Query 000413
Match_columns 1545
No_of_seqs 275 out of 1673
Neff 4.2
Searched_HMMs 29240
Date Tue Mar 26 16:39:43 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000413.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_192-196//hhsearch_pdb/000413hhsearch_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 1 349.3 26.1 366 1010-1545 2-384 (646)
2 2gk6_A Regulator of nonsense t 1.0 1 1 285.2 29.5 348 1004-1544 1-356 (624)
3 2xzl_A ATP-dependent helicase 1.0 1 1 283.0 26.9 353 999-1544 174-534 (802)
4 2wjy_A Regulator of nonsense t 1.0 1 1 280.7 28.6 352 999-1544 172-532 (800)
5 3e1s_A Exodeoxyribonuclease V, 1.0 1 1 97.0 9.3 66 1203-1332 187-252 (574)
6 3lfu_A DNA helicase II; SF1 he 1.0 1 1 94.3 9.2 15 1525-1539 564-578 (647)
7 1w36_D RECD, exodeoxyribonucle 1.0 1 1 90.3 9.0 67 1207-1333 151-217 (608)
8 3upu_A ATP-dependent DNA helic 1.0 1 1 89.0 9.4 71 1204-1332 24-94 (459)
9 1uaa_A REP helicase, protein ( 1.0 1 1 76.3 8.6 22 584-605 180-201 (673)
10 1pjr_A PCRA; DNA repair, DNA r 1.0 1 1 75.4 9.7 24 583-606 188-211 (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=349.33 Aligned_cols=366 Identities=23% Similarity=0.271 Sum_probs=233.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCCCCCE----EEEEEEE-EECCEEEEEEEECCC---CCCCCCCC
Q ss_conf 6956799854467999999999842310144---33342250----7999554-408739999960599---87444478
Q 000413 1010 QSPEQFVSIFRPLVLEEFKAQLHSSFLEMSS---WEDMYYGS----LSVLSVE-RVDDFHLVRFVHDDN---DSVTSKIF 1078 (1545)
Q Consensus 1010 sSveEYl~vFePLLLEE~rAQL~sS~eEiss---aE~~~~g~----IsVlSle-rvDdF~lVkfs~~~~---d~le~~~f 1078 (1545)
.++++|++.|.+||..|..+++.+....... .+....|. +.+.+.. ..++.+.++|..... ...+...|
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 CCCCEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCCHHHHHHHHHCCCCEEEHHCCCCCHHHHH
Q ss_conf 99969999823999999733599999985125788851999999931785003787642201441000210231477699
Q 000413 1079 SENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLRE 1158 (1545)
Q Consensus 1079 sEGDLVLLSk~kPe~s~~~~~~LGkVerie~dnkr~~~iItIRl~L~n~ssrLnq~~~~L~~rSkW~l~KL~SLTTi~RE 1158 (1545)
..||+|+++...+... ..+.|.|.++..+ .+++++.-.. .....+.....|.+.++.|.+|+.|+
T Consensus 82 ~~Gd~v~~~~~~~~~~---~~~~g~v~~~~~~------~i~v~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~r~ 146 (646)
T 4b3f_X 82 TSGDIVGLYDAANEGS---QLATGILTRVTQK------SVTVAFDESH------DFQLSLDRENSYRLLKLANDVTYRRL 146 (646)
T ss_dssp CTTCEEEEEETTTTSC---CCEEEEEEEEETT------EEEEECC-------------CCCSSCCEEEEEECCHHHHHHH
T ss_pred CCCCEEEEEECCCCCC---CEEEEEEEEEECC------EEEEEECCCC------CCCCCCCCCCCEEEEEECCCHHHHHH
T ss_conf 9899899996689987---1489999999499------9999988865------33335578984799980660689999
Q ss_pred HHHHCCCCCCC------CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCEEE
Q ss_conf 98403298899------722215888888888887334223123788886017899999999999804999866766178
Q 000413 1159 FHALSSLKSIP------LLPIILNPVNVSRGYNESRELDLGKLSQLQQILKTSFNESQLQAISVAIGLSSSWKKDCELSL 1232 (1545)
Q Consensus 1159 y~AL~sL~~~P------L~d~ILsP~~~~~~~~~s~~v~~~kip~L~~~Lk~~LNeSQ~qAI~aALs~~~~~~~~~gitL 1232 (1545)
+.||..+.... +.+.|++..++.+.... .. ..+++.+||++|.+||..|+... +++|
T Consensus 147 ~~al~~l~~~~~~~~~~l~~~l~~~~~p~~~~~~-~~---------~~~~~~~LN~~Q~~AV~~al~~~-------~~~l 209 (646)
T 4b3f_X 147 KKALIALKKYHSGPASSLIEVLFGRSAPSPASEI-HP---------LTFFNTCLDTSQKEAVLFALSQK-------ELAI 209 (646)
T ss_dssp HHHHHHHHTCCSSTTHHHHHHHTTSSCCCCCCCC-CC---------CCCSSTTCCHHHHHHHHHHHHCS-------SEEE
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCC-CC---------CCCCCCCCCHHHHHHHHHHHCCC-------CCEE
T ss_conf 9999985212467257799987499999976555-76---------53257888999999999996589-------9659
Q ss_pred EECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 85589997057899999999960489975455576655578876641489998888899974311221111244456699
Q 000413 1233 IQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSVR 1312 (1545)
Q Consensus 1233 IQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~ss~~~~rp~~s~s~avar~W~daala~ql~~d~~~~~~ss~~~~k 1312 (1545)
||||||||||+||+.+|..++.. +
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 82999928728899999999826977899986789566974545447888543179999999988530269976411222
Q 000413 1313 ARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKTVHPNSLPFFIDTLVDHRLAEERMHLTDPKNEFCTR 1392 (1545)
Q Consensus 1313 ~RILVCAPSNAAVDEIV~RLl~~GI~d~dGk~ykPnIVRIG~~eaIhs~V~dVsLD~LVeqrL~~e~m~~~~sk~d~~~~ 1392 (1545)
.+||||||||.||||+++||...+ .+++|+|...+++..+..+++|..+... +....
