Query 003880
Match_columns 789
No_of_seqs 240 out of 557
Neff 5.7
Searched_HMMs 29240
Date Mon Mar 25 07:02:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003880.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/003880hhsearch_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 5E-229 2E-233 1974.6 55.7 767 1-789 4-837 (899)
2 3pie_A 5'->3' exoribonuclease 100.0 2E-191 8E-196 1699.9 55.5 643 1-720 1-663 (1155)
3 2y35_A LD22664P; hydrolase-DNA 100.0 2E-177 5E-182 1600.6 44.5 582 1-721 1-586 (1140)
4 1b43_A Protein (FEN-1); nuclea 98.5 1.9E-07 6.6E-12 101.5 9.9 151 50-240 23-180 (340)
5 1a76_A Flap endonuclease-1 pro 98.4 5.6E-07 1.9E-11 97.4 8.2 92 190-356 143-235 (326)
6 1rxw_A Flap structure-specific 98.2 8.4E-06 2.9E-10 88.5 14.3 24 334-357 223-246 (336)
7 3qe9_Y Exonuclease 1; exonucle 98.1 2.1E-05 7.3E-10 86.0 13.2 172 1-240 1-178 (352)
8 3ory_A Flap endonuclease 1; hy 98.0 0.00011 3.7E-09 80.8 16.3 134 157-369 138-272 (363)
9 1ul1_X Flap endonuclease-1; pr 97.7 0.00017 5.8E-09 79.6 11.6 229 2-355 1-241 (379)
10 3q8k_A Flap endonuclease 1; he 97.5 0.00035 1.2E-08 76.1 11.5 176 2-240 1-185 (341)
11 2izo_A FEN1, flap structure-sp 97.5 0.00076 2.6E-08 73.5 13.1 212 50-356 20-244 (346)
12 1exn_A 5'-exonuclease, 5'-nucl 96.4 0.049 1.7E-06 58.0 14.9 145 50-251 21-166 (290)
13 1dsq_A Nucleic acid binding pr 88.9 0.16 5.6E-06 34.5 1.6 18 262-279 3-20 (26)
14 1nc8_A Nucleocapsid protein; H 88.8 0.2 6.7E-06 35.0 2.0 19 261-279 6-24 (29)
15 1a6b_B Momulv, zinc finger pro 87.9 0.29 1E-05 36.9 2.6 22 260-281 9-30 (40)
16 1u6p_A GAG polyprotein; MLV, A 82.5 0.65 2.2E-05 37.6 2.4 22 261-282 23-44 (56)
17 2ysa_A Retinoblastoma-binding 78.0 0.9 3.1E-05 36.6 1.8 18 261-278 7-24 (55)
18 2bl6_A Nucleocapsid protein P1 68.0 1.9 6.6E-05 31.3 1.4 17 262-278 20-36 (37)
19 2ec7_A GAG polyprotein (PR55GA 66.2 2.5 8.4E-05 32.8 1.8 19 261-279 6-24 (49)
20 2a51_A Nucleocapsid protein; s 63.2 3 0.0001 30.7 1.7 17 262-278 22-38 (39)
21 2a51_A Nucleocapsid protein; s 60.7 3 0.0001 30.7 1.2 17 263-279 2-18 (39)
22 1cl4_A Protein (GAG polyprotei 60.4 4.2 0.00014 32.7 2.2 21 261-281 30-50 (60)
23 2ec7_A GAG polyprotein (PR55GA 57.2 4.2 0.00014 31.5 1.6 18 262-279 28-45 (49)
24 2bl6_A Nucleocapsid protein P1 56.4 4.2 0.00014 29.5 1.4 17 263-279 2-18 (37)
25 2cqf_A RNA-binding protein LIN 55.2 5.6 0.00019 32.5 2.1 20 261-280 29-48 (63)
26 3ts2_A Protein LIN-28 homolog 54.2 5.5 0.00019 38.1 2.2 16 263-278 99-114 (148)
27 3nyb_B Protein AIR2; polya RNA 53.6 4.9 0.00017 34.9 1.6 20 260-279 45-64 (83)
28 2li8_A Protein LIN-28 homolog 53.4 6.6 0.00023 33.2 2.3 16 263-278 48-63 (74)
29 2ihx_A Nucleocapsid (NC) prote 53.3 4.5 0.00016 32.7 1.3 19 262-280 31-49 (61)
30 1a1t_A Nucleocapsid protein; s 52.5 4.6 0.00016 31.8 1.1 19 261-279 12-30 (55)
31 1a1t_A Nucleocapsid protein; s 51.0 5.8 0.0002 31.2 1.5 18 262-279 34-51 (55)
32 2ihx_A Nucleocapsid (NC) prote 49.5 6.4 0.00022 31.8 1.5 20 261-280 4-23 (61)
33 1cl4_A Protein (GAG polyprotei 48.2 3.8 0.00013 32.9 0.0 18 263-280 3-20 (60)
34 2cqf_A RNA-binding protein LIN 46.3 8.5 0.00029 31.3 1.9 19 261-279 7-25 (63)
35 3nyb_B Protein AIR2; polya RNA 43.2 8.5 0.00029 33.3 1.5 19 261-279 5-23 (83)
36 2li8_A Protein LIN-28 homolog 39.9 12 0.00041 31.6 1.9 18 262-279 25-42 (74)
37 3ts2_A Protein LIN-28 homolog 38.4 11 0.00036 36.0 1.5 18 264-281 122-139 (148)
38 2lli_A Protein AIR2; RNA surve 24.6 28 0.00096 31.7 1.7 19 260-278 104-122 (124)
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=4.9e-229 Score=1974.61 Aligned_cols=767 Identities=44% Similarity=0.760 Sum_probs=602.3
Q ss_pred CcchhHHHHHHhhCCcccccccccCcccc-CCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCCCCCHHHHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVI-DGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPAPTTFDEVFQ 79 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~-~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~~~~p~t~~e~~~ 79 (789)
||||+|||||++|||+|+++|+|+.|..+ ||..+|+|+++|||||.+|||||||||||||+|+|+++.+.+.|+++||.
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 HHHHHHHHHHhhccccceEEEeecCCCcchhhHHHhhhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCC--CCCCCCcc
Q 003880 80 CMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPK--SDSQVFDS 157 (789)
Q Consensus 80 ~if~yid~l~~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~~~~~~~~~~~~l~~~~~~~g~~~~~~--~~~~~fDs 157 (789)
+||+|||+||++|||||+||||||||||||||||||+||||+|++++++..+.+++++++.++| .+++. ...+.|||
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 9999999999999999999999999999999999999999999999998877788888888888 33321 23578999
Q ss_pred CcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHH
Q 003880 158 NVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLI 237 (789)
Q Consensus 158 n~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLI 237 (789)
|||||||+||.+|+.+|+|||+.||++||+|++++|||||++||||||||||+|||+||++|+|||||+|||||+|||||
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 HHHhhcCCceEEEeecccccCCCCccccccCCCCCcccccccccccccCCCCcCCCccccCCCCceEeeHHHHHHHHHHH
Q 003880 238 MLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYE 317 (789)
Q Consensus 238 mL~Lathe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~LReyL~~e 317 (789)
||||+||||||+||||+|+++. +|.||.+.+|.|..+. ++++++. .....++|+||||++|||||..|
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 9999999999999999998754 6889999999997665 4444432 23456889999999999999999
Q ss_pred hcCCCCCCccchhhhhhHHHHHhhhccCCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHHHHHHH
Q 003880 318 FRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQAV 397 (789)
Q Consensus 318 ~~~~~~~~~~d~eriIDDfVfLcf~vGNDFLPhlp~l~I~~g~id~L~~~Yk~~l~~~~gYLt~~G~inl~rl~~fl~~l 397 (789)
|.++++||++|+||+||||||||||||||||||||+|+|++|||+.|+.+||+.|+++|||||++|+||++||+.||+.|
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--CCCCCC---cc-------cccccCCCCCCCCCCC
Q 003880 398 GSYEDRIFQKRARLHQRHAERIKREKAQARRGDDV------EPL--AQPDSL---VP-------VSRFHGSRLASGPSPS 459 (789)
Q Consensus 398 ~~~E~~iF~~r~~~~~r~~e~~k~~k~~~~~~~~~------~~~--~~~~~~---~~-------~~~~~~~~l~~~~~~~ 459 (789)
|++|++||++|.+.++++.++.||++.+.++.... ... ..+... .+ .....+......+...
