Query 004471
Match_columns 751
No_of_seqs 328 out of 1688
Neff 8.3
Searched_HMMs 29240
Date Tue Mar 26 02:11:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004471.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/004471hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1nc8_A Nucleocapsid protein; H 95.9 0.0031 1.1E-07 40.9 1.7 23 728-750 3-25 (29)
2 1a6b_B Momulv, zinc finger pro 95.3 0.01 3.6E-07 41.4 2.9 24 727-750 6-29 (40)
3 1u6p_A GAG polyprotein; MLV, A 95.1 0.011 3.8E-07 44.6 2.5 25 726-750 18-42 (56)
4 1dsq_A Nucleic acid binding pr 94.5 0.02 6.7E-07 36.0 2.2 20 731-750 2-21 (26)
5 2ayd_A WRKY transcription fact 93.0 0.24 8.1E-06 39.7 6.5 40 212-251 34-73 (76)
6 2ec7_A GAG polyprotein (PR55GA 92.6 0.062 2.1E-06 39.4 2.5 20 731-750 27-46 (49)
7 1wj2_A Probable WRKY transcrip 91.4 0.28 9.6E-06 39.4 5.2 40 212-251 37-76 (78)
8 2a51_A Nucleocapsid protein; s 89.4 0.17 5.9E-06 35.0 2.0 15 734-748 24-38 (39)
9 2bl6_A Nucleocapsid protein P1 88.5 0.19 6.5E-06 34.3 1.7 19 731-749 19-37 (37)
10 2a51_A Nucleocapsid protein; s 88.3 0.22 7.5E-06 34.5 2.0 18 732-749 1-18 (39)
11 1a1t_A Nucleocapsid protein; s 86.8 0.2 6.9E-06 37.6 1.2 21 730-750 32-52 (55)
12 2ysa_A Retinoblastoma-binding 85.0 0.35 1.2E-05 36.2 1.7 22 728-749 4-25 (55)
13 2bl6_A Nucleocapsid protein P1 82.3 0.37 1.3E-05 32.8 0.8 17 733-749 2-18 (37)
14 2cqf_A RNA-binding protein LIN 82.0 0.87 3E-05 35.1 2.9 21 730-750 28-48 (63)
15 2ec7_A GAG polyprotein (PR55GA 80.9 0.56 1.9E-05 34.2 1.4 23 728-750 3-25 (49)
16 1a1t_A Nucleocapsid protein; s 80.6 0.55 1.9E-05 35.1 1.3 22 729-750 10-31 (55)
17 2li8_A Protein LIN-28 homolog 80.3 0.95 3.3E-05 36.2 2.6 20 730-749 45-64 (74)
18 2ihx_A Nucleocapsid (NC) prote 80.2 0.57 1.9E-05 35.9 1.2 19 732-750 31-49 (61)
19 1cl4_A Protein (GAG polyprotei 79.7 0.91 3.1E-05 34.6 2.3 21 730-750 29-49 (60)
20 2rpr_A Flywch-type zinc finger 77.2 3.7 0.00013 33.7 5.5 46 200-252 26-74 (87)
21 2ihx_A Nucleocapsid (NC) prote 76.1 0.89 3E-05 34.8 1.2 21 730-750 3-23 (61)
22 2cqf_A RNA-binding protein LIN 74.5 1.2 4.2E-05 34.3 1.7 21 730-750 6-26 (63)
23 3ts2_A Protein LIN-28 homolog 74.4 1.1 3.9E-05 41.0 1.7 21 730-750 118-138 (148)
24 3hot_A Transposable element ma 70.1 36 0.0012 35.1 12.5 63 380-445 184-253 (345)
25 3nyb_B Protein AIR2; polya RNA 68.4 1.8 6.1E-05 35.4 1.4 21 730-750 45-65 (83)
26 2li8_A Protein LIN-28 homolog 67.5 1.8 6.3E-05 34.5 1.3 21 730-750 23-43 (74)
27 1cl4_A Protein (GAG polyprotei 64.7 1.4 4.6E-05 33.6 0.0 19 732-750 2-20 (60)
28 3ts2_A Protein LIN-28 homolog 62.6 2.7 9.2E-05 38.5 1.6 22 729-750 95-116 (148)
29 3l3u_A POL polyprotein; DNA in 60.1 25 0.00086 31.7 8.0 66 369-448 9-74 (163)
30 3kks_A Integrase, IN; beta-str 54.4 32 0.0011 30.2 7.6 65 370-448 3-67 (152)
31 2lli_A Protein AIR2; RNA surve 52.3 6.6 0.00023 34.6 2.3 20 731-750 64-83 (124)
32 2lli_A Protein AIR2; RNA surve 52.3 7.7 0.00026 34.1 2.7 23 728-750 102-124 (124)
33 1cxq_A Avian sarcoma virus int 52.0 39 0.0014 30.4 7.8 71 369-448 11-81 (162)
34 2ezd_A High mobility group pro 51.7 10 0.00035 23.0 2.2 17 706-722 2-18 (26)
35 1c0m_A Protein (integrase); HI 50.7 36 0.0012 33.2 7.8 70 370-448 11-80 (238)
36 1bco_A MUA domain II, bacterio 48.1 42 0.0015 34.5 8.2 73 369-448 16-96 (327)
37 3alr_A Nanos protein; zinc-fin 40.9 8.4 0.00029 32.3 1.0 21 730-750 70-93 (106)
38 2xzm_5 Ribosomal protein S26E 40.8 17 0.0006 31.2 3.0 27 706-739 2-28 (119)
39 3av9_A Integrase, IN; protein- 38.9 48 0.0016 30.6 6.2 66 369-448 29-94 (183)
40 3hph_A Integrase, IN; protein- 37.1 71 0.0024 30.3 7.4 66 370-449 61-126 (219)
41 3u5c_a 40S ribosomal protein S 36.3 22 0.00076 30.6 2.9 27 706-739 2-28 (119)
42 3f9k_A Integrase; protein-prot 31.4 88 0.003 29.5 6.9 65 370-448 60-124 (210)
43 1c6v_A Protein (SIV integrase) 30.9 1.1E+02 0.0037 27.0 7.2 66 369-448 9-74 (164)
44 2x78_A Integrase; viral protei 29.8 84 0.0029 29.1 6.4 69 370-448 14-83 (200)
45 1ex4_A Integrase; SH3-like dom 22.8 1E+02 0.0036 29.7 5.7 65 370-448 10-74 (239)
