Query 001209
Match_columns 1123
No_of_seqs 278 out of 564
Neff 4.6
Searched_HMMs 29240
Date Mon Mar 25 16:33:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001209.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/001209hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3fqd_A Protein DHP1, 5'-3' exo 100.0 9E-235 3E-239 2076.8 58.3 802 1-826 4-872 (899)
2 3pie_A 5'->3' exoribonuclease 100.0 1E-191 4E-196 1745.5 54.6 704 1-832 1-723 (1155)
3 2y35_A LD22664P; hydrolase-DNA 100.0 8E-176 3E-180 1623.8 44.6 581 1-720 1-585 (1140)
4 1b43_A Protein (FEN-1); nuclea 98.4 6.7E-07 2.3E-11 100.1 11.6 151 50-240 23-180 (340)
5 1a76_A Flap endonuclease-1 pro 98.3 1.2E-06 4.2E-11 97.5 8.1 91 190-355 143-234 (326)
6 1rxw_A Flap structure-specific 98.1 1.5E-05 5E-10 89.2 13.6 41 301-356 205-245 (336)
7 3qe9_Y Exonuclease 1; exonucle 98.1 3E-05 1E-09 87.6 14.5 172 1-240 1-178 (352)
8 3ory_A Flap endonuclease 1; hy 97.8 0.00017 5.8E-09 81.8 14.3 134 157-369 138-272 (363)
9 1ul1_X Flap endonuclease-1; pr 97.5 0.00047 1.6E-08 78.5 12.5 229 2-355 1-241 (379)
10 2izo_A FEN1, flap structure-sp 97.4 0.0011 3.8E-08 74.5 13.0 211 50-356 20-244 (346)
11 3q8k_A Flap endonuclease 1; he 97.3 0.0023 7.7E-08 72.1 13.9 232 2-355 1-241 (341)
12 1exn_A 5'-exonuclease, 5'-nucl 96.1 0.057 2E-06 59.7 14.3 145 50-251 21-166 (290)
13 1nc8_A Nucleocapsid protein; H 84.7 0.43 1.5E-05 35.3 2.0 19 261-279 6-24 (29)
14 1dsq_A Nucleic acid binding pr 84.5 0.36 1.2E-05 34.9 1.5 18 262-279 3-20 (26)
15 1a6b_B Momulv, zinc finger pro 82.8 0.7 2.4E-05 37.0 2.6 21 260-280 9-29 (40)
16 1u6p_A GAG polyprotein; MLV, A 76.4 1.2 4E-05 38.1 2.1 21 261-281 23-43 (56)
17 2ysa_A Retinoblastoma-binding 70.2 1.5 5.1E-05 37.4 1.3 18 261-278 7-24 (55)
18 2bl6_A Nucleocapsid protein P1 58.6 3.7 0.00013 31.6 1.5 17 262-278 20-36 (37)
19 2ec7_A GAG polyprotein (PR55GA 55.6 4.7 0.00016 33.0 1.7 19 261-279 6-24 (49)
20 1cl4_A Protein (GAG polyprotei 52.5 6.8 0.00023 33.1 2.2 20 261-280 30-49 (60)
21 2a51_A Nucleocapsid protein; s 52.1 5.7 0.00019 30.9 1.6 17 262-278 22-38 (39)
22 2cqf_A RNA-binding protein LIN 48.6 8 0.00027 33.2 2.1 20 261-280 29-48 (63)
23 2a51_A Nucleocapsid protein; s 48.2 5.9 0.0002 30.8 1.1 17 263-279 2-18 (39)
24 2ec7_A GAG polyprotein (PR55GA 47.9 7.4 0.00025 31.8 1.7 18 262-279 28-45 (49)
25 3ts2_A Protein LIN-28 homolog 46.9 8.2 0.00028 38.6 2.2 16 263-278 99-114 (148)
26 2li8_A Protein LIN-28 homolog 45.8 10 0.00034 33.9 2.3 16 263-278 48-63 (74)
27 2ihx_A Nucleocapsid (NC) prote 45.7 6.9 0.00023 33.4 1.2 19 262-280 31-49 (61)
28 2bl6_A Nucleocapsid protein P1 43.8 8.4 0.00029 29.6 1.3 17 263-279 2-18 (37)
29 1a1t_A Nucleocapsid protein; s 42.8 7.9 0.00027 32.1 1.1 19 261-279 12-30 (55)
30 2ihx_A Nucleocapsid (NC) prote 41.9 9.6 0.00033 32.5 1.6 20 261-280 4-23 (61)
31 1a1t_A Nucleocapsid protein; s 41.7 9.7 0.00033 31.6 1.5 18 262-279 34-51 (55)
32 1cl4_A Protein (GAG polyprotei 39.7 6.2 0.00021 33.4 0.0 19 262-280 2-20 (60)
33 3nyb_B Protein AIR2; polya RNA 39.3 11 0.00037 34.4 1.6 19 261-279 46-64 (83)
34 2cqf_A RNA-binding protein LIN 38.2 13 0.00045 31.9 1.9 19 261-279 7-25 (63)
35 3nyb_B Protein AIR2; polya RNA 33.7 15 0.0005 33.6 1.5 19 261-279 5-23 (83)
36 2li8_A Protein LIN-28 homolog 32.3 17 0.00059 32.4 1.7 19 261-279 24-42 (74)
37 3ts2_A Protein LIN-28 homolog 30.5 17 0.00057 36.3 1.4 18 264-281 122-139 (148)
No 1
>3fqd_A Protein DHP1, 5'-3' exoribonuclease 2; protein-protein complex, exonuclease, hydrolase, mRNA proces nuclease, nucleus, rRNA processing, transcription; 2.20A {Schizosaccharomyces pombe}
Probab=100.00 E-value=9.5e-235 Score=2076.79 Aligned_cols=802 Identities=43% Similarity=0.754 Sum_probs=635.4
Q ss_pred CcchhHHHHHHhhCCcccccccccCcccc-CCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCCCCCHHHHHH
Q 001209 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVI-DGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPAPTTFDEVFQ 79 (1123)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~viE~~~~~~-dG~~iP~d~s~pNPNg~efDNLYLDMNGIIHpC~Hpe~~p~p~te~Emf~ 79 (1123)
||||+|||||++|||+|+++|+|+.|.++ ||..||+|+++|||||.||||||||||||||+|+|+++.+.+.|++|||.
T Consensus 4 MGVP~ffRWLs~rYP~i~~~~~e~~~~~~~~g~~~p~d~~~pnpng~e~DnLYlDmNgIIH~c~h~~~~~~~~te~e~~~ 83 (899)
T 3fqd_A 4 MGVPALFRLLSRKFAKVITPVIEAPTEKLPDGTEIEPDLSLPNPNGVECDNLYLDMNGIVHPCSHPEDRPAPETEDEMMV 83 (899)
T ss_dssp CCHHHHHHHHHHHCGGGEEECCCCCCEECTTSCEECCCTTSCCTTSSCEEEEEEETHHHHHHHHSCSSSCCCCSHHHHHH
T ss_pred cchHHHHHHHHHHCCccchhhcccccccccCCccccccccCCCCCCcccceEEEecchhhhhhcCCCCCCCCCCHHHHHH
Confidence 99999999999999999999999999888 89999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhccccceEEEEecCCCchhhhHHHHhhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCC--CCCCCCcc
Q 001209 80 CMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPK--SDSQVFDS 157 (1123)
Q Consensus 80 ~If~yIDrL~~iVRPrKlLyiAIDGVAPRAKMNQQRsRRFrsakea~~~~~~~~~l~~e~~~eg~~lp~~--~~~~~fDS 157 (1123)
+||+|||+||.+|||||+||||||||||||||||||+||||+|++++++.++.++++++++++| .+++. ...+.|||
T Consensus 84 ~If~yid~l~~~vrPrklly~AiDGVAPrAKmnQQRsRRfrsa~~~~~~~~~~~~~~~~~~~~g-~~~~~~~~~~~~fDs 162 (899)
T 3fqd_A 84 AVFEYTDRILAMVRPRQLLFIAIDGVAPRAKMNQQRSRRFRSSREAALKEEELQAFIEEAKQQG-IPIDENATKKKSWDS 162 (899)
T ss_dssp HHHHHHHHHHHHHCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-CCBCHHHHSCCCCCG
T ss_pred HHHHHHHHHHHHcCcceeEEEeecCCCCchHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHhcC-CCCccccccccCCCc
Confidence 9999999999999999999999999999999999999999999999998888888999999998 34321 24578999
Q ss_pred CcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHH
Q 001209 158 NVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLI 237 (1123)
Q Consensus 158 N~ITPGT~FM~kLs~~L~~yI~~kl~~Dp~W~~lkVIlSda~VPGEGEHKImdfIR~qr~~p~ydPNt~HcIYGlDADLI 237 (1123)
|||||||+||++|+.+|+|||+.||++||+|++++|||||++||||||||||+|||+||++|+|||||+|||||+|||||
T Consensus 163 N~ITPGT~FM~~L~~~L~~~i~~kl~~dp~W~~~~VIlSd~~vPGEGEHKIm~fIR~~r~~p~ydpN~~HcIyGlDADLI 242 (899)
T 3fqd_A 163 NCITPGTPFMDTLAKSLRYYIINKLNSDPCWRNVRFILSDASVPGEGEHKIMEFIRSQRVKPEYDPNTHHVVYGLDADLI 242 (899)
T ss_dssp GGSSTTSHHHHHHHHHHHHHHHHHHTSCGGGTTCEEEEECTTSCSCHHHHHHHHHHHHHTSTTSCTTCCEEEECCCTTHH
T ss_pred CccCCccHHHHHHHHHHHHHHHHHhhcCcccccceEEEeCCCCCCccHHHHHHHHHHHhcCCCCCCCCeEEEEccCccHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCCceEEEcccccccCCCCCcccccCCCCCcccccccccccccCCCCcCCCcccCCCCCeEEEehhHHHHHHHHH
Q 001209 238 MLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYE 317 (1123)
Q Consensus 238 mLgLatHep~f~ILRE~Vf~~~~~~~c~~cgQ~gH~~~~c~g~~k~k~~e~~e~~~~~~~~~~~f~~l~I~vLREYL~~E 317 (1123)
||||+||||||+||||+|++.. +|.||.+.+|.|..+. ++++++. .....++|+||||++|||||+.|
T Consensus 243 mL~LatHep~f~ILRE~v~~~~--------~q~~~~~~~~~~~~k~--~~~~~~~--~~~~~~~f~~l~i~iLREYL~~E 310 (899)
T 3fqd_A 243 MLGLATHEPHFRVLREDVFFQQ--------GSTKKTKEERLGIKRL--DDVSETN--KVPVKKPFIWLNVSILREYLEVE 310 (899)
T ss_dssp HHHHHTTCSSEEEEEECCC-----------------CTTTTTCCBT--TC------------CCEEEEEHHHHHHHHHHH
T ss_pred HHhhhccCCceEEEeeecccCc--------Cccccchhhhcccccc--ccccccc--cccccCceEEEeHHHHHHHHHHH
Confidence 9999999999999999998753 6889999999997665 5555432 23456899999999999999999
Q ss_pred hcCCCCCCccchhhhhhHHHHhhhhcccCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHHHHHHH
Q 001209 318 FRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQAV 397 (1123)
Q Consensus 318 l~~~~~pf~~DlERiIDDfVfLcffvGNDFLPhLPsLeIreGaID~Li~iYKk~Lp~~ggYLT~~G~INl~rl~~fl~~L 397 (1123)
|.++++||++|+|||||||||||||||||||||||+|+|++||||+|+.+||++|+++|||||++|+|||+||+.||+.|
T Consensus 311 ~~~~~~~f~~d~ERiIDDfVfmcFfvGNDFLPhlP~l~I~egaid~L~~~Yk~~l~~~~gYlt~~G~inl~rl~~~l~~L 390 (899)
T 3fqd_A 311 LYVPNLPFPFDLERAIDDWVFFIFFVGNDFLPHLPSLDIRDGAVERLTEIWRASLPHMGGYLTLDGSVNLARAEVILSAV 390 (899)
T ss_dssp HCCTTCSSCCCHHHHHHHHHHHGGGGCCSSSCCCTTCCGGGTHHHHHHHHHHHHHHHHSSCSEETTEECHHHHHHHHHHH
T ss_pred hcccCCCCCchhhhhhhhhhhhhHhhCcccCCCCCccCcCCChHHHHHHHHHHHHHHcCCeeecCCEEcHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCC------CCC--CCCCC---ccc-------cccccCCCCCCCCCCC
Q 001209 398 GSYEDRIFQKRARLHQRHAERIKREKAQARRGDDV------EPL--AQPDS---LVP-------VSRFHGSRLASGPSPS 459 (1123)
Q Consensus 398 ~~~Ed~iF~~r~~~e~r~~e~~kr~k~~~~~~~~~------~~~--~~~~~---~~p-------~~~~~~~~l~~~~~~~ 459 (1123)
|++|++||++|.+.++++.++.||++.+.+..... ... ..+.. ..+ .....+......+...
