Query 000248
Match_columns 1789
No_of_seqs 283 out of 1698
Neff 4.3
Searched_HMMs 29240
Date Tue Mar 26 16:01:41 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000248.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_28-31//hhsearch_pdb/000248hhsearch_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 1 334.6 26.5 365 1255-1789 3-384 (646)
2 2gk6_A Regulator of nonsense t 1.0 1 1 280.7 25.6 347 1248-1788 1-356 (624)
3 2xzl_A ATP-dependent helicase 1.0 1 1 275.7 28.1 352 1243-1788 174-534 (802)
4 2wjy_A Regulator of nonsense t 1.0 1 1 271.9 29.8 352 1243-1788 172-532 (800)
5 3e1s_A Exodeoxyribonuclease V, 1.0 1 1 95.1 9.2 66 1447-1576 187-252 (574)
6 3lfu_A DNA helicase II; SF1 he 1.0 1 1 94.4 9.3 25 1557-1581 348-372 (647)
7 1w36_D RECD, exodeoxyribonucle 1.0 1 1 89.0 8.8 67 1451-1577 151-217 (608)
8 3upu_A ATP-dependent DNA helic 1.0 1 1 87.2 9.3 71 1448-1576 24-94 (459)
9 1uaa_A REP helicase, protein ( 1.0 1 1 77.6 7.4 26 210-235 47-73 (673)
10 1pjr_A PCRA; DNA repair, DNA r 1.0 1 1 76.9 8.3 19 672-690 354-372 (724)
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=334.63 Aligned_cols=365 Identities=24% Similarity=0.278 Sum_probs=230.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CC-CCCCCC----EEEEEEEEE-ECCEEEEEEEECCC---CCCCCCCCC
Q ss_conf 96689996459999999999972110025--43-224225----079995544-18749999861599---874444789
Q 000248 1255 SPEQFVSIFRPLVLEEFKAQLHSSFLEMS--SW-EDMYYG----SLSVLSVER-VDDFHLVRFVHDDN---DSVTSKIFS 1323 (1789)
Q Consensus 1255 SveEYi~tFePLLLEE~rAQLqsSleEis--sa-Ed~~~g----~IsVlS~er-vDdF~lV~f~~~~~---d~le~~~ls 1323 (1789)
+.++|++.|.+||..|..+++.+...... +. +....| .+.+.+... .++.+.+.|..... ...+...|.
T Consensus 3 ~~~~~~~~~~~Ll~~E~~~e~~~~~~~~~~~~~~~~~~~G~~~~~l~~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~~~~ 82 (646)
T 4b3f_X 3 AVESFVTKQLDLLELERDAEVEERRSWQENISLKELQSRGVCLLKLQVSSQRTGLYGRLLVTFEPRRYGSAAALPSNSFT 82 (646)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCHHHHGGGTSEEEEEEEEEEEECSSSCEEEEEEESCC---CCCCCCCCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCEECCEEEEEEEECCCCEEEEEEEECCCCCCCCCCCCCCC
T ss_conf 18999999999999999999999999986299999996796032648888896579859999983577887778667899
Q ss_pred CCCEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCHHHHHHHHHHCCCCHHHHHCCCCCHHHHHH
Q ss_conf 99699998239999998357999999851257788519999998227850037875321014401013202413898999
Q 000248 1324 ENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLREF 1403 (1789)
Q Consensus 1324 egDLVLLSke~Pe~s~~~~h~LG~Ve~~e~d~~r~~~iL~IRi~L~n~ssrLnq~~~~L~~~S~w~l~KL~SLTTi~REy 1403 (1789)
.||+|+++...+... ..+.|+|.+...+ .+++++.... .....+.....|.+.++.|.+|+.|++
T Consensus 83 ~Gd~v~~~~~~~~~~---~~~~g~v~~~~~~------~i~v~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~r~~ 147 (646)
T 4b3f_X 83 SGDIVGLYDAANEGS---QLATGILTRVTQK------SVTVAFDESH------DFQLSLDRENSYRLLKLANDVTYRRLK 147 (646)
T ss_dssp TTCEEEEEETTTTSC---CCEEEEEEEEETT------EEEEECC-------------CCCSSCCEEEEEECCHHHHHHHH
T ss_pred CCCEEEEEECCCCCC---CEEEEEEEEEECC------EEEEEECCCC------CCCCCCCCCCCEEEEEECCCHHHHHHH
T ss_conf 899899996689987---1489999999499------9999988865------333355789847999806606899999
