534 (802)
T ss_dssp -----HHHHHHHHHHHHHHHHTCSEEEEETTGGGCTTC----------------CS-CCSEEEETTGGGSCHHHH
T ss_pred -----HHHHHHHHHHHHHHHCCCCEEEECHHHCCHHHH----------------HC-CCCEEEEECCCCCCHHHH
T ss_conf -----888999999999875239999833233172777----------------55-699999988503244789
No 4
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A
Probab=1.00 E-value=1 Score=275.62 Aligned_cols=352 Identities=22% Similarity=0.255 Sum_probs=214.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCEEEEEEEECCCCCCCCCCC
Q ss_conf 26566468545896689996459999999999983221015422242250799955440874999996159987444478
Q 000249 1242 HCKLKEVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSSWEDMYYGSLSVLSVERVDDFHLVRFVHDDNDSVTSKIF 1321 (1788)
Q Consensus 1242 ~~~LkkVP~TFsS~eEYi~tFePLLLEE~rAQL~sSleEiss~E~~~~g~IsVlS~ervDdF~lV~f~~~~~d~lk~~~l 1321 (1788)
...+.+|+++|.|..+|.++|.||+..|.+++... .|.... ..+.+......++.....|..+.. .....+
T Consensus 172 ~~~~~~v~~~y~~~~~Y~~~~~~l~~lE~~~~~~~--~e~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~l 242 (800)
T 2wjy_A 172 DEEPQHVLLRYEDAYQYQNIFGPLVKLEADYDKKL--KESQTQ-----DNITVRWDLGLNKKRIAYFTLPKT--DSDMRL 242 (800)
T ss_dssp --CCCCCCSCCSCHHHHHHHHHHHHHHHHHHHHHH--HHHTCE-----EEECCEEEECTTCCEEEEECCCBC--CC--CC
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH--HHHHHC-----CCEEEEEEECCCCEEEEEEEECCC--CCCCCC
T ss_conf 44546634445999999999999999999761434--455422-----662898772689806899995365--578878
Q ss_pred CCCCEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCHHHHHHHHHHCCCCHHHHHCCCCCHHHHH
Q ss_conf 99969999823999999835799999985135788851999999831785102787532101430101320241489899
Q 000249 1322 SENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLRE 1401 (1788)
Q Consensus 1322 segDLVLLSke~P~~s~~~~h~LG~Ve~~e~d~~~~~~~I~IRi~l~n~s~rLnq~~~~L~~~S~w~l~KL~SLTTi~RE 1401 (1788)
..||+|.++...+.. ....+.|.|.+..... ...+.+.+.... ... ......+.+.++.+.+|+.|+
T Consensus 243 ~~GD~v~l~~~~~~~--~~~~~~g~V~~v~~~~---~~~v~l~~~~~~-~~p-------~~~~~~~~v~~~~~~~~~~r~ 309 (800)
T 2wjy_A 243 MQGDEICLRYKGDLA--PLWKGIGHVIKVPDNY---GDEIAIELRSSV-GAP-------VEVTHNFQVDFVWKSTSFDRM 309 (800)
T ss_dssp CTTCEEEEEECSSSS--CCEEEEEEEEECSBTT---BSCEEEEESCCT-TCC-------TTCCSCEEEEECCCCHHHHHH
T ss_pred CCCCEEEEEECCCCC--CCCEEEEEEEEECCCC---CCEEEEEECCCC-CCC-------CCCCCCCEEEEEECCCHHHHH
T ss_conf 999989999788878--8734589999976788---888999982688-884-------003777049996068759999
Q ss_pred HHHHCCCCCC--C----CCCCCCCCCCCCCCCCCCCCCCCCCHHH-HHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCEE
Q ss_conf 9840439889--9----6000049988888877874342242136-7878501899989999999980499986777616
Q 000249 1402 FHALSSLKSI--P----LLPIILNPVNVSRGYNESRELDLGKLSQ-LQQILKTSFNESQLQAISVAIGLSSSWKKDCELS 1474 (1788)
Q Consensus 1402 y~AL~sL~~l--P----L~~~ILsP~~~~~~~~~s~~v~~~~ip~-L~~~Lk~~LNeSQleAI~aALs~~~~~~~~~gIs 1474 (1788)