46 1fme_A FSD-EY peptide; beta-BE 22.4 58 0.002 19.5 2.1 20 177-196 6-25 (28)
47 2l0z_A Glycoprotein G2; zinc-b 22.1 32 0.0011 23.6 1.1 15 626-640 21-35 (42)
No 1
>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=95.86 E-value=0.0031 Score=40.88 Aligned_cols=23 Identities=35% Similarity=0.908 Sum_probs=20.4
Q ss_pred CcceeeCcccCcCCCCCCCCCCC
Q 004471 728 VKRVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 728 ~k~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
+++..+|-+|++.||..+.|+.|
T Consensus 3 ~r~~~~C~nCgk~GH~ar~C~~p 25 (29)
T 1nc8_A 3 QRKVIRCWNCGKEGHSARQCRAP 25 (29)
T ss_dssp CCCCCBCTTTSCBSSCGGGCCSS
T ss_pred CCCCCEEEECCccccCHhHCccc
Confidence 45668899999999999999987
No 2
>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=95.34 E-value=0.01 Score=41.37 Aligned_cols=24 Identities=21% Similarity=0.606 Sum_probs=20.7
Q ss_pred CCcceeeCcccCcCCCCCCCCCCC
Q 004471 727 RVKRVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 727 ~~k~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
......+|-.|++.||.++.||++
T Consensus 6 ~~~~~~~C~~Cgk~GH~ardCP~~ 29 (40)
T 1a6b_B 6 SQLDRDQCAYCKEKGHWAKDCPKK 29 (40)
T ss_dssp CSCCSSSCSSSCCTTCCTTSCSSS
T ss_pred CCCCCCeeeECCCCCcchhhCcCC
Confidence 344568999999999999999986
No 3
>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=95.05 E-value=0.011 Score=44.58 Aligned_cols=25 Identities=20% Similarity=0.569 Sum_probs=21.3
Q ss_pred CCCcceeeCcccCcCCCCCCCCCCC
Q 004471 726 GRVKRVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 726 ~~~k~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
.......+|-.||+.||..+.||.+
T Consensus 18 ~~~~~~~~C~~Cge~GH~ardCp~~ 42 (56)
T 1u6p_A 18 RSQLDRDQCAYCKEKGHWAKDCPKK 42 (56)
T ss_dssp STTCCTTBCSSSCCBSSCGGGCTTC
T ss_pred CCCCCCCcceeCCCCCcccccCcCC
Confidence 3455678899999999999999975
No 4
>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=94.47 E-value=0.02 Score=35.99 Aligned_cols=20 Identities=30% Similarity=0.733 Sum_probs=18.0
Q ss_pred eeeCcccCcCCCCCCCCCCC
Q 004471 731 VVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 731 ~~~Cs~C~~~GHn~rtC~~~ 750 (751)
..+|-+|++.||..|.||.+
T Consensus 2 ~~~Cf~CG~~GH~ardC~~~ 21 (26)
T 1dsq_A 2 GPVCFSCGKTGHIKRDCKEE 21 (26)
T ss_dssp CCBCTTTCCBSSCTTTTTCC
T ss_pred CCeeEeCCCCCcccccCCCc
Confidence 35799999999999999986
No 5
>2ayd_A WRKY transcription factor 1; beta strands, zinc finger; 1.60A {Arabidopsis thaliana}
Probab=93.03 E-value=0.24 Score=39.66 Aligned_cols=40 Identities=23% Similarity=0.399 Sum_probs=35.0
Q ss_pred cEEEEEecCCCCceEEEEEEcCCCCcEEEEeecCCccccC
Q 004471 212 TRFTAKCAAEGCPWRIHAAKLPGVPTFTIRTIHESHTCGG 251 (751)
Q Consensus 212 ~r~~~~C~~~gC~w~i~a~~~~~~~~w~I~~~~~~Hnc~~ 251 (751)
-|-.++|+..||+++-.+.+..++....++++..+|||+.
T Consensus 34 PRsYYrCt~~gC~a~K~Ver~~~d~~~~~~tY~G~H~H~~ 73 (76)
T 2ayd_A 34 PRSYYRCSSPGCPVKKHVERSSHDTKLLITTYEGKHDHDM 73 (76)
T ss_dssp CEEEEEECSTTCCCEEEEEECSSSTTEEEEEEESCCSSCC
T ss_pred ceeEeEcCCCCCCceeeEEEECCCCCEEEEEEccCcCCCC
Confidence 4666899999999999999987778888999999999974
No 6
>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=92.63 E-value=0.062 Score=39.42 Aligned_cols=20 Identities=30% Similarity=0.742 Sum_probs=14.3
Q ss_pred eeeCcccCcCCCCCCCCCCC
Q 004471 731 VVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 731 ~~~Cs~C~~~GHn~rtC~~~ 750 (751)
...|-+|++.||..+.||..
T Consensus 27 ~~~C~~Cg~~GH~~~~C~~~ 46 (49)
T 2ec7_A 27 RQGCWKCGKTGHVMAKCPER 46 (49)
T ss_dssp CCSCSSSCCSSCCGGGCCSS
T ss_pred CCeeCcCCCcCCccCCCcCC
Confidence 45677777777777777753
No 7
>1wj2_A Probable WRKY transcription factor 4; DNA-binding domain, zinc-binding, structural genomics; NMR {Arabidopsis thaliana} SCOP: g.79.1.1 PDB: 2lex_A*
Probab=91.44 E-value=0.28 Score=39.40 Aligned_cols=40 Identities=25% Similarity=0.371 Sum_probs=34.6
Q ss_pred cEEEEEecCCCCceEEEEEEcCCCCcEEEEeecCCccccC
Q 004471 212 TRFTAKCAAEGCPWRIHAAKLPGVPTFTIRTIHESHTCGG 251 (751)
Q Consensus 212 ~r~~~~C~~~gC~w~i~a~~~~~~~~w~I~~~~~~Hnc~~ 251 (751)
-|-.++|+..||+++-.+.+...+....++++..+|||+.