Q ss_pred HHHCCCCCCC------CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCEEEE
Q ss_conf 8605488899------6000049988888877874342242136787850179998999999998049998667761578
Q 000248 1404 HALSSLKSIP------LLPIILNPVNVSRGYNESRELDLGKLSQLQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLI 1477 (1789)
Q Consensus 1404 ~AL~sL~~lP------L~d~ILsP~~~~~~~~~s~~v~~~~ip~L~~~Lk~~LNeSQleAI~sALs~~~~~~~~~gISLI 1477 (1789)
.||..+...+ +.+.|+...++.+... ... ..+++.+||++|.+||..++... +++||
T Consensus 148 ~al~~l~~~~~~~~~~l~~~l~~~~~p~~~~~-~~~---------~~~~~~~LN~~Q~~AV~~al~~~-------~~~lI 210 (646)
T 4b3f_X 148 KALIALKKYHSGPASSLIEVLFGRSAPSPASE-IHP---------LTFFNTCLDTSQKEAVLFALSQK-------ELAII 210 (646)
T ss_dssp HHHHHHHTCCSSTTHHHHHHHTTSSCCCCCCC-CCC---------CCCSSTTCCHHHHHHHHHHHHCS-------SEEEE
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCC-CCC---------CCCCCCCCCHHHHHHHHHHHCCC-------CCEEE
T ss_conf 99998521246725779998749999997655-576---------53257888999999999996589-------96599
Q ss_pred ECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf 57899971568999999999603899754555766555888766504799988888999753112210112454444687
Q 000248 1478 QGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSVRA 1557 (1789)
Q Consensus 1478 QGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~avar~W~d~alarql~~d~~~~~~s~~~~~k~ 1557 (1789)
|||||||||+||+.+|..++.. +.
T Consensus 211 ~GPPGTGKT~ti~~~I~~l~~~--------------------------------------------------------~~ 234 (646)
T 4b3f_X 211 HGPPGTGKTTTVVEIILQAVKQ--------------------------------------------------------GL 234 (646)
T ss_dssp ECCTTSCHHHHHHHHHHHHHHT--------------------------------------------------------TC
T ss_pred ECCCCCCHHHHHHHHHHHHHHC--------------------------------------------------------CC
T ss_conf 8899988899999999999848--------------------------------------------------------98
Q ss_pred EEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 19999075589999999988258768999867893889844554368875431789999998885303699752001220
Q 000248 1558 RVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKTVHPNSLPFFIDTLVDHRLAEERMHLTDPKNEFCTRS 1637 (1789)
Q Consensus 1558 RILVCAPSNAAVDEIV~RLlk~GI~d~dGk~ykPnIVRIG~~eaIhs~Vk~vsLD~LV~qrLs~e~~~~~dak~~~~~es 1637 (1789)
+||||||||.|||++++||...| .+++|+|...++++.+..+++|..+... +. ....
T Consensus 235 ~ILv~a~TN~AvD~i~erL~~~~----------~~ilRlG~~~r~~~~~~~~~l~~~~~~~---------~~----~~~~ 291 (646)
T 4b3f_X 235 KVLCCAPSNIAVDNLVERLALCK----------QRILRLGHPARLLESIQQHSLDAVLARS---------DS----AQIV 291 (646)
T ss_dssp CEEEEESSHHHHHHHHHHHHHTT----------CCEEECSCCSSCCHHHHTTBHHHHHTTT---------TC----SSTH
T ss_pred EEEEECCCHHHHHHHHHHHHHCC----------CCEEEECCHHHHHHHHHHHHHHHHHHHC---------HH----HHHH
T ss_conf 29999185188879999998627----------7658823656520255430188898504---------17----8899
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 58999999999899999986402468999998864211124887666669999999999999999999998999998779
Q 000248 1638 STLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQEKKS 1717 (1789)
Q Consensus 1638 S~LrskLekL~~ei~~~ea~R~~~~~g~s~~k~~l~~~~~kg~~~gls~~eLe~kL~kL~eqrrqL~~EL~~~~~~ekk~ 1717 (1789)
..++.+++.+.. ... . ..+...+ .. .. .++. ..