+.||..+... . +...++....+..... ..+|. +.......+|++|.+||..++.. +++
T Consensus 310 ~~aL~~~~~~e~~~~~~l~~~ll~~~~~~~~~~-------~~l~~~~~~~~~~~Ln~~Q~~Av~~~l~~--------~~~ 374 (800)
T 2wjy_A 310 QSALKTFAVDETSVSGYIYHKLLGHEVEDVIIK-------CQLPKRFTAQGLPDLNHSQVYAVKTVLQR--------PLS 374 (800)
T ss_dssp HHHHHHHHHCTTSBCHHHHHHHTTCCCCCCCCC-------CCCCSCCSCTTSCCCCHHHHHHHHHHHTS--------SEE
T ss_pred HHHHHHHHHHHCCHHHHHHHHHCCCCCCCHHHC-------CCCCCCCCCCCCCCCCHHHHHHHHHHCCC--------CEE
T ss_conf 999999987400116899998518888713322-------45720036434667799999999874259--------917
Q ss_pred EEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 78678999824579999999996038997545557565557887665147999788889998531122101124544446
Q 000249 1475 LIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSV 1554 (1788)
Q Consensus 1475 LIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~avar~W~~~alarql~~d~~~~~~s~~~~~ 1554 (1788)
+||||||||||+|+..++..++.. .
T Consensus 375 lI~GppGTGKT~ti~~~i~~l~~~-------------------------------------------------------~ 399 (800)
T 2wjy_A 375 LIQGPPGTGKTVTSATIVYHLARQ-------------------------------------------------------G 399 (800)
T ss_dssp EEECCTTSCHHHHHHHHHHHHHTT-------------------------------------------------------C
T ss_pred EEECCCCCCHHHHHHHHHHHHHHC-------------------------------------------------------C
T ss_conf 998699999899999999999974-------------------------------------------------------8
Q ss_pred CCEEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCC--CCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 8719999075589999999988259768999866894889834555--46888543178999999898520369975200
Q 000249 1555 RARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKT--VHPNSLPFFIDTLVDHRLAEERMHLTDPKNEF 1632 (1788)
Q Consensus 1555 k~RILVCAPSNAAVDEIV~RLlk~GI~d~dGk~ykP~IVRIG~~~a--ihs~vl~vsLD~LV~qrL~~e~~~~~d~k~~~ 1632 (1788)
+.+||||||||.|+|++.+|+.+.|+ +++|+|...+ +...+..++++.++... +.
T Consensus 400 ~~~ilv~a~tn~A~~~l~~~l~~~g~----------~vvRlg~~~r~~i~~~~~~~tlh~~~~~~---------~~---- 456 (800)
T 2wjy_A 400 NGPVLVCAPSNIAVDQLTEKIHQTGL----------KVVRLCAKSREAIDSPVSFLALHNQIRNM---------DS---- 456 (800)
T ss_dssp SSCEEEEESSHHHHHHHHHHHHTTTC----------CEEECCCGGGGGCCCTTGGGBHHHHHHTC---------TT----
T ss_pred CCCEEEECCCHHHHHHHHHHHHHHCC----------CEEEECCCCHHHHCCHHHHHHHHHHHHCC---------CC----
T ss_conf 98199986968999999999987275----------41762332143313615565399999727---------64----
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 12215899999999989999998640246899999886421112488766566999999999999999999999899999
Q 000249 1633 CTRSSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQ 1712 (1788)
Q Consensus 1633 ~~e~s~Lr~kLekL~~ei~~~ea~R~~~~~g~~~~k~~l~~~~~kg~~~gls~~eL~~kL~kL~eqrrqL~~eL~~~~~~ 1712 (1788)
. .++.++.. .+.. . +.++...