T Consensus 391 ~~~E~~iF~~r~~~e~~~~~~~krr~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 470 (899)
T 3fqd_A 391 GNQEDDIFKRLKQQEDRRNENYRRRQQRESNQESESYVDNVVIQRSVETQSTEVVTSSKSTSVDTKPPKKTQKIDAPAPV 470 (899)
T ss_dssp HTTHHHHHHHHHHHHTTTC-------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccccccccccccccccccccccccccccccccccccccccCcccc
Confidence 99999999999998887777777665443211110 000 00000 000 0000000000000000
Q ss_pred CCccc--ccc-ccccCCCCCCCCCCccc---------ccCCCcchhhHHHhhh-------ccCCCCcc-cc--------H
Q 001209 460 PYQQS--ECV-GRLDNGKGTSGRPHKVP---------RLSSGATIGAAIVEAE-------NSFETDPQ-EN--------K 511 (1123)
Q Consensus 460 ~~~~~--~~~-~~~~~~~~~~~~~~k~~---------~~s~~~~~~~~~~~~e-------~~~~~~~~-~~--------~ 511 (1123)
++... ... .............+.+. ..+..+..+++.++.. .....++. +. .
T Consensus 471 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~n~~~a~~lk~~l~~~~~~~~~~~~~~~~~~~~~e~~~~ 550 (899)
T 3fqd_A 471 DLVNLSEKTSNRSLGATNRELINNRAANRLGLSREAAAVSSVNKLAASALKAQLVSNETLQNVPLEDSIASSSAYEDTDS 550 (899)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccccccccccccchhhhhhhhhhcchhhhhhhhhhhhhhcccchhHHHHHHHHhhccccccccccccccccccccccccc
Confidence 00000 000 00000000000000000 0000000001111100 00000000 00 0
Q ss_pred HHHHHHHHHHHhh-------hcc--cCCCCCcchhhhccCCCchhHHHHHHhcCCCChhHHHHHHHHHHHHHHhhHHHHh
Q 001209 512 EEFKAKLKELLRD-------KSD--AFNSDNPEEDKVKLGEPGWKERYYEEKFNAKTPEEREETRKDVVLRYTEGLCWVM 582 (1123)
Q Consensus 512 eelk~~l~~~~~~-------k~d--~~~~~~~~eD~VkL~e~g~K~rYY~~KF~v~~~~di~~~r~~vv~~YvEGL~WVL 582 (1123)
.+......+.+++ ++. ...++.+.+|.|+|||+|||+|||++||+++..+ ++++++||++|||||||||
T Consensus 551 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~v~l~e~g~K~rYY~~KF~~~~~d--~e~~~~v~~~YvEGL~WVL 628 (899)
T 3fqd_A 551 IESSTPVVHPIDTKVSNVGQKRKAPDSTEENENTDTVRLYEPGYRERYYEQKFHISPDE--PEKIREAVKHYVHGLCWVL 628 (899)
T ss_dssp ----------------------------------CCSCTTSTTHHHHHHHHTSCCCTTC--THHHHHHHHHHHHHHHHHH
T ss_pred ccccccchhhhhccccccccccccccccccccchhhhhhcccchHHHHHHHhcCCCCCC--HHHHHHHHHHHHHHHHHHH
Confidence 0000000000000 000 0011123568899999999999999999997544 4789999999999999999
Q ss_pred hhhccCcCcccccccCCCCcccccccccccccceecCCCCCChhhhhhhcCCCCCCCCCcHHHHhhhcCCCCCCcccCCC
Q 001209 583 HYYYEGVCSWQWFYPYHYAPFASDLKDLDQFNISFELGHPFKPFNQLLGVFPSASSHALPEHYRKLMTDPNSPISDFYPT 662 (1123)
Q Consensus 583 ~YYyqGcpSW~WYYPYHYAPfaSDl~~l~~~~i~Fe~G~Pf~PfEQLMsVLPaaS~~~LP~~~r~LMtdp~SpIiDFYP~ 662 (1123)
+|||||||||+||||||||||||||+++.+++|+|++|+||+|||||||||||+|+++||++||+||+||+|||+||||+
T Consensus 629 ~YYYqGc~SW~WyYPYHYAPfaSD~~~~~~~~i~Fe~G~PF~PfEQLMaVLPaaS~~~LP~~y~~LMtdp~SpIiDFYP~ 708 (899)
T 3fqd_A 629 LYYYQGCPSWTWYYPYHYAPFAADFKDLASIDVKFELNQPFKPYEQLLGVLPAASKNNLPEKLQTLMTDENSEIIDFYPE 708 (899)
T ss_dssp HHHHTCCSCSSCCCCCSSCCCGGGCCSCTTCCCCCCCCCCCCHHHHHHHHCCGGGGGGSCHHHHHHHHCTTCTTGGGCCS
T ss_pred HHHhCCCCCCcccCcccccchHHHHhhcccCceecCCCCCCChHHHHHhhcCHhhhCcccHHHHHHhcCCCCcchhhCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCcccccceeccCCCChHHHHHHHHhhcCCCCHHHHhhccCCCcEEEEecCCCcchhhhhhhhHhhhhhhhhh
Q 001209 663 DFEVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEEARRNSIMADMLFVLLSHPLSASIYTLDEHCKQLKIKER 742 (1123)
Q Consensus 663 dF~ID~NGKk~~WqGVaLLPFIDe~rLl~a~~~~~~~LT~eE~~RN~~g~d~Lfv~~~~~l~~~i~~l~~~~~~~~~~~~ 742 (1123)
||+|||||||++||||||||||||+|||+||++++++||+||++||++|.++||++++||+++. .++.+|++++
T Consensus 709 dFeiDmNGKk~~WqgVvlLPFIDE~RLL~A~~~~~~~LT~eEk~RN~~G~~~lf~~~~~~l~~~------~~~~~y~~~~ 782 (899)
T 3fqd_A 709 NFTIDLNGKKFEWQGVALLPFIDENRLLNAVSKIYPQLTEEESKRNEDGSTLLFISEHHPMFSE------LVKQLYSKKR 782 (899)
T ss_dssp CCCEECSSSSCTTSSEECCCCCCHHHHHHHHHTTGGGSCHHHHHTTSCCCCEEEEETTSTTHHH------HHHHHTSSSC
T ss_pred cccccCCCCccccceEEecCccCHHHHHHHHHHhhccCCHHHHHhccCCCcEEEEeCCCchHHH------HHHHhccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999874 3455666666
Q ss_pred hhhhhcCCCCccccCCCceEEEecCCCCCCCCcccCCCC--CCcC------CCCCeEEEEEecCCC-CCCCCCCCCCCCC
Q 001209 743 VEVKERLNPELSMCSDGMNGYISPCAGDPHPPVFRSPVA--SMED------IMGNQVLCAIYKLPD-AHKHVTRPPAGVI 813 (1123)
Q Consensus 743 ~~~~~~i~~~~~~~~~G~~G~v~~~~~~~~~~~~~sPi~--~l~d------i~~n~~~~~~y~~P~-~~~h~s~ll~g~~ 813 (1123)
...+++|||++ |+||+|+|++++.+.++++|.|||. +||| |.+|++|||.|++|+ .+.|+||||+||+
T Consensus 783 ~~~~~~~~~~~---s~gl~G~v~~~~~~~p~~~~~sP~~~~~~~~~~~~~~i~~n~~~~~~y~~P~~~~~~~s~lL~g~~ 859 (899)
T 3fqd_A 783 QGKPLKLSGKM---AHGLFGKVNTNDSVIPNVSVQCPIDVTSADALQKYGSIDDNQSISLVFEVPKSHFVHKSMLLRGVK 859 (899)
T ss_dssp SSSCEECCGGG---GTTCCSEEEECTTSCSCCCBCCSSCCCSHHHHHHSCCBSSCCEEEEEEECCCCSSCCCCSCCTTCC
T ss_pred cCcccccCccc---ccCcceEEEeCCCcCCCCeecCCCCccCCCCccccccccCCcEEEEEEeCCCCCCCcCCcCCCCCC
Confidence 66678899999 9999999999999888899999997 9999 999999999999999 6999999999999
Q ss_pred cCCCCCCcccCCC
Q 001209 814 FPKKIVQLEDLKP 826 (1123)
Q Consensus 814 ~p~~~l~~~d~~~ 826 (1123)
+|+++|++.|++.
T Consensus 860 ~p~~~l~~~D~~~ 872 (899)
T 3fqd_A 860 MPNRVLTPEDINQ 872 (899)
T ss_dssp CCCCCCCHHHHHH
T ss_pred CCCCCCCHHHHHH
Confidence 9999999999983
No 2
>3pie_A 5'->3' exoribonuclease (XRN1); beta berrel, tudor domain, chromo domain, mRNA turnover, RRN processing, RNA binding, DNA binding; 2.90A {Kluyveromyces lactis} PDB: 3pif_A
Probab=100.00 E-value=1.2e-191 Score=1745.52 Aligned_cols=704 Identities=37% Similarity=0.674 Sum_probs=535.9
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCC--CCCCHHHHH
Q 001209 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRP--APTTFDEVF 78 (1123)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~viE~~~~~~dG~~iP~d~s~pNPNg~efDNLYLDMNGIIHpC~Hpe~~p--~p~te~Emf 78 (1123)
||||+|||||++|||+|+.. + ++..+| +|||||||||||||+|+|+++.+ .+.|++|||
T Consensus 1 MGVP~ffrwl~~ryP~i~~~-~-------~~~~~p-----------e~DnLYlDmNgIIH~c~h~~~~~~~~~~te~e~~ 61 (1155)
T 3pie_A 1 MGIPKFFHFISERWPQISQL-I-------DGSQIP-----------EFDNLYLDMNSILHNCTHGDGSEVNSRLSEEEVY 61 (1155)
T ss_pred CChHHHHHHHHHhCcchhhc-c-------cCCCCC-----------cCCeEEEecccceeeeecCCCCccccCCCHHHHH
Confidence 99999999999999998643 2 233444 89999999999999999999876 588999999
Q ss_pred HHHHHHHHHHHhhccccceEEEEecCCCchhhhHHHHhhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCCCCCCccC
Q 001209 79 QCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFDSN 158 (1123)
Q Consensus 79 ~~If~yIDrL~~iVRPrKlLyiAIDGVAPRAKMNQQRsRRFrsakea~~~~~~~~~l~~e~~~eg~~lp~~~~~~~fDSN 158 (1123)
.+||+|||+||++|||||+||||||||||||||||||+||||+|++++++. ++..++|..+|. .+.||||
T Consensus 62 ~~if~yid~l~~~vrPrkllyiAiDGVAPrAKmnqQR~RRfrsa~~~~~~~-------~~~~~~g~~~~~---~~~fdsn 131 (1155)
T 3pie_A 62 SKIFSYIDHLFHTIKPKQTFYMAIDGVAPRAKMNQQRARRFRTAMDAEKAL-------QKAIENGDELPK---GEPFDSN 131 (1155)
T ss_pred HHHHHHHHHHHHhcCcceEEEEEecCCCChhHHHHHHHHHHHhhhhhhHHH-------HHHHhcCCcCCc---ccccccc
Confidence 999999999999999999999999999999999999999999999876432 223456777763 3689999
Q ss_pred cccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHH
Q 001209 159 VITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIM 238 (1123)
Q Consensus 159 ~ITPGT~FM~kLs~~L~~yI~~kl~~Dp~W~~lkVIlSda~VPGEGEHKImdfIR~qr~~p~ydPNt~HcIYGlDADLIm 238 (1123)
||||||+||.+|+.+|+|||+.|+++||.|++++|||||++||||||||||+|||++|++|+|||||+|||||+||||||
T Consensus 132 ~ITPGT~FM~~L~~~L~~~i~~k~~~d~~w~~~~vi~S~~~vPGEGEhKIm~~IR~~r~~p~y~pn~~H~IyG~DADLIm 211 (1155)
T 3pie_A 132 AITPGTEFMAKLTENLKYFIHDKITNDTRWQNVKVIFSGHEVPGEGQHKIMDYIRAIRAQEDYNPNTRHCIYGLDADLII 211 (1155)
T ss_pred cccCCcHHHHHHHHHHHHHHHHHhhCCcCccccEEEEeCCCCCCccHHHHHHHHHHhccCCCCCCCCeEEEeccChhHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCceEEEcccccccCCCCCcccccCCCCCcccccccccccccCCCCcCCCcccCCCCCeEEEehhHHHHHHHHHh
Q 001209 239 LALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEF 318 (1123)
Q Consensus 239 LgLatHep~f~ILRE~Vf~~~~~~~c~~cgQ~gH~~~~c~g~~k~k~~e~~e~~~~~~~~~~~f~~l~I~vLREYL~~El 318 (1123)
|||+||||||+||||+|++..+... + .....++|+||||++|||||+.||
T Consensus 212 L~L~thep~f~iLRe~v~f~~~~~~------------------~------------~~~~~~~f~~l~i~~LREyL~~ef 261 (1155)
T 3pie_A 212 LGLSTHDHHFCLLREEVTFGKRSSS------------------V------------KTLETQNFFLLHLSILREYLALEF 261 (1155)
T ss_pred hhhccCCCcEEEEeeccccCccccc------------------c------------cccccCCeEEEEHHHHHHHHHHHH
Confidence 9999999999999999866432100 0 011246799999999999999999
Q ss_pred cC--CCCCCccchhhhhhHHHHhhhhcccCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHHHHHH
Q 001209 319 RI--PNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQA 396 (1123)
Q Consensus 319 ~~--~~~pf~~DlERiIDDfVfLcffvGNDFLPhLPsLeIreGaID~Li~iYKk~Lp~~ggYLT~~G~INl~rl~~fl~~ 396 (1123)
.. +.++|++|+|||||||||||||||||||||||+|+|++||||.|+++||+.|+++|||||++|+|||+||+.||+.