T Consensus 292 ~~~~~~~~~~~~------------~~~-----~-~~~~~~~---~~-~~------------------~~~~-------~l 324 (646)
T 4b3f_X 292 ADIRKDIDQVFV------------KNK-----K-TQDKREK---SN-FR------------------NEIK-------LL 324 (646)
T ss_dssp HHHHHHHTTSST------------TTT-----C-------C---CS-SH------------------HHHH-------HH
T ss_pred HHHHHHHHHHHH------------HHH-----H-HHHHHHH---HH-HH------------------HHHH-------HH
T ss_conf 999988899998------------634-----3-2237888---77-78------------------8999-------99
Q ss_pred HHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCC
Q ss_conf 999999999999988515959998187887675334444445765589998999999999268421002479
Q 000248 1718 YEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHEL 1789 (1789)
Q Consensus 1718 ~rele~~Rrkir~~IL~EAdIICSTLSGSGsells~c~et~aaakf~~ll~~~~FDtVIIDEAAQAVElStL 1789 (1789)
.++++..++....++|.+|+|||+|++++++..... .+....||+||||||+|++|+++|
T Consensus 325 ~~~l~~~~~~~~~~~l~~~~vv~~t~~~a~~~~~~~------------~~~~~~Fd~vIIDEAsQ~~e~~~l 384 (646)
T 4b3f_X 325 RKELKEREEAAMLESLTSANVVLATNTGASADGPLK------------LLPESYFDVVVIDECAQALEASCW 384 (646)
T ss_dssp HHHHHHHHHHHHHHHHHHCSEEEEETTTTCSSSGGG------------GSCTTCCSEEEETTGGGSCHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHH------------HHHHCCCCEEEECCCCCCCHHHHH
T ss_conf 999988888888988763354222201222335887------------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=280.73 Aligned_cols=347 Identities=22% Similarity=0.266 Sum_probs=212.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCCCCE
Q ss_conf 46854489668999645999999999997211002543224225079995544187499998615998744447899969
Q 000248 1248 EVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSSWEDMYYGSLSVLSVERVDDFHLVRFVHDDNDSVTSKIFSENDL 1327 (1789)
Q Consensus 1248 kVP~TFsSveEYi~tFePLLLEE~rAQLqsSleEissaEd~~~g~IsVlS~ervDdF~lV~f~~~~~d~le~~~lsegDL 1327 (1789)
+|+.+|.|..+|+++|.|||..|.+++... .+... . ..+.+......++.+.+.|..+.. .....+..||+
T Consensus 1 ~~~~~~~~~~~y~~~~~~ll~~E~~~~~~~--~~~~~-~----~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~Gd~ 71 (624)
T 2gk6_A 1 PLGSRYEDAYQYQNIFGPLVKLEADYDKKL--KESQT-Q----DNITVRWDLGLNKKRIAYFTLPKT--DSDMRLMQGDE 71 (624)
T ss_dssp --CCCCSSHHHHHHHHHHHHHHHHHHHHHH--HHHTC-E----EEECEEEEECTTSCEEEEEECC---------CCTTCE
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH--HHHHH-C----CCCEEEEEECCCCCEEEEEEECCC--CCCCCCCCCCE
T ss_conf 967765999999999999999999997888--76540-4----582587663478816999970643--35796899998
Q ss_pred EEEEECCCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCHHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHHHC
Q ss_conf 99982399999983579999998512577885199999982278500378753210144010132024138989998605
Q 000248 1328 VLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLREFHALS 1407 (1789)
Q Consensus 1328 VLLSke~Pe~s~~~~h~LG~Ve~~e~d~~r~~~iL~IRi~L~n~ssrLnq~~~~L~~~S~w~l~KL~SLTTi~REy~AL~ 1407 (1789)
|+++...+.. ....+.|.|.+...+. ...+.+.+.... .. . ......+.+.++.+.+|+.|++.||.