T Consensus 457 ---~----~~l~~l~~-------~~~~--~------------------~~~~~~~------------------------- 477 (800)
T 2wjy_A 457 ---M----PELQKLQQ-------LKDE--T------------------GELSSAD------------------------- 477 (800)
T ss_dssp ---C----HHHHHHHH-------HHTT--T------------------SCCCHHH-------------------------
T ss_pred ---H----HHHHHHHH-------HHHH--H------------------CCCCHHH-------------------------
T ss_conf ---9----99999999-------9875--3------------------3468678-------------------------
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf 877999999999999998850595999817788777533444444676569999899999999926842100247
Q 000249 1713 EKKSYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHE 1787 (1788)
Q Consensus 1713 ekk~~rele~~Rrkir~~IL~eAdIVCSTLSGSGsell~~c~et~aaakf~~l~~~~~FDtVIIDEAAQAvElSt 1787 (1788)
.++.+..++.+..++|++++|||+|++++++..+ ....||+||||||+|+.|+++
T Consensus 478 ----~~~~~~~~~~~~~~~l~~a~VI~~T~~~~~~~~l----------------~~~~fd~viIDEAsQ~~e~~~ 532 (800)
T 2wjy_A 478 ----EKRYRALKRTAERELLMNADVICCTCVGAGDPRL----------------AKMQFRSILIDESTQATEPEC 532 (800)
T ss_dssp ----HHHHHHHHHHHHHHHHHHCSEEEEETGGGGCTTT----------------TTCCCSEEEETTGGGSCHHHH
T ss_pred ----HHHHHHHHHHHHHHHHCCCCEEEECHHHHCCHHH----------------HCCCCCEEEEECCCCCCCHHH
T ss_conf ----9999999987777543369899974045287245----------------458989899989778776999
No 5
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
Probab=1.00 E-value=1 Score=95.72 Aligned_cols=66 Identities=26% Similarity=0.375 Sum_probs=55.4
Q ss_pred HCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 01899989999999980499986777616786789998245799999999960389975455575655578876651479
Q 000249 1446 KTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAA 1525 (1788)
Q Consensus 1446 k~~LNeSQleAI~aALs~~~~~~~~~gIsLIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~a 1525 (1788)
...||+.|.+|+..++.. ++.+|+||||||||+|+.+++..+...
T Consensus 187 ~~~L~~~Q~~Av~~~~~~--------~~~~I~G~pGTGKTt~i~~l~~~l~~~--------------------------- 231 (574)
T 3e1s_A 187 RKGLSEEQASVLDQLAGH--------RLVVLTGGPGTGKSTTTKAVADLAESL--------------------------- 231 (574)
T ss_dssp TTTCCHHHHHHHHHHTTC--------SEEEEECCTTSCHHHHHHHHHHHHHHT---------------------------
T ss_pred CCCCCHHHHHHHHHHHHC--------CEEEEECCCCCCHHHHHHHHHHHHHHC---------------------------
T ss_conf 379999999999999768--------879999599998899999999999856---------------------------
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHH
Q ss_conf 99788889998531122101124544446871999907558999999998
Q 000249 1526 IARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRI 1575 (1788)
Q Consensus 1526 var~W~~~alarql~~d~~~~~~s~~~~~k~RILVCAPSNAAVDEIV~RL 1575 (1788)
+.+|++||||+.|.+++.+++
T Consensus 232 -----------------------------g~~Vl~~ApT~~Aa~~L~e~~ 252 (574)
T 3e1s_A 232 -----------------------------GLEVGLCAPTGKAARRLGEVT 252 (574)
T ss_dssp -----------------------------TCCEEEEESSHHHHHHHHHHH
T ss_pred -----------------------------CCEEEEECCCHHHHHHHHHHH
T ss_conf -----------------------------982999648589999767663
No 6
>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*
Probab=1.00 E-value=1 Score=94.80 Aligned_cols=26 Identities=19% Similarity=0.204 Sum_probs=16.7
Q ss_pred CCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf 95999817788777533444444676569999899999999926842
Q 000249 1735 AEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQ 1781 (1788)
Q Consensus 1735 AdIVCSTLSGSGsell~~c~et~aaakf~~l~~~~~FDtVIIDEAAQ 1781 (1788)
..|.++|+.+|- ..+|++|+|=-..+
T Consensus 552 ~~V~l~TiH~aK---------------------GLEf~~Vfl~gl~e 577 (647)
T 3lfu_A 552 DAVQLMTLHSAK---------------------GLEFPQVFIVGMEE 577 (647)
T ss_dssp CCEEEEETGGGT---------------------TCCEEEEEECCCBT
T ss_pred CCEEEEEEECCC---------------------CCCCCEEEEECCCC
T ss_conf 957999600025---------------------76677799927767
No 7
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*
Probab=1.00 E-value=1 Score=89.45 Aligned_cols=67 Identities=31% Similarity=0.459 Sum_probs=50.1
Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 99899999999804999867776167867899982457999999999603899754555756555788766514799978
Q 000249 1450 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARA 1529 (1788)
Q Consensus 1450 NeSQleAI~aALs~~~~~~~~~gIsLIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~avar~ 1529 (1788)
++.|..||..++.. ++.+|+||||||||+|+..++..+.....