T Consensus 37 PRsYYrCt~~gC~a~K~Ver~~~d~~~~~~tY~G~H~H~~ 76 (78)
T 1wj2_A 37 PRSYYKCTTPGCGVRKHVERAATDPKAVVTTYEGKHNHDL 76 (78)
T ss_dssp CEEEEEEECSSCEEEEEEEEETTTTSEEEEEEESCCSSCC
T ss_pred eeEEeecCcCCCCcEeeEEEEcCCCCEEEEEEeeEcCCCC
Confidence 3566899999999999999987777788889999999974
No 8
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=89.38 E-value=0.17 Score=35.01 Aligned_cols=15 Identities=27% Similarity=0.709 Sum_probs=8.0
Q ss_pred CcccCcCCCCCCCCC
Q 004471 734 CSRCNQTGHFRTTCA 748 (751)
Q Consensus 734 Cs~C~~~GHn~rtC~ 748 (751)
|-+|++.||..+.||
T Consensus 24 C~~Cg~~GH~~~~C~ 38 (39)
T 2a51_A 24 CWNCGSKEHRFAQCP 38 (39)
T ss_dssp CTTTCCSSSCTTTSC
T ss_pred cccCCCCCCccCcCc
Confidence 445555555555554
No 9
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=88.47 E-value=0.19 Score=34.32 Aligned_cols=19 Identities=37% Similarity=0.920 Sum_probs=14.7
Q ss_pred eeeCcccCcCCCCCCCCCC
Q 004471 731 VVHCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 731 ~~~Cs~C~~~GHn~rtC~~ 749 (751)
...|-+|++.||..+.||+
T Consensus 19 ~~~C~~Cg~~GH~a~~C~~ 37 (37)
T 2bl6_A 19 PKVCFKCKQPGHFSKQCRS 37 (37)
T ss_dssp BTTCSSCCCTTGGGGTTCC
T ss_pred cCeEccCCCcCCccCcCcC
Confidence 3778888888888888874
No 10
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=88.27 E-value=0.22 Score=34.46 Aligned_cols=18 Identities=28% Similarity=0.809 Sum_probs=16.1
Q ss_pred eeCcccCcCCCCCCCCCC
Q 004471 732 VHCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 732 ~~Cs~C~~~GHn~rtC~~ 749 (751)
++|-+|++.||..+.||+
T Consensus 1 i~C~~Cg~~GH~a~~C~~ 18 (39)
T 2a51_A 1 LTCFNCGKPGHTARMCRQ 18 (39)
T ss_dssp CBCTTTCCBSSCTTTCCS
T ss_pred CeeeccCCCCcccccCCC
Confidence 369999999999999984
No 11
>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=86.79 E-value=0.2 Score=37.57 Aligned_cols=21 Identities=29% Similarity=0.694 Sum_probs=16.4
Q ss_pred ceeeCcccCcCCCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
+...|-+|++.||..+.||.+
T Consensus 32 ~~~~C~~Cg~~GH~~~~C~~~ 52 (55)
T 1a1t_A 32 RKKGCWKCGKEGHQMKDCTER 52 (55)
T ss_dssp SCCBCTTTCCBSSCGGGCSSS
T ss_pred CCCEeCCCCCcCCccCCCcCc
Confidence 456788888888888888864
No 12
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=85.05 E-value=0.35 Score=36.17 Aligned_cols=22 Identities=27% Similarity=0.714 Sum_probs=18.8
Q ss_pred CcceeeCcccCcCCCCCCCCCC
Q 004471 728 VKRVVHCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 728 ~k~~~~Cs~C~~~GHn~rtC~~ 749 (751)
..+.+.|=+|++.||..+.||.
T Consensus 4 ~p~~~~C~kCGk~GH~~k~Cp~ 25 (55)
T 2ysa_A 4 GSSGYTCFRCGKPGHYIKNCPT 25 (55)
T ss_dssp SSSSCCCTTTCCTTSCGGGCSG
T ss_pred CCCCCccccCCCcCcccccCCC
Confidence 3456789999999999999993
No 13
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=82.31 E-value=0.37 Score=32.83 Aligned_cols=17 Identities=35% Similarity=1.024 Sum_probs=15.7
Q ss_pred eCcccCcCCCCCCCCCC
Q 004471 733 HCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 733 ~Cs~C~~~GHn~rtC~~ 749 (751)
+|-+|++.||..+.||.
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 69999999999999985
No 14
>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=81.98 E-value=0.87 Score=35.14 Aligned_cols=21 Identities=19% Similarity=0.581 Sum_probs=16.9
Q ss_pred ceeeCcccCcCCCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
+...|-+|++.||..+.||..
T Consensus 28 ~~~~C~~Cg~~GH~ar~Cp~~ 48 (63)
T 2cqf_A 28 QPKKCHFCQSISHMVASCPLK 48 (63)
T ss_dssp CSSCCTTTCCSSSCTTTCTGG
T ss_pred CCCccCCcCCcCCccCcCCCc
Confidence 467888888888888888853
No 15
>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=80.89 E-value=0.56 Score=34.20 Aligned_cols=23 Identities=35% Similarity=0.908 Sum_probs=20.3
Q ss_pred CcceeeCcccCcCCCCCCCCCCC
Q 004471 728 VKRVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 728 ~k~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
+++..+|-+|++.||..+.||.|
T Consensus 3 ~~r~~~C~~Cg~~GH~a~~C~~~ 25 (49)
T 2ec7_A 3 QRKVIRCWNCGKEGHSARQCRAP 25 (49)
T ss_dssp CCCCCBCTTTCCBTCCTTTCCCS
T ss_pred CCCcCeeeecCCCCcChhhCcCC
Confidence 45678999999999999999975
No 16
>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=80.62 E-value=0.55 Score=35.13 Aligned_cols=22 Identities=36% Similarity=1.002 Sum_probs=19.5
Q ss_pred cceeeCcccCcCCCCCCCCCCC
Q 004471 729 KRVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 729 k~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
++..+|-+|++.||..+.||.|
T Consensus 10 ~~~~~C~~Cg~~GH~a~~C~~~ 31 (55)
T 1a1t_A 10 RKTVKCFNCGKEGHIAKNCRAP 31 (55)
T ss_dssp GGTCBCTTTCCBSSCGGGCSSC
T ss_pred CCCcceeeeCCCCcChhhcCCC
Confidence 4567899999999999999975
No 17
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=80.26 E-value=0.95 Score=36.17 Aligned_cols=20 Identities=20% Similarity=0.620 Sum_probs=14.6
Q ss_pred ceeeCcccCcCCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~~ 749 (751)
+...|-+|++.||..+.||.