T Consensus 234 ~~ILv~a~TN~AvD~i~erL~~~~----------~~ilRlG~~~r~~~~~~~~~l~~~~~~~-------------~~~~~ 290 (646)
T 4b3f_X 234 LKVLCCAPSNIAVDNLVERLALCK----------QRILRLGHPARLLESIQQHSLDAVLARS-------------DSAQI 290 (646)
T ss_dssp CCEEEEESSHHHHHHHHHHHHHTT----------CCEEECSCCSSCCHHHHTTBHHHHHTTT-------------TCSST
T ss_pred CEEEEECCCHHHHHHHHHHHHHCC----------CCEEEECCHHHHHHHHHHHHHHHHHHHC-------------HHHHH
T ss_conf 829999185188879999998627----------7658823656520255430188898504-------------17889
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 14799999999999999999861126999999887643334687766667999999999899999999999798999766
Q 000413 1393 SSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQEKK 1472 (1545)
Q Consensus 1393 ss~Lr~eLekL~~~Ir~~ea~R~~~~~~~~d~~~~l~~~s~kg~~~~lsd~eLe~kL~kL~~qRrql~~eL~~~~~kekk 1472 (1545)
...++.+++.+.. .. + ...+...+ ..+..++..
T Consensus 291 ~~~~~~~~~~~~~----------~~-------~-~~~~~~~~----------------------~~~~~~~~~------- 323 (646)
T 4b3f_X 291 VADIRKDIDQVFV----------KN-------K-KTQDKREK----------------------SNFRNEIKL------- 323 (646)
T ss_dssp HHHHHHHHTTSST----------TT-------T-C------C----------------------CSSHHHHHH-------
T ss_pred HHHHHHHHHHHHH----------HH-------H-HHHHHHHH----------------------HHHHHHHHH-------
T ss_conf 9999988899998----------63-------4-32237888----------------------777889999-------
Q ss_pred HHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCC
Q ss_conf 7999999999999977237929998188777563223344456765599999998769999168433012479
Q 000413 1473 SYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHEL 1545 (1545)
Q Consensus 1473 ~~re~e~~Rrkir~eIL~EAdVVCSTLSGSG~ell~~c~e~~~~~kf~~~~~~~~FDtVIIDEAAQAVElStl 1545 (1545)
..++.+..++....++|..|+|||+|++++++...... .....||+||||||+|+.|+++|
T Consensus 324 l~~~l~~~~~~~~~~~l~~~~vv~~t~~~a~~~~~~~~------------~~~~~Fd~vIIDEAsQ~~e~~~l 384 (646)
T 4b3f_X 324 LRKELKEREEAAMLESLTSANVVLATNTGASADGPLKL------------LPESYFDVVVIDECAQALEASCW 384 (646)
T ss_dssp HHHHHHHHHHHHHHHHHHHCSEEEEETTTTCSSSGGGG------------SCTTCCSEEEETTGGGSCHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHH------------HHHCCCCEEEECCCCCCCHHHHH
T ss_conf 99999888888889887633542222012223358876------------43126888997175444557887
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=285.25 Aligned_cols=348 Identities=22% Similarity=0.239 Sum_probs=213.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCCCCE
Q ss_conf 23733369567998544679999999998423101443334225079995544087399999605998744447899969
Q 000413 1004 EVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSSWEDMYYGSLSVLSVERVDDFHLVRFVHDDNDSVTSKIFSENDL 1083 (1545)
Q Consensus 1004 kIP~TFsSveEYl~vFePLLLEE~rAQL~sS~eEissaE~~~~g~IsVlSlervDdF~lVkfs~~~~d~le~~~fsEGDL 1083 (1545)
+|+.+|.|..+|+++|.|||..|.+++... .|.. .. ..+.+......++.+...|..+.. .....+..||+
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 EEEEECCCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCCHHHHHHHHHCCCCEEEHHCCCCCHHHHHHHHHC
Q ss_conf 99982399999973359999998512578885199999993178500378764220144100021023147769998403
Q 000413 1084 VLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLREFHALS 1163 (1545)
Q Consensus 1084 VLLSk~kPe~s~~~~~~LGkVerie~dnkr~~~iItIRl~L~n~ssrLnq~~~~L~~rSkW~l~KL~SLTTi~REy~AL~ 1163 (1545)
|+++...+.. ....+.|.|.++.... ...+.+.+..... . +. .....+.+.++.+.+|+.|++.||.