T Consensus 262 ~~~~~~~~~~~d~ERiiDDfVflcf~vGNDFLPhlP~l~I~~g~i~~L~~~Yk~~l~~~~gYlt~~G~inl~rl~~~l~~ 341 (1155)
T 3pie_A 262 EEITDSVQFEYDFERVLDDFIFVLFTIGNDFLPNLPDLHLKKGAFPVLLQTFKEALQHMDGYINEQGKINLARFSIWLKY 341 (1155)
T ss_pred HhhccccCCCccHhHhhcceeeehhhhCcccCCCCCccCcCCChHHHHHHHHHHHHHhcCCeeccCCEEcHHHHHHHHHH
Confidence 75 6789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhHHHHHHHHHHHHHHHH---HHHH--HHHHHhhcCCCCCCCCCCCCccccccccCCCCCCCCCCCCCcccccc-ccc
Q 001209 397 VGSYEDRIFQKRARLHQRHA---ERIK--REKAQARRGDDVEPLAQPDSLVPVSRFHGSRLASGPSPSPYQQSECV-GRL 470 (1123)
Q Consensus 397 L~~~Ed~iF~~r~~~e~r~~---e~~k--r~k~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~~~~-~~~ 470 (1123)
||++|++||++|...++... +++. .++.+++.++......+.+....+..+.... .+...+......... ..+
T Consensus 342 L~~~E~~~F~~~~~d~~~~~~k~~~~~~~~~~~r~~~~~~~~~~~q~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l 420 (1155)
T 3pie_A 342 LSDFEYLNFEKKDIDVEWFNQQLENISLEGERKRTRMGKKLLMKQQKKLIGAVKPWLLKT-VQRKVTSELQDADFEIFPL 420 (1155)
T ss_pred HHHHHHHHHHHHhhHHHHHHHhhhhhhhhhHHHhhhhcccccchhHHhhhhccchhhhcc-ccccccccccccccccccc
Confidence 99999999999976432221 1110 0001111111000000000000000000000 000000000000000 000
Q ss_pred cCCCCCCCCCCcccccCCCcchhhHHHhhhccCCCCccccHHHHHHHH--HHHHhhhccc-C---CCCCcchhhhccCCC
Q 001209 471 DNGKGTSGRPHKVPRLSSGATIGAAIVEAENSFETDPQENKEEFKAKL--KELLRDKSDA-F---NSDNPEEDKVKLGEP 544 (1123)
Q Consensus 471 ~~~~~~~~~~~k~~~~s~~~~~~~~~~~~e~~~~~~~~~~~eelk~~l--~~~~~~k~d~-~---~~~~~~eD~VkL~e~ 544 (1123)
.+. ......+...+ ..+ .+... .... ....+....++ .......++. . +.....++.+..+.+
T Consensus 421 ~~~-~~~~~~~~~~~-------~~a-~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~~~~~~~~~~~ 489 (1155)
T 3pie_A 421 EDK-ELVRANLDFLK-------EFA-FDLGL-ILAH-SKSKDLYYFKLDLDSINXXXXXXXXXXXXXXXXXXXIYSERFV 489 (1155)
T ss_pred Cch-hhhhhhHHHHH-------HHH-Hhhcc-cccc-cccccccceecccccccccccccccccccccccccccchhhhh
Confidence 000 00000000000 000 00000 0000 00000000000 0000000000 0 000011223344557
Q ss_pred chhHHHHHHhcCCCChhHHHHHHHHHHHHHHhhHHHHhhhhccCcCcccccccCCCCcccccccccccccceecCCCCCC
Q 001209 545 GWKERYYEEKFNAKTPEEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPFASDLKDLDQFNISFELGHPFK 624 (1123)
Q Consensus 545 g~K~rYY~~KF~v~~~~di~~~r~~vv~~YvEGL~WVL~YYyqGcpSW~WYYPYHYAPfaSDl~~l~~~~i~Fe~G~Pf~ 624 (1123)
|||+|||++||+++.. +. +++++||++|||||||||+|||+|||||+||||||||||||||+++.+++|+|++|+||+
T Consensus 490 ~~k~rYY~~Kf~~~~~-~~-e~~~~v~~~YveGL~WVL~YYy~Gc~SW~WyYPYHYAPfasDl~~~~~~~i~F~~g~Pf~ 567 (1155)
T 3pie_A 490 EWKDQYYKDKLDFSIN-DT-DSLKEMTENYVGGLQWVLYYYYRGCPSWSWYYRYHYAPRISDVIKGIDQNIEFHKGQPFK 567 (1155)
T ss_pred hHHHHHHHHhcCCCcC-CH-HHHHHHHHHHHHHHHhHHHHHhCCCCCccccCccccccHHHHHHhhcccceeecCCCCCC
Confidence 9999999999999753 33 467899999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhcCCCCCCCCCcHHHHhhhcCCCCCCcccCCCcccccCCCCcccccceeccCCCChHHHHHHHHhhcCCCCHHH
Q 001209 625 PFNQLLGVFPSASSHALPEHYRKLMTDPNSPISDFYPTDFEVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEE 704 (1123)
Q Consensus 625 PfEQLMsVLPaaS~~~LP~~~r~LMtdp~SpIiDFYP~dF~ID~NGKk~~WqGVaLLPFIDe~rLl~a~~~~~~~LT~eE 704 (1123)
|||||||||||+|+++||++|++||+||+|||+||||++|+|||||||++||||||||||||+|||+||++++++||+||
T Consensus 568 PfeQLm~VLP~~S~~~LP~~~~~LM~d~~SpIidFYP~dF~iD~NGKk~~WqgVvlLPFIDe~rLl~a~~~~~~~Lt~eE 647 (1155)
T 3pie_A 568 PFQQLMAVLPERSKNLIPVVYRPLMYDEHSPILDFYPNEVELDLNGKTADWEAVVKISFVDQKRLVEAMAPYDAKLSPDE 647 (1155)
T ss_pred cHHHHhhhcChhhhccCcHhHHHhhcCCCCchhhhCccceeecCCCCccceeeEEECCcCCHHHHHHHHhhccccCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhccCCCcEEEEecCCCcchhhhhhhhHhhhhhhhhhhhhhhcCCCCccccCCCceEEEecCCCCCCCCcccCCCC-CC
Q 001209 705 ARRNSIMADMLFVLLSHPLSASIYTLDEHCKQLKIKERVEVKERLNPELSMCSDGMNGYISPCAGDPHPPVFRSPVA-SM 783 (1123)
Q Consensus 705 ~~RN~~g~d~Lfv~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~i~~~~~~~~~G~~G~v~~~~~~~~~~~~~sPi~-~l 783 (1123)
++||++|.++||+++..- + .++.||++ .+
T Consensus 648 ~~RN~~g~~~lf~~~~~~---------------------------~-----------------------~~~~s~l~~~f 677 (1155)
T 3pie_A 648 KKRNSFGTDLIFIFNPQV---------------------------D-----------------------TVYKTPLAGLF 677 (1155)
T ss_pred HhhccCCCcEEEEecCCC---------------------------C-----------------------ceeCCCccccC
Confidence 999999999999876411 0 12345664 46
Q ss_pred cCCCCCeEEEEEecCCCCC--CCCCCCCCCCCcCCCCCCcccCCCCCcccC
Q 001209 784 EDIMGNQVLCAIYKLPDAH--KHVTRPPAGVIFPKKIVQLEDLKPAPVLWH 832 (1123)
Q Consensus 784 ~di~~n~~~~~~y~~P~~~--~h~s~ll~g~~~p~~~l~~~d~~~~~~lw~ 832 (1123)
|||.++.|+...|.+|... .-+..|++|+++-...|.. .|+|.|
T Consensus 678 ~~i~~~~~~~~~~~~p~~~~~~~~~~l~~g~~~g~~~l~G-----FPtl~~ 723 (1155)
T 3pie_A 678 NDIEHNHCIEREFIPESMENVKFLFGLPKGAKLGASSLAG-----FPSLKT 723 (1155)
T ss_pred CCcccceEEEEeecCCCcccceecccCCcccccCccccCC-----CCcccc
Confidence 8999999999999999753 3357888998876655442 466643
No 3
>2y35_A LD22664P; hydrolase-DNA complex, RNA degradation, exonuclease 5'-3', R interference; 3.20A {Drosophila melanogaster}
Probab=100.00 E-value=7.6e-176 Score=1623.80 Aligned_cols=581 Identities=42% Similarity=0.805 Sum_probs=475.9
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCCC--CCHHHHH
Q 001209 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPAP--TTFDEVF 78 (1123)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~viE~~~~~~dG~~iP~d~s~pNPNg~efDNLYLDMNGIIHpC~Hpe~~p~p--~te~Emf 78 (1123)
||||+|||||++|||+|+..+.+ ..+| +|||||||||||||+|+|+++.+.+ .||+|||
T Consensus 1 MGVp~ffrwl~~ryP~~~~~~~~--------~~~~-----------e~DnLYlDmNgIIH~c~h~~~~~~~~~~~e~e~~ 61 (1140)
T 2y35_A 1 MGVPKFFRYISERYPCLSELARE--------HCIP-----------EFDNLYLDMNGIVHNCSHPDDNNIHFHLEEEQIF 61 (1140)
T ss_dssp CCSCHHHHHHHHHSGGGEEEEET--------TTSC-----------CCSEEEEEHHHHHHHHHCC------CCCCHHHHH
T ss_pred CChhHHHHHHHHHCCchhhhccc--------cCCC-----------cCCeEEEecchhhhhhcCCCCCCCCCCCCHHHHH
Confidence 99999999999999987543221 1122 8999999999999999999987554 6899999
Q ss_pred HHHHHHHHHHHhhccccceEEEEecCCCchhhhHHHHhhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCCCCCCccC
Q 001209 79 QCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFDSN 158 (1123)
Q Consensus 79 ~~If~yIDrL~~iVRPrKlLyiAIDGVAPRAKMNQQRsRRFrsakea~~~~~~~~~l~~e~~~eg~~lp~~~~~~~fDSN 158 (1123)
.+||+|||+||.+|||||+||||||||||||||||||+||||+|+++++..+ +..++|... ..+.||||
T Consensus 62 ~~if~yid~l~~~vrPrkll~iAiDGvAPrAKmnqQR~RRfrsa~~~~~~~~-------~~~~~g~~~----~~~~fdsn 130 (1140)
T 2y35_A 62 QEIFNYVDKLFYLIKPQRLFFLSVDGVAPRAKMNQQRSRRFRTAREAEQQEA-------KAAQRGELR----EHERFDSN 130 (1140)
T ss_dssp HHHHHHHHHHHHHHCCSSEEEEECCCSCCHHHHHHHHHHHHHHHHHHHHHHH-------HHHHC-----------CCCSG
T ss_pred HHHHHHHHHHHheeccceeEEEEecCCCchhHHHHHHHHHhhhhhhhhhhHH-------HHhhcCCcc----ccccCCcc
Confidence 9999999999999999999999999999999999999999999998765332 223445432 24689999
Q ss_pred cccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHH
Q 001209 159 VITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIM 238 (1123)
Q Consensus 159 ~ITPGT~FM~kLs~~L~~yI~~kl~~Dp~W~~lkVIlSda~VPGEGEHKImdfIR~qr~~p~ydPNt~HcIYGlDADLIm 238 (1123)
||||||+||.+|+++|++||+.|+++||.|++++|||||++||||||||||+|||.+|++|+|||||+|||||+||||||
T Consensus 131 ~ITPGT~FM~~l~~~L~~~i~~k~~~d~~w~~~~Vi~S~~~vPGEGEhKIm~~IR~~~~~p~~~pn~~HciyG~DADLIm 210 (1140)
T 2y35_A 131 CITPGTEFMVRLQEGLRAFLKTKISTDPLWQRCTVILSGQEAPGEGEHKIMDYIRYMKTQPDYDPNTRHCLYGLDAALII 210 (1140)
T ss_dssp GGSTTSHHHHHHHHHHHHHHHHHHHHCGGGSSSEEEEECSSSCSCHHHHHHHHHHHHHHSTTCCTTCCEEEECCSHHHHH
T ss_pred ccCCCcHHHHHHHHHHHHHHHHHhccCccccceEEEEeCCCCCCchHHHHHHHHHHHhhCCCCCCCCeEEEEccCHhHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCceEEEcccccccCCCCCcccccCCCCCcccccccccccccCCCCcCCCcccCCCCCeEEEehhHHHHHHHHHh
Q 001209 239 LALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEF 318 (1123)
Q Consensus 239 LgLatHep~f~ILRE~Vf~~~~~~~c~~cgQ~gH~~~~c~g~~k~k~~e~~e~~~~~~~~~~~f~~l~I~vLREYL~~El 318 (1123)