T Consensus 45 ~~~~C~~Cg~~GH~ar~Cp~ 64 (74)
T 2li8_A 45 QPKKCHFCQSISHMVASCPL 64 (74)
T ss_dssp CCCCCTTTCCTTSCGGGCTT
T ss_pred CCCccCCcCCcCCccCcCcC
Confidence 35677777777777777775
No 18
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=80.20 E-value=0.57 Score=35.95 Aligned_cols=19 Identities=32% Similarity=0.711 Sum_probs=15.4
Q ss_pred eeCcccCcCCCCCCCCCCC
Q 004471 732 VHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 732 ~~Cs~C~~~GHn~rtC~~~ 750 (751)
..|-+|++.||..+.||++
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 5688888888888888864
No 19
>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=79.72 E-value=0.91 Score=34.58 Aligned_cols=21 Identities=24% Similarity=0.638 Sum_probs=18.7
Q ss_pred ceeeCcccCcCCCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
+...|-+|++.||..+.||++
T Consensus 29 ~~~~C~~Cg~~GH~ar~C~~~ 49 (60)
T 1cl4_A 29 VPGLCPRCKRGKHWANECKSK 49 (60)
T ss_dssp CCCSCSSCSSCSSCSTTCCCT
T ss_pred CCcceeECCCCCCccCcCCCc
Confidence 457899999999999999975
No 20
>2rpr_A Flywch-type zinc finger-containing protein 1; flywch domain, alternative splicing, DNA-binding, metal- binding, nucleus, metal binding protein; NMR {Homo sapiens}
Probab=77.16 E-value=3.7 Score=33.75 Aligned_cols=46 Identities=20% Similarity=0.179 Sum_probs=33.2
Q ss_pred cCeeEEEEeecCcEEEEEecC---CCCceEEEEEEcCCCCcEEEEeecCCccccCc
Q 004471 200 LHFEMQTIKSDKTRFTAKCAA---EGCPWRIHAAKLPGVPTFTIRTIHESHTCGGI 252 (751)
Q Consensus 200 ~gf~i~~~ks~~~r~~~~C~~---~gC~w~i~a~~~~~~~~w~I~~~~~~Hnc~~~ 252 (751)
.||.|...+....+..-.|.+ .+|++++.... +. |. ....|||+|.
T Consensus 26 ~Gy~Y~~~~~~~~~~yWrC~~~~~~kCrARi~T~~----~~--~~-~~~~HnH~p~ 74 (87)
T 2rpr_A 26 ESFLYRKEKAAGEKVYWMCRDQARLGCRSRAITQG----HR--IM-VMRSHCHQPD 74 (87)
T ss_dssp TTEEEEEEEECSSCEEEEEGGGTTSCCCCEEEEET----TE--EE-ECSCCSSCCC
T ss_pred CCEEEEeeecCCCcEEEEecCCCCCCCCEEEEEcC----CC--EE-CCCCcCCCCc
Confidence 467777777667777799986 58999988754 12 32 5678999874
No 21
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=76.09 E-value=0.89 Score=34.82 Aligned_cols=21 Identities=24% Similarity=0.705 Sum_probs=18.3
Q ss_pred ceeeCcccCcCCCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
+...|-+|++.||..+.||.+
T Consensus 3 ~~~~C~~Cg~~GH~a~~C~~~ 23 (61)
T 2ihx_A 3 ARGLCYTCGSPGHYQAQCPKK 23 (61)
T ss_dssp CTTBCSSSCCBTCCGGGCTTT
T ss_pred CCCcccccCCCCeehhhCcCC
Confidence 356799999999999999974
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=74.53 E-value=1.2 Score=34.28 Aligned_cols=21 Identities=24% Similarity=0.581 Sum_probs=18.5
Q ss_pred ceeeCcccCcCCCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
+...|-+|++.||..+.||.+
T Consensus 6 r~~~C~~Cg~~GH~a~~C~~~ 26 (63)
T 2cqf_A 6 SGDRCYNCGGLDHHAKECKLP 26 (63)
T ss_dssp SCCCCSSSCCSSSCTTTCCSC
T ss_pred CCCcccccCCCCcChhhCCCC
Confidence 457899999999999999964
No 23
>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=74.37 E-value=1.1 Score=41.02 Aligned_cols=21 Identities=19% Similarity=0.581 Sum_probs=16.4
Q ss_pred ceeeCcccCcCCCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
+..+|-+|++.||..+.||+.
T Consensus 118 ~~~~C~~Cg~~GH~~r~Cp~~ 138 (148)
T 3ts2_A 118 QPKKCHFCQSINHMVASCPLK 138 (148)
T ss_dssp CCCCCTTTCCSSCCGGGCTTT
T ss_pred CCCcccccCCcCCEeccCcCC
Confidence 357788888888888888864
No 24
>3hot_A Transposable element mariner, complete CDS; protein-DNA complex, synaptic complex, transposase, inverted DNA, DNA binding protein-DNA complex; HET: 5IU; 3.25A {Drosophila mauritiana} PDB: 3hos_A*
Probab=70.10 E-value=36 Score=35.13 Aligned_cols=63 Identities=16% Similarity=0.269 Sum_probs=41.6
Q ss_pred ccccCcceEEEEEecCCCCeEEEEEEEee---cCchhhHHHHHHHHHHHhccccCC----CCceEEeecCccc
Q 004471 380 KSKYLGTLLLATGFDGDGALFPLAFGVVD---EENDDNWMWFLSELHNLLEINTEN----MPRLTILSDRQKG 445 (751)
Q Consensus 380 ~~~y~~~ll~~~g~d~~~~~~~la~alv~---~E~~es~~w~l~~l~~~~~~~~~~----~~p~~iitD~~~~ 445 (751)
...+.+.++++.+.+..| .+++.++. .-+.+.|.-+|+.+...+...... ..+.+|+.|....