T Consensus 72 v~l~~~~~~~--~~~~~~g~v~~~~~~~---~~~v~v~~~~~~~-~------~~-~~~~~~~~~~~~~~~~~~r~~~al~ 138 (624)
T 2gk6_A 72 ICLRYKGDLA--PLWKGIGHVIKVPDNY---GDEIAIELRSSVG-A------PV-EVTHNFQVDFVWKSTSFDRMQSALK 138 (624)
T ss_dssp EEEEECSSSS--CCCEEEEEEEECSCSS---CSEEEEEESCCTT-C------CC-SCCSSEEEEECCCCHHHHHHHHHHH
T ss_pred EEEEECCCCC--CCCEEEEEEEEECCCC---CCEEEEEECCCCC-C------CC-CCCCCEEEEEEECCCHHHHHHHHHH
T ss_conf 9999788888--8747899999964778---8789999826888-8------63-3566558999957726999999999
Q ss_pred CCCCC-----C-CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEECCC
Q ss_conf 29889-----9-72221588888888888733422312378888601789999999999980499986676617885589
Q 000413 1164 SLKSI-----P-LLPIILNPVNVSRGYNESRELDLGKLSQLQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPP 1237 (1545)
Q Consensus 1164 sL~~~-----P-L~d~ILsP~~~~~~~~~s~~v~~~kip~L~~~Lk~~LNeSQ~qAI~aALs~~~~~~~~~gitLIQGPP 1237 (1545)
.+... + +.+.+++...+........+ ..+..+ ....+|++|.+||..++.. +++||||||
T Consensus 139 ~~~~~~~~~~~~~~~~ll~~~~~~~~~~~~~~-~~~~~~-----~~~~ln~~Q~~av~~~l~~--------~~~li~Gpp 204 (624)
T 2gk6_A 139 TFAVDETSVSGYIYHKLLGHEVEDVIIKCQLP-KRFTAQ-----GLPDLNHSQVYAVKTVLQR--------PLSLIQGPP 204 (624)
T ss_dssp HHHHCTTSBCSHHHHHHTTCCCCCCCCCCCCC-SCCSCT-----TSCCCCHHHHHHHHHHHTC--------SEEEEECCT
T ss_pred HHHHCCCCCHHHHHHHHCCCCCCCCCCCCCCC-CCCCCC-----CCCCCCHHHHHHHHHHHCC--------CCEEEECCC
T ss_conf 98760455127789986188876421245675-212544-----5678999999999999628--------976998999
Q ss_pred CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEE
Q ss_conf 99705789999999996048997545557665557887664148999888889997431122111124445669982999
Q 000413 1238 GTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSVRARVLI 1317 (1545)
Q Consensus 1238 GTGKTkTIvgLIsaLLs~~~~~~s~~~~~~ss~~~~rp~~s~s~avar~W~daala~ql~~d~~~~~~ss~~~~k~RILV 1317 (1545)
|||||+|+..++..++.. .+.+||+
T Consensus 205 GTGKT~~~~~~i~~l~~~-------------------------------------------------------~~~~ilv 229 (624)
T 2gk6_A 205 GTGKTVTSATIVYHLARQ-------------------------------------------------------GNGPVLV 229 (624)
T ss_dssp TSCHHHHHHHHHHHHHTS-------------------------------------------------------SSCCEEE
T ss_pred CCCHHHHHHHHHHHHHHC-------------------------------------------------------CCCEEEE
T ss_conf 987899999999999974-------------------------------------------------------8980999
Q ss_pred EECCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCC--CCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHH
Q ss_conf 9287288999999998269778999867895669745454--47888543179999999988530269976411222147
Q 000413 1318 CAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKT--VHPNSLPFFIDTLVDHRLAEERMHLTDPKNEFCTRSST 1395 (1545)
Q Consensus 1318 CAPSNAAVDEIV~RLl~~GI~d~dGk~ykPnIVRIG~~ea--Ihs~V~dVsLD~LVeqrL~~e~m~~~~sk~d~~~~ss~ 1395 (1545)
|||||.|+|++..|+.+.|+ +++|+|...+ +...+..++++.++.. .+ . .