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 99999999999998887777777665543221110 000 000000 00 0000000000000000
Q ss_pred ccccccccccccCC----CCCCCCCCCc--cc-------cCCCcchhhHHHhhhc-------CCCCCCcccH--------
Q 003880 460 PYQQSECVGRLDNG----KGTSGRPHKV--PR-------LSSGATIGAAIVEAEN-------SFETDPQENK-------- 511 (789)
Q Consensus 460 ~~~~~~~~~~~~~~----~~~~~~~~k~--~~-------~~~~~~~~~~~~~~~~-------~~~~~~~~~~-------- 511 (789)
+.... ..+..... .......+.+ +. .+..+..+++.++... ....++..+.
T Consensus 471 ~~~~~-~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~n~~~a~~lk~~l~~~~~~~~~~~~~~~~~~~~~e~~~ 549 (899)
T 3fqd_A 471 DLVNL-SEKTSNRSLGATNRELINNRAANRLGLSREAAAVSSVNKLAASALKAQLVSNETLQNVPLEDSIASSSAYEDTD 549 (899)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccccc-cccccccchhhhhhhhhhcchhhhhhhhhhhhhhcccchhHHHHHHHHhhcccccccccccccccccccccccc
Confidence 00000 00000000 0000000000 00 0000001111111100 0000000000
Q ss_pred -HHHHHHHHHHHhh-------hcc--cCCCCCcchhhcccCCCchhHHHHHHhcCCCChhHHHHHHHHHHHHHHhHHHHH
Q 003880 512 -EEFKAKLKELLRD-------KSD--AFNSDNPEEDKVKLGEPGWKERYYEEKFNAKTPEEREETRKDVVLRYTEGLCWV 581 (789)
Q Consensus 512 -~~~~~~~~~~~~~-------~~~--~~~~~~~~~d~v~l~e~g~k~rYY~~Kf~~~~~~~~~~~~~~v~~~YveGL~WV 581 (789)
.+......+.+.+ .+. ....+.+.+|.|+||++|||+|||++|||++..+ ++++++||++||||||||
T Consensus 550 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~v~l~e~g~K~rYY~~KF~~~~~d--~e~~~~v~~~YvEGL~WV 627 (899)
T 3fqd_A 550 SIESSTPVVHPIDTKVSNVGQKRKAPDSTEENENTDTVRLYEPGYRERYYEQKFHISPDE--PEKIREAVKHYVHGLCWV 627 (899)
T ss_dssp -----------------------------------CCSCTTSTTHHHHHHHHTSCCCTTC--THHHHHHHHHHHHHHHHH
T ss_pred cccccccchhhhhccccccccccccccccccccchhhhhhcccchHHHHHHHhcCCCCCC--HHHHHHHHHHHHHHHHHH
Confidence 0000000000000 000 0001122568899999999999999999997544 478999999999999999
Q ss_pred hhhhhcCcccccccccCCCCccccccccccCccccccCCCCCChhhhhhhcCCCCCCCCCcHHHHhhhcCCCCCCcccCC
Q 003880 582 MHYYYEGVCSWQWFYPYHYAPFASDLKDLDQFNISFELGHPFKPFNQLLGVFPSASSHALPEHYRKLMTDPNSPISDFYP 661 (789)
Q Consensus 582 L~YYy~Gc~SW~WyYPyHYAPfasDl~~l~~~~i~F~~g~Pf~PfeQLm~VLP~~S~~~LP~~~~~LM~d~~SpI~dfYP 661 (789)
|+|||||||||+||||||||||||||+++.+++|+|++|+||+|||||||||||+|+++||++||+||+||+|||+||||
T Consensus 628 L~YYYqGc~SW~WyYPYHYAPfaSD~~~~~~~~i~Fe~G~PF~PfEQLMaVLPaaS~~~LP~~y~~LMtdp~SpIiDFYP 707 (899)
T 3fqd_A 628 LLYYYQGCPSWTWYYPYHYAPFAADFKDLASIDVKFELNQPFKPYEQLLGVLPAASKNNLPEKLQTLMTDENSEIIDFYP 707 (899)
T ss_dssp HHHHHTCCSCSSCCCCCSSCCCGGGCCSCTTCCCCCCCCCCCCHHHHHHHHCCGGGGGGSCHHHHHHHHCTTCTTGGGCC
T ss_pred HHHHhCCCCCCcccCcccccchHHHHhhcccCceecCCCCCCChHHHHHhhcCHhhhCcccHHHHHHhcCCCCcchhhCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccCCCCccccceeeeccCCChHHHHHHHhhccCCCCHHHHhhccCCCceEEEecCCCcchhhhhhhhhhhhhchhh
Q 003880 662 TDFEVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEEARRNSIMADMLFVLLSHPLSASIYTLDEHCKQLKIKE 741 (789)
Q Consensus 662 ~~F~iD~nGkk~~WqgV~lLPFIDe~rLl~a~~~~~~~Lt~eE~~RN~~g~~~lf~~~~~~l~~~~~~l~~~~~~~~~~~ 741 (789)
++|+|||||||++||||||||||||+|||+||++++++||+||++||++|.++||++++||+++. .++.+|+++
T Consensus 708 ~dFeiDmNGKk~~WqgVvlLPFIDE~RLL~A~~~~~~~LT~eEk~RN~~G~~~lf~~~~~~l~~~------~~~~~y~~~ 781 (899)
T 3fqd_A 708 ENFTIDLNGKKFEWQGVALLPFIDENRLLNAVSKIYPQLTEEESKRNEDGSTLLFISEHHPMFSE------LVKQLYSKK 781 (899)
T ss_dssp SCCCEECSSSSCTTSSEECCCCCCHHHHHHHHHTTGGGSCHHHHHTTSCCCCEEEEETTSTTHHH------HHHHHTSSS
T ss_pred ccccccCCCCccccceEEecCccCHHHHHHHHHHhhccCCHHHHHhccCCCcEEEEeCCCchHHH------HHHHhcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999864 445667666
Q ss_pred hhhhccccCCCCCCCcceeeecCCCCCCCCccccCCC--CCCC------CCCCccC
Q 003880 742 RVEVKERLNPELSDGMNGYISPCAGDPHPPVFRSPVA--SMED------IMGNQVL 789 (789)
Q Consensus 742 ~~~~~~~~~~~~~~g~~g~v~~~~~~~~~~~~~~p~~--~~~~------i~~~~~~ 789 (789)
+...+++|||++|+||+|+|++++.+++++++.|||. +||| |.+|++|
T Consensus 782 ~~~~~~~~~~~~s~gl~G~v~~~~~~~p~~~~~sP~~~~~~~~~~~~~~i~~n~~~ 837 (899)
T 3fqd_A 782 RQGKPLKLSGKMAHGLFGKVNTNDSVIPNVSVQCPIDVTSADALQKYGSIDDNQSI 837 (899)
T ss_dssp CSSSCEECCGGGGTTCCSEEEECTTSCSCCCBCCSSCCCSHHHHHHSCCBSSCCEE
T ss_pred ccCcccccCcccccCcceEEEeCCCcCCCCeecCCCCccCCCCccccccccCCcEE
Confidence 6666788999999999999999999999999999998 9999 9999975
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=2.3e-191 Score=1699.85 Aligned_cols=643 Identities=38% Similarity=0.723 Sum_probs=499.2
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCC--CCCCHHHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRP--APTTFDEVF 78 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~~~--~p~t~~e~~ 78 (789)
||||+|||||++|||+|++.+ ++..+| +|||||||||||||+|+|+++.+ .+.|+++||
T Consensus 1 MGVP~ffrwl~~ryP~i~~~~--------~~~~~p-----------e~DnLYlDmNgIIH~c~h~~~~~~~~~~te~e~~ 61 (1155)
T 3pie_A 1 MGIPKFFHFISERWPQISQLI--------DGSQIP-----------EFDNLYLDMNSILHNCTHGDGSEVNSRLSEEEVY 61 (1155)
T ss_pred CChHHHHHHHHHhCcchhhcc--------cCCCCC-----------cCCeEEEecccceeeeecCCCCccccCCCHHHHH
Confidence 999999999999999986432 233444 89999999999999999999876 588999999
Q ss_pred HHHHHHHHHHHhhccccceEEEeecCCCcchhhHHHhhhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCCCCCCccC
Q 003880 79 QCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFDSN 158 (789)
Q Consensus 79 ~~if~yid~l~~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~fDsn 158 (789)
.+||+|||+||++|||||+||||||||||||||||||+||||+|++++.+. ++..++|..+|. .+.||||
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 999999999999999999999999999999999999999999999876532 223456777764 3689999
Q ss_pred cccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHH
Q 003880 159 VITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIM 238 (789)
Q Consensus 159 ~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLIm 238 (789)
||||||+||.+|+.+|+|||+.|+++||.|++++|||||++||||||||||+|||++|++|+|||||+|||||+||||||
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 HHhhcCCceEEEeecccccCCCCccccccCCCCCcccccccccccccCCCCcCCCccccCCCCceEeeHHHHHHHHHHHh
Q 003880 239 LALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEF 318 (789)
Q Consensus 239 L~Lathe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~LReyL~~e~ 318 (789)
|||+||||||+||||+|++..+... + .....++|+||||++|||||+.||
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 9999999999999999876432110 0 011246799999999999999999
Q ss_pred cC--CCCCCccchhhhhhHHHHHhhhccCCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHHHHHH
Q 003880 319 RI--PNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQA 396 (789)
Q Consensus 319 ~~--~~~~~~~d~eriIDDfVfLcf~vGNDFLPhlp~l~I~~g~id~L~~~Yk~~l~~~~gYLt~~G~inl~rl~~fl~~ 396 (789)
.. +.++|++|+||+||||||||||+|||||||||+|+|++|||+.|+++||+.++++|||||++|+||++||+.||+.