T Consensus 72 v~l~~~~~~~--~~~~~~g~v~~~~~~~---~~~v~v~~~~~~-~~------~-~~~~~~~~~~~~~~~~~~~r~~~al~ 138 (624)
T 2gk6_A 72 ICLRYKGDLA--PLWKGIGHVIKVPDNY---GDEIAIELRSSV-GA------P-VEVTHNFQVDFVWKSTSFDRMQSALK 138 (624)
T ss_dssp EEEEECSSSS--CCCEEEEEEEECSCSS---CSEEEEEESCCT-TC------C-CSCCSSEEEEECCCCHHHHHHHHHHH
T ss_pred EEEEECCCCC--CCCEEEEEEEEECCCC---CCEEEEEECCCC-CC------C-CCCCCCEEEEEEECCCHHHHHHHHHH
T ss_conf 9999788888--8747899999964778---878999982688-88------6-33566558999957726999999999
Q ss_pred CCCCC-----C-CCCCCCCCCCCCCCCCCCCCCCCCCHHH-HHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEECC
Q ss_conf 48889-----9-6000049988888877874342242136-787850179998999999998049998667761578578
Q 000248 1408 SLKSI-----P-LLPIILNPVNVSRGYNESRELDLGKLSQ-LQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGP 1480 (1789)
Q Consensus 1408 sL~~l-----P-L~d~ILsP~~~~~~~~~s~~v~~~~ip~-L~~~Lk~~LNeSQleAI~sALs~~~~~~~~~gISLIQGP 1480 (1789)
.+... + +...++....+...... .+|. +.......+|++|.+||..++.. +++|||||
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 99971568999999999603899754555766555888766504799988888999753112210112454444687199
Q 000248 1481 PGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSVRARVL 1560 (1789)
Q Consensus 1481 PGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~avar~W~d~alarql~~d~~~~~~s~~~~~k~RIL 1560 (1789)
||||||+||..++..++.. .+.+||
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 99075589999999988258768999867893889844554--3688754317899999988853036997520012205
Q 000248 1561 ICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKT--VHPNSLPFFIDTLVDHRLAEERMHLTDPKNEFCTRSS 1638 (1789)
Q Consensus 1561 VCAPSNAAVDEIV~RLlk~GI~d~dGk~ykPnIVRIG~~ea--Ihs~Vk~vsLD~LV~qrLs~e~~~~~dak~~~~~esS 1638 (1789)
||||||.|+|++.+|+.+.|+ +++|+|...+ +...+..++++.++.. .+. .
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 89999999998999999864024689999988642111248876666699999999999999999999989999987799
Q 000248 1639 TLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQEKKSY 1718 (1789)
Q Consensus 1639 ~LrskLekL~~ei~~~ea~R~~~~~g~s~~k~~l~~~~~kg~~~gls~~eLe~kL~kL~eqrrqL~~EL~~~~~~ekk~~ 1718 (1789)
.++.++.. .+ + ..+.++... .
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 9999999999998851595999818788767533444444576558999899999999926842100247
Q 000248 1719 EETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHE 1788 (1789)
Q Consensus 1719 rele~~Rrkir~~IL~EAdIICSTLSGSGsells~c~et~aaakf~~ll~~~~FDtVIIDEAAQAVElSt 1788 (1789)
+..+..++.+...+|++++|||+|++++++..+. ...||+||||||+|+.|+++
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=275.72 Aligned_cols=352 Identities=25% Similarity=0.271 Sum_probs=215.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEEECCEEEEEEEECCCCCCCCCCC
Q ss_conf 26566468544896689996459999999999972110025432242250799955441874999986159987444478
Q 000248 1243 HCKLKEVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSSWEDMYYGSLSVLSVERVDDFHLVRFVHDDNDSVTSKIF 1322 (1789)
Q Consensus 1243 ~~~LkkVP~TFsSveEYi~tFePLLLEE~rAQLqsSleEissaEd~~~g~IsVlS~ervDdF~lV~f~~~~~d~le~~~l 1322 (1789)
..++.+||++|.|..+|.++|.||+..|.+++... .+..... .+.+......++.+.+.|..+... .....+
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 99969999823999999835799999985125778851999999822785003787532101440101320241389899
Q 000248 1323 SENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLRE 1402 (1789)
Q Consensus 1323 segDLVLLSke~Pe~s~~~~h~LG~Ve~~e~d~~r~~~iL~IRi~L~n~ssrLnq~~~~L~~~S~w~l~KL~SLTTi~RE 1402 (1789)
..||.|+++...+.. ......|.|.+..... ...+.+++......... .....+.+.++.+.+|+.|+
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 986054888--99----6000049988888877874342242136-7878501799989999999980499986677615
Q 000248 1403 FHALSSLKS--IP----LLPIILNPVNVSRGYNESRELDLGKLSQ-LQQILKTSFNESQLQAISVAIGLSSSWKKDCELS 1475 (1789)
Q Consensus 1403 y~AL~sL~~--lP----L~d~ILsP~~~~~~~~~s~~v~~~~ip~-L~~~Lk~~LNeSQleAI~sALs~~~~~~~~~gIS 1475 (1789)
+.||..+.. .. +.+.++....+...... .+|. +.......+|++|.+||..++.. +++
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 78578999715689999999996038997545557665558887665047999888889997531122101124544446
Q 000248 1476 LIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSV 1555 (1789)
Q Consensus 1476 LIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~avar~W~d~alarql~~d~~~~~~s~~~~~ 1555 (1789)
|||||||||||+||+.++..++.. .