T Consensus 230 ~a~tn~A~~~l~~~l~~~~~----------~~~R~~~~~r~~~~~~~~~~tl~~~~~~---------~~----~---~-- 281 (624)
T 2gk6_A 230 CAPSNIAVDQLTEKIHQTGL----------KVVRLCAKSREAIDSPVSFLALHNQIRN---------MD----S---M-- 281 (624)
T ss_dssp EESSHHHHHHHHHHHHTTTC----------CEEECCCTGGGSCCCTTTTTBHHHHHTS---------CS----S---C--
T ss_pred EECCHHHHHHHHHHHHHCCC----------EEEEECCCCCHHHCCCHHHHHHHHHHHH---------CC----C---H--
T ss_conf 92718999999999986197----------5896053220111130456659999980---------52----3---6--
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999861126999999887643334687766667999999999899999999999798999766799
Q 000413 1396 LRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQEKKSYE 1475 (1545)
Q Consensus 1396 Lr~eLekL~~~Ir~~ea~R~~~~~~~~d~~~~l~~~s~kg~~~~lsd~eLe~kL~kL~~qRrql~~eL~~~~~kekk~~r 1475 (1545)
.++.++.. . +.....++..+ .+
T Consensus 282 --~~l~~l~~-----------~----------------~~~~~~~~~~~-----------------------------~~ 303 (624)
T 2gk6_A 282 --PELQKLQQ-----------L----------------KDETGELSSAD-----------------------------EK 303 (624)
T ss_dssp --HHHHHHHT-----------T----------------CC----CCHHH-----------------------------HH
T ss_pred --HHHHHHHH-----------H----------------HHHHCCCCHHH-----------------------------HH
T ss_conf --99999999-----------9----------------87642137778-----------------------------99
Q ss_pred HHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf 999999999997723792999818877756322334445676559999999876999916843301247
Q 000413 1476 ETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHE 1544 (1545)
Q Consensus 1476 e~e~~Rrkir~eIL~EAdVVCSTLSGSG~ell~~c~e~~~~~kf~~~~~~~~FDtVIIDEAAQAVElSt 1544 (1545)
..+..++.+...+|++|+|||+|++++|+..+. ...||+||||||+|+.|+++
T Consensus 304 ~~~~~~~~~~~~~l~~~~vI~~T~~~~~~~~l~----------------~~~fd~viIDEAsQ~~e~~~ 356 (624)
T 2gk6_A 304 RYRALKRTAERELLMNADVICCTCVGAGDPRLA----------------KMQFRSILIDESTQATEPEC 356 (624)
T ss_dssp HHHHHHHHHHHHHHHTCSEEEEETGGGGCGGGT----------------TCCCSEEEETTGGGSCHHHH
T ss_pred HHHHHHHHHHHHHHHCCCEEEECCHHHCCHHHH----------------CCCCCEEEEECCCCCCCHHH
T ss_conf 999999988999871499999927011514664----------------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=283.04 Aligned_cols=353 Identities=24% Similarity=0.256 Sum_probs=217.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCEEEEEEEECCCCCCCCCCC
Q ss_conf 04555237333695679985446799999999984231014433342250799955440873999996059987444478
Q 000413 999 HCKLKEVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSSWEDMYYGSLSVLSVERVDDFHLVRFVHDDNDSVTSKIF 1078 (1545)
Q Consensus 999 ~~kLkkIP~TFsSveEYl~vFePLLLEE~rAQL~sS~eEissaE~~~~g~IsVlSlervDdF~lVkfs~~~~d~le~~~f 1078 (1545)
..++.+||++|.|..+|.++|.||+..|.+++... .+..... .+.+......++.+.+.|..+... .....+
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 CCCCEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCCHHHHHHHHHCCCCEEEHHCCCCCHHHHH
Q ss_conf 99969999823999999733599999985125788851999999931785003787642201441000210231477699
Q 000413 1079 SENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLRE 1158 (1545)
Q Consensus 1079 sEGDLVLLSk~kPe~s~~~~~~LGkVerie~dnkr~~~iItIRl~L~n~ssrLnq~~~~L~~rSkW~l~KL~SLTTi~RE 1158 (1545)
..||.|+++...+.. ......|.|.++.... ...+.+++....... + ......+.+.++.+.+|+.|+
T Consensus 246 ~~GD~v~l~~~~~~~--~~~~~~g~V~~v~~~~---~~~v~v~~~~~~~~~------p-~~~~~~~~v~~~~~~~~~~r~ 313 (802)
T 2xzl_A 246 AIGDEMILWYSGMQH--PDWEGRGYIVRLPNSF---QDTFTLELKPSKTPP------P-THLTTGFTAEFIWKGTSYDRM 313 (802)
