Query 007308
Match_columns 608
No_of_seqs 255 out of 1737
Neff 9.4
Searched_HMMs 29240
Date Mon Mar 25 22:30:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007308.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/007308hhsearch_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 95.0 0.01 3.6E-07 35.6 1.8 21 587-607 4-24 (29)
2 2ayd_A WRKY transcription fact 94.8 0.063 2.2E-06 40.1 5.9 41 77-117 34-74 (76)
3 1wj2_A Probable WRKY transcrip 93.8 0.12 4.2E-06 38.7 5.6 41 77-117 37-77 (78)
4 1a6b_B Momulv, zinc finger pro 93.6 0.033 1.1E-06 36.0 2.1 19 589-607 10-28 (40)
5 1dsq_A Nucleic acid binding pr 93.5 0.034 1.2E-06 32.3 1.7 18 590-607 3-20 (26)
6 1u6p_A GAG polyprotein; MLV, A 92.3 0.073 2.5E-06 37.3 2.3 20 588-607 22-41 (56)
7 2ec7_A GAG polyprotein (PR55GA 90.3 0.14 4.8E-06 34.9 2.2 19 589-607 27-45 (49)
8 2a51_A Nucleocapsid protein; s 88.7 0.18 6.1E-06 32.5 1.7 18 590-607 22-39 (39)
9 3hot_A Transposable element ma 88.3 6.5 0.00022 38.9 13.9 58 246-306 186-254 (345)
10 2bl6_A Nucleocapsid protein P1 86.7 0.29 9.9E-06 31.0 1.7 15 592-606 22-36 (37)
11 2ysa_A Retinoblastoma-binding 86.7 0.27 9.4E-06 34.2 1.7 20 588-607 6-25 (55)
12 2a51_A Nucleocapsid protein; s 85.9 0.34 1.2E-05 31.1 1.7 17 591-607 2-18 (39)
13 2bl6_A Nucleocapsid protein P1 84.4 0.42 1.4E-05 30.3 1.6 17 591-607 2-18 (37)
14 2rpr_A Flywch-type zinc finger 84.4 1.3 4.3E-05 34.3 4.8 46 65-117 26-74 (87)
15 1a1t_A Nucleocapsid protein; s 83.1 0.45 1.5E-05 33.2 1.5 20 588-607 32-51 (55)
16 2ec7_A GAG polyprotein (PR55GA 80.8 0.63 2.2E-05 31.6 1.5 21 587-607 4-24 (49)
17 1a1t_A Nucleocapsid protein; s 79.8 0.69 2.3E-05 32.3 1.5 21 587-607 10-30 (55)
18 1c0m_A Protein (integrase); HI 79.6 7.4 0.00025 36.2 9.2 69 233-306 10-78 (238)
19 1cxq_A Avian sarcoma virus int 78.4 8.7 0.0003 33.1 8.7 69 233-306 11-79 (162)
20 2li8_A Protein LIN-28 homolog 78.0 1.3 4.6E-05 33.0 2.7 19 589-607 46-64 (74)
21 2cqf_A RNA-binding protein LIN 75.9 1.2 4.2E-05 32.0 1.9 17 590-606 30-46 (63)
22 2ihx_A Nucleocapsid (NC) prote 75.7 1 3.4E-05 32.2 1.4 18 590-607 31-48 (61)
23 1cl4_A Protein (GAG polyprotei 74.4 1.4 4.9E-05 31.2 1.9 20 588-607 29-48 (60)
24 2ihx_A Nucleocapsid (NC) prote 74.2 1.2 4.2E-05 31.8 1.5 19 589-607 4-22 (61)
25 3kks_A Integrase, IN; beta-str 70.4 9.2 0.00032 32.2 6.7 64 234-307 3-66 (152)
26 2cqf_A RNA-binding protein LIN 69.8 1.7 5.8E-05 31.3 1.4 20 588-607 6-25 (63)
27 3f9k_A Integrase; protein-prot 69.6 22 0.00075 32.0 9.5 64 233-306 59-122 (210)
28 1ex4_A Integrase; SH3-like dom 68.6 14 0.00049 34.2 8.1 64 233-306 9-72 (239)
29 2ezd_A High mobility group pro 66.4 4.8 0.00016 22.5 2.4 14 566-579 2-15 (26)
30 3alr_A Nanos protein; zinc-fin 66.3 2.1 7.2E-05 33.5 1.3 20 588-607 70-92 (106)
31 3ts2_A Protein LIN-28 homolog 66.1 2.7 9.3E-05 36.1 2.2 19 589-607 119-137 (148)
32 2li8_A Protein LIN-28 homolog 66.1 2.5 8.6E-05 31.4 1.7 20 588-607 23-42 (74)
33 1cl4_A Protein (GAG polyprotei 62.0 1.6 5.6E-05 30.9 0.0 18 590-607 2-19 (60)