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 74 5778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhHHHHHHHHHHHHHHH---HHHHH--HHHHHhhcCCCCCCCCCCCCCcccccccCCCCCCCCCCCcccccccc-ccc
Q 003880 397 VGSYEDRIFQKRARLHQRH---AERIK--REKAQARRGDDVEPLAQPDSLVPVSRFHGSRLASGPSPSPYQQSECV-GRL 470 (789)
Q Consensus 397 l~~~E~~iF~~r~~~~~r~---~e~~k--~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-~~~ 470 (789)
||++|++||++|...++.. .++.. ..+.+.+.++......+......+..+... ..+...+......... ...
T Consensus 342 L~~~E~~~F~~~~~d~~~~~~k~~~~~~~~~~~r~~~~~~~~~~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l 420 (1155)
T 3pie_A 342 LSDFEYLNFEKKDIDVEWFNQQLENISLEGERKRTRMGKKLLMKQQKKLIGAVKPWLLK-TVQRKVTSELQDADFEIFPL 420 (1155)
T ss_pred HHHHHHHHHHHHhhHHHHHHHhhhhhhhhhHHHhhhhcccccchhHHhhhhccchhhhc-cccccccccccccccccccc
Confidence 9999999999997653221 11110 001111111110000000000000000000 0000000000000000 000
Q ss_pred cCCCCCCCCCCCccc-cCCCcchhhHHHhhh--cC--CC--CC---CcccHHHHHHHHHHHHhhhcccCCCCCcchhhcc
Q 003880 471 DNGKGTSGRPHKVPR-LSSGATIGAAIVEAE--NS--FE--TD---PQENKEEFKAKLKELLRDKSDAFNSDNPEEDKVK 540 (789)
Q Consensus 471 ~~~~~~~~~~~k~~~-~~~~~~~~~~~~~~~--~~--~~--~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~v~ 540 (789)
.+ .......++.++ ++. ..+..++... .. .. .+ ..+.+++... . +.....++.+.
T Consensus 421 ~~-~~~~~~~~~~~~~~a~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ee~~~---------~---~~~~~~~~~~~ 485 (1155)
T 3pie_A 421 ED-KELVRANLDFLKEFAF--DLGLILAHSKSKDLYYFKLDLDSINXXXXXXXXXX---------X---XXXXXXXXIYS 485 (1155)
T ss_pred Cc-hhhhhhhHHHHHHHHH--hhcccccccccccccceeccccccccccccccccc---------c---cccccccccch
Confidence 00 000000000000 000 0000000000 00 00 00 0000000000 0 00001123334
Q ss_pred cCCCchhHHHHHHhcCCCChhHHHHHHHHHHHHHHhHHHHHhhhhhcCcccccccccCCCCccccccccccCccccccCC
Q 003880 541 LGEPGWKERYYEEKFNAKTPEEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPFASDLKDLDQFNISFELG 620 (789)
Q Consensus 541 l~e~g~k~rYY~~Kf~~~~~~~~~~~~~~v~~~YveGL~WVL~YYy~Gc~SW~WyYPyHYAPfasDl~~l~~~~i~F~~g 620 (789)
.+.+|||+|||++|||++..+ ++++++||++|||||||||+|||+|||||+||||||||||||||+++.+++|+|++|
T Consensus 486 ~~~~~~k~rYY~~Kf~~~~~~--~e~~~~v~~~YveGL~WVL~YYy~Gc~SW~WyYPYHYAPfasDl~~~~~~~i~F~~g 563 (1155)
T 3pie_A 486 ERFVEWKDQYYKDKLDFSIND--TDSLKEMTENYVGGLQWVLYYYYRGCPSWSWYYRYHYAPRISDVIKGIDQNIEFHKG 563 (1155)
T ss_pred hhhhhHHHHHHHHhcCCCcCC--HHHHHHHHHHHHHHHHhHHHHHhCCCCCccccCccccccHHHHHHhhcccceeecCC
Confidence 455899999999999997533 346789999999999999999999999999999999999999999999999999999
Q ss_pred CCCChhhhhhhcCCCCCCCCCcHHHHhhhcCCCCCCcccCCCcccccCCCCccccceeeeccCCChHHHHHHHhhccCCC
Q 003880 621 HPFKPFNQLLGVFPSASSHALPEHYRKLMTDPNSPISDFYPTDFEVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTL 700 (789)
Q Consensus 621 ~Pf~PfeQLm~VLP~~S~~~LP~~~~~LM~d~~SpI~dfYP~~F~iD~nGkk~~WqgV~lLPFIDe~rLl~a~~~~~~~L 700 (789)
+||+|||||||||||+|+++||++||+||+||+|||+||||++|+|||||||++||||||||||||+|||+||+++++.|
T Consensus 564 ~Pf~PfeQLm~VLP~~S~~~LP~~~~~LM~d~~SpIidFYP~dF~iD~NGKk~~WqgVvlLPFIDe~rLl~a~~~~~~~L 643 (1155)
T 3pie_A 564 QPFKPFQQLMAVLPERSKNLIPVVYRPLMYDEHSPILDFYPNEVELDLNGKTADWEAVVKISFVDQKRLVEAMAPYDAKL 643 (1155)
T ss_pred CCCCcHHHHhhhcChhhhccCcHhHHHhhcCCCCchhhhCccceeecCCCCccceeeEEECCcCCHHHHHHHHhhccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHhhccCCCceEEEecC
Q 003880 701 TEEEARRNSIMADMLFVLLS 720 (789)
Q Consensus 701 t~eE~~RN~~g~~~lf~~~~ 720 (789)
|+||++||++|.+++|+++.