T ss_dssp CTTCEEEEEECSSSS--SCEEEEEEEEECCC------CCEEEEECCCSSCC------C-TTCCSSEEEEECCCCHHHHHH
T ss_pred CCCCEEEEEECCCCC--CCEEEEEEEEEECCCC---CCEEEEEEECCCCCC------C-CCCCCCEEEEEEECCCHHHHH
T ss_conf 999989999789888--9515789999987888---878999996788899------6-002777489997568618999
Q ss_pred HHHHCCCCC--CC----CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCEEE
Q ss_conf 984032988--99----722215888888888887334223123788886017899999999999804999866766178
Q 000413 1159 FHALSSLKS--IP----LLPIILNPVNVSRGYNESRELDLGKLSQLQQILKTSFNESQLQAISVAIGLSSSWKKDCELSL 1232 (1545)
Q Consensus 1159 y~AL~sL~~--~P----L~d~ILsP~~~~~~~~~s~~v~~~kip~L~~~Lk~~LNeSQ~qAI~aALs~~~~~~~~~gitL 1232 (1545)
+.||..+.. .. +.+.+++...+........+ .....+ ....||++|.+||..++.. +++|
T Consensus 314 ~~AL~~~~~~~~~~~~~l~~~ll~~~~~~~~~~~~lp-~~~~~~-----~~~~Ln~~Q~~Av~~~l~~--------~~~l 379 (802)
T 2xzl_A 314 QDALKKFAIDKKSISGYLYYKILGHQVVDISFDVPLP-KEFSIP-----NFAQLNSSQSNAVSHVLQR--------PLSL 379 (802)
T ss_dssp HHHHHHHHHCTTSBCHHHHHHHHTCCCCCCCCCCCCC-SCCSCT-----TSCCCCHHHHHHHHHHTTC--------SEEE
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCCC-CCCCCC-----CCCCCCHHHHHHHHHHHCC--------CCEE
T ss_conf 9999998751334036788876077656543465685-111543-----4556899999999998639--------9779
Q ss_pred EECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 85589997057899999999960489975455576655578876641489998888899974311221111244456699
Q 000413 1233 IQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSVR 1312 (1545)
Q Consensus 1233 IQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~ss~~~~rp~~s~s~avar~W~daala~ql~~d~~~~~~ss~~~~k 1312 (1545)
||||||||||+||+.++..++.. .+
T Consensus 380 I~GppGTGKT~~i~~~i~~l~~~-------------------------------------------------------~~ 404 (802)
T 2xzl_A 380 IQGPPGTGKTVTSATIVYHLSKI-------------------------------------------------------HK 404 (802)
T ss_dssp EECSTTSSHHHHHHHHHHHHHHH-------------------------------------------------------HC
T ss_pred EECCCCCCHHHHHHHHHHHHHHC-------------------------------------------------------CC
T ss_conf 98789977899999999999867-------------------------------------------------------99
Q ss_pred CEEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCC--CCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 829999287288999999998269778999867895669745454--478885431799999999885302699764112
Q 000413 1313 ARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKT--VHPNSLPFFIDTLVDHRLAEERMHLTDPKNEFC 1390 (1545)
Q Consensus 1313 ~RILVCAPSNAAVDEIV~RLl~~GI~d~dGk~ykPnIVRIG~~ea--Ihs~V~dVsLD~LVeqrL~~e~m~~~~sk~d~~ 1390 (1545)
.+||||||||.|+|++..||.+.| .+++|+|...+ +...+...+++.++... .+
T Consensus 405 ~~ILv~a~tn~A~d~l~~rL~~~g----------~~ilR~g~~~r~~i~~~~~~~tl~~~~~~~----------~~---- 460 (802)
T 2xzl_A 405 DRILVCAPSNVAVDHLAAKLRDLG----------LKVVRLTAKSREDVESSVSNLALHNLVGRG----------AK---- 460 (802)
T ss_dssp CCEEEEESSHHHHHHHHHHHHHTT----------CCEEECCCGGGTTSCCTTGGGBHHHHHHTT----------CC----
T ss_pred CEEEEECCCHHHHHHHHHHHHHHC----------CCEEEECCCCHHHHCCHHHHHHHHHHHHHH----------CH----
T ss_conf 729998485799999999998627----------507862223222103156564299999851----------68----
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 22147999999999999999998611269999998876433346877666679999999998999999999997989997
Q 000413 1391 TRSSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQE 1470 (1545)
Q Consensus 1391 ~~ss~Lr~eLekL~~~Ir~~ea~R~~~~~~~~d~~~~l~~~s~kg~~~~lsd~eLe~kL~kL~~qRrql~~eL~~~~~ke 1470 (1545)
. ++.++.... . .. ..++..+.