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 8719999075589999999988258768999867893889844554--36887543178999999888530369975200
Q 000248 1556 RARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKT--VHPNSLPFFIDTLVDHRLAEERMHLTDPKNEF 1633 (1789)
Q Consensus 1556 k~RILVCAPSNAAVDEIV~RLlk~GI~d~dGk~ykPnIVRIG~~ea--Ihs~Vk~vsLD~LV~qrLs~e~~~~~dak~~~ 1633 (1789)
+.+||||||||.|+|++.+||.+.|+ +++|+|...+ +...+..++++.++... ..
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 12205899999999989999998640246899999886421112488766666999999999999999999999899999
Q 000248 1634 CTRSSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQ 1713 (1789)
Q Consensus 1634 ~~esS~LrskLekL~~ei~~~ea~R~~~~~g~s~~k~~l~~~~~kg~~~gls~~eLe~kL~kL~eqrrqL~~EL~~~~~~ 1713 (1789)
. .+.++..... . . ++++..+.
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 877999999999999998851595999818788767533444444576558999899999999926842100247
Q 000248 1714 EKKSYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHE 1788 (1789)
Q Consensus 1714 ekk~~rele~~Rrkir~~IL~EAdIICSTLSGSGsells~c~et~aaakf~~ll~~~~FDtVIIDEAAQAVElSt 1788 (1789)
+..+...++....+|+.++|||+|++++++..+ .. .||.||||||+|+.|++.
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=271.90 Aligned_cols=352 Identities=22% Similarity=0.254 Sum_probs=213.9
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEEECCEEEEEEEECCCCCCCCCCC
Q ss_conf 26566468544896689996459999999999972110025432242250799955441874999986159987444478
Q 000248 1243 HCKLKEVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSSWEDMYYGSLSVLSVERVDDFHLVRFVHDDNDSVTSKIF 1322 (1789)
Q Consensus 1243 ~~~LkkVP~TFsSveEYi~tFePLLLEE~rAQLqsSleEissaEd~~~g~IsVlS~ervDdF~lV~f~~~~~d~le~~~l 1322 (1789)
...+.+|+++|.|..+|.++|.||+..|.++.... .+.... ..+.+......++.....|..+.. .....+
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 99969999823999999835799999985125778851999999822785003787532101440101320241389899
Q 000248 1323 SENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLRE 1402 (1789)
Q Consensus 1323 segDLVLLSke~Pe~s~~~~h~LG~Ve~~e~d~~r~~~iL~IRi~L~n~ssrLnq~~~~L~~~S~w~l~KL~SLTTi~RE 1402 (1789)
..||+|.++...+.. ......|.|.+..... ...+.+.+... .... ......+.+.++.+.+|+.|+
T Consensus 243 ~~GD~v~l~~~~~~~--~~~~~~g~V~~v~~~~---~~~v~l~~~~~-~~~p-------~~~~~~~~v~~~~~~~~~~r~ 309 (800)
T 2wjy_A 243 MQGDEICLRYKGDLA--PLWKGIGHVIKVPDNY---GDEIAIELRSS-VGAP-------VEVTHNFQVDFVWKSTSFDRM 309 (800)
T ss_dssp CTTCEEEEEECSSSS--CCEEEEEEEEECSBTT---BSCEEEEESCC-TTCC-------TTCCSCEEEEECCCCHHHHHH
T ss_pred CCCCEEEEEECCCCC--CCCEEEEEEEEECCCC---CCEEEEEECCC-CCCC-------CCCCCCCEEEEEECCCHHHHH
T ss_conf 999989999788878--8734589999976788---88899998268-8884-------003777049996068759999
Q ss_pred HHHHCCCCCC--C----CCCCCCCCCCCCCCCCCCCCCCCCCHHH-HHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCEE
Q ss_conf 9860548889--9----6000049988888877874342242136-7878501799989999999980499986677615
Q 000248 1403 FHALSSLKSI--P----LLPIILNPVNVSRGYNESRELDLGKLSQ-LQQILKTSFNESQLQAISVAIGLSSSWKKDCELS 1475 (1789)
Q Consensus 1403 y~AL~sL~~l--P----L~d~ILsP~~~~~~~~~s~~v~~~~ip~-L~~~Lk~~LNeSQleAI~sALs~~~~~~~~~gIS 1475 (1789)
+.||..+... . +...++....+..... ..+|. +.......+|++|.+||..++.. +++
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 78578999715689999999996038997545557665558887665047999888889997531122101124544446
Q 000248 1476 LIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSV 1555 (1789)
Q Consensus 1476 LIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~avar~W~d~alarql~~d~~~~~~s~~~~~ 1555 (1789)
+||||||||||+||..++..++.. .