|||+||||||+||||+|++....+ +. ......|++|||++|||||+.||
T Consensus 211 L~L~the~~f~ilRe~v~f~~~~~--------------------~~-----------~~~~~~f~~l~i~~lReyL~~ef 259 (1140)
T 2y35_A 211 LGLCTHELHFVVLREEVKFGRNVK--------------------RT-----------SVEETRFFLLHLGLLREYLELEF 259 (1140)
T ss_dssp HHHHTTCSSEEEEEESSCTTCCTT--------------------CC-----------CGGGCEEEEEEHHHHHHHHHHHG
T ss_pred HHHccCCCcEEEeecccccccccc--------------------cc-----------cccccceEEEEehHHHHHHHHHh
Confidence 999999999999999986542110 00 01135799999999999999999
Q ss_pred cCC-CCCCccchhhhhhHHHHhhhhcccCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHHHHHHH
Q 001209 319 RIP-NPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQAV 397 (1123)
Q Consensus 319 ~~~-~~pf~~DlERiIDDfVfLcffvGNDFLPhLPsLeIreGaID~Li~iYKk~Lp~~ggYLT~~G~INl~rl~~fl~~L 397 (1123)
... ..+|++|+||+||||||||||+|||||||||+|+|++||||+|+++|++.++++|||||++|+||+++|+.||+.|
T Consensus 260 ~~~~~~~~~~d~eriidDfVfl~fl~GNDFLP~lp~l~I~~gai~~L~~~Y~~~~~~~~gyl~~~g~in~~~l~~~l~~l 339 (1140)
T 2y35_A 260 DALRTDEHKLDIAQLIDDWVLMGFLVGNDFIPHLPCLHISSNALPLLYRTYIGIYPTLGGNINENGKLNLRRLQIFISAL 339 (1140)
T ss_dssp GGGCCSSSCCCHHHHHHHHHHHHHHHCCTTSCCCTTCCTTTTHHHHHHHHHHHHGGGSSSCSEETTEECHHHHHHHHHHH
T ss_pred hhhccccccccHHHHHHHHHHHHHHhCCccCCCCCccccCCCHHHHHHHHHHHHHHHcCCcccCCCEEcHHHHHHHHHHH
Confidence 753 3579999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCccccccccCCCCCCCCCCCCCccccccccccCCCCCC
Q 001209 398 GSYEDRIFQKRARLHQRHAERIKREKAQARRGDDVEPLAQPDSLVPVSRFHGSRLASGPSPSPYQQSECVGRLDNGKGTS 477 (1123)
Q Consensus 398 ~~~Ed~iF~~r~~~e~r~~e~~kr~k~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 477 (1123)
++.|+++|++|.+..+.. +.|.++ .+ .. +. .+... ..+ .
T Consensus 340 ~~~E~~~f~~~~~~~~~~--~~k~~~-----~~-~~----------~~-----~~~~~---~~~-----~---------- 378 (1140)
T 2y35_A 340 TEVELDHFKEHADDLKYM--NNKSEA-----FD-MD----------VG-----EITES---QNL-----D---------- 378 (1140)
T ss_dssp HHHHHHHHHHHSCC------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHh--hhcchh-----cc-cc----------hh-----hcccc---ccc-----h----------
Confidence 999999998874321110 000000 00 00 00 00000 000 0
Q ss_pred CCCCcccccCCCcchhhHHHhhhccCCCCccccHHHHHHHHHHHHhhhcccCCCCCcchhhhccC-CCchhHHHHHHhcC
Q 001209 478 GRPHKVPRLSSGATIGAAIVEAENSFETDPQENKEEFKAKLKELLRDKSDAFNSDNPEEDKVKLG-EPGWKERYYEEKFN 556 (1123)
Q Consensus 478 ~~~~k~~~~s~~~~~~~~~~~~e~~~~~~~~~~~eelk~~l~~~~~~k~d~~~~~~~~eD~VkL~-e~g~K~rYY~~KF~ 556 (1123)
.... +.++. ..+....+.+ .+...++.+.++ .++||++||++||+
T Consensus 379 ------------~~~~-~~~~~--~~~~~~~~~~-------------------~~~~~e~~~~~~~~~~~k~~YY~~Kf~ 424 (1140)
T 2y35_A 379 ------------SDLG-ALINK--SMLLYDDDSE-------------------EDCSDENAVLLKEFQNYKRNFYRNKFK 424 (1140)
T ss_dssp ---------------------------------------------------------CHHHHHHHHHHHHHHHHHHHHHC
T ss_pred ------------hHHH-HHHHh--hhhccccccc-------------------cccchhhhhhhhhhhHHHHHHHHHHhC
Confidence 0000 00000 0000000000 000111122222 36899999999999
Q ss_pred CCChhHHHHHHHHHHHHHHhhHHHHhhhhccCcCcccccccCCCCcccccccccccccceecCCCCCChhhhhhhcCCCC
Q 001209 557 AKTPEEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPFASDLKDLDQFNISFELGHPFKPFNQLLGVFPSA 636 (1123)
Q Consensus 557 v~~~~di~~~r~~vv~~YvEGL~WVL~YYyqGcpSW~WYYPYHYAPfaSDl~~l~~~~i~Fe~G~Pf~PfEQLMsVLPaa 636 (1123)
++..+ +++++||++|||||||||+|||+|||||+||||||||||||||+++.+++|+|++|+||+|||||||||||+
T Consensus 425 ~~~~~---~~~~~~~~~YveGl~Wvl~YYy~G~~SW~WyYpyhYAP~~sDl~~~~~~~i~F~~g~Pf~PfeQLm~VLP~~ 501 (1140)
T 2y35_A 425 RDPND---ELIEELCHHYVNALQWVLDYYYRGVQSWDWYYPFHYTPFISDLKNIEQVEIAFHMGTPFLPFQQLLAVLPAA 501 (1140)
T ss_dssp SCCCH---HHHHHHHHHHHHHHHHHHHHHHTSCSCSSCCCCCSSCCCGGGCCCCTTCCCCCCCCCCCCHHHHHHHHCCGG
T ss_pred CCCcH---HHHHHHHHHHHHHHHHHHHHhcCCCCCCCcccCCCcCchHHHHHhhccccccccCCCCCChHHHHHhhcChh
Confidence 87543 567899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcHHHHhhhcCCCCCCcccCCCcccccCCCCcccccceeccCCCChHHHHHHHHhhcCCCCHHHHhhccCCCcEEE
Q 001209 637 SSHALPEHYRKLMTDPNSPISDFYPTDFEVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEEARRNSIMADMLF 716 (1123)
Q Consensus 637 S~~~LP~~~r~LMtdp~SpIiDFYP~dF~ID~NGKk~~WqGVaLLPFIDe~rLl~a~~~~~~~LT~eE~~RN~~g~d~Lf 716 (1123)
|+++||++|++||++|+|||+||||++|+||||||+++||||||||||||+|||+||+++++.||+||++||++|.+++|
T Consensus 502 S~~~LP~~~~~Lm~~~~Spi~dfYP~~f~iD~nGk~~~we~VvllPFIde~~Ll~a~~~~~~~Lt~eE~~RN~~g~~~~~ 581 (1140)
T 2y35_A 502 SAKLLPVAYHDLMLLPTSPLAEFYPLEFESDLNGKKHDWEAVVLIPFIDEGRLLAAMLPCEAQLSLEERERNRHGPMYVY 581 (1140)
T ss_dssp GGGGSCGGGHHHHHCTTCTTGGGSCSSCCCCCSSCCSGGGSCCCCCCCCHHHHHHTTHHHHHHSCHHHHHTTSCCCEEEE
T ss_pred hhhhCCHHHHHhhcCCCCchhHhCccceeecCCCCcCcEEeEEECCcCCHHHHHHHHHhccccCCHHHHhhcccCCceEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecC
Q 001209 717 VLLS 720 (1123)
Q Consensus 717 v~~~ 720 (1123)
..+.
T Consensus 582 ~~~~ 585 (1140)
T 2y35_A 582 KYST 585 (1140)
T ss_dssp EECS
T ss_pred Eecc
Confidence 8764
No 4
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A
Probab=98.44 E-value=6.7e-07 Score=100.10 Aligned_cols=151 Identities=13% Similarity=0.172 Sum_probs=79.8
Q ss_pred eEEEeccccccccccCCC---CCCCCC-HHHHHHHHHHHHHHHHhhc-cccceEEEEecCCCchhhhHHHHhhhccchhH
Q 001209 50 NLYLDMNGIIHPCFHPED---RPAPTT-FDEVFQCMFDYIDRLFVMV-RPRKLLYMAIDGVAPRAKMNQQRSRRFRASKD 124 (1123)
Q Consensus 50 NLYLDMNGIIHpC~Hpe~---~p~p~t-e~Emf~~If~yIDrL~~iV-RPrKlLyiAIDGVAPRAKMNQQRsRRFrsake 124 (1123)
-|-||.++.||-+.+.-. ...-.+ .-+.-..|+.++.+++.++ .|-+ +++++||.+|-.|......||-+....
T Consensus 23 ~l~ID~~~~l~r~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~l~~ll~~~i~-pv~VFDG~~~~~K~~~~~~R~~~r~~~ 101 (340)
T 1b43_A 23 KIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLFYRTINLMEAGIK-PVYVFDGEPPEFKKKELEKRREAREEA 101 (340)
T ss_dssp EEEEEHHHHHHHHHHHSBCTTSCBCBCTTSCBCHHHHHHHHHHHHHHHTTCE-EEEEECCSCCCCSSCSSTTCCCCTTHH
T ss_pred EEEEEhHHHHHHHHHHhccccCCccccccCCchHHHHHHHHHHHHHHhCCCE-EEEEecCCCchhhhhhHHHHHHHHHHH
Confidence 789999999998765321 000000 0001123444444444444 4544 567899999988877665555544322
Q ss_pred HHhHHHHHHHHHHHHHHhCCCCCCCCCCCCC--ccCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCC
Q 001209 125 AADSAAEEERLRQEFEREGRKLPPKSDSQVF--DSNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPG 202 (1123)
Q Consensus 125 a~~~~~~~~~l~~e~~~eg~~lp~~~~~~~f--DSN~ITPGT~FM~kLs~~L~~yI~~kl~~Dp~W~~lkVIlSda~VPG 202 (1123)
.+.. .+.+ +.|..-. ...| .++.||| +.+.. ++..+.. + ++.+|. .|+
T Consensus 102 ~~~~-------~~~y-k~g~~~~----~~~~~~~~~~vt~--~~~~~----~~~lL~~-~-------gip~i~----ap~ 151 (340)
T 1b43_A 102 EEKW-------REAL-EKGEIEE----ARKYAQRATRVNE--MLIED----AKKLLEL-M-------GIPIVQ----APS 151 (340)
T ss_dssp HHHH-------HHHH-HHSCHHH----HHHHHHTSGGGTH--HHHHH----HHHHHHH-H-------TCCEEE----CSS
T ss_pred HHHH-------HHHH-HcCCHHH----HHHHHHhcCCCCH--HHHHH----HHHHHHH-c-------CCcEEE----cCh
Confidence 1111 0011 1111000 0011 2234444 22222 3333322 1 466776 479
Q ss_pred ChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHH
Q 001209 203 EGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLA 240 (1123)
Q Consensus 203 EGEHKImdfIR~qr~~p~ydPNt~HcIYGlDADLImLg 240 (1123)
|+|-=|-..-+. ....+|++.|.||++++
T Consensus 152 EADa~iA~La~~---------g~~~~i~S~D~D~l~~g 180 (340)
T 1b43_A 152 EGEAQAAYMAAK---------GSVYASASQDYDSLLFG 180 (340)
T ss_dssp CHHHHHHHHHHH---------TSSSEEECSSSHHHHTT
T ss_pred hHHHHHHHHHHc---------CCEEEEEccCCCcceec
Confidence 999988877764 14578999999999987
No 5
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A
Probab=98.25 E-value=1.2e-06 Score=97.50 Aligned_cols=91 Identities=25% Similarity=0.420 Sum_probs=61.1
Q ss_pred ccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhhcCCceEEEcccccccCCCCCcccccCC
Q 001209 190 KIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQ 269 (1123)
Q Consensus 190 ~lkVIlSda~VPGEGEHKImdfIR~qr~~p~ydPNt~HcIYGlDADLImLgLatHep~f~ILRE~Vf~~~~~~~c~~cgQ 269 (1123)
++.+|. .|||+|-=|--+-+. +...+|++.|.||++|+ + ++ |+|-.. .