T Consensus 644 t~eE~~RN~~g~~~lf~~~~ 663 (1155)
T 3pie_A 644 SPDEKKRNSFGTDLIFIFNP 663 (1155)
T ss_pred CHHHHhhccCCCcEEEEecC
Confidence 99999999999999999864
No 3
>2y35_A LD22664P; hydrolase-DNA complex, RNA degradation, exonuclease 5'-3', R interference; 3.20A {Drosophila melanogaster}
Probab=100.00 E-value=1.5e-177 Score=1600.58 Aligned_cols=582 Identities=42% Similarity=0.805 Sum_probs=476.5
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCC--CCCHHHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPA--PTTFDEVF 78 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~~~~--p~t~~e~~ 78 (789)
||||+|||||++|||+++..+.+ ..+| +|||||||||||||+|+|+++.+. +.++++||
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 99999999999999987643221 1122 899999999999999999988755 46899999
Q ss_pred HHHHHHHHHHHhhccccceEEEeecCCCcchhhHHHhhhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCCCCCCccC
Q 003880 79 QCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFDSN 158 (789)
Q Consensus 79 ~~if~yid~l~~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~fDsn 158 (789)
.+||+|||+||++|||||+||||||||||||||||||+||||+|++++.... +..+.|... ..+.||||
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 9999999999999999999999999999999999999999999998765432 223445432 24689999
Q ss_pred cccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHH
Q 003880 159 VITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIM 238 (789)
Q Consensus 159 ~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLIm 238 (789)
||||||+||.+|+.+|++||+.|+++||.|++++|||||++||||||||||+|||+||++|+|||||+|||||+||||||
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 HHhhcCCceEEEeecccccCCCCccccccCCCCCcccccccccccccCCCCcCCCccccCCCCceEeeHHHHHHHHHHHh
Q 003880 239 LALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEF 318 (789)
Q Consensus 239 L~Lathe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~LReyL~~e~ 318 (789)
|||+||+|||+||||+|++....++ . ......|+++||++|||||+.||
T Consensus 211 L~L~the~~f~ilRe~v~f~~~~~~--------------------~-----------~~~~~~f~~l~i~~lReyL~~ef 259 (1140)
T 2y35_A 211 LGLCTHELHFVVLREEVKFGRNVKR--------------------T-----------SVEETRFFLLHLGLLREYLELEF 259 (1140)
T ss_dssp HHHHTTCSSEEEEEESSCTTCCTTC--------------------C-----------CGGGCEEEEEEHHHHHHHHHHHG
T ss_pred HHHccCCCcEEEeeccccccccccc--------------------c-----------cccccceEEEEehHHHHHHHHHh
Confidence 9999999999999999876432110 0 01235799999999999999999
Q ss_pred cCC-CCCCccchhhhhhHHHHHhhhccCCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHHHHHHH
Q 003880 319 RIP-NPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQAV 397 (789)
Q Consensus 319 ~~~-~~~~~~d~eriIDDfVfLcf~vGNDFLPhlp~l~I~~g~id~L~~~Yk~~l~~~~gYLt~~G~inl~rl~~fl~~l 397 (789)
... ..++++|+||+||||||||||+|||||||||+|+|++|||++|+++|++.++++|||||++|+||++||+.||+.|
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 3468999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcccccccCCCCCCCCCCCccccccccccccCCCCCC
Q 003880 398 GSYEDRIFQKRARLHQRHAERIKREKAQARRGDDVEPLAQPDSLVPVSRFHGSRLASGPSPSPYQQSECVGRLDNGKGTS 477 (789)
Q Consensus 398 ~~~E~~iF~~r~~~~~r~~e~~k~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 477 (789)
|++|+++|++|.+..+.. +.|.++ . +.. +. .+... ..+.
T Consensus 340 ~~~E~~~f~~~~~~~~~~--~~k~~~-----~-~~~----------~~-----~~~~~---~~~~--------------- 378 (1140)
T 2y35_A 340 TEVELDHFKEHADDLKYM--NNKSEA-----F-DMD----------VG-----EITES---QNLD--------------- 378 (1140)
T ss_dssp HHHHHHHHHHHSCC------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHh--hhcchh-----c-ccc----------hh-----hcccc---ccch---------------
Confidence 999999998765321110 000000 0 000 00 00000 0000
Q ss_pred CCCCCccccCCCcchhhHHHhhhcCCCCCCcccHHHHHHHHHHHHhhhcccCCCCCcchhhccc-CCCchhHHHHHHhcC
Q 003880 478 GRPHKVPRLSSGATIGAAIVEAENSFETDPQENKEEFKAKLKELLRDKSDAFNSDNPEEDKVKL-GEPGWKERYYEEKFN 556 (789)
Q Consensus 478 ~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~v~l-~e~g~k~rYY~~Kf~ 556 (789)
...++ .++.. ......+.++ +...++.+.+ ..+|||++||++||+
T Consensus 379 ------------~~~~~-~~~~~--~~~~~~~~~~-------------------~~~~e~~~~~~~~~~~k~~YY~~Kf~ 424 (1140)
T 2y35_A 379 ------------SDLGA-LINKS--MLLYDDDSEE-------------------DCSDENAVLLKEFQNYKRNFYRNKFK 424 (1140)
T ss_dssp ---------------------------------------------------------CHHHHHHHHHHHHHHHHHHHHHC
T ss_pred ------------hHHHH-HHHhh--hhcccccccc-------------------ccchhhhhhhhhhhHHHHHHHHHHhC
Confidence 00000 00000 0000000000 0000111111 236899999999999
Q ss_pred CCChhHHHHHHHHHHHHHHhHHHHHhhhhhcCcccccccccCCCCccccccccccCccccccCCCCCChhhhhhhcCCCC
Q 003880 557 AKTPEEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPFASDLKDLDQFNISFELGHPFKPFNQLLGVFPSA 636 (789)
Q Consensus 557 ~~~~~~~~~~~~~v~~~YveGL~WVL~YYy~Gc~SW~WyYPyHYAPfasDl~~l~~~~i~F~~g~Pf~PfeQLm~VLP~~ 636 (789)
++..+ +++++||++|||||||||+|||+|||||+||||||||||||||.++.+++++|++|+||+|||||||||||+
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 CCCCCcHHHHhhhcCCCCCCcccCCCcccccCCCCccccceeeeccCCChHHHHHHHhhccCCCCHHHHhhccCCCceEE
Q 003880 637 SSHALPEHYRKLMTDPNSPISDFYPTDFEVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEEARRNSIMADMLF 716 (789)
Q Consensus 637 S~~~LP~~~~~LM~d~~SpI~dfYP~~F~iD~nGkk~~WqgV~lLPFIDe~rLl~a~~~~~~~Lt~eE~~RN~~g~~~lf 716 (789)
|+++||++||+||++|+|||+||||++|+||||||+++|||||||||||++||++||+++++.||+||++||++|.+++|
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 EecCC
Q 003880 717 VLLSH 721 (789)
Q Consensus 717 ~~~~~ 721 (789)
.++..
T Consensus 582 ~~~~~ 586 (1140)
T 2y35_A 582 KYSTV 586 (1140)
T ss_dssp EECSS
T ss_pred Eeccc
Confidence 87643
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=98.52 E-value=1.9e-07 Score=101.53 Aligned_cols=151 Identities=14% Similarity=0.190 Sum_probs=79.2
Q ss_pred eEEEeccccccccccCC----CCCCCCCHHHHHHHHHHHHHHHHhhc-cccceEEEeecCCCcchhhHHHhhhhccchhH
Q 003880 50 NLYLDMNGIIHPCFHPE----DRPAPTTFDEVFQCMFDYIDRLFVMV-RPRKLLYMAIDGVAPRAKMNQQRSRRFRASKD 124 (789)
Q Consensus 50 nLYlDmNgIIH~c~h~~----~~~~p~t~~e~~~~if~yid~l~~~v-rPrkllyiAiDGVAPrAKmnQQRsRRfrsa~~ 124 (789)
-|-||.++.||.+.|.- +.+--...-..-..|+.++.++++++ .|-+ +++++||.+|-.|......||-+....