T Consensus 184 ~~~~~~~~~v~~~~~~~g---~~~~~~~~~~~~~~~~~y~~~L~~~~~~~~~~~p~~~~~~~~~~~~~Dna~~ 253 (345)
T 3hot_A 184 PNRFGKKTMLCVWWDQSG---VIYYELLKPGETVNAARYQQQLINLNRALQRKRPEYQKRQHRVIFLHDNAPS 253 (345)
T ss_dssp CCTTCCEEEEEEEEESSS---EEEEEEECSSCCCCHHHHHHHHHHHHHHHHHHSTTCC---CCCEEECCCCTT
T ss_pred ccCcCCcEEEEEEEcccC---ceeeEecCCCCcccHHHHHHHHHHHHHHHHHhchhhhcCCCceEEEECCCCc
Confidence 344566777777888777 57777776 567888888888776554321111 2367899999663
No 25
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=68.36 E-value=1.8 Score=35.40 Aligned_cols=21 Identities=29% Similarity=0.817 Sum_probs=18.8
Q ss_pred ceeeCcccCcCCCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
..+.|-+|++.||..+.||.+
T Consensus 45 ~~~~CYnCG~~GH~~rdC~~~ 65 (83)
T 3nyb_B 45 HTIYCYNCGGKGHFGDDCKEK 65 (83)
T ss_dssp CCCBCSSSSCBSSCGGGCSSC
T ss_pred CCCeecccCCCCcCcccCCcc
Confidence 457899999999999999975
No 26
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=67.50 E-value=1.8 Score=34.48 Aligned_cols=21 Identities=24% Similarity=0.627 Sum_probs=18.4
Q ss_pred ceeeCcccCcCCCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
+..+|-+|++.||..+.||.+
T Consensus 23 r~~~C~~Cg~~GH~a~~C~~~ 43 (74)
T 2li8_A 23 KGDRCYNCGGLDHHAKECKLP 43 (74)
T ss_dssp TTSCCTTTCCSSSCTTTCSSC
T ss_pred CCCcccccCCcCcCcccCCCC
Confidence 457899999999999999963
No 27
>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=64.75 E-value=1.4 Score=33.59 Aligned_cols=19 Identities=32% Similarity=0.887 Sum_probs=0.0
Q ss_pred eeCcccCcCCCCCCCCCCC
Q 004471 732 VHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 732 ~~Cs~C~~~GHn~rtC~~~ 750 (751)
..|-+|++.||..+.||.+
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 3699999999999999975
No 28
>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=62.62 E-value=2.7 Score=38.47 Aligned_cols=22 Identities=27% Similarity=0.591 Sum_probs=19.2
Q ss_pred cceeeCcccCcCCCCCCCCCCC
Q 004471 729 KRVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 729 k~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
++..+|-+|++.||..+.||.+
T Consensus 95 ~~~~~C~~Cg~~GH~a~~C~~~ 116 (148)
T 3ts2_A 95 KGGDRCYNCGGLDHHAKECKLP 116 (148)
T ss_dssp CCSCCCTTTCCSSCCGGGCCSC
T ss_pred CCCCcccEeCCccchhhhCCCC
Confidence 3467899999999999999973
No 29
>3l3u_A POL polyprotein; DNA integration, AIDS, integrase, endonuclease, polynucleotidyl transferase, DNA binding, viral protein; 1.40A {Human immunodeficiency virus 1} PDB: 3ao1_A 3l3v_A* 3ovn_A* 3ao2_A* 3ao3_A* 3ao4_A* 3ao5_A* 2itg_A 1biz_A 1biu_A 1b9d_A 4dmn_A* 2b4j_A 1itg_A 1b92_A 1bl3_A 1bi4_A 1bis_A 1b9f_A 1bi4_B ...
Probab=60.14 E-value=25 Score=31.66 Aligned_cols=66 Identities=18% Similarity=0.189 Sum_probs=45.1
Q ss_pred CCceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccc
Q 004471 369 RPLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 369 ~~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
..++.+|.|+..++ ++++.+|...+.. +++.+ ..++.+...-++..+...++ +.+|.||+.....+
T Consensus 9 ~~~w~~D~t~~~g~-----y~~~~iD~~sr~~-~~~~~-~~~~~~~~~~~l~~~~~~~~-------~~~i~sD~G~~f~s 74 (163)
T 3l3u_A 9 PGIWQLDCTHLEGK-----VILVAVHVASGYI-EAEVI-PAETGQETAYFLLKLAGRWP-------VKTVHTDNGSNFTS 74 (163)
T ss_dssp TTEEEEEEEEETTE-----EEEEEEETTTCCE-EEEEE-SSCCHHHHHHHHHHHHHHSC-------CCEEEECCCGGGGS
T ss_pred CCEEEEEecccCCc-----EEEEEEecCCCcE-EEEEe-CCCcHHHHHHHHHHHHHHcC-------CcEEeecChHhhhh
Confidence 46889999998653 4667777777654 66665 45566666666655544433 47999999887654
No 30
>3kks_A Integrase, IN; beta-strands flanked by alpha-helices, DNA binding protein; 2.20A {Bovine immunodeficiency virus} PDB: 3kkr_A
Probab=54.44 E-value=32 Score=30.24 Aligned_cols=65 Identities=17% Similarity=0.141 Sum_probs=42.8
Q ss_pred CceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccc
Q 004471 370 PLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 370 ~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
.++.+|.|+..++ ++++.+|..-+.. +++.+- +++.+...-+|..+.... +|.+|.||+.....+
T Consensus 3 ~~w~~D~t~~~~~-----y~~~~iD~~sr~~-~~~~~~-~~~~~~~~~~l~~~~~~~-------gp~~i~sDnG~~f~s 67 (152)
T 3kks_A 3 HLWQMDNTHWNKT-----IIWVAVETNSGLV-EAQVIP-EETALQVALCILQLIQRY-------TVLHLHSDNGPCFTA 67 (152)
T ss_dssp CEEEEEEEEETTE-----EEEEEEETTTCCE-EEEEES-SSCHHHHHHHHHHHHHHS-------CCSEEEECSCHHHHS
T ss_pred cEEEEeeeeeCCE-----EEEEEEEcCCCcE-EEEEeC-CcCHHHHHHHHHHHHHHh-------CCcEEecCCchHhhH
Confidence 5788999988433 5666777776655 566554 666666555555443332 289999999887654
No 31
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=52.29 E-value=6.6 Score=34.55 Aligned_cols=20 Identities=25% Similarity=0.685 Sum_probs=17.7
Q ss_pred eeeCcccCcCCCCCCCCCCC
Q 004471 731 VVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 731 ~~~Cs~C~~~GHn~rtC~~~ 750 (751)
...|-+|++.||..+.||.+
T Consensus 64 ~~~C~~Cg~~GH~~~~Cp~~ 83 (124)
T 2lli_A 64 KVQCTLCKSKKHSKERCPSI 83 (124)
T ss_dssp CCSSSSSCSSCCCTTTCCCS
T ss_pred CccCCCCCcCCcchhhCCCc
Confidence 46899999999999999974
No 32
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=52.26 E-value=7.7 Score=34.11 Aligned_cols=23 Identities=26% Similarity=0.673 Sum_probs=19.8
Q ss_pred CcceeeCcccCcCCCCCCCCCCC
Q 004471 728 VKRVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 728 ~k~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
+...+.|-+|++.||..+.||+.