T Consensus 143 gi~~i~----apgEAD~~ia~La~~---------g~~~~I~S~D~Dll~~~-~---~~--v~~~~~-~------------ 190 (326)
T 1a76_A 143 GIPYVE----APSEGEAQASYMAKK---------GDVWAVVSQDYDALLYG-A---PR--VVRNLT-T------------ 190 (326)
T ss_dssp TCCEEE----CSSCHHHHHHHHHHT---------TSSSEEECSSSGGGGGT-C---SE--EEESSS-S------------
T ss_pred CCCeEE----CCccHHHHHHHHHHC---------CCEEEEecCCcccceec-C---CE--EEEeec-C------------
Confidence 456664 589999977777663 34589999999999997 2 33 333210 0
Q ss_pred CCCcccccccccccccCCCCcCCCcccCCCCCeEEEehhHHHHHHHHHhcCCCCCCccchhhhhhHHHHhhhhcccCCCC
Q 001209 270 PGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLP 349 (1123)
Q Consensus 270 ~gH~~~~c~g~~k~k~~e~~e~~~~~~~~~~~f~~l~I~vLREYL~~El~~~~~pf~~DlERiIDDfVfLcffvGNDFLP 349 (1123)
+ .+.+++++...+.+.+ . ++. +.||.+|.|+|+||+|
T Consensus 191 ---------------------~-------~~~~~~~~~~~v~~~~----g-------l~~----~q~id~~~L~GsD~~p 227 (326)
T 1a76_A 191 ---------------------T-------KEMPELIELNEVLEDL----R-------ISL----DDLIDIAIFMGTDYNP 227 (326)
T ss_dssp ---------------------C-------SSCCEEEEHHHHHHHH----T-------CCH----HHHHHHHHHHCCTTST
T ss_pred ---------------------C-------CCceEEEEHHHHHHHc----C-------CCH----HHHHHHHHHcCCCCCC
Confidence 0 0146678876655443 2 222 4688899999999999
Q ss_pred -CCCccc
Q 001209 350 -HMPTLE 355 (1123)
Q Consensus 350 -hLPsLe 355 (1123)
.+|++-
T Consensus 228 ~GvpGiG 234 (326)
T 1a76_A 228 GGVKGIG 234 (326)
T ss_dssp TTTTTCC
T ss_pred CCCCCcC
Confidence 999874
No 6
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' FLA site, hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A
Probab=98.14 E-value=1.5e-05 Score=89.20 Aligned_cols=41 Identities=12% Similarity=0.230 Sum_probs=29.0
Q ss_pred CeEEEehhHHHHHHHHHhcCCCCCCccchhhhhhHHHHhhhhcccCCCCCCCcccc
Q 001209 301 PYQFLHIWTLREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEI 356 (1123)
Q Consensus 301 ~f~~l~I~vLREYL~~El~~~~~pf~~DlERiIDDfVfLcffvGNDFLPhLPsLeI 356 (1123)
.+++++...+.+.+ . ++ -+.||.+|.|+|+||+|.+|++-+
T Consensus 205 ~~~~~~~~~v~~~~----g-------l~----~~q~id~~~L~GsD~ipGv~GiG~ 245 (336)
T 1rxw_A 205 KPEIIILESNLKRL----G-------LT----REQLIDIAILVGTDYNEGVKGVGV 245 (336)
T ss_dssp CCEEEEHHHHHHHH----T-------CC----HHHHHHHHHHHCBTTBCCCTTCCH
T ss_pred ceEEeEHHHHHHHc----C-------CC----HHHHHHHHhhcCCCCCCCCCCcCH
Confidence 45677776655543 2 22 246888999999999999998543
No 7
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Probab=98.07 E-value=3e-05 Score=87.58 Aligned_cols=172 Identities=17% Similarity=0.282 Sum_probs=88.2
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCC----CCCCCCCHHH
Q 001209 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPE----DRPAPTTFDE 76 (1123)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~viE~~~~~~dG~~iP~d~s~pNPNg~efDNLYLDMNGIIHpC~Hpe----~~p~p~te~E 76 (1123)
|||.+|..||...-+.+- ++ ...|. -|=||....||-..... ..-.+++ .
T Consensus 1 MGI~GL~~~L~~~~~~~~---l~----~l~Gk-----------------~vaIDas~wL~~~~~~~~~~l~~G~~t~--~ 54 (352)
T 3qe9_Y 1 MGIQGLLQFIKEASEPIH---VR----KYKGQ-----------------VVAVDTYCWLHKGAIACAEKLAKGEPTD--R 54 (352)
T ss_dssp -CCTTHHHHTTTSEEEEE---GG----GGTTS-----------------EEEEETHHHHHHHHHHTHHHHHTTCCCC--H
T ss_pred CCcchHHHHHHhhCCcCC---HH----HhCCc-----------------EEEEecHHHHHHhhhccchhhcCCCCcH--H
Confidence 999999999976533221 11 11222 56788888888632211 0112222 1
Q ss_pred HHHHHHHHHHHHH-hhccccceEEEEecCCCchhhhHHHHhhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCCCCCC
Q 001209 77 VFQCMFDYIDRLF-VMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVF 155 (1123)
Q Consensus 77 mf~~If~yIDrL~-~iVRPrKlLyiAIDGVAPRAKMNQQRsRRFrsakea~~~~~~~~~l~~e~~~eg~~lp~~~~~~~f 155 (1123)
++.-++..+..|. .-|+| ++.+||.+|-.|-....+||.+.....+...+ ..++|.. +...+.|
T Consensus 55 l~~~~~r~l~~L~~~gI~P----vfVFDG~~~p~Kk~~~~~Rr~~r~~~~~~~~~--------~~~~g~~---~~a~~~f 119 (352)
T 3qe9_Y 55 YVGFCMKFVNMLLSHGIKP----ILVFDGCTLPSKKEVERSRRERRQANLLKGKQ--------LLREGKV---SEARECF 119 (352)
T ss_dssp HHHHHHHHHHHHHHTTCEE----EEEECCSCCTTTHHHHHHHHHHHHHHHHHHHH--------HTTSSCC---HHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCEE----EEEECCCCcHHHHHHHHHHHHHHHHHHHHHHH--------HHHhCCH---HHHHHHH
Confidence 2222222233221 12344 56699999988877665555543322111110 1111210 0000112
Q ss_pred -ccCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecCh
Q 001209 156 -DSNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDA 234 (1123)
Q Consensus 156 -DSN~ITPGT~FM~kLs~~L~~yI~~kl~~Dp~W~~lkVIlSda~VPGEGEHKImdfIR~qr~~p~ydPNt~HcIYGlDA 234 (1123)
.+..||| + +...++..+.. -+|.+|.+ |+|+|-=|--.-+. .....|++.|.
T Consensus 120 ~~~~~vt~--~----~~~~i~~~L~~--------~gIp~i~a----p~EADaqiA~La~~---------g~~~~I~S~D~ 172 (352)
T 3qe9_Y 120 TRSINITH--A----MAHKVIKAARS--------QGVDCLVA----PYEADAQLAYLNKA---------GIVQAIITEDS 172 (352)
T ss_dssp GGGCCCCH--H----HHHHHHHHHHH--------TTCEEEEC----SSCHHHHHHHHHHT---------TSCSEEECSCG
T ss_pred hhcCCCCH--H----HHHHHHHHHHH--------cCCcEEEC----CcchHHHHHHHHHC---------CCeEEEEeCCc
Confidence 1235676 2 23334444432 25788874 79999977665551 34579999999
Q ss_pred hHHHHH
Q 001209 235 DLIMLA 240 (1123)
Q Consensus 235 DLImLg 240 (1123)
||++|+
T Consensus 173 Dll~~~ 178 (352)
T 3qe9_Y 173 ALLAFG 178 (352)
T ss_dssp GGGGGT
T ss_pred Cccccc
Confidence 998877
No 8
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus}
Probab=97.79 E-value=0.00017 Score=81.84 Aligned_cols=134 Identities=19% Similarity=0.267 Sum_probs=74.3
Q ss_pred cCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhH
Q 001209 157 SNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADL 236 (1123)
Q Consensus 157 SN~ITPGT~FM~kLs~~L~~yI~~kl~~Dp~W~~lkVIlSda~VPGEGEHKImdfIR~qr~~p~ydPNt~HcIYGlDADL 236 (1123)
+..||| +.+..+.+.|+.+ +|.+|.+ |||+|-=|--.-+ -....+|++-|.|+
T Consensus 138 ~~~vt~--~~~~~i~~lL~~~------------GIp~i~a----pgEADaqiA~La~---------~g~~~~I~S~D~D~ 190 (363)
T 3ory_A 138 SAKLTE--EMVRDAKSLLDAM------------GIPWVQA----PAEGEAQAAYIVK---------KGDAYASASQDYDS 190 (363)
T ss_dssp CCCCCH--HHHHHHHHHHHHH------------TCCEEEC----SSCHHHHHHHHHH---------TTSCSEEECSSSHH
T ss_pred cccCCH--HHHHHHHHHHHHC------------CCCEEEe----CccHHHHHHHHHH---------CCCeEEEECCCcCc
Confidence 446776 4455555555433 4666665 8899985544332 13568999999999
Q ss_pred HHHHhhcCCceEEEcccccccCCCCCcccccCCCCCcccccccccccccCCCCcCCCcccCCCCCeEEEehhHHHHHHHH
Q 001209 237 IMLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDY 316 (1123)
Q Consensus 237 ImLgLatHep~f~ILRE~Vf~~~~~~~c~~cgQ~gH~~~~c~g~~k~k~~e~~e~~~~~~~~~~~f~~l~I~vLREYL~~ 316 (1123)
++|+- ++ |+|-. +..+ +|. . . .++ ......+++++...+.+.+
T Consensus 191 l~fg~----~~--v~~~l-~~~~---~~~-----------------~-p----~~~---~~v~~~~~~~~~~~v~~~~-- 233 (363)
T 3ory_A 191 LLFGS----PK--LVRNL-TISG---RRK-----------------L-P----RKN---EYVEVKPELIELDKLLVQL-- 233 (363)
T ss_dssp HHTTC----SE--EEEST-TTCE---EEE-----------------C-S----STT---CEEEECCEEEEHHHHHHHH--
T ss_pred cccCC----Ce--EEEEe-eccc---ccc-----------------C-C----ccc---cccccceEEEcHHHHHHHh--
Confidence 99873 22 33321 1100 000 0 0 000 0000124677777665543
Q ss_pred HhcCCCCCCccchhhhhhHHHHhhhhcccCCCC-CCCccccccchHHHHHHHHH
Q 001209 317 EFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLP-HMPTLEIREGAINLLMAVYK 369 (1123)
Q Consensus 317 El~~~~~pf~~DlERiIDDfVfLcffvGNDFLP-hLPsLeIreGaID~Li~iYK 369 (1123)
. ++. +-||-+|.|+|+||+| .+|++-.. .|+. |+.-|.