34 1k6y_A Integrase; HIV-1, domai 57.8 57 0.0019 29.1 9.9 64 233-306 58-121 (212)
35 3ts2_A Protein LIN-28 homolog 56.1 4.6 0.00016 34.7 1.8 19 589-607 97-115 (148)
36 3l3u_A POL polyprotein; DNA in 56.0 24 0.00083 30.0 6.7 65 233-307 9-73 (163)
37 3nyb_B Protein AIR2; polya RNA 50.4 6.1 0.00021 30.1 1.5 19 589-607 46-64 (83)
38 3hph_A Integrase, IN; protein- 50.0 30 0.001 31.2 6.7 64 234-307 61-124 (219)
39 2lli_A Protein AIR2; RNA surve 44.7 9.4 0.00032 31.5 1.9 18 590-607 65-82 (124)
40 2lli_A Protein AIR2; RNA surve 44.4 24 0.00082 29.0 4.4 20 588-607 104-123 (124)
41 2qh9_A UPF0215 protein AF_1433 39.9 1E+02 0.0036 27.1 8.1 67 234-304 8-74 (184)
42 1bco_A MUA domain II, bacterio 39.6 47 0.0016 32.4 6.5 72 233-307 16-95 (327)
43 3av9_A Integrase, IN; protein- 39.5 38 0.0013 29.6 5.3 66 232-307 28-93 (183)
44 2zjr_Z 50S ribosomal protein L 38.6 10 0.00034 26.8 1.0 42 566-607 7-48 (60)
45 2nrr_A Uvrabc system protein C 37.6 47 0.0016 28.5 5.2 62 234-314 37-99 (159)
46 1fme_A FSD-EY peptide; beta-BE 36.1 23 0.00079 19.5 1.9 18 44-61 8-25 (28)
47 2bw3_A Transposase; DNA recomb 36.0 1E+02 0.0034 32.2 8.9 67 263-333 131-201 (534)
48 2l0z_A Glycoprotein G2; zinc-b 35.8 12 0.00041 23.7 0.9 15 492-506 21-35 (42)
49 2lju_A Putative oxidoreductase 35.6 45 0.0015 26.6 4.4 28 42-73 60-87 (108)
50 2nrt_A Uvrabc system protein C 34.9 73 0.0025 29.0 6.3 62 234-314 42-104 (220)
51 2x78_A Integrase; viral protei 34.2 77 0.0026 27.8 6.6 69 233-307 13-82 (200)
52 3f2k_A Histone-lysine N-methyl 33.5 82 0.0028 28.7 6.8 123 243-369 65-210 (226)
53 2jya_A AGR_C_3324P, uncharacte 32.3 40 0.0014 26.8 3.6 29 42-74 52-80 (106)
54 1c6v_A Protein (SIV integrase) 30.4 95 0.0033 25.9 6.4 64 233-306 9-72 (164)
55 2aus_D NOP10, ribosome biogene 27.0 25 0.00086 24.7 1.4 20 588-608 4-23 (60)
56 3v2d_5 50S ribosomal protein L 26.4 8 0.00027 27.3 -1.2 43 566-608 7-49 (60)
57 4fcy_A Transposase; rnaseh, DD 26.3 5.5E+02 0.019 26.4 15.0 73 234-308 188-267 (529)
58 3oym_A PFV integrase, P42IN; p 25.4 1.9E+02 0.0066 28.5 8.5 69 233-306 125-193 (395)
59 2apo_B Ribosome biogenesis pro 24.4 29 0.00099 24.4 1.3 20 588-608 5-24 (60)
60 2ahq_A Sigma-54, RNA polymeras 23.7 1.5E+02 0.0052 21.9 5.2 47 125-172 16-65 (76)
61 2lsn_A Reverse transcriptase; 23.3 2.1E+02 0.007 24.6 7.0 74 232-306 6-88 (165)
62 2p5k_A Arginine repressor; DNA 21.8 1.5E+02 0.005 20.3 4.9 37 134-171 10-46 (64)
63 3c65_A Uvrabc system protein C 21.4 89 0.003 28.6 4.4 63 234-314 34-102 (226)
64 1q1v_A DEK protein; winged-hel 21.1 2.4E+02 0.0082 20.4 7.0 42 123-164 10-54 (70)
65 1pdn_C Protein (PRD paired); p 20.6 1.2E+02 0.004 24.0 4.8 37 132-169 82-123 (128)
66 1mus_A TN5 transposase; hairpi 20.2 4.9E+02 0.017 26.6 10.1 63 246-310 121-197 (477)
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=95.01 E-value=0.01 Score=35.59 Aligned_cols=21 Identities=24% Similarity=0.855 Sum_probs=18.2
Q ss_pred cceeecCCcCCCCcCccCCCC
Q 007308 587 KRSLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 587 kr~~~C~~C~~~gHn~~tC~~ 607 (608)
++...|-+|++.||..+.|+.