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 78999999999876531 11100000000123333444444433 4555 567899999988877665555544322
Q ss_pred HHhHHHHHHHHHHHHHHhCCCCCCCCCCCCC--ccCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCC
Q 003880 125 AADSAAEEERLRQEFEREGRKLPPKSDSQVF--DSNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPG 202 (789)
Q Consensus 125 ~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~f--Dsn~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPG 202 (789)
.+.. .+.+ +.|..- ....| .++.||| ..... ++..+... ++.+|. .|+
T Consensus 102 ~~~~-------~~~y-k~g~~~----~~~~~~~~~~~vt~--~~~~~----~~~lL~~~--------gip~i~----ap~ 151 (340)
T 1b43_A 102 EEKW-------REAL-EKGEIE----EARKYAQRATRVNE--MLIED----AKKLLELM--------GIPIVQ----APS 151 (340)
T ss_dssp HHHH-------HHHH-HHSCHH----HHHHHHHTSGGGTH--HHHHH----HHHHHHHH--------TCCEEE----CSS
T ss_pred HHHH-------HHHH-HcCCHH----HHHHHHHhcCCCCH--HHHHH----HHHHHHHc--------CCcEEE----cCh
Confidence 1111 0011 111100 00011 2233444 22222 33333221 456666 479
Q ss_pred ChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHH
Q 003880 203 EGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLA 240 (789)
Q Consensus 203 EGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLImL~ 240 (789)
|+|-=|-..-|. ...++|++.|.|+++++
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 999988877763 24578999999999987
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=98.36 E-value=5.6e-07 Score=97.38 Aligned_cols=92 Identities=24% Similarity=0.406 Sum_probs=60.9
Q ss_pred ccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhhcCCceEEEeecccccCCCCccccccCC
Q 003880 190 KIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQ 269 (789)
Q Consensus 190 ~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLImL~Lathe~~f~ILRE~v~~~~~~~~c~~c~q 269 (789)
++.+|. .|||+|-=|-.+-+. +..++|++.|.|+++++ + ++ ++|-. ..
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--VVRNL---TT---------- 190 (326)
T ss_dssp TCCEEE----CSSCHHHHHHHHHHT---------TSSSEEECSSSGGGGGT-C---SE--EEESS---SS----------
T ss_pred CCCeEE----CCccHHHHHHHHHHC---------CCEEEEecCCcccceec-C---CE--EEEee---cC----------
Confidence 345553 589999977777663 35689999999999997 2 33 33321 00
Q ss_pred CCCcccccccccccccCCCCcCCCccccCCCCceEeeHHHHHHHHHHHhcCCCCCCccchhhhhhHHHHHhhhccCCCCC
Q 003880 270 PGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLP 349 (789)
Q Consensus 270 ~gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~LReyL~~e~~~~~~~~~~d~eriIDDfVfLcf~vGNDFLP 349 (789)
+ .+.+++++...+.+.+ . ++. +.||.+|.|+|+||+|
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 0145677776555433 2 222 4677799999999999
Q ss_pred -CCCcccc
Q 003880 350 -HMPTLEI 356 (789)
Q Consensus 350 -hlp~l~I 356 (789)
.+|++-.
T Consensus 228 ~GvpGiG~ 235 (326)
T 1a76_A 228 GGVKGIGF 235 (326)
T ss_dssp TTTTTCCH
T ss_pred CCCCCcCH
Confidence 9999743
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=98.24 E-value=8.4e-06 Score=88.50 Aligned_cols=24 Identities=17% Similarity=0.462 Sum_probs=20.0
Q ss_pred hHHHHHhhhccCCCCCCCCccccc
Q 003880 334 DDFIFMCFFVGNDFLPHMPTLEIR 357 (789)
Q Consensus 334 DDfVfLcf~vGNDFLPhlp~l~I~ 357 (789)
+.|+.+|.|+|+||+|.+|++-.+
T Consensus 223 ~q~id~~~L~GsD~ipGv~GiG~K 246 (336)
T 1rxw_A 223 EQLIDIAILVGTDYNEGVKGVGVK 246 (336)
T ss_dssp HHHHHHHHHHCBTTBCCCTTCCHH
T ss_pred HHHHHHHhhcCCCCCCCCCCcCHH
Confidence 467789999999999999985443
No 7
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Probab=98.08 E-value=2.1e-05 Score=86.02 Aligned_cols=172 Identities=17% Similarity=0.281 Sum_probs=88.5
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCC----CCCCCCCHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPE----DRPAPTTFDE 76 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~----~~~~p~t~~e 76 (789)
|||.+|..||...-+.+- ++ ...|. -|=||..+.+|...... ....+++ .
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 999999999976543221 11 11121 56788888888632210 0112222 1
Q ss_pred HHHHHHHHHHHHH-hhccccceEEEeecCCCcchhhHHHhhhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCCCCCC
Q 003880 77 VFQCMFDYIDRLF-VMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVF 155 (789)
Q Consensus 77 ~~~~if~yid~l~-~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~f 155 (789)
+..-+++.+..|. .-|+| ++.+||.+|-.|-....+||-+.....+... +..++|..- ...+.|
T Consensus 55 l~~~~~r~l~~L~~~gI~P----vfVFDG~~~p~Kk~~~~~Rr~~r~~~~~~~~--------~~~~~g~~~---~a~~~f 119 (352)
T 3qe9_Y 55 YVGFCMKFVNMLLSHGIKP----ILVFDGCTLPSKKEVERSRRERRQANLLKGK--------QLLREGKVS---EARECF 119 (352)
T ss_dssp HHHHHHHHHHHHHHTTCEE----EEEECCSCCTTTHHHHHHHHHHHHHHHHHHH--------HHTTSSCCH---HHHHHH
T ss_pred HHHHHHHHHHHHHHcCCEE----EEEECCCCcHHHHHHHHHHHHHHHHHHHHHH--------HHHHhCCHH---HHHHHH
Confidence 2221222233221 22444 5669999998887766555554332211110 001112100 000112
Q ss_pred -ccCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecCh
Q 003880 156 -DSNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDA 234 (789)
Q Consensus 156 -Dsn~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DA 234 (789)
.+..||| . +...++..+.. -++.+|.+ |+|+|-=|--.-+. +....|++.|.
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 1235666 2 23334444432 25677764 89999977666551 45689999999
Q ss_pred hHHHHH
Q 003880 235 DLIMLA 240 (789)
Q Consensus 235 DLImL~ 240 (789)
|+++++
T Consensus 173 Dll~~~ 178 (352)
T 3qe9_Y 173 ALLAFG 178 (352)
T ss_dssp GGGGGT
T ss_pred Cccccc
Confidence 998887
No 8
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus}
Probab=97.97 E-value=0.00011 Score=80.81 Aligned_cols=134 Identities=21% Similarity=0.285 Sum_probs=73.7
Q ss_pred cCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhH
Q 003880 157 SNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADL 236 (789)
Q Consensus 157 sn~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADL 236 (789)
+..||| +.+..+.+.|+.+ ++.+|.+ |||+|-=|-..-+ .+....|++.|.|+
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 345776 4455555555433 3556654 8999986544432 14568999999999
Q ss_pred HHHHhhcCCceEEEeecccccCCCCccccccCCCCCcccccccccccccCCCCcCCCccccCCCCceEeeHHHHHHHHHH
Q 003880 237 IMLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDY 316 (789)
Q Consensus 237 ImL~Lathe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~LReyL~~ 316 (789)
++++- ++ ++|-. +..+ +|. .++ ++ ......+++++...+.+.+
T Consensus 191 l~fg~----~~--v~~~l-~~~~---~~~---~p~-------------------~~---~~v~~~~~~~~~~~v~~~~-- 233 (363)
T 3ory_A 191 LLFGS----PK--LVRNL-TISG---RRK---LPR-------------------KN---EYVEVKPELIELDKLLVQL-- 233 (363)
T ss_dssp HHTTC----SE--EEEST-TTCE---EEE---CSS-------------------TT---CEEEECCEEEEHHHHHHHH--
T ss_pred cccCC----Ce--EEEEe-eccc---ccc---CCc-------------------cc---cccccceEEEcHHHHHHHh--
Confidence 99873 22 33321 1100 000 000 00 0000124677776655543
Q ss_pred HhcCCCCCCccchhhhhhHHHHHhhhccCCCCC-CCCccccccchHHHHHHHHH
Q 003880 317 EFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLP-HMPTLEIREGAINLLMAVYK 369 (789)
Q Consensus 317 e~~~~~~~~~~d~eriIDDfVfLcf~vGNDFLP-hlp~l~I~~g~id~L~~~Yk 369 (789)
. ++.+ -||-+|.|+|+||+| .+|++-.. .|+. |+.-|.