T Consensus 461 ---~----~l~~l~~~~------~-~~--------------------~~ls~~~~------------------------- 481 (802)
T 2xzl_A 461 ---G----ELKNLLKLK------D-EV--------------------GELSASDT------------------------- 481 (802)
T ss_dssp ---T----HHHHHHHHH------H-HH--------------------SCCCHHHH-------------------------
T ss_pred ---H----HHHHHHHHH------H-HH--------------------CCCCHHHH-------------------------
T ss_conf ---9----999999998------8-64--------------------45788899-------------------------
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf 66799999999999997723792999818877756322334445676559999999876999916843301247
Q 000413 1471 KKSYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHE 1544 (1545)
Q Consensus 1471 kk~~re~e~~Rrkir~eIL~EAdVVCSTLSGSG~ell~~c~e~~~~~kf~~~~~~~~FDtVIIDEAAQAVElSt 1544 (1545)
+..+...++....+|+.|+|||+|++++++..+. . .||+||||||+|+.|+.+
T Consensus 482 ----~~~~~~~~~~~~~~l~~a~VI~~T~~~~~~~~L~----------------~-~fd~viIDEA~q~~e~~~ 534 (802)
T 2xzl_A 482 ----KRFVKLVRKTEAEILNKADVVCCTCVGAGDKRLD----------------T-KFRTVLIDESTQASEPEC 534 (802)
T ss_dssp ----HHHHHHHHHHHHHHHHTCSEEEEETTGGGCTTCC----------------S-CCSEEEETTGGGSCHHHH
T ss_pred ----HHHHHHHHHHHHHHHCCCCEEEECHHHCCHHHHH----------------C-CCCEEEEECCCCCCHHHH
T ss_conf ----8889999999998752399998332331727775----------------5-699999988503244789
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=280.67 Aligned_cols=352 Identities=22% Similarity=0.255 Sum_probs=215.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCEEEEEEEECCCCCCCCCCC
Q ss_conf 04555237333695679985446799999999984231014433342250799955440873999996059987444478
Q 000413 999 HCKLKEVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSSWEDMYYGSLSVLSVERVDDFHLVRFVHDDNDSVTSKIF 1078 (1545)
Q Consensus 999 ~~kLkkIP~TFsSveEYl~vFePLLLEE~rAQL~sS~eEissaE~~~~g~IsVlSlervDdF~lVkfs~~~~d~le~~~f 1078 (1545)
.+.+.+|+++|.|..+|.++|.||+..|.+++... .|.... ..+.+......++.....|..... .....+
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 CCCCEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCCHHHHHHHHHCCCCEEEHHCCCCCHHHHH
Q ss_conf 99969999823999999733599999985125788851999999931785003787642201441000210231477699
Q 000413 1079 SENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLRE 1158 (1545)
Q Consensus 1079 sEGDLVLLSk~kPe~s~~~~~~LGkVerie~dnkr~~~iItIRl~L~n~ssrLnq~~~~L~~rSkW~l~KL~SLTTi~RE 1158 (1545)
..||+|.++..++.. ....+.|.|.++.... ...+.+.+... ... + ......+.+.++.+.+|+.|+
T Consensus 243 ~~GD~v~l~~~~~~~--~~~~~~g~V~~v~~~~---~~~v~l~~~~~-~~~------p-~~~~~~~~v~~~~~~~~~~r~ 309 (800)
T 2wjy_A 243 MQGDEICLRYKGDLA--PLWKGIGHVIKVPDNY---GDEIAIELRSS-VGA------P-VEVTHNFQVDFVWKSTSFDRM 309 (800)
T ss_dssp CTTCEEEEEECSSSS--CCEEEEEEEEECSBTT---BSCEEEEESCC-TTC------C-TTCCSCEEEEECCCCHHHHHH
T ss_pred CCCCEEEEEECCCCC--CCCEEEEEEEEECCCC---CCEEEEEECCC-CCC------C-CCCCCCCEEEEEECCCHHHHH
T ss_conf 999989999788878--8734589999976788---88899998268-888------4-003777049996068759999
Q ss_pred HHHHCCCCCC--C----CCCCCCCCCCCCCCCCCCCCCCCCCHHH-HHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCEE
Q ss_conf 9840329889--9----7222158888888888873342231237-8888601789999999999980499986676617
Q 000413 1159 FHALSSLKSI--P----LLPIILNPVNVSRGYNESRELDLGKLSQ-LQQILKTSFNESQLQAISVAIGLSSSWKKDCELS 1231 (1545)
Q Consensus 1159 y~AL~sL~~~--P----L~d~ILsP~~~~~~~~~s~~v~~~kip~-L~~~Lk~~LNeSQ~qAI~aALs~~~~~~~~~git 1231 (1545)
+.||..+... . +...+++...+...... .++. +.......||++|.+||..++.. +++
T Consensus 310 ~~aL~~~~~~e~~~~~~l~~~ll~~~~~~~~~~~-------~l~~~~~~~~~~~Ln~~Q~~Av~~~l~~--------~~~ 374 (800)
T 2wjy_A 310 QSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKC-------QLPKRFTAQGLPDLNHSQVYAVKTVLQR--------PLS 374 (800)
T ss_dssp HHHHHHHHHCTTSBCHHHHHHHTTCCCCCCCCCC-------CCCSCCSCTTSCCCCHHHHHHHHHHHTS--------SEE
T ss_pred HHHHHHHHHHHCCHHHHHHHHHCCCCCCCHHHCC-------CCCCCCCCCCCCCCCHHHHHHHHHHCCC--------CEE
T ss_conf 9999999874001168999985188887133224-------5720036434667799999999874259--------917
Q ss_pred EEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 88558999705789999999996048997545557665557887664148999888889997431122111124445669
Q 000413 1232 LIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSV 1311 (1545)
Q Consensus 1232 LIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~ss~~~~rp~~s~s~avar~W~daala~ql~~d~~~~~~ss~~~~ 1311 (1545)
+||||||||||+|+..++..++.. .