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 8719999075589999999988258768999867893889844554--36887543178999999888530369975200
Q 000248 1556 RARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKT--VHPNSLPFFIDTLVDHRLAEERMHLTDPKNEF 1633 (1789)
Q Consensus 1556 k~RILVCAPSNAAVDEIV~RLlk~GI~d~dGk~ykPnIVRIG~~ea--Ihs~Vk~vsLD~LV~qrLs~e~~~~~dak~~~ 1633 (1789)
+.+||||||||.|+|++.+|+.+.|+ +++|+|...+ +...+..++++.++... +.
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 12205899999999989999998640246899999886421112488766666999999999999999999999899999
Q 000248 1634 CTRSSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQ 1713 (1789)
Q Consensus 1634 ~~esS~LrskLekL~~ei~~~ea~R~~~~~g~s~~k~~l~~~~~kg~~~gls~~eLe~kL~kL~eqrrqL~~EL~~~~~~ 1713 (1789)
. .++.++.. .+.. . +.++...
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 877999999999999998851595999818788767533444444576558999899999999926842100247
Q 000248 1714 EKKSYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHE 1788 (1789)
Q Consensus 1714 ekk~~rele~~Rrkir~~IL~EAdIICSTLSGSGsells~c~et~aaakf~~ll~~~~FDtVIIDEAAQAVElSt 1788 (1789)
.++.+..++.+..++|++++|||+|++++++..+ ....||+||||||+|+.|++.
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=95.07 Aligned_cols=66 Identities=26% Similarity=0.391 Sum_probs=55.3
Q ss_pred HCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 01799989999999980499986677615785789997156899999999960389975455576655588876650479
Q 000248 1447 KTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAA 1526 (1789)
Q Consensus 1447 k~~LNeSQleAI~sALs~~~~~~~~~gISLIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~a 1526 (1789)
...+|+.|.+|+..++.. ++.+|+||||||||+|+..++..+..
T Consensus 187 ~~~L~~~Q~~Av~~~~~~--------~~~~I~G~pGTGKTt~i~~l~~~l~~---------------------------- 230 (574)
T 3e1s_A 187 RKGLSEEQASVLDQLAGH--------RLVVLTGGPGTGKSTTTKAVADLAES---------------------------- 230 (574)
T ss_dssp TTTCCHHHHHHHHHHTTC--------SEEEEECCTTSCHHHHHHHHHHHHHH----------------------------
T ss_pred CCCCCHHHHHHHHHHHHC--------CEEEEECCCCCCHHHHHHHHHHHHHH----------------------------
T ss_conf 379999999999999768--------87999959999889999999999985----------------------------
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHH
Q ss_conf 99888889997531122101124544446871999907558999999998
Q 000248 1527 IARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRI 1576 (1789)
Q Consensus 1527 var~W~d~alarql~~d~~~~~~s~~~~~k~RILVCAPSNAAVDEIV~RL 1576 (1789)
.+.+|++||||+.|.+++.+++
T Consensus 231 ----------------------------~g~~Vl~~ApT~~Aa~~L~e~~ 252 (574)
T 3e1s_A 231 ----------------------------LGLEVGLCAPTGKAARRLGEVT 252 (574)
T ss_dssp ----------------------------TTCCEEEEESSHHHHHHHHHHH
T ss_pred ----------------------------CCCEEEEECCCHHHHHHHHHHH
T ss_conf ----------------------------6982999648589999767663
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=94.37 Aligned_cols=25 Identities=24% Similarity=0.209 Sum_probs=13.0
Q ss_pred CEEEEEECCHHHHHHHHHHHHHCCC
Q ss_conf 7199990755899999999882587
Q 000248 1557 ARVLICAQSNAAVDELVSRISKEGL 1581 (1789)