T Consensus 102 ~~~~~~Cy~Cg~~GH~a~dCp~~ 124 (124)
T 2lli_A 102 PFHTIYCYNCGGKGHFGDDCKEK 124 (124)
T ss_dssp CCCCCCTTTTSSSCTTTTTSCCC
T ss_pred CCCCCCcCCCCCCCcCcccCcCC
Confidence 34568999999999999999973
No 33
>1cxq_A Avian sarcoma virus integrase; mixed beta-sheet surrounded by alpha-helices, transferase; HET: EPE; 1.02A {Avian sarcoma virus} SCOP: c.55.3.2 PDB: 1cxu_A* 1czb_A* 1cz9_A* 1asu_A* 1asw_A* 1asv_A 1a5v_A* 1a5w_A* 1a5x_A* 1vsf_A* 1vse_A* 3o4n_A* 1vsm_A 3o4q_A* 1vsd_A* 1vsh_A* 1vsi_A* 1vsj_A* 1vsk_A 1vsl_A
Probab=52.02 E-value=39 Score=30.39 Aligned_cols=71 Identities=11% Similarity=-0.051 Sum_probs=46.8
Q ss_pred CCceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccc
Q 004471 369 RPLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 369 ~~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
..++.+|.|+.... ++..++++.+|..-+. ++++.+- +.+.+.-.-+|+.+....+ .|.+|.||+.....+
T Consensus 11 ~~~~~~D~~~~~~~-~g~~yl~~~iD~~Sr~-i~~~~~~-~~~~~~v~~~l~~~~~~~g------~p~~i~sDnG~~f~s 81 (162)
T 1cxq_A 11 LQIWQTDFTLEPRM-APRSWLAVTVDTASSA-IVVTQHG-RVTSVAAQHHWATAIAVLG------RPKAIKTDNGSCFTS 81 (162)
T ss_dssp CCEEEEEEEECGGG-TTSCEEEEEEETTTCC-EEEEEES-SCCHHHHHHHHHHHHHHHC------CCSEEECCSCHHHHS
T ss_pred CCEEEeeeeecccC-CCCEEEEEEEEcCCCe-EEEEECC-CccHHHHHHHHHHHHHHHC------CCeEEEeCCchhhhh
Confidence 35789999987643 3456667778877654 4666665 5666655555555544443 467999999887654
No 34
>2ezd_A High mobility group protein HMG-I/HMG-Y; DNA binding protein, minor groove DNA binding, transcriptional CO-activator, architectural factor; HET: DNA; NMR {Homo sapiens} SCOP: j.10.1.1 PDB: 2eze_A*
Probab=51.74 E-value=10 Score=22.98 Aligned_cols=17 Identities=35% Similarity=0.817 Sum_probs=11.5
Q ss_pred CCCCCCCCCCCcccccc
Q 004471 706 PKSLRPPGRPRKKRVRA 722 (751)
Q Consensus 706 P~~~r~~GRPkk~R~~~ 722 (751)
|..+|++||||-...++
T Consensus 2 ptpKrpRgRpkGSKNk~ 18 (26)
T 2ezd_A 2 PTPKRPRGRPKGSKNKG 18 (26)
T ss_dssp CSCCCCSSCCTTCCCCS
T ss_pred CCCcCCCCCcCcccccC
Confidence 34467889998765543
No 35
>1c0m_A Protein (integrase); HIV, X-RAY crystallography, protein structure, transferase; 2.53A {Rous sarcoma virus} SCOP: b.34.7.1 c.55.3.2 PDB: 1c1a_A
Probab=50.65 E-value=36 Score=33.16 Aligned_cols=70 Identities=11% Similarity=-0.042 Sum_probs=47.9
Q ss_pred CceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccc
Q 004471 370 PLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 370 ~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
.++.+|.|+.... ++..++++.+|..-+ +++|+.+- .++.+...-+|..+....+ .|.+|.||+.....+
T Consensus 11 ~~w~~D~~~~~~~-~g~~yl~~~iD~~Sr-~i~~~~~~-~~~~~~v~~~l~~~~~~~g------~p~~i~sDnG~~f~s 80 (238)
T 1c0m_A 11 QIWQTDFTLEPRM-APRSWLAVTVDTASS-AIVVTQHG-RVTSVAVQHHWATAIAVLG------RPKAIKTDNGSCFTS 80 (238)
T ss_dssp SEEEEEEEECGGG-CSSCEEEEEEETTTC-CEEEEEES-SCCHHHHHHHHHHHHHHHC------CCSEEEECSCHHHHS
T ss_pred CEEEEeecccccc-CCCEEEEEEEECCCC-CEEEEEcc-CCCHHHHHHHHHHHHHHhC------CCcEEEECCCCcccc
Confidence 5789999987643 344566677777655 45667765 7777766666666555544 378999999887644
No 36
>1bco_A MUA domain II, bacteriophage MU transposase; polynucleotidyl transferase, DNA binding, endonuclease, integrase; 2.40A {Enterobacteria phage MU} SCOP: b.48.1.1 c.55.3.3 PDB: 1bcm_A
Probab=48.14 E-value=42 Score=34.52 Aligned_cols=73 Identities=14% Similarity=-0.054 Sum_probs=50.0
Q ss_pred CCceeeeeeeecccc---Cc---ceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCce--EEee
Q 004471 369 RPLLGLDRTFLKSKY---LG---TLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRL--TILS 440 (751)
Q Consensus 369 ~~Vv~iD~T~~~~~y---~~---~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~--~iit 440 (751)
..++.+|+|+..... .| ...+.+.+|..-+ .++|+.+...++.++..-+|.......+ .|. +|.|
T Consensus 16 ~~~w~~D~t~~d~~~~~~~g~~~r~~l~~~iD~~SR-~ivg~~~~~~~~~~~v~~aL~~a~~~~G------~P~~~~i~s 88 (327)
T 1bco_A 16 MQWINGDGYLHNVFVRWFNGDVIRPKTWFWQDVKTR-KILGWRCDVSENIDSIRLSFMDVVTRYG------IPEDFHITI 88 (327)
T ss_dssp TTEEEEEEEECSBCEECTTSCEECCEEEEEEETTTC-CEEEEEEESSCCHHHHHHHHHHHHHHHC------EESSCEEEC
T ss_pred CcEEEecCCEEEEEEECCCCccceeEEEEEEECCCC-cEEEEEEECCCCHHHHHHHHHHHHHhcC------CCCCcEEEe
Confidence 468899999765421 23 3456666777665 4589999888887777666666555443 356 9999
Q ss_pred cCcccccc
Q 004471 441 DRQKGIVD 448 (751)
Q Consensus 441 D~~~~l~~ 448 (751)
|+.....+
T Consensus 89 DnG~~f~s 96 (327)
T 1bco_A 89 DNTRGAAN 96 (327)
T ss_dssp CCTTSTTT
T ss_pred eCchhhcc
Confidence 99987754
No 37
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=40.95 E-value=8.4 Score=32.25 Aligned_cols=21 Identities=33% Similarity=0.740 Sum_probs=18.2
Q ss_pred ceeeCcccCcCC---CCCCCCCCC
Q 004471 730 RVVHCSRCNQTG---HFRTTCAAP 750 (751)
Q Consensus 730 ~~~~Cs~C~~~G---Hn~rtC~~~ 750 (751)
|.+.|..||..| |+.+-||+.