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 9829999287288999999998269778999867895669745454--47888543179999999988530269976411
Q 000413 1312 RARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKT--VHPNSLPFFIDTLVDHRLAEERMHLTDPKNEF 1389 (1545)
Q Consensus 1312 k~RILVCAPSNAAVDEIV~RLl~~GI~d~dGk~ykPnIVRIG~~ea--Ihs~V~dVsLD~LVeqrL~~e~m~~~~sk~d~ 1389 (1545)
+.+||+|||||.|+|++..|+...|+ +++|+|...+ +...+...+++.++... +
T Consensus 400 ~~~ilv~a~tn~A~~~l~~~l~~~g~----------~vvRlg~~~r~~i~~~~~~~tlh~~~~~~---------~----- 455 (800)
T 2wjy_A 400 NGPVLVCAPSNIAVDQLTEKIHQTGL----------KVVRLCAKSREAIDSPVSFLALHNQIRNM---------D----- 455 (800)
T ss_dssp SSCEEEEESSHHHHHHHHHHHHTTTC----------CEEECCCGGGGGCCCTTGGGBHHHHHHTC---------T-----
T ss_pred CCCEEEECCCHHHHHHHHHHHHHHCC----------CEEEECCCCHHHHCCHHHHHHHHHHHHCC---------C-----
T ss_conf 98199986968999999999987275----------41762332143313615565399999727---------6-----
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 22214799999999999999999861126999999887643334687766667999999999899999999999798999
Q 000413 1390 CTRSSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQ 1469 (1545)
Q Consensus 1390 ~~~ss~Lr~eLekL~~~Ir~~ea~R~~~~~~~~d~~~~l~~~s~kg~~~~lsd~eLe~kL~kL~~qRrql~~eL~~~~~k 1469 (1545)
... ++.++.. .+... ..++..+
T Consensus 456 --~~~----~l~~l~~-------~~~~~--------------------~~~~~~~------------------------- 477 (800)
T 2wjy_A 456 --SMP----ELQKLQQ-------LKDET--------------------GELSSAD------------------------- 477 (800)
T ss_dssp --TCH----HHHHHHH-------HHTTT--------------------SCCCHHH-------------------------
T ss_pred --CHH----HHHHHHH-------HHHHH--------------------CCCCHHH-------------------------
T ss_conf --499----9999999-------98753--------------------3468678-------------------------
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf 766799999999999997723792999818877756322334445676559999999876999916843301247
Q 000413 1470 EKKSYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHE 1544 (1545)
Q Consensus 1470 ekk~~re~e~~Rrkir~eIL~EAdVVCSTLSGSG~ell~~c~e~~~~~kf~~~~~~~~FDtVIIDEAAQAVElSt 1544 (1545)
.+..+..++.+..++|++|+|||+|++++|+..+. ...||+||||||+|+.|+.+
T Consensus 478 ----~~~~~~~~~~~~~~~l~~a~VI~~T~~~~~~~~l~----------------~~~fd~viIDEAsQ~~e~~~ 532 (800)
T 2wjy_A 478 ----EKRYRALKRTAERELLMNADVICCTCVGAGDPRLA----------------KMQFRSILIDESTQATEPEC 532 (800)
T ss_dssp ----HHHHHHHHHHHHHHHHHHCSEEEEETGGGGCTTTT----------------TCCCSEEEETTGGGSCHHHH
T ss_pred ----HHHHHHHHHHHHHHHHCCCCEEEECHHHHCCHHHH----------------CCCCCEEEEECCCCCCCHHH
T ss_conf ----99999999877775433698999740452872454----------------58989899989778776999
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=97.01 Aligned_cols=66 Identities=26% Similarity=0.375 Sum_probs=55.3
Q ss_pred HCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 01789999999999980499986676617885589997057899999999960489975455576655578876641489
Q 000413 1203 KTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAA 1282 (1545)
Q Consensus 1203 k~~LNeSQ~qAI~aALs~~~~~~~~~gitLIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~ss~~~~rp~~s~s~a 1282 (1545)
...||+.|.+||..++.. ++.+|+||||||||+|+.+++..+...