Q Consensus 1557 ~RILVCAPSNAAVDEIV~RLlk~GI 1581 (1789)
..|.|.+++|.-...+...|.+.||
T Consensus 348 ~diaVL~r~~~~~~~l~~~l~~~~I 372 (647)
T 3lfu_A 348 AECAILYRSNAQSRVLEEALLQASM 372 (647)
T ss_dssp GGEEEEESSGGGHHHHHHHHHHTTC
T ss_pred CCEEEEEECCHHHHHHHHHHHHCCC
T ss_conf 6789998474439999999997799
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=89.04 Aligned_cols=67 Identities=31% Similarity=0.459 Sum_probs=50.2
Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 99899999999804999866776157857899971568999999999603899754555766555888766504799988
Q 000248 1451 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARA 1530 (1789)
Q Consensus 1451 NeSQleAI~sALs~~~~~~~~~gISLIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~avar~ 1530 (1789)
++.|..||..++.. ++.+|+||||||||+|+..++..+.....
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 88899975311221011245444468719999075589999999988
Q 000248 1531 WQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRIS 1577 (1789)
Q Consensus 1531 W~d~alarql~~d~~~~~~s~~~~~k~RILVCAPSNAAVDEIV~RLl 1577 (1789)
..+.+|++||||+.|.+++.+.+.
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=87.22 Aligned_cols=71 Identities=27% Similarity=0.361 Sum_probs=53.3
Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 17999899999999804999866776157857899971568999999999603899754555766555888766504799
Q 000248 1448 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1527 (1789)
Q Consensus 1448 ~~LNeSQleAI~sALs~~~~~~~~~gISLIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~~s~~~~rp~~s~s~av 1527 (1789)
..+|+.|.+|+...+..- ....++.+|+||||||||+++..++..+....
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 9888889997531122101124544446871999907558999999998
Q 000248 1528 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRI 1576 (1789)
Q Consensus 1528 ar~W~d~alarql~~d~~~~~~s~~~~~k~RILVCAPSNAAVDEIV~RL 1576 (1789)
..+|++|||||.|.+++..++
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
>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19
Probab=1.00 E-value=1 Score=77.59 Aligned_cols=26 Identities=19% Similarity=0.457 Sum_probs=11.4
Q ss_pred CEEEEEECCH-HHHHHHHHHHHHHHCC
Q ss_conf 7066641031-5479999999998187
Q 000248 210 PGVFALFFFN-RRVRTIGRRLARSMGK 235 (1789)
Q Consensus 210 Pgvy~lL~h~-~~~R~~a~~~ar~~g~ 235 (1789)
|.-.+.+-|+ .+++....++...+|.
T Consensus 47 ~~~IL~lTfT~~Aa~em~~Rl~~~l~~ 73 (673)
T 1uaa_A 47 ARHIAAVTFTNKAAREMKERVGQTLGR 73 (673)
T ss_dssp GGGEEEEESSHHHHHHHHHHHHHHSCT
T ss_pred HHHEEEEECCHHHHHHHHHHHHHHCCC
T ss_conf 789587854689999999999987073
No 10
>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*
Probab=1.00 E-value=1 Score=76.86 Aligned_cols=19 Identities=21% Similarity=0.279 Sum_probs=8.3
Q ss_pred EECCCCCCHHHHHHHHHHH
Q ss_conf 1002499814767899999
Q 000248 672 ILSLVDPNDNVRQFGKCIL 690 (1789)
Q Consensus 672 il~l~~~~~~~r~~~~~~l 690 (1789)
|--|+-.|...|.+-..+.
T Consensus 354 iAIL~R~~~~~~~le~~L~ 372 (724)
T 1pjr_A 354 FAVLYRTNAQSRVMEEMLL 372 (724)
T ss_dssp EEEEESSGGGHHHHHHHHH
T ss_pred EEEEEECCHHHHHHHHHHH
T ss_conf 3564305214899999998
Done!