T Consensus 151 ~~~Q~~Ai~~~l~~--------~~~vi~G~pGTGKTt~l~~ll~~l~~~~~----------------------------- 193 (608)
T 1w36_D 151 INWQKVAAAVALTR--------RISVISGGPGTGKTTTVAKLLAALIQMAD----------------------------- 193 (608)
T ss_dssp CCHHHHHHHHHHTB--------SEEEEECCTTSTHHHHHHHHHHHHHHTCS-----------------------------
T ss_pred CHHHHHHHHHHHCC--------CCEEEEECCCCCHHHHHHHHHHHHHHHHH-----------------------------
T ss_conf 99999999999629--------98999949999789999999999998630-----------------------------
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHH
Q ss_conf 88899985311221011245444468719999075589999999988
Q 000249 1530 WQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRIS 1576 (1788)
Q Consensus 1530 W~~~alarql~~d~~~~~~s~~~~~k~RILVCAPSNAAVDEIV~RLl 1576 (1788)
..+.+|++||||+.|.+++.+.+.
T Consensus 194 -----------------------~~~~~vll~APTg~AA~~L~e~~~ 217 (608)
T 1w36_D 194 -----------------------GERCRIRLAAPTGKAAARLTESLG 217 (608)
T ss_dssp -----------------------SCCCCEEEEBSSHHHHHHHHHHHT
T ss_pred -----------------------CCCCEEEEEECCHHHHHHHHHHHH
T ss_conf -----------------------579759999187368999999999
No 8
>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}
Probab=1.00 E-value=1 Score=87.85 Aligned_cols=71 Identities=27% Similarity=0.361 Sum_probs=53.3
Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 18999899999999804999867776167867899982457999999999603899754555756555788766514799
Q 000249 1447 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1526 (1788)
Q Consensus 1447 ~~LNeSQleAI~aALs~~~~~~~~~gIsLIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~av 1526 (1788)
..+|+.|.+|+...+..- ....++.+|+||||||||+++..++..+....
T Consensus 24 ~~Ln~~Q~~av~~~~~~i---~~~~~~~li~G~aGTGKT~ll~~~~~~l~~~~--------------------------- 73 (459)
T 3upu_A 24 DDLTEGQKNAFNIVMKAI---KEKKHHVTINGPAGTGATTLTKFIIEALISTG--------------------------- 73 (459)
T ss_dssp SCCCHHHHHHHHHHHHHH---HSSSCEEEEECCTTSCHHHHHHHHHHHHHHTT---------------------------
T ss_pred CCCCHHHHHHHHHHHHHH---HCCCCEEEEEECCCCCHHHHHHHHHHHHHHCC---------------------------
T ss_conf 348999999999999987---36897799996999989999999999998649---------------------------
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHH
Q ss_conf 9788889998531122101124544446871999907558999999998
Q 000249 1527 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRI 1575 (1788)
Q Consensus 1527 ar~W~~~alarql~~d~~~~~~s~~~~~k~RILVCAPSNAAVDEIV~RL 1575 (1788)
..+|++|||||.|.+++..++
T Consensus 74 ----------------------------~~~il~~a~T~~Aa~~l~~~~ 94 (459)
T 3upu_A 74 ----------------------------ETGIILAAPTHAAKKILSKLS 94 (459)
T ss_dssp ----------------------------CCCEEEEESSHHHHHHHHHHH
T ss_pred ----------------------------CCEEEEECCCHHHHHHHHHHH
T ss_conf ----------------------------960999667578999887661
No 9
>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*
Probab=1.00 E-value=1 Score=65.83 Aligned_cols=65 Identities=25% Similarity=0.372 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf 89998999999998049998677761678678999824579999999996038997545557565557887665147999
Q 000249 1448 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1527 (1788)
Q Consensus 1448 ~LNeSQleAI~aALs~~~~~~~~~gIsLIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~ava 1527 (1788)
++|+.|.+||. ...+-.||.|.||||||+|++.-|..++..