T Consensus 234 --g-------l~~~----q~id~~~L~GsDy~p~GVpGIG~K-tA~k-Ll~~~g 272 (363)
T 3ory_A 234 --G-------ITLE----NLIDIGILLGTDYNPDGFEGIGPK-KALQ-LVKAYG 272 (363)
T ss_dssp --T-------CCHH----HHHHHHHHHCBTTBTTCSTTCCHH-HHHH-HHHHHT
T ss_pred --C-------cCHH----HHHHHHHHhCCCCCCCCCCCcCHH-HHHH-HHHHcC
Confidence 1 2233 566799999999999 99986533 3443 555553
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=97.67 E-value=0.00017 Score=79.59 Aligned_cols=229 Identities=19% Similarity=0.292 Sum_probs=115.9
Q ss_pred cchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCC--CCCCCHH-H--
Q 003880 2 GVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDR--PAPTTFD-E-- 76 (789)
Q Consensus 2 GVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~~--~~p~t~~-e-- 76 (789)
||++|...|...-|.+++.+- +.. -.| --|-||.+++||-+.|.-.. ..-.+.+ +
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 899999999999887665431 000 012 27899999999998774311 0000100 1
Q ss_pred -HHHHHHHHHHHHHhh-ccccceEEEeecCCCcchhhHH--Hhh-hhccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCC
Q 003880 77 -VFQCMFDYIDRLFVM-VRPRKLLYMAIDGVAPRAKMNQ--QRS-RRFRASKDAADSAAEEERLRQEFEREGRKLPPKSD 151 (789)
Q Consensus 77 -~~~~if~yid~l~~~-vrPrkllyiAiDGVAPrAKmnQ--QRs-RRfrsa~~~~~~~~~~~~l~~~~~~~g~~~~~~~~ 151 (789)
-+..+|..+-+|+.. ++| +| ++||..|-.|-.. +|. +|-.+...... ...+|. |+.
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 122223333344443 566 34 8999998555332 222 22211111100 001111 100
Q ss_pred CCCCc--cCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEE
Q 003880 152 SQVFD--SNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCL 229 (789)
Q Consensus 152 ~~~fD--sn~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~I 229 (789)
-..|. +..||+. -+..+.+.|+.+ ++.+|. .|||+|-=|--.-+. ....+|
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 345554 499999988887774 234789
Q ss_pred EecChhHHHHHhhcCCceEEEeecccccCCCCccccccCCCCCcccccccccccccCCCCcCCCccccCCCCceEeeHHH
Q 003880 230 YGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWT 309 (789)
Q Consensus 230 yG~DADLImL~Lathe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~ 309 (789)
.+.|.|+++++ + ++ ++|-..+. + ..+.++..++...
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 99999999998 2 33 33321000 0 0012456777765
Q ss_pred HHHHHHHHhcCCCCCCccchhhhhhHHHHHhhhccCCCCCCCCccc
Q 003880 310 LREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLE 355 (789)
Q Consensus 310 LReyL~~e~~~~~~~~~~d~eriIDDfVfLcf~vGNDFLPhlp~l~ 355 (789)
+.+.+ . ++. +.||.+|.|+|+||.+++|++-
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 54432 2 222 4577799999999999999863
No 10
>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=97.53 E-value=0.00035 Score=76.12 Aligned_cols=176 Identities=16% Similarity=0.158 Sum_probs=90.2
Q ss_pred cchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCC--CCCCCC-HHHHH
Q 003880 2 GVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPED--RPAPTT-FDEVF 78 (789)
Q Consensus 2 GVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~--~~~p~t-~~e~~ 78 (789)
||.|+...|...-|.+++.+.=+ ... | --+-||.++.||-+.|.-. +..-.+ .-+.-
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---SYF--------------G---RKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60 (341)
T ss_dssp CCTTHHHHHHHHCGGGEEEEEGG---GGT--------------T---CEEEEEHHHHHHHHHHHCEETTEECBCTTSCBC
T ss_pred CchhHHHHHHHhhhhccccccHH---HhC--------------C---CEEEEecHHHHHHHHHccccccCCCCCCCCCCc
Confidence 89999999999999887654110 001 1 1578999999988766321 000000 00111
Q ss_pred HHHHHHHHHHHhhcc-ccceEEEeecCCCcchh--hHHHhhhhccchhH-HHhHHH--HHHHHHHHHHHhCCCCCCCCCC
Q 003880 79 QCMFDYIDRLFVMVR-PRKLLYMAIDGVAPRAK--MNQQRSRRFRASKD-AADSAA--EEERLRQEFEREGRKLPPKSDS 152 (789)
Q Consensus 79 ~~if~yid~l~~~vr-PrkllyiAiDGVAPrAK--mnQQRsRRfrsa~~-~~~~~~--~~~~l~~~~~~~g~~~~~~~~~ 152 (789)
..|+.++.+++.+++ --+-+| ++||.+|-.| +..+|..|-..+.+ ..++.. ..+.+.....
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 233444444444443 222244 7999999554 45554432222211 110000 0011111110
Q ss_pred CCCccCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEec
Q 003880 153 QVFDSNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGL 232 (789)
Q Consensus 153 ~~fDsn~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~ 232 (789)
.+..||+. -+..+.+.|+.+ ++.+|.+ |||+|-=|-..-+. +...+|.+.
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 222233333322 3556653 79999988877763 245678899
Q ss_pred ChhHHHHH
Q 003880 233 DADLIMLA 240 (789)
Q Consensus 233 DADLImL~ 240 (789)
|.|+++++
T Consensus 178 D~D~l~~~ 185 (341)
T 3q8k_A 178 DMDCLTFG 185 (341)
T ss_dssp CTHHHHTT
T ss_pred CccccccC
Confidence 99999997
No 11
>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=97.46 E-value=0.00076 Score=73.46 Aligned_cols=212 Identities=17% Similarity=0.245 Sum_probs=95.7
Q ss_pred eEEEeccccccccccCCCC---CCCCC----HHHHHHHHHHHHHHHHhh-ccccceEEEeecCCCcchhhHH--Hhhhhc
Q 003880 50 NLYLDMNGIIHPCFHPEDR---PAPTT----FDEVFQCMFDYIDRLFVM-VRPRKLLYMAIDGVAPRAKMNQ--QRSRRF 119 (789)
Q Consensus 50 nLYlDmNgIIH~c~h~~~~---~~p~t----~~e~~~~if~yid~l~~~-vrPrkllyiAiDGVAPrAKmnQ--QRsRRf 119 (789)
-|-||.++.+|-+.|.-.. ..-.+ ....+..++..+-+|+.. ++| ++++||..|-.|-.. +|..+-
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 6889999999987664310 00000 011233334444455555 788 689999988555433 332211
Q ss_pred cchhHHHhHHHHHHHHHHHHHHhCCCCCCCCCCCCCc--cCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcC
Q 003880 120 RASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFD--SNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSD 197 (789)
Q Consensus 120 rsa~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~fD--sn~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sd 197 (789)
..+.+ .+.+ ....|.. .....|- +..||| +.+..+.+.|+.+ ++.+|.