T Consensus 70 R~Y~CpiCGATGd~AHT~kYCP~~ 93 (106)
T 3alr_A 70 RQYKCPLCGATGAKAHTKRFCPMV 93 (106)
T ss_dssp GGCCCTTTCCCGGGCCCGGGCTTC
T ss_pred ccccCCCCCCcCCcccceecCCCC
Confidence 578999999988 999999963
No 38
>2xzm_5 Ribosomal protein S26E containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_5
Probab=40.84 E-value=17 Score=31.21 Aligned_cols=27 Identities=37% Similarity=0.752 Sum_probs=18.1
Q ss_pred CCCCCCCCCCCccccccccCCCCcceeeCcccCc
Q 004471 706 PKSLRPPGRPRKKRVRAEDRGRVKRVVHCSRCNQ 739 (751)
Q Consensus 706 P~~~r~~GRPkk~R~~~~~~~~~k~~~~Cs~C~~ 739 (751)
|+.+|..||-|+.|-. -...+|.+|++
T Consensus 2 ~kKRrN~GR~KkgrGh-------v~~V~C~nCgr 28 (119)
T 2xzm_5 2 PVKRRNAGRSQKNRGH-------TRTVPCTNCGR 28 (119)
T ss_dssp CCCCSSTTCCCCSSSC-------CCEEECTTTCC
T ss_pred CcccccCCCCCCCCCC-------CccEeeCCccc
Confidence 4566667777765332 25788999986
No 39
>3av9_A Integrase, IN; protein-protein interactions, HIV, recombination-inhibitor C; 1.70A {Human immunodeficiency virus type 1} PDB: 3ava_A 3avb_A 3avc_A 3avg_A 3avh_A 3avi_A 3avj_A 3avk_A 3avl_A 3avm_A 3avn_A 3nf6_A* 3nf7_A* 3nf8_A* 3nf9_A* 3nfa_A* 3avf_A
Probab=38.90 E-value=48 Score=30.63 Aligned_cols=66 Identities=20% Similarity=0.210 Sum_probs=38.9
Q ss_pred CCceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccc
Q 004471 369 RPLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 369 ~~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
..++.+|.|+..++| + ++.+|..-+.. +|+.+- +.+.....-++..+.... ++.+|.||+.....+
T Consensus 29 ~~~w~~D~~~~~g~~---~--l~~vD~~Sr~~-~~~~~~-~~~~~~~~~~~~~~~~~~-------~~~~i~sDnG~ef~s 94 (183)
T 3av9_A 29 PGIWQLDCTHLEGKV---I--LVAVHVASGYI-EAEVIP-AETGQETAYFLLKLAGRW-------PVKTVHTDNGSNFTS 94 (183)
T ss_dssp TTEEEEEEEEETTEE---E--EEEEETTTTEE-EEEEES-SCCHHHHHHHHHHHHHHS-------CCCEEECSSHHHHHC
T ss_pred CCEEEEeccccCCcE---E--EEEEECCCCCE-EEEEeC-CccchHHHHHHHHHHHHc-------CCcEEEecCchhcch
Confidence 468899999884432 3 34447666654 676554 444444443333333332 248999999876643
No 40
>3hph_A Integrase, IN; protein-protein complex, tetramer, DNA integration, endonucl magnesium, metal-binding, multifunctional enzyme; 2.64A {Maedi visna virus} PDB: 3hpg_A
Probab=37.05 E-value=71 Score=30.29 Aligned_cols=66 Identities=15% Similarity=0.154 Sum_probs=42.1
Q ss_pred CceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCccccccc
Q 004471 370 PLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVDG 449 (751)
Q Consensus 370 ~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~A 449 (751)
.++.+|.|+..++ ++++.+|..-+.. +++.+ .+.+.....-+|..+.... + |.+|.||+.....++
T Consensus 61 ~~w~~D~t~~~~~-----y~~~~iD~~Sr~~-~~~~~-~~~~~~~~~~~l~~~~~~~-----g--p~~i~sDnG~~F~s~ 126 (219)
T 3hph_A 61 DHWQVDYTHYEDK-----IILVWVETNSGLI-YAERV-KGETGQEFRVQTMKWYAMF-----A--PKSLQSDNGPAFVAE 126 (219)
T ss_dssp CEEEEEEEEETTE-----EEEEEEETTTCCE-EEEEE-SCCCHHHHHHHHHHHHHHH-----C--CCEEEECCCHHHHSH
T ss_pred ceEEEEEecCCCE-----EEEEEEeCCCCcE-EEEEe-CCCCHHHHHHHHHHHHHHh-----C--CcEEEeCCCchhhhH
Confidence 5778999876543 5667777777665 55554 4555555555554443332 2 789999998876543
No 41
>3u5c_a 40S ribosomal protein S26-A, 40S ribosomal protein S25-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_a
Probab=36.34 E-value=22 Score=30.61 Aligned_cols=27 Identities=33% Similarity=0.651 Sum_probs=18.0
Q ss_pred CCCCCCCCCCCccccccccCCCCcceeeCcccCc
Q 004471 706 PKSLRPPGRPRKKRVRAEDRGRVKRVVHCSRCNQ 739 (751)
Q Consensus 706 P~~~r~~GRPkk~R~~~~~~~~~k~~~~Cs~C~~ 739 (751)
|+.+|..||-|+-|-. -...+|++|+.
T Consensus 2 ~kKRrN~GR~KkgrGh-------v~~V~C~nCgr 28 (119)
T 3u5c_a 2 PKKRASNGRNKKGRGH-------VKPVRCVNCSK 28 (119)
T ss_dssp CCCCSSTTSCCCSCSC-------CCEEECTTTCC
T ss_pred CcccccCCCCCCCCCC-------CccEeeccccc
Confidence 4566677777765332 25788999985
No 42
>3f9k_A Integrase; protein-protein complex, AIDS, DNA integration, endonuclease magnesium, metal-binding, multifunctional enzyme; 3.20A {Human immunodeficiency virus type 2} PDB: 1e0e_A
Probab=31.44 E-value=88 Score=29.47 Aligned_cols=65 Identities=17% Similarity=0.150 Sum_probs=41.7
Q ss_pred CceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccc
Q 004471 370 PLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 370 ~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
.++.+|-|+..++ ++++.+|..-+ +.+++.+-. ++.+...-++..+....+ +.+|.||+......