T Consensus 10 ~~t~eQ~~~i~----------~~~~~~~v~a~AGSGKT~vl~~ri~~ll~~----------------------------- 50 (1232)
T 3u4q_A 10 TWTDDQWNAIV----------STGQDILVAAAAGSGKTAVLVERMIRKITA----------------------------- 50 (1232)
T ss_dssp CCCHHHHHHHH----------CCSSCEEEEECTTCCHHHHHHHHHHHHHSC-----------------------------
T ss_pred CCCHHHHHHHH----------CCCCCEEEEECCCCCHHHHHHHHHHHHHHC-----------------------------
T ss_conf 98999999983----------899998999659876899999999999866-----------------------------
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCC---CCCEEEEEECCHHHHHHHHHHH
Q ss_conf 78888999853112210112454444---6871999907558999999998
Q 000249 1528 RAWQDAALARQINEDSERDKKSSESS---VRARVLICAQSNAAVDELVSRI 1575 (1788)
Q Consensus 1528 r~W~~~alarql~~d~~~~~~s~~~~---~k~RILVCAPSNAAVDEIV~RL 1575 (1788)
.. ...+||+.+++|+|.+|+-.|+
T Consensus 51 ------------------------~~~~~~~~~il~~Tft~~aa~e~~~ri 77 (1232)
T 3u4q_A 51 ------------------------EENPIDVDRLLVVTFTNASAAEMKHRI 77 (1232)
T ss_dssp ------------------------SSSCCCGGGEEEECSSHHHHHHHHHHH
T ss_pred ------------------------CCCCCCCCCEEEEECCHHHHHHHHHHH
T ss_conf ------------------------787898021588854699999999999
No 10
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}
Probab=1.00 E-value=1 Score=60.59 Aligned_cols=58 Identities=24% Similarity=0.400 Sum_probs=0.0
Q ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 77761678678999824579999999996038997545557565557887665147999788889998531122101124
Q 000249 1469 KDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKK 1548 (1788)
Q Consensus 1469 ~~~gIsLIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~avar~W~~~alarql~~d~~~~~~ 1548 (1788)
....+++|.||||||||+.|..++.
T Consensus 159 ~~~~v~~I~G~aGsGKTt~I~~~~~------------------------------------------------------- 183 (446)
T 3vkw_A 159 SSAKVVLVDGVPGCGKTKEILSRVN------------------------------------------------------- 183 (446)
T ss_dssp CCSEEEEEEECTTSCHHHHHHHHCC-------------------------------------------------------
T ss_pred CCCCEEEEECCCCCCHHHHHHHHHC-------------------------------------------------------
T ss_conf 6531899992798988999999863-------------------------------------------------------
Q ss_pred CCCCCCCCEEEEEECCHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 544446871999907558999999998825976899986
Q 000249 1549 SSESSVRARVLICAQSNAAVDELVSRISKEGLYGSDGKT 1587 (1788)
Q Consensus 1549 s~~~~~k~RILVCAPSNAAVDEIV~RLlk~GI~d~dGk~ 1587 (1788)
..++||++|+|+|.+++-.++.+.|........
T Consensus 184 ------~~~~lVlTpT~~aa~~l~~kl~~~~~~~~~~~~ 216 (446)
T 3vkw_A 184 ------FEEDLILVPGRQAAEMIRRRANASGIIVATKDN 216 (446)
T ss_dssp ------TTTCEEEESCHHHHHHHHHHHTTTSCCCCCTTT
T ss_pred ------CCCEEEEECCHHHHHHHHHHHHHCCCCCCCCCE
T ss_conf ------087299908889999999986542766556515
Done!