T Consensus 96 ~~~~~---------~l~~-~~~~g~~----~~a~~~~~~~~~vt~--~~~~~~~~lL~~~------------gi~~i~-- 145 (346)
T 2izo_A 96 EEAER---------KLER-AKSEGKI----EELRKYSQAILRLSN--IMVEESKKLLRAM------------GIPIVQ-- 145 (346)
T ss_dssp -------------------------------------------CH--HHHHHHHHHHHHH------------TCCEEE--
T ss_pred HHhHH---------HHHH-HHhcCCH----HHHHHHHhhccCCCH--HHHHHHHHHHHHC------------CCCEEE--
Confidence 11111 0110 0111110 0001122 223332 3344444444422 345665
Q ss_pred CCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhhcCCceEEEeecccccCCCCccccccCCCCCccccc
Q 003880 198 ANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANC 277 (789)
Q Consensus 198 s~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLImL~Lathe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c 277 (789)
.|||+|-=|--.-+. +...+|++.|.|+++++- ++ ++|-.. ..+ +| ..+
T Consensus 146 --ap~EADa~ia~La~~---------g~~~~I~S~D~D~l~~~~----~~--v~~~~~-~~~---~~---~~p------- 194 (346)
T 2izo_A 146 --APSEGEAEAAYLNKL---------GLSWAAASQDYDAILFGA----KR--LVRNLT-ITG---KR---KLP------- 194 (346)
T ss_dssp --CSSCHHHHHHHHHHT---------TSSSEEECSSSHHHHTTC----SE--EEESSC-C--------------------
T ss_pred --cCCcHHHHHHHHHhC---------CCeEEEECCCCCcceecC----Ce--EEEEec-ccc---cc---cCc-------
Confidence 499999988766651 356899999999999882 33 333210 000 00 000
Q ss_pred ccccccccCCCCcCCCccccCCCCceEeeHHHHHHHHHHHhcCCCCCCccchhhhhhHHHHHhhhccCCCCC-CCCcccc
Q 003880 278 EGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLP-HMPTLEI 356 (789)
Q Consensus 278 ~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~LReyL~~e~~~~~~~~~~d~eriIDDfVfLcf~vGNDFLP-hlp~l~I 356 (789)
. ++ ......+++++...+.+.+ . +.. +.||.+|.|+|+||+| .+|++-.
T Consensus 195 -----~-------~~---~~~~~~~~~~~~~~v~~~~----g-------l~~----~q~id~~~L~G~D~~p~Gv~GIG~ 244 (346)
T 2izo_A 195 -----N-------KD---VYVEIKPELIETEILLKKL----G-------ITR----EQLIDIGILIGTDYNPDGIRGIGP 244 (346)
T ss_dssp -------------------CCCCCCEEEEHHHHHHHH----T-------CCH----HHHHHHHHHHCCSSSTTCSTTCCH
T ss_pred -----c-------cc---cccccceEEEEHHHHHHHc----C-------CCH----HHHHHHHHHcCCCCCCCCCCCcCH
Confidence 0 00 0000135677776554432 2 222 4677799999999999 9999754
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=96.37 E-value=0.049 Score=58.00 Aligned_cols=145 Identities=16% Similarity=0.157 Sum_probs=81.2
Q ss_pred eEEEeccccccccccCCCCCCCCCHHHHHHHHHHHHHHHHhhccccceEEEeecCCCcchhhHHHhhhhccchhHHHhHH
Q 003880 50 NLYLDMNGIIHPCFHPEDRPAPTTFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSA 129 (789)
Q Consensus 50 nLYlDmNgIIH~c~h~~~~~~p~t~~e~~~~if~yid~l~~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~~~~~~~ 129 (789)
-|-||.++++|-++|..++. | ....++..+-+++...+|..++ +|+||..| .-|..-|-.-|......
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 2444555666677778898764 89998766 44554444433222111
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCCCCCccCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCC-ChhhhH
Q 003880 130 AEEERLRQEFEREGRKLPPKSDSQVFDSNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPG-EGEHKI 208 (789)
Q Consensus 130 ~~~~~l~~~~~~~g~~~~~~~~~~~fDsn~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPG-EGEHKI 208 (789)
..+ .......+++ .|+..+.+.|+.+ ++ + +.+| .+|| |++==|
T Consensus 89 ----------p~~----------~~~~~e~L~~--q~~~~ikell~~~---~~----g---ip~i----~~~g~EADDvi 132 (290)
T 1exn_A 89 ----------YAQ----------RTEEEKALDE--QFFEYLKDAFELC---KT----T---FPTF----TIRGVEADDMA 132 (290)
T ss_dssp ----------HHT----------SCHHHHHHHH--HHHHHHHHHHHHH---TT----T---SCEE----CCTTBCHHHHH
T ss_pred ----------Ccc----------ccccchhHHH--hhHHHHHHHHHhh---CC----C---CcEE----EECCcCHHHHH
Confidence 000 0000000000 0122233323221 11 2 3343 3799 999988
Q ss_pred HHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhhcCCceEEEe
Q 003880 209 MSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALATHEVHFSIL 251 (789)
Q Consensus 209 m~fIR~qr~~p~~dpn~~H~IyG~DADLImL~Lathe~~f~IL 251 (789)
--.-++-... ....+|++.|-|+..|. .+++.++
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 8877764432 23588999999997665 3566665
No 13
>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=88.87 E-value=0.16 Score=34.53 Aligned_cols=18 Identities=39% Similarity=1.150 Sum_probs=16.2
Q ss_pred ccccccCCCCCccccccc
Q 003880 262 DKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 262 ~~c~~c~q~gh~~~~c~g 279 (789)
..|+.||+.||.+.+|..
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 14
>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=88.80 E-value=0.2 Score=34.98 Aligned_cols=19 Identities=37% Similarity=0.947 Sum_probs=16.7
Q ss_pred CccccccCCCCCccccccc
Q 003880 261 QDKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~g 279 (789)
..+|+.||+.||++.+|..
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 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=87.92 E-value=0.29 Score=36.91 Aligned_cols=22 Identities=36% Similarity=0.890 Sum_probs=18.5
Q ss_pred CCccccccCCCCCccccccccc
Q 003880 260 QQDKCFLCGQPGHLAANCEGKA 281 (789)
Q Consensus 260 ~~~~c~~c~q~gh~~~~c~g~~ 281 (789)
...+|+.||+.||.+.+|....
T Consensus 9 ~~~~C~~Cgk~GH~ardCP~~~ 30 (40)
T 1a6b_B 9 DRDQCAYCKEKGHWAKDCPKKP 30 (40)
T ss_dssp CSSSCSSSCCTTCCTTSCSSSC
T ss_pred CCCeeeECCCCCcchhhCcCCc
Confidence 4568999999999999997643
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=82.55 E-value=0.65 Score=37.56 Aligned_cols=22 Identities=36% Similarity=0.918 Sum_probs=18.4
Q ss_pred CccccccCCCCCcccccccccc
Q 003880 261 QDKCFLCGQPGHLAANCEGKAK 282 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~g~~k 282 (789)
..+|+.||+.||.+.+|....+
T Consensus 23 ~~~C~~Cge~GH~ardCp~~~~ 44 (56)
T 1u6p_A 23 RDQCAYCKEKGHWAKDCPKKPR 44 (56)
T ss_dssp TTBCSSSCCBSSCGGGCTTCCC
T ss_pred CCcceeCCCCCcccccCcCCcc
Confidence 4689999999999999976543
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=78.00 E-value=0.9 Score=36.59 Aligned_cols=18 Identities=50% Similarity=1.220 Sum_probs=16.2
Q ss_pred CccccccCCCCCcccccc
Q 003880 261 QDKCFLCGQPGHLAANCE 278 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~ 278 (789)
...|+.|||.||.+.+|.
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 457999999999999995
No 18
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=68.04 E-value=1.9 Score=31.35 Aligned_cols=17 Identities=47% Similarity=1.249 Sum_probs=13.3
Q ss_pred ccccccCCCCCcccccc
Q 003880 262 DKCFLCGQPGHLAANCE 278 (789)
Q Consensus 262 ~~c~~c~q~gh~~~~c~ 278 (789)
..|+.|++.||.+.+|.
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 46888888888888774
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=66.25 E-value=2.5 Score=32.81 Aligned_cols=19 Identities=37% Similarity=0.947 Sum_probs=13.6
Q ss_pred CccccccCCCCCccccccc
Q 003880 261 QDKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~g 279 (789)
...|+.||+.||.+.+|..
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
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=63.24 E-value=3 Score=30.67 Aligned_cols=17 Identities=35% Similarity=0.905 Sum_probs=13.4
Q ss_pred ccccccCCCCCcccccc
Q 003880 262 DKCFLCGQPGHLAANCE 278 (789)
Q Consensus 262 ~~c~~c~q~gh~~~~c~ 278 (789)
..|+.||+.||.+.+|.