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 99888889997431122111124445669982999928728899999999
Q 000413 1283 IARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRI 1332 (1545)
Q Consensus 1283 var~W~daala~ql~~d~~~~~~ss~~~~k~RILVCAPSNAAVDEIV~RL 1332 (1545)
+.+|++||||+.|++++..++
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=94.29 Aligned_cols=15 Identities=20% Similarity=0.089 Sum_probs=9.9
Q ss_pred CCCCCEEEEECCCCC
Q ss_conf 998769999168433
Q 000413 1525 NTLFDAVVIDEAAQV 1539 (1545)
Q Consensus 1525 ~~~FDtVIIDEAAQA 1539 (1545)
+.+|++|+|=-...-
T Consensus 564 GLEf~~Vfl~gl~eg 578 (647)
T 3lfu_A 564 GLEFPQVFIVGMEEG 578 (647)
T ss_dssp TCCEEEEEECCCBTB
T ss_pred CCCCCEEEEECCCCC
T ss_conf 766777999277678
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=90.31 Aligned_cols=67 Identities=31% Similarity=0.459 Sum_probs=53.4
Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 99999999999804999866766178855899970578999999999604899754555766555788766414899988
Q 000413 1207 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARA 1286 (1545)
Q Consensus 1207 NeSQ~qAI~aALs~~~~~~~~~gitLIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~ss~~~~rp~~s~s~avar~ 1286 (1545)
++.|..||..++.. ++++|+||||||||+|+..++..+.....
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 88899974311221111244456699829999287288999999998
Q 000413 1287 WQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRIS 1333 (1545)
Q Consensus 1287 W~daala~ql~~d~~~~~~ss~~~~k~RILVCAPSNAAVDEIV~RLl 1333 (1545)
..+.+|++||||+.|.+++...+.
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=88.97 Aligned_cols=71 Identities=27% Similarity=0.350 Sum_probs=54.9
Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 17899999999999804999866766178855899970578999999999604899754555766555788766414899
Q 000413 1204 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1283 (1545)
Q Consensus 1204 ~~LNeSQ~qAI~aALs~~~~~~~~~gitLIQGPPGTGKTkTIvgLIsaLLs~~~~~~s~~~~~~ss~~~~rp~~s~s~av 1283 (1545)
..||+.|.+|+...+... ....++.+|+||||||||+++..++..+...
T Consensus 24 ~~Ln~~Q~~av~~~~~~i---~~~~~~~li~G~aGTGKT~ll~~~~~~l~~~---------------------------- 72 (459)
T 3upu_A 24 DDLTEGQKNAFNIVMKAI---KEKKHHVTINGPAGTGATTLTKFIIEALIST---------------------------- 72 (459)
T ss_dssp SCCCHHHHHHHHHHHHHH---HSSSCEEEEECCTTSCHHHHHHHHHHHHHHT----------------------------
T ss_pred CCCCHHHHHHHHHHHHHH---HCCCCEEEEEECCCCCHHHHHHHHHHHHHHC----------------------------
T ss_conf 348999999999999987---3689779999699998999999999999864----------------------------
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHH
Q ss_conf 9888889997431122111124445669982999928728899999999
Q 000413 1284 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRI 1332 (1545)
Q Consensus 1284 ar~W~daala~ql~~d~~~~~~ss~~~~k~RILVCAPSNAAVDEIV~RL 1332 (1545)
...+|++|||||.|.+++..|+
T Consensus 73 ---------------------------~~~~il~~a~T~~Aa~~l~~~~ 94 (459)
T 3upu_A 73 ---------------------------GETGIILAAPTHAAKKILSKLS 94 (459)
T ss_dssp ---------------------------TCCCEEEEESSHHHHHHHHHHH
T ss_pred ---------------------------CCCEEEEECCCHHHHHHHHHHH
T ss_conf ---------------------------9960999667578999887661
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=76.30 Aligned_cols=22 Identities=18% Similarity=0.064 Sum_probs=9.4
Q ss_pred CCCCCCCCCHHHHHHHCHHHHH
Q ss_conf 2345443321555551001232
Q 000413 584 FLDYSLCQMTCIRVLEILPVVF 605 (1545)
Q Consensus 584 ~~~~~~~~~tc~r~~e~lp~v~ 605 (1545)
.+|+.-...-+.++|+-.|-+.
T Consensus 180 ~lDfdDll~~~~~lL~~~~~~~ 201 (673)
T 1uaa_A 180 VLDFDDLILLPTLLLQANEEVR 201 (673)
T ss_dssp CEEHHHHHHHHHHHHHHCHHHH
T ss_pred CCCHHHHHHHHHHHHHHCHHHH
T ss_conf 9988999999999987496899
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=75.36 Aligned_cols=24 Identities=29% Similarity=0.420 Sum_probs=13.1
Q ss_pred CCCCCCCCCCHHHHHHHCHHHHHC
Q ss_conf 323454433215555510012321
Q 000413 583 TFLDYSLCQMTCIRVLEILPVVFG 606 (1545)
Q Consensus 583 ~~~~~~~~~~tc~r~~e~lp~v~~ 606 (1545)
..+|+.-..+-+.++|+-.|-+.+
T Consensus 188 ~~lDf~Dll~~~~~ll~~~~~v~~ 211 (724)
T 1pjr_A 188 HSLDFDDLIMTTIQLFDRVPDVLH 211 (724)
T ss_dssp TEECTTHHHHHHHHHHHHCHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHCHHHHH
T ss_conf 999999999999999865979999
Done!