T Consensus 60 ~~w~~D~~~~~~~-----y~l~~vD~~sr-~~~~~~~~~-~~~~~~~~~l~~~~~~~g-------~~~i~sDnG~~F~s 124 (210)
T 3f9k_A 60 GTWQMDCTHLEGK-----IIIVAVHVASG-FIEAEVIPQ-ESGRQTALFLLKLASRWP-------ITHLHTDNGANFTS 124 (210)
T ss_dssp TEEEEEEEEETTE-----EEEEEEETTTT-EEEEEEESS-CCHHHHHHHHHHHHTTSC-------CSEEEECCCTTTSS
T ss_pred CeEeEeecccCCe-----EEEEEEEcCCC-cEEEEEeCC-cchHHHHHHHHHHHHHcC-------CCEEEeCCCchhhH
Confidence 4788999888654 35666777766 566665544 566666555554433322 34699999987754
No 43
>1c6v_A Protein (SIV integrase); DNA integration, DNA binding protein; 3.00A {Simian immunodeficiency virus} SCOP: c.55.3.2
Probab=30.93 E-value=1.1e+02 Score=26.97 Aligned_cols=66 Identities=18% Similarity=0.171 Sum_probs=39.9
Q ss_pred CCceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccc
Q 004471 369 RPLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 369 ~~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
..++.+|.|+. ++. +.++.+|..-+ +.+++.+- +.+.+.+.-++.. .+. ..+|.+|.||+.....+
T Consensus 9 ~~~w~~D~~~~----~g~-~~l~~iD~~Sr-~~~~~~~~-~~~~~~~~~~~~~---~~~----~~~~~~i~sDnG~~f~s 74 (164)
T 1c6v_A 9 LGTWQMDCTHL----EGK-IVIVAVHVASG-FIEAEVIP-QETGRQTALFLLK---LAG----RWPITHLHTDNGANFAS 74 (164)
T ss_dssp TTEEEEEEEEE----TTE-EEEEEECTTSC-CEEEEECS-SCSHHHHHHHHHH---HHT----TSCCCEEECCCCSSTTS
T ss_pred CCEEEEeeccc----CCE-EEEEEEEccCC-EEEEEEcC-CCchHHHHHHHHH---HHH----hcCCCEEEeCCchhhhh
Confidence 35789999988 233 34444887666 44566544 4555555444433 333 12468999999887654
No 44
>2x78_A Integrase; viral protein, DNA-directed DNA polyme nucleotidyltransferase, DNA integration, aspartyl protease, recombination, transferase; 2.00A {Human spumaretrovirus} PDB: 2x6n_A 2x6s_A 2x74_A 3dlr_A
Probab=29.83 E-value=84 Score=29.14 Aligned_cols=69 Identities=16% Similarity=0.076 Sum_probs=43.8
Q ss_pred Cceeeee-eeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccc
Q 004471 370 PLLGLDR-TFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 370 ~Vv~iD~-T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
.++.+|- ++.... +|..++++.+|..-+. .+++.+ ...+.+...-+| ..++. ...|.+|.||+.....+
T Consensus 14 ~~~~~D~~~~~~~~-~g~~y~~~~iD~~Sr~-~~~~~~-~~~~~~~~~~~l---~~~~~----~g~p~~i~sDnG~~f~s 83 (200)
T 2x78_A 14 DKFFIDYIGPLPPS-QGYLYVLVVVDGMTGF-TWLYPT-KAPSTSATVKSL---NVLTS----IAIPRVIHSDQGAAFTS 83 (200)
T ss_dssp SEEEEEEECCCSCB-TTBCEEEEEEETTTCC-EEEEEE-SSSCHHHHHHHH---HHHTT----TCCCSEEEECSCHHHHS
T ss_pred cEEEEEEeCCCccC-CCCeEEEEEEeCCCCc-EEEEEC-CCCCHHHHHHHH---HHHHH----hCCCcEEEecCCcceeh
Confidence 5788887 555443 5567778888877664 456665 566655544444 33333 13578999999876543
No 45
>1ex4_A Integrase; SH3-like domain, nonspecific DNA binding beta sheet, CIS-Pro viral protein; HET: CPS; 2.80A {Human immunodeficiency virus 1} SCOP: b.34.7.1 c.55.3.2 PDB: 1qmc_A 1ihv_A 1ihw_A
Probab=22.82 E-value=1e+02 Score=29.67 Aligned_cols=65 Identities=22% Similarity=0.226 Sum_probs=38.3
Q ss_pred CceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccc
Q 004471 370 PLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 370 ~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
.++.+|.|+..++| .++.+|..-+ +.+|+.+- .++.....-++..+... .++.+|.||+.....+
T Consensus 10 ~~w~~D~t~~~g~~-----~l~~vD~~Sr-~i~~~~~~-~~~~~~~~~~~~~~~~~-------~~~~~i~sDnG~eF~s 74 (239)
T 1ex4_A 10 GIWQLDCTHLEGKV-----ILVAVHVASG-YIEAEVIP-AETGQETAYFLLKLAGR-------WPVKTIHTDNGSNFTG 74 (239)
T ss_dssp GEEEEEEEEETTEE-----EEEEECTTTC-CEEEECCS-SSSTTHHHHHHHHHHHH-------SCCCEEEECCCHHHHC
T ss_pred CEEEEeccccCCeE-----EEEEEECCCC-eEEEEEeC-CCCHHHHHHHHHHHHHh-------cCCcEEEecCcHHHHH
Confidence 47899999984332 3334466554 45677555 44544444443333332 2358999999887643
No 46
>1fme_A FSD-EY peptide; beta-BETA-alpha, zinc finger, designed protein, de novo protein; NMR {Synthetic} SCOP: k.12.1.1 PDB: 1fsd_A 1fsv_A 2k6r_A* 1psv_A
Probab=22.45 E-value=58 Score=19.54 Aligned_cols=20 Identities=20% Similarity=0.233 Sum_probs=17.0
Q ss_pred cccCCeeCCHHHHHHHHHHH
Q 004471 177 LAVGQEFPDVKSCRRALRDT 196 (751)
Q Consensus 177 ~~vG~~F~s~ee~~~a~~~y 196 (751)
-+.|.+|.+..+++.++..|
T Consensus 6 kykgrtfrnekelrdfiekf 25 (28)
T 1fme_A 6 KYKGRTFRNEKELRDFIEKF 25 (28)
T ss_dssp ESSSCEECCHHHHHHHHHHC
T ss_pred hhcccccccHHHHHHHHHHh
Confidence 35789999999999999764
No 47
>2l0z_A Glycoprotein G2; zinc-binding domain, virus envelope glycoprotein, GPC, junin arenavirus, viral protein; NMR {Junin virus}
Probab=22.12 E-value=32 Score=23.57 Aligned_cols=15 Identities=20% Similarity=0.401 Sum_probs=12.9
Q ss_pred CccccCCcccccCCc
Q 004471 626 NRCCLCRGWQLYGLP 640 (751)
Q Consensus 626 ~~~CsC~~~~~~GiP 640 (751)
...|+|++|...|.|
T Consensus 21 ~~~C~CG~y~~~~kp 35 (42)
T 2l0z_A 21 LGGCRCGKYPNLKKP 35 (42)
T ss_dssp TSSBTTTTBCCCCCC
T ss_pred CceeccccccCCCCc
Confidence 468999999999876
Done!