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 56888888888888773
No 21
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=60.66 E-value=3 Score=30.73 Aligned_cols=17 Identities=53% Similarity=1.265 Sum_probs=15.3
Q ss_pred cccccCCCCCccccccc
Q 003880 263 KCFLCGQPGHLAANCEG 279 (789)
Q Consensus 263 ~c~~c~q~gh~~~~c~g 279 (789)
+|+.|++.||.+.+|..
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 58999999999999964
No 22
>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=60.40 E-value=4.2 Score=32.66 Aligned_cols=21 Identities=29% Similarity=0.599 Sum_probs=17.6
Q ss_pred CccccccCCCCCccccccccc
Q 003880 261 QDKCFLCGQPGHLAANCEGKA 281 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~g~~ 281 (789)
...|+.|++.||++.+|....
T Consensus 30 ~~~C~~Cg~~GH~ar~C~~~~ 50 (60)
T 1cl4_A 30 PGLCPRCKRGKHWANECKSKT 50 (60)
T ss_dssp CCSCSSCSSCSSCSTTCCCTT
T ss_pred CcceeECCCCCCccCcCCCcc
Confidence 467999999999999997643
No 23
>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=57.17 E-value=4.2 Score=31.45 Aligned_cols=18 Identities=39% Similarity=1.102 Sum_probs=16.0
Q ss_pred ccccccCCCCCccccccc
Q 003880 262 DKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 262 ~~c~~c~q~gh~~~~c~g 279 (789)
..|+.||+.||.+.+|..
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 24
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=56.41 E-value=4.2 Score=29.51 Aligned_cols=17 Identities=47% Similarity=1.425 Sum_probs=15.2
Q ss_pred cccccCCCCCccccccc
Q 003880 263 KCFLCGQPGHLAANCEG 279 (789)
Q Consensus 263 ~c~~c~q~gh~~~~c~g 279 (789)
.|+.|++.||.+.+|..
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 59999999999999964
No 25
>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=55.16 E-value=5.6 Score=32.47 Aligned_cols=20 Identities=35% Similarity=0.790 Sum_probs=15.2
Q ss_pred CccccccCCCCCcccccccc
Q 003880 261 QDKCFLCGQPGHLAANCEGK 280 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~g~ 280 (789)
...|+.|++.||++.+|...
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 45788888888888888653
No 26
>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=54.25 E-value=5.5 Score=38.07 Aligned_cols=16 Identities=38% Similarity=1.059 Sum_probs=8.5
Q ss_pred cccccCCCCCcccccc
Q 003880 263 KCFLCGQPGHLAANCE 278 (789)
Q Consensus 263 ~c~~c~q~gh~~~~c~ 278 (789)
+|+.||+.||.+.+|.
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 27
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=53.58 E-value=4.9 Score=34.86 Aligned_cols=20 Identities=30% Similarity=0.904 Sum_probs=17.3
Q ss_pred CCccccccCCCCCccccccc
Q 003880 260 QQDKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 260 ~~~~c~~c~q~gh~~~~c~g 279 (789)
....|..||+.||++.+|..
T Consensus 45 ~~~~CYnCG~~GH~~rdC~~ 64 (83)
T 3nyb_B 45 HTIYCYNCGGKGHFGDDCKE 64 (83)
T ss_dssp CCCBCSSSSCBSSCGGGCSS
T ss_pred CCCeecccCCCCcCcccCCc
Confidence 34689999999999999964
No 28
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=53.36 E-value=6.6 Score=33.24 Aligned_cols=16 Identities=38% Similarity=1.005 Sum_probs=8.0
Q ss_pred cccccCCCCCcccccc
Q 003880 263 KCFLCGQPGHLAANCE 278 (789)
Q Consensus 263 ~c~~c~q~gh~~~~c~ 278 (789)
.|+.||+.||++.+|.
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 29
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=53.25 E-value=4.5 Score=32.71 Aligned_cols=19 Identities=37% Similarity=0.922 Sum_probs=16.6
Q ss_pred ccccccCCCCCcccccccc
Q 003880 262 DKCFLCGQPGHLAANCEGK 280 (789)
Q Consensus 262 ~~c~~c~q~gh~~~~c~g~ 280 (789)
..|+.|++.||++.+|...
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 30
>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=52.55 E-value=4.6 Score=31.83 Aligned_cols=19 Identities=53% Similarity=1.200 Sum_probs=15.5
Q ss_pred CccccccCCCCCccccccc
Q 003880 261 QDKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~g 279 (789)
...|+.|++.||++.+|..
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 3579999999999998854
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=50.96 E-value=5.8 Score=31.20 Aligned_cols=18 Identities=33% Similarity=1.003 Sum_probs=16.1
Q ss_pred ccccccCCCCCccccccc
Q 003880 262 DKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 262 ~~c~~c~q~gh~~~~c~g 279 (789)
..|+.||+.||.+.+|..
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
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=49.46 E-value=6.4 Score=31.84 Aligned_cols=20 Identities=45% Similarity=1.154 Sum_probs=17.1
Q ss_pred CccccccCCCCCcccccccc
Q 003880 261 QDKCFLCGQPGHLAANCEGK 280 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~g~ 280 (789)
...|+.|++.||.+.+|...
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 33
>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=48.25 E-value=3.8 Score=32.93 Aligned_cols=18 Identities=50% Similarity=1.250 Sum_probs=0.0
Q ss_pred cccccCCCCCcccccccc
Q 003880 263 KCFLCGQPGHLAANCEGK 280 (789)
Q Consensus 263 ~c~~c~q~gh~~~~c~g~ 280 (789)
.|+.|++.||++.+|...
T Consensus 3 ~Cf~Cg~~GH~a~~C~~~ 20 (60)
T 1cl4_A 3 SCFKCGKKGHFAKNCHEH 20 (60)
T ss_dssp ------------------
T ss_pred ccccCCCCCcCHhhCcCC
Confidence 699999999999999653
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=46.25 E-value=8.5 Score=31.34 Aligned_cols=19 Identities=37% Similarity=0.880 Sum_probs=16.7
Q ss_pred CccccccCCCCCccccccc
Q 003880 261 QDKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~g 279 (789)
...|+.|++.||.+.+|..
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=43.20 E-value=8.5 Score=33.33 Aligned_cols=19 Identities=26% Similarity=0.658 Sum_probs=15.5
Q ss_pred CccccccCCCCCccccccc
Q 003880 261 QDKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~g 279 (789)
+..|+.|++.||.+.+|..
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=39.87 E-value=12 Score=31.60 Aligned_cols=18 Identities=39% Similarity=0.947 Sum_probs=16.2
Q ss_pred ccccccCCCCCccccccc
Q 003880 262 DKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 262 ~~c~~c~q~gh~~~~c~g 279 (789)
..|+.||+.||.+.+|..
T Consensus 25 ~~C~~Cg~~GH~a~~C~~ 42 (74)
T 2li8_A 25 DRCYNCGGLDHHAKECKL 42 (74)
T ss_dssp SCCTTTCCSSSCTTTCSS
T ss_pred CcccccCCcCcCcccCCC
Confidence 579999999999999964
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=38.45 E-value=11 Score=36.04 Aligned_cols=18 Identities=39% Similarity=0.857 Sum_probs=15.8
Q ss_pred ccccCCCCCccccccccc
Q 003880 264 CFLCGQPGHLAANCEGKA 281 (789)
Q Consensus 264 c~~c~q~gh~~~~c~g~~ 281 (789)
|..|++.||++.+|...+
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 889999999999997654
No 38
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=24.64 E-value=28 Score=31.69 Aligned_cols=19 Identities=32% Similarity=0.966 Sum_probs=16.6
Q ss_pred CCccccccCCCCCcccccc
Q 003880 260 QQDKCFLCGQPGHLAANCE 278 (789)
Q Consensus 260 ~~~~c~~c~q~gh~~~~c~ 278 (789)
....|+.||+.||++.+|.
T Consensus 104 ~~~~Cy~Cg~~GH~a~dCp 122 (124)
T 2lli_A 104 HTIYCYNCGGKGHFGDDCK 122 (124)
T ss_dssp CCCCTTTTSSSCTTTTTSC
T ss_pred CCCCcCCCCCCCcCcccCc
Confidence 3468999999999999994
Done!