T Consensus 234 --g-------l~~----~q~id~~~L~GsDy~p~GVpGIG~K-tA~k-Ll~~~g 272 (363)
T 3ory_A 234 --G-------ITL----ENLIDIGILLGTDYNPDGFEGIGPK-KALQ-LVKAYG 272 (363)
T ss_dssp --T-------CCH----HHHHHHHHHHCBTTBTTCSTTCCHH-HHHH-HHHHHT
T ss_pred --C-------cCH----HHHHHHHHHhCCCCCCCCCCCcCHH-HHHH-HHHHcC
Confidence 1 223 3577799999999999 99975433 3444 455553
No 9
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2
Probab=97.51 E-value=0.00047 Score=78.46 Aligned_cols=229 Identities=17% Similarity=0.289 Sum_probs=116.4
Q ss_pred cchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCC--CCCCCHH-HHH
Q 001209 2 GVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDR--PAPTTFD-EVF 78 (1123)
Q Consensus 2 GVP~FfRWL~~rYP~ii~~viE~~~~~~dG~~iP~d~s~pNPNg~efDNLYLDMNGIIHpC~Hpe~~--p~p~te~-Emf 78 (1123)
||++|...|...-|..+..+- +.. -.| --|-||.+.+||-+.|.-.. ..-.+.+ +.-
T Consensus 1 GI~GL~~~L~~~~~~~~~~~~-------------l~~----l~g---~~l~IDg~~~lyr~~~a~~~~~~~l~~~~G~~t 60 (379)
T 1ul1_X 1 GIQGLAKLIADVAPSAIREND-------------IKS----YFG---RKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60 (379)
T ss_dssp CCTTHHHHHHTTCTTSCCEEC-------------GGG----GTT---CCEEEEHHHHHHHHHSCC-------------CC
T ss_pred CcChhHHHHHHhccccceeeC-------------HHH----cCC---CEEEEEchHHHHHHHHhCCCcccccCcCCCCCc
Confidence 899999999998886654421 000 011 26889999999998875311 0001110 111
Q ss_pred HHHHHHHHH---HHhh-ccccceEEEEecCCCchhhhHH--HH-hhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCC
Q 001209 79 QCMFDYIDR---LFVM-VRPRKLLYMAIDGVAPRAKMNQ--QR-SRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSD 151 (1123)
Q Consensus 79 ~~If~yIDr---L~~i-VRPrKlLyiAIDGVAPRAKMNQ--QR-sRRFrsakea~~~~~~~~~l~~e~~~eg~~lp~~~~ 151 (1123)
..|+.++.+ |+.. ++| +| ++||..|-.|-.. .| .+|-.+.....+ ...+|. |++
T Consensus 61 ~~l~g~~~~~~~ll~~~i~P---~~-VFDG~~~~~K~~~~~~yk~~R~~~~~~~~~-----------~~~~g~--~~~-- 121 (379)
T 1ul1_X 61 SHLMGMFYRTIRMMENGIKP---VY-VFDGKPPQLKSGELAKRSERRAEAEKQLQQ-----------AQAAGA--EQE-- 121 (379)
T ss_dssp HHHHHHHHHHHHHHHTTCCE---EE-EECCSCCSCCCCCCCCC-------------------------------------
T ss_pred hHHHHHHHHHHHHHHCCCCe---EE-EEeCCCcccccchHHHHHhhhhHHHHHHHH-----------HHHcCC--HHH--
Confidence 123344444 4443 555 44 8999998555332 22 222211111100 011111 110
Q ss_pred CCCCc--cCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEE
Q 001209 152 SQVFD--SNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCL 229 (1123)
Q Consensus 152 ~~~fD--SN~ITPGT~FM~kLs~~L~~yI~~kl~~Dp~W~~lkVIlSda~VPGEGEHKImdfIR~qr~~p~ydPNt~HcI 229 (1123)
-..|. +..||+- -+..+.+.|+.+ ++.+|. .|||+|-=|--.-+. ....+|
T Consensus 122 ~~~~~~~~~~vt~~--~~~~~~~lL~~~------------Gi~~i~----apgEADd~iA~La~~---------g~~~~i 174 (379)
T 1ul1_X 122 VEKFTKRLVKVTKQ--HNDECKHLLSLM------------GIPYLD----APSEAEASCAALVKA---------GKVYAA 174 (379)
T ss_dssp -------CCCCCCS--CHHHHHHHHHHH------------TCCEEE----CSSCHHHHHHHHHHH---------TSSSEE
T ss_pred HHHHHhhccCCCHH--HHHHHHHHHHHc------------CCCeec----CCCcHHHHHHHHHhc---------CCeEEE
Confidence 01121 2233332 233333333322 356665 489999988887764 234789
Q ss_pred EecChhHHHHHhhcCCceEEEcccccccCCCCCcccccCCCCCcccccccccccccCCCCcCCCcccCCCCCeEEEehhH
Q 001209 230 YGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWT 309 (1123)
Q Consensus 230 YGlDADLImLgLatHep~f~ILRE~Vf~~~~~~~c~~cgQ~gH~~~~c~g~~k~k~~e~~e~~~~~~~~~~~f~~l~I~v 309 (1123)
.+-|.||++++ + ++ |+|-..+. + ..+..++.++...
T Consensus 175 iS~D~Dll~~g-~---~~--v~~~~~~~-~-------------------------------------~~k~~~~~~~~~~ 210 (379)
T 1ul1_X 175 ATEDMDCLTFG-S---PV--LMRHLTAS-E-------------------------------------AKKLPIQEFHLSR 210 (379)
T ss_dssp ECSCTHHHHTT-C---SE--EEECSSCC-C--------------------------------------CCCCEEEEEHHH
T ss_pred EecCcCccccc-c---ce--EEEEeccc-c-------------------------------------cCcCCeEEEeHHH
Confidence 99999999987 2 33 33321000 0 0012466777766
Q ss_pred HHHHHHHHhcCCCCCCccchhhhhhHHHHhhhhcccCCCCCCCccc
Q 001209 310 LREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLE 355 (1123)
Q Consensus 310 LREYL~~El~~~~~pf~~DlERiIDDfVfLcffvGNDFLPhLPsLe 355 (1123)
+.+.+ . ++. +.||.||.|+|+||.+.||++-
T Consensus 211 v~~~~----g-------l~~----~q~id~~~L~G~D~~d~IpGIG 241 (379)
T 1ul1_X 211 ILQEL----G-------LNQ----EQFVDLCILLGSDYCESIRGIG 241 (379)
T ss_dssp HHHHH----T-------CCH----HHHHHHHHHHHCSSSCCCTTCC
T ss_pred HHHHh----C-------CCH----HHHHHHHHHhCCCcCCCCCCcC
Confidence 54433 2 222 4677899999999999999863
No 10
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus}
Probab=97.36 E-value=0.0011 Score=74.50 Aligned_cols=211 Identities=17% Similarity=0.222 Sum_probs=96.3
Q ss_pred eEEEeccccccccccCCCC---CCCCC----HHHHHHHHHHHHHHHHhh-ccccceEEEEecCCCchhhhHH--HHh-hh
Q 001209 50 NLYLDMNGIIHPCFHPEDR---PAPTT----FDEVFQCMFDYIDRLFVM-VRPRKLLYMAIDGVAPRAKMNQ--QRS-RR 118 (1123)
Q Consensus 50 NLYLDMNGIIHpC~Hpe~~---p~p~t----e~Emf~~If~yIDrL~~i-VRPrKlLyiAIDGVAPRAKMNQ--QRs-RR 118 (1123)
-|-||.+++||-+.+.-.. ..-.+ ....+..+|..+-+|+.. ++| ++++||..|-.|-.. .|. +|
T Consensus 20 ~l~IDg~~~l~r~~~a~~~~~g~~l~~~~G~~t~al~g~~~~~~~ll~~~i~P----v~vFDG~~~~~r~~~~~~yk~~R 95 (346)
T 2izo_A 20 RVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSHLSGLFYRTINILEEGVIP----IYVFDGKPPEQKSEELERRRKAK 95 (346)
T ss_dssp EEEEEHHHHHHHHHHSCCCC---CCBCSSSCBCHHHHHHHHHHHHHHHHTEEE----EEEECC-----------------
T ss_pred EEEEEhHHHHHHHHHhccccccccccccCCCccHHHHHHHHHHHHHHHCCCcE----EEEECCCCcchhhhHHHHHHHHH
Confidence 6889999999987664311 00000 011233334444455554 788 689999988555433 332 22
Q ss_pred ccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCCCCCCc--cCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEc
Q 001209 119 FRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFD--SNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILS 196 (1123)
Q Consensus 119 Frsakea~~~~~~~~~l~~e~~~eg~~lp~~~~~~~fD--SN~ITPGT~FM~kLs~~L~~yI~~kl~~Dp~W~~lkVIlS 196 (1123)
-.+..+ +. ++...|.. .....|- +..||| +.+..+.+.|+.+ ++.+|.
T Consensus 96 ~~~~~~----------l~-~~~~~g~~----~~a~~~~~~~~~vt~--~~~~~~~~lL~~~------------gi~~i~- 145 (346)
T 2izo_A 96 EEAERK----------LE-RAKSEGKI----EELRKYSQAILRLSN--IMVEESKKLLRAM------------GIPIVQ- 145 (346)
T ss_dssp --------------------------------------------CH--HHHHHHHHHHHHH------------TCCEEE-
T ss_pred HHhHHH----------HH-HHHhcCCH----HHHHHHHhhccCCCH--HHHHHHHHHHHHC------------CCCEEE-
Confidence 211111 11 01111210 0001122 223332 3444444444422 456665
Q ss_pred CCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhhcCCceEEEcccccccCCCCCcccccCCCCCcccc
Q 001209 197 DANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAAN 276 (1123)
Q Consensus 197 da~VPGEGEHKImdfIR~qr~~p~ydPNt~HcIYGlDADLImLgLatHep~f~ILRE~Vf~~~~~~~c~~cgQ~gH~~~~ 276 (1123)
.|||+|-=|--.-+. ....+|++.|.||++|+- +++ +|-. ...+ +|. .
T Consensus 146 ---ap~EADa~ia~La~~---------g~~~~I~S~D~D~l~~~~----~~v--~~~~-~~~~---~~~---~------- 193 (346)
T 2izo_A 146 ---APSEGEAEAAYLNKL---------GLSWAAASQDYDAILFGA----KRL--VRNL-TITG---KRK---L------- 193 (346)
T ss_dssp ---CSSCHHHHHHHHHHT---------TSSSEEECSSSHHHHTTC----SEE--EESS-CC-------------------
T ss_pred ---cCCcHHHHHHHHHhC---------CCeEEEECCCCCcceecC----CeE--EEEe-cccc---ccc---C-------
Confidence 589999987766651 345899999999999872 333 3321 0000 000 0
Q ss_pred cccccccccCCCCcCCCcccCCCCCeEEEehhHHHHHHHHHhcCCCCCCccchhhhhhHHHHhhhhcccCCCC-CCCccc
Q 001209 277 CEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLP-HMPTLE 355 (1123)
Q Consensus 277 c~g~~k~k~~e~~e~~~~~~~~~~~f~~l~I~vLREYL~~El~~~~~pf~~DlERiIDDfVfLcffvGNDFLP-hLPsLe 355 (1123)
+. + .......+++++...+.+.+ . ++. +.||.||.|+|+||+| .+|++-
T Consensus 194 ----p~--------~---~~~~~~~~~~~~~~~v~~~~----g-------l~~----~q~id~~~L~G~D~~p~Gv~GIG 243 (346)
T 2izo_A 194 ----PN--------K---DVYVEIKPELIETEILLKKL----G-------ITR----EQLIDIGILIGTDYNPDGIRGIG 243 (346)
T ss_dssp --------------------CCCCCCEEEEHHHHHHHH----T-------CCH----HHHHHHHHHHCCSSSTTCSTTCC
T ss_pred ----cc--------c---ccccccceEEEEHHHHHHHc----C-------CCH----HHHHHHHHHcCCCCCCCCCCCcC
Confidence 00 0 00000135678776655433 2 222 4688899999999999 999874
Q ss_pred c
Q 001209 356 I 356 (1123)
Q Consensus 356 I 356 (1123)
+
T Consensus 244 ~ 244 (346)
T 2izo_A 244 P 244 (346)
T ss_dssp H
T ss_pred H
Confidence 4
No 11
>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase-DNA complex, DNA repair, replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A* 3q8m_A*
Probab=97.25 E-value=0.0023 Score=72.08 Aligned_cols=232 Identities=19% Similarity=0.235 Sum_probs=121.7
Q ss_pred cchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCC--CCCCCC-HHHHH
Q 001209 2 GVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPED--RPAPTT-FDEVF 78 (1123)
Q Consensus 2 GVP~FfRWL~~rYP~ii~~viE~~~~~~dG~~iP~d~s~pNPNg~efDNLYLDMNGIIHpC~Hpe~--~p~p~t-e~Emf 78 (1123)
||.++...|...-|.+++.+-=+ +..| --|-||.++.||-+.|.-. ...-.+ .-+.-
T Consensus 1 GI~GL~~~l~~~~p~~~~~~~l~---~l~g-----------------k~l~IDgs~~lyr~~~a~~~~~~~l~~~~G~~T 60 (341)
T 3q8k_A 1 GIQGLAKLIADVAPSAIRENDIK---SYFG-----------------RKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60 (341)
T ss_dssp CCTTHHHHHHHHCGGGEEEEEGG---GGTT-----------------CEEEEEHHHHHHHHHHHCEETTEECBCTTSCBC
T ss_pred CchhHHHHHHHhhhhccccccHH---HhCC-----------------CEEEEecHHHHHHHHHccccccCCCCCCCCCCc
Confidence 89999999999999877654110 0111 1578999999988766321 000000 00111
Q ss_pred HHHHHHHHHHHhhcc-ccceEEEEecCCCchhh--hHHHHh-hhccchhHHHhHHH--HHHHHHHHHHHhCCCCCCCCCC
Q 001209 79 QCMFDYIDRLFVMVR-PRKLLYMAIDGVAPRAK--MNQQRS-RRFRASKDAADSAA--EEERLRQEFEREGRKLPPKSDS 152 (1123)
Q Consensus 79 ~~If~yIDrL~~iVR-PrKlLyiAIDGVAPRAK--MNQQRs-RRFrsakea~~~~~--~~~~l~~e~~~eg~~lp~~~~~ 152 (1123)
..|+.++.+++.+++ --+-+| ++||.+|-.| +...|. +|-.+.+...++.. ..+++.+...
T Consensus 61 ~al~g~~~~~~~ll~~~i~P~~-VFDg~~~~~r~~~~~~yk~~R~~~~~~~~~a~r~~~pe~l~~~~~------------ 127 (341)
T 3q8k_A 61 SHLMGMFYRTIRMMENGIKPVY-VFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTK------------ 127 (341)
T ss_dssp HHHHHHHHHHHHHHTTTCEEEE-EECCCCCGGGHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH------------
T ss_pred hHHHHHHHHHHHHHHCCCCceE-EEeCCCcccchhhhHHHHHHHhHhHHHHHHHHhcCCHHHHHHHHh------------
Confidence 244455555555444 223344 7999999554 455543 33222111111000 0011111111
Q ss_pred CCCccCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEec
Q 001209 153 QVFDSNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGL 232 (1123)
Q Consensus 153 ~~fDSN~ITPGT~FM~kLs~~L~~yI~~kl~~Dp~W~~lkVIlSda~VPGEGEHKImdfIR~qr~~p~ydPNt~HcIYGl 232 (1123)
.+..||+. -+..+.+.|+.+ +|.+|.. |||+|-=|--.-+. ....+|.+-
T Consensus 128 ---~~~~vt~~--q~~~~~~lL~~~------------gip~i~a----p~EADd~ia~La~~---------g~v~~i~s~ 177 (341)
T 3q8k_A 128 ---RLVKVTKQ--HNDECKHLLSLM------------GIPYLDA----PSEAEASCAALVKA---------GKVYAAATE 177 (341)
T ss_dssp ---HTCCCCHH--HHHHHHHHHHHH------------TCCEEEC----SSCHHHHHHHHHHT---------TSSSEEECS
T ss_pred ---hcccCCHH--HHHHHHHHHHHc------------CCCEEEC----CccHHHHHHHHHhc---------CCeEEEEcC
Confidence 01123332 222333333322 4566664 79999988877763 235678899
Q ss_pred ChhHHHHHhhcCCceEEEcccccccCCCCCcccccCCCCCcccccccccccccCCCCcCCCcccCCCCCeEEEehhHHHH
Q 001209 233 DADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLRE 312 (1123)
Q Consensus 233 DADLImLgLatHep~f~ILRE~Vf~~~~~~~c~~cgQ~gH~~~~c~g~~k~k~~e~~e~~~~~~~~~~~f~~l~I~vLRE 312 (1123)
|.|+++++- ++ |+|-..+ .+ + ...++..++...+.+
T Consensus 178 D~D~l~~~~----~~--v~~~~~~-~~-------------------------------~------~~~~~~~~~~~~v~~ 213 (341)
T 3q8k_A 178 DMDCLTFGS----PV--LMRHLTA-SE-------------------------------A------KKLPIQEFHLSRILQ 213 (341)
T ss_dssp CTHHHHTTC----SE--EEESCCC-CS-------------------------------S------CCCEEEEEEHHHHHH
T ss_pred CccccccCC----cE--EEEcccc-cc-------------------------------c------CCCceEEEcHHHHHH
Confidence 999999972 22 3332100 00 0 012356677665544
Q ss_pred HHHHHhcCCCCCCccchhhhhhHHHHhhhhcccCCCCCCCccc
Q 001209 313 YLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLE 355 (1123)
Q Consensus 313 YL~~El~~~~~pf~~DlERiIDDfVfLcffvGNDFLPhLPsLe 355 (1123)
-+ .++.+ .||-+|.|+|+|++|.+|++-
T Consensus 214 ~~-----------gl~~~----q~id~~~L~G~D~~~gipGiG 241 (341)
T 3q8k_A 214 EL-----------GLNQE----QFVDLCILLGSDYCESIRGIG 241 (341)
T ss_dssp HH-----------TCCHH----HHHHHHHHHCCSSSCCCTTCC
T ss_pred Hh-----------CCCHH----HHHHHHHhcCCCCCCCCCCcc
Confidence 32 22333 567799999999999999753
No 12
>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A
Probab=96.13 E-value=0.057 Score=59.70 Aligned_cols=145 Identities=16% Similarity=0.161 Sum_probs=80.8
Q ss_pred eEEEeccccccccccCCCCCCCCCHHHHHHHHHHHHHHHHhhccccceEEEEecCCCchhhhHHHHhhhccchhHHHhHH
Q 001209 50 NLYLDMNGIIHPCFHPEDRPAPTTFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSA 129 (1123)
Q Consensus 50 NLYLDMNGIIHpC~Hpe~~p~p~te~Emf~~If~yIDrL~~iVRPrKlLyiAIDGVAPRAKMNQQRsRRFrsakea~~~~ 129 (1123)
-|-||.+++||-++|..++. | .+..++..|-+|+...+|..++ +|+||..| .-|..-|-.-|......
T Consensus 21 lllIDg~~llyRa~~~~~G~-p-----av~Gf~~~l~~ll~~~~p~~~v-vvFD~~~~-----tfR~~~~~~YKa~R~~~ 88 (290)
T 1exn_A 21 LMIVDGTNLGFRFKHNNSKK-P-----FASSYVSTIQSLAKSYSARTTI-VLGDKGKS-----VFRLEHLPEYKGNRDEK 88 (290)
T ss_dssp EEEEEHHHHHHHHHHHCSSS-C-----CHHHHHHHHHHHHHHTTEEEEE-EECCBSCC-----HHHHHHCTTTTHHHHHH
T ss_pred EEEEECcHHHHHHHhCCCCc-h-----HHHHHHHHHHHHHHHcCCCeEE-EEEcCCCc-----hhhhhCcHHHHcCCCCC
Confidence 68999999999998843332 2 3444555666667778898764 89998766 44554444433322111
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCCCCCccCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCC-ChhhhH
Q 001209 130 AEEERLRQEFEREGRKLPPKSDSQVFDSNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPG-EGEHKI 208 (1123)
Q Consensus 130 ~~~~~l~~e~~~eg~~lp~~~~~~~fDSN~ITPGT~FM~kLs~~L~~yI~~kl~~Dp~W~~lkVIlSda~VPG-EGEHKI 208 (1123)
. .+ .......+++ .|+..+.+.|+.+ ++ ++.+| .+|| |++==|
T Consensus 89 p----------~~----------~~~~~e~L~~--q~~~~ikell~~~---~~-------gip~i----~~~g~EADDvi 132 (290)
T 1exn_A 89 Y----------AQ----------RTEEEKALDE--QFFEYLKDAFELC---KT-------TFPTF----TIRGVEADDMA 132 (290)
T ss_dssp H----------HT----------SCHHHHHHHH--HHHHHHHHHHHHH---TT-------TSCEE----CCTTBCHHHHH
T ss_pred C----------cc----------ccccchhHHH--hhHHHHHHHHHhh---CC-------CCcEE----EECCcCHHHHH
Confidence 1 00 0000000000 0122233333221 11 23444 3789 999888
Q ss_pred HHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhhcCCceEEEc
Q 001209 209 MSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALATHEVHFSIL 251 (1123)
Q Consensus 209 mdfIR~qr~~p~ydPNt~HcIYGlDADLImLgLatHep~f~IL 251 (1123)
--.-++-... ....+|++.|-||..|. .++++|+
T Consensus 133 atLa~~~~~~-----G~~v~IvS~DkDl~Qlv----~~~v~v~ 166 (290)
T 1exn_A 133 AYIVKLIGHL-----YDHVWLISTDGDWDTLL----TDKVSRF 166 (290)
T ss_dssp HHHHHHHGGG-----SSCEEEECSCGGGGGGC----CSSEEEE
T ss_pred HHHHHHHHHC-----CCcEEEEeCCCChhhcC----CCCEEEE
Confidence 8777764432 23588999999997665 3566554
No 13
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A
Probab=84.74 E-value=0.43 Score=35.29 Aligned_cols=19 Identities=37% Similarity=0.947 Sum_probs=16.6
Q ss_pred CCcccccCCCCCccccccc
Q 001209 261 QDKCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g 279 (1123)
..+|+.||+.||++.+|..
T Consensus 6 ~~~C~nCgk~GH~ar~C~~ 24 (29)
T 1nc8_A 6 VIRCWNCGKEGHSARQCRA 24 (29)
T ss_dssp CCBCTTTSCBSSCGGGCCS
T ss_pred CCEEEECCccccCHhHCcc
Confidence 3579999999999999965
No 14
>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1
Probab=84.46 E-value=0.36 Score=34.89 Aligned_cols=18 Identities=39% Similarity=1.150 Sum_probs=16.3
Q ss_pred CcccccCCCCCccccccc
Q 001209 262 DKCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 262 ~~c~~cgQ~gH~~~~c~g 279 (1123)
..|+.||+.||++.+|..
T Consensus 3 ~~Cf~CG~~GH~ardC~~ 20 (26)
T 1dsq_A 3 PVCFSCGKTGHIKRDCKE 20 (26)
T ss_dssp CBCTTTCCBSSCTTTTTC
T ss_pred CeeEeCCCCCcccccCCC
Confidence 579999999999999964
No 15
>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1
Probab=82.79 E-value=0.7 Score=36.99 Aligned_cols=21 Identities=38% Similarity=0.928 Sum_probs=18.1
Q ss_pred CCCcccccCCCCCcccccccc
Q 001209 260 QQDKCFLCGQPGHLAANCEGK 280 (1123)
Q Consensus 260 ~~~~c~~cgQ~gH~~~~c~g~ 280 (1123)
...+|+.||+.||.+.+|...
T Consensus 9 ~~~~C~~Cgk~GH~ardCP~~ 29 (40)
T 1a6b_B 9 DRDQCAYCKEKGHWAKDCPKK 29 (40)
T ss_dssp CSSSCSSSCCTTCCTTSCSSS
T ss_pred CCCeeeECCCCCcchhhCcCC
Confidence 356899999999999999654
No 16
>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A
Probab=76.35 E-value=1.2 Score=38.13 Aligned_cols=21 Identities=38% Similarity=0.918 Sum_probs=18.0
Q ss_pred CCcccccCCCCCccccccccc
Q 001209 261 QDKCFLCGQPGHLAANCEGKA 281 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g~~ 281 (1123)
..+|+.||+.||.+.+|....
T Consensus 23 ~~~C~~Cge~GH~ardCp~~~ 43 (56)
T 1u6p_A 23 RDQCAYCKEKGHWAKDCPKKP 43 (56)
T ss_dssp TTBCSSSCCBSSCGGGCTTCC
T ss_pred CCcceeCCCCCcccccCcCCc
Confidence 468999999999999997643
No 17
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=70.22 E-value=1.5 Score=37.36 Aligned_cols=18 Identities=50% Similarity=1.220 Sum_probs=16.2
Q ss_pred CCcccccCCCCCcccccc
Q 001209 261 QDKCFLCGQPGHLAANCE 278 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~ 278 (1123)
...|+.|||.||.+.+|.
T Consensus 7 ~~~C~kCGk~GH~~k~Cp 24 (55)
T 2ysa_A 7 GYTCFRCGKPGHYIKNCP 24 (55)
T ss_dssp SCCCTTTCCTTSCGGGCS
T ss_pred CCccccCCCcCcccccCC
Confidence 357999999999999995
No 18
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=58.57 E-value=3.7 Score=31.62 Aligned_cols=17 Identities=47% Similarity=1.249 Sum_probs=13.5
Q ss_pred CcccccCCCCCcccccc
Q 001209 262 DKCFLCGQPGHLAANCE 278 (1123)
Q Consensus 262 ~~c~~cgQ~gH~~~~c~ 278 (1123)
..|+.|++.||++.+|.
T Consensus 20 ~~C~~Cg~~GH~a~~C~ 36 (37)
T 2bl6_A 20 KVCFKCKQPGHFSKQCR 36 (37)
T ss_dssp TTCSSCCCTTGGGGTTC
T ss_pred CeEccCCCcCCccCcCc
Confidence 46888888888888874
No 19
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1
Probab=55.59 E-value=4.7 Score=32.98 Aligned_cols=19 Identities=37% Similarity=0.947 Sum_probs=13.6
Q ss_pred CCcccccCCCCCccccccc
Q 001209 261 QDKCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g 279 (1123)
...|+.|++.||++.+|..
T Consensus 6 ~~~C~~Cg~~GH~a~~C~~ 24 (49)
T 2ec7_A 6 VIRCWNCGKEGHSARQCRA 24 (49)
T ss_dssp CCBCTTTCCBTCCTTTCCC
T ss_pred cCeeeecCCCCcChhhCcC
Confidence 3467778888887777754
No 20
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A
Probab=52.52 E-value=6.8 Score=33.10 Aligned_cols=20 Identities=30% Similarity=0.619 Sum_probs=17.3
Q ss_pred CCcccccCCCCCcccccccc
Q 001209 261 QDKCFLCGQPGHLAANCEGK 280 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g~ 280 (1123)
...|+.|++.||++.+|...
T Consensus 30 ~~~C~~Cg~~GH~ar~C~~~ 49 (60)
T 1cl4_A 30 PGLCPRCKRGKHWANECKSK 49 (60)
T ss_dssp CCSCSSCSSCSSCSTTCCCT
T ss_pred CcceeECCCCCCccCcCCCc
Confidence 36799999999999999764
No 21
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=52.11 E-value=5.7 Score=30.92 Aligned_cols=17 Identities=35% Similarity=0.905 Sum_probs=14.0
Q ss_pred CcccccCCCCCcccccc
Q 001209 262 DKCFLCGQPGHLAANCE 278 (1123)
Q Consensus 262 ~~c~~cgQ~gH~~~~c~ 278 (1123)
..|+.||+.||++.+|.
T Consensus 22 ~~C~~Cg~~GH~~~~C~ 38 (39)
T 2a51_A 22 EGCWNCGSKEHRFAQCP 38 (39)
T ss_dssp SSCTTTCCSSSCTTTSC
T ss_pred CccccCCCCCCccCcCc
Confidence 57888999999888884
No 22
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=48.58 E-value=8 Score=33.25 Aligned_cols=20 Identities=35% Similarity=0.790 Sum_probs=15.6
Q ss_pred CCcccccCCCCCcccccccc
Q 001209 261 QDKCFLCGQPGHLAANCEGK 280 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g~ 280 (1123)
...|+.|++.||++.+|...
T Consensus 29 ~~~C~~Cg~~GH~ar~Cp~~ 48 (63)
T 2cqf_A 29 PKKCHFCQSISHMVASCPLK 48 (63)
T ss_dssp SSCCTTTCCSSSCTTTCTGG
T ss_pred CCccCCcCCcCCccCcCCCc
Confidence 45788888888888888654
No 23
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=48.24 E-value=5.9 Score=30.81 Aligned_cols=17 Identities=53% Similarity=1.265 Sum_probs=15.4
Q ss_pred cccccCCCCCccccccc
Q 001209 263 KCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 263 ~c~~cgQ~gH~~~~c~g 279 (1123)
+|+.|++.||++.+|..
T Consensus 2 ~C~~Cg~~GH~a~~C~~ 18 (39)
T 2a51_A 2 TCFNCGKPGHTARMCRQ 18 (39)
T ss_dssp BCTTTCCBSSCTTTCCS
T ss_pred eeeccCCCCcccccCCC
Confidence 59999999999999964
No 24
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1
Probab=47.94 E-value=7.4 Score=31.78 Aligned_cols=18 Identities=39% Similarity=1.102 Sum_probs=16.0
Q ss_pred CcccccCCCCCccccccc
Q 001209 262 DKCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 262 ~~c~~cgQ~gH~~~~c~g 279 (1123)
..|+.||+.||++.+|..
T Consensus 28 ~~C~~Cg~~GH~~~~C~~ 45 (49)
T 2ec7_A 28 QGCWKCGKTGHVMAKCPE 45 (49)
T ss_dssp CSCSSSCCSSCCGGGCCS
T ss_pred CeeCcCCCcCCccCCCcC
Confidence 479999999999999954
No 25
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*
Probab=46.90 E-value=8.2 Score=38.56 Aligned_cols=16 Identities=38% Similarity=1.059 Sum_probs=8.7
Q ss_pred cccccCCCCCcccccc
Q 001209 263 KCFLCGQPGHLAANCE 278 (1123)
Q Consensus 263 ~c~~cgQ~gH~~~~c~ 278 (1123)
+|+.|++.||++.+|.
T Consensus 99 ~C~~Cg~~GH~a~~C~ 114 (148)
T 3ts2_A 99 RCYNCGGLDHHAKECK 114 (148)
T ss_dssp CCTTTCCSSCCGGGCC
T ss_pred cccEeCCccchhhhCC
Confidence 3555555555555554
No 26
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=45.76 E-value=10 Score=33.91 Aligned_cols=16 Identities=38% Similarity=1.005 Sum_probs=8.3
Q ss_pred cccccCCCCCcccccc
Q 001209 263 KCFLCGQPGHLAANCE 278 (1123)
Q Consensus 263 ~c~~cgQ~gH~~~~c~ 278 (1123)
.|+.|++.||++.+|.
T Consensus 48 ~C~~Cg~~GH~ar~Cp 63 (74)
T 2li8_A 48 KCHFCQSISHMVASCP 63 (74)
T ss_dssp CCTTTCCTTSCGGGCT
T ss_pred ccCCcCCcCCccCcCc
Confidence 4555555555555553
No 27
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=45.66 E-value=6.9 Score=33.37 Aligned_cols=19 Identities=37% Similarity=0.922 Sum_probs=16.6
Q ss_pred CcccccCCCCCcccccccc
Q 001209 262 DKCFLCGQPGHLAANCEGK 280 (1123)
Q Consensus 262 ~~c~~cgQ~gH~~~~c~g~ 280 (1123)
..|+.|++.||++.+|...
T Consensus 31 ~~C~~Cg~~GH~ar~C~~~ 49 (61)
T 2ihx_A 31 ERCQLCNGMGHNAKQCRKR 49 (61)
T ss_dssp SBCTTTCCBSSCGGGCCCC
T ss_pred CeeCCCCCCCCCcCCCcCC
Confidence 5799999999999999653
No 28
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=43.83 E-value=8.4 Score=29.60 Aligned_cols=17 Identities=47% Similarity=1.425 Sum_probs=15.2
Q ss_pred cccccCCCCCccccccc
Q 001209 263 KCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 263 ~c~~cgQ~gH~~~~c~g 279 (1123)
.|+.|++.||.+.+|..
T Consensus 2 ~C~~Cg~~GH~~~~C~~ 18 (37)
T 2bl6_A 2 TCYNCGKPGHLSSQCRA 18 (37)
T ss_dssp CBSSSCCSSCCTTTSSC
T ss_pred cccccCCCCcchhhCcC
Confidence 59999999999999954
No 29
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A
Probab=42.79 E-value=7.9 Score=32.11 Aligned_cols=19 Identities=53% Similarity=1.200 Sum_probs=15.4
Q ss_pred CCcccccCCCCCccccccc
Q 001209 261 QDKCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g 279 (1123)
...|+.|++.||++.+|..
T Consensus 12 ~~~C~~Cg~~GH~a~~C~~ 30 (55)
T 1a1t_A 12 TVKCFNCGKEGHIAKNCRA 30 (55)
T ss_dssp TCBCTTTCCBSSCGGGCSS
T ss_pred CcceeeeCCCCcChhhcCC
Confidence 3579999999999888854
No 30
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=41.91 E-value=9.6 Score=32.46 Aligned_cols=20 Identities=45% Similarity=1.154 Sum_probs=17.1
Q ss_pred CCcccccCCCCCcccccccc
Q 001209 261 QDKCFLCGQPGHLAANCEGK 280 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g~ 280 (1123)
...|+.|++.||++.+|...
T Consensus 4 ~~~C~~Cg~~GH~a~~C~~~ 23 (61)
T 2ihx_A 4 RGLCYTCGSPGHYQAQCPKK 23 (61)
T ss_dssp TTBCSSSCCBTCCGGGCTTT
T ss_pred CCcccccCCCCeehhhCcCC
Confidence 35799999999999999653
No 31
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A
Probab=41.73 E-value=9.7 Score=31.58 Aligned_cols=18 Identities=33% Similarity=1.003 Sum_probs=16.2
Q ss_pred CcccccCCCCCccccccc
Q 001209 262 DKCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 262 ~~c~~cgQ~gH~~~~c~g 279 (1123)
..|+.||+.||++.+|..
T Consensus 34 ~~C~~Cg~~GH~~~~C~~ 51 (55)
T 1a1t_A 34 KGCWKCGKEGHQMKDCTE 51 (55)
T ss_dssp CBCTTTCCBSSCGGGCSS
T ss_pred CEeCCCCCcCCccCCCcC
Confidence 579999999999999954
No 32
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A
Probab=39.66 E-value=6.2 Score=33.35 Aligned_cols=19 Identities=47% Similarity=1.186 Sum_probs=0.0
Q ss_pred CcccccCCCCCcccccccc
Q 001209 262 DKCFLCGQPGHLAANCEGK 280 (1123)
Q Consensus 262 ~~c~~cgQ~gH~~~~c~g~ 280 (1123)
..|+.|++.||++.+|...
T Consensus 2 ~~Cf~Cg~~GH~a~~C~~~ 20 (60)
T 1cl4_A 2 GSCFKCGKKGHFAKNCHEH 20 (60)
T ss_dssp -------------------
T ss_pred CccccCCCCCcCHhhCcCC
Confidence 3699999999999999653
No 33
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=39.27 E-value=11 Score=34.45 Aligned_cols=19 Identities=32% Similarity=0.931 Sum_probs=16.9
Q ss_pred CCcccccCCCCCccccccc
Q 001209 261 QDKCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g 279 (1123)
...|+.||+.||++.+|..
T Consensus 46 ~~~CYnCG~~GH~~rdC~~ 64 (83)
T 3nyb_B 46 TIYCYNCGGKGHFGDDCKE 64 (83)
T ss_dssp CCBCSSSSCBSSCGGGCSS
T ss_pred CCeecccCCCCcCcccCCc
Confidence 4679999999999999964
No 34
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=38.18 E-value=13 Score=31.87 Aligned_cols=19 Identities=37% Similarity=0.880 Sum_probs=16.7
Q ss_pred CCcccccCCCCCccccccc
Q 001209 261 QDKCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g 279 (1123)
...|+.|++.||++.+|..
T Consensus 7 ~~~C~~Cg~~GH~a~~C~~ 25 (63)
T 2cqf_A 7 GDRCYNCGGLDHHAKECKL 25 (63)
T ss_dssp CCCCSSSCCSSSCTTTCCS
T ss_pred CCcccccCCCCcChhhCCC
Confidence 4579999999999999964
No 35
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=33.66 E-value=15 Score=33.61 Aligned_cols=19 Identities=26% Similarity=0.658 Sum_probs=15.5
Q ss_pred CCcccccCCCCCccccccc
Q 001209 261 QDKCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g 279 (1123)
+..|+.|++.||++.+|..
T Consensus 5 ~~~C~~Cg~~GH~~~~Cp~ 23 (83)
T 3nyb_B 5 KVQCTLCKSKKHSKERCPS 23 (83)
T ss_dssp --CCSSSCCSSSCGGGCGG
T ss_pred cCCCCCCCCCCCccccCCC
Confidence 3579999999999999954
No 36
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=32.26 E-value=17 Score=32.35 Aligned_cols=19 Identities=37% Similarity=0.880 Sum_probs=16.6
Q ss_pred CCcccccCCCCCccccccc
Q 001209 261 QDKCFLCGQPGHLAANCEG 279 (1123)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g 279 (1123)
...|+.|++.||++.+|..
T Consensus 24 ~~~C~~Cg~~GH~a~~C~~ 42 (74)
T 2li8_A 24 GDRCYNCGGLDHHAKECKL 42 (74)
T ss_dssp TSCCTTTCCSSSCTTTCSS
T ss_pred CCcccccCCcCcCcccCCC
Confidence 3579999999999999964
No 37
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*
Probab=30.55 E-value=17 Score=36.32 Aligned_cols=18 Identities=39% Similarity=0.857 Sum_probs=15.8
Q ss_pred ccccCCCCCccccccccc
Q 001209 264 CFLCGQPGHLAANCEGKA 281 (1123)
Q Consensus 264 c~~cgQ~gH~~~~c~g~~ 281 (1123)
|+.|++.||++.+|...+
T Consensus 122 C~~Cg~~GH~~r~Cp~~~ 139 (148)
T 3ts2_A 122 CHFCQSINHMVASCPLKA 139 (148)
T ss_dssp CTTTCCSSCCGGGCTTTT
T ss_pred ccccCCcCCEeccCcCCC
Confidence 889999999999997653
Done!