T Consensus 4 r~~~~C~nCgk~GH~ar~C~~ 24 (29)
T 1nc8_A 4 RKVIRCWNCGKEGHSARQCRA 24 (29)
T ss_dssp CCCCBCTTTSCBSSCGGGCCS
T ss_pred CCCCEEEECCccccCHhHCcc
Confidence 345789999999999999985
No 2
>2ayd_A WRKY transcription factor 1; beta strands, zinc finger; 1.60A {Arabidopsis thaliana}
Probab=94.80 E-value=0.063 Score=40.08 Aligned_cols=41 Identities=24% Similarity=0.416 Sum_probs=35.9
Q ss_pred eEEEEEEeccCCCeEEEEEEcCCcceEEEEeccCccccccc
Q 007308 77 HRVTVKCKCQGCPWRIYASRLSTTQLVCIKKMNSKHTCEGA 117 (608)
Q Consensus 77 ~r~~~~C~~~gC~~~v~~~~~~~~~~~~V~~~~~~H~c~~~ 117 (608)
-|-.++|+..||+++-.+.+..+.....++.+.++|||..+
T Consensus 34 PRsYYrCt~~gC~a~K~Ver~~~d~~~~~~tY~G~H~H~~p 74 (76)
T 2ayd_A 34 PRSYYRCSSPGCPVKKHVERSSHDTKLLITTYEGKHDHDMP 74 (76)
T ss_dssp CEEEEEECSTTCCCEEEEEECSSSTTEEEEEEESCCSSCCC
T ss_pred ceeEeEcCCCCCCceeeEEEECCCCCEEEEEEccCcCCCCC
Confidence 37779999999999999999877777889999999999864
No 3
>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=93.77 E-value=0.12 Score=38.71 Aligned_cols=41 Identities=24% Similarity=0.364 Sum_probs=35.2
Q ss_pred eEEEEEEeccCCCeEEEEEEcCCcceEEEEeccCccccccc
Q 007308 77 HRVTVKCKCQGCPWRIYASRLSTTQLVCIKKMNSKHTCEGA 117 (608)
Q Consensus 77 ~r~~~~C~~~gC~~~v~~~~~~~~~~~~V~~~~~~H~c~~~ 117 (608)
-|-.++|+..||+++-.+.+..+.....++.+.++|||..+
T Consensus 37 PRsYYrCt~~gC~a~K~Ver~~~d~~~~~~tY~G~H~H~~p 77 (78)
T 1wj2_A 37 PRSYYKCTTPGCGVRKHVERAATDPKAVVTTYEGKHNHDLP 77 (78)
T ss_dssp CEEEEEEECSSCEEEEEEEEETTTTSEEEEEEESCCSSCCC
T ss_pred eeEEeecCcCCCCcEeeEEEEcCCCCEEEEEEeeEcCCCCC
Confidence 36779999999999999999776667788899999999864
No 4
>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=93.63 E-value=0.033 Score=36.03 Aligned_cols=19 Identities=42% Similarity=0.772 Sum_probs=17.5
Q ss_pred eeecCCcCCCCcCccCCCC
Q 007308 589 SLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 589 ~~~C~~C~~~gHn~~tC~~ 607 (608)
...|-.|++.||-.+.||.
T Consensus 10 ~~~C~~Cgk~GH~ardCP~ 28 (40)
T 1a6b_B 10 RDQCAYCKEKGHWAKDCPK 28 (40)
T ss_dssp SSSCSSSCCTTCCTTSCSS
T ss_pred CCeeeECCCCCcchhhCcC
Confidence 4789999999999999996
No 5
>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=93.48 E-value=0.034 Score=32.33 Aligned_cols=18 Identities=39% Similarity=0.853 Sum_probs=16.6
Q ss_pred eecCCcCCCCcCccCCCC
Q 007308 590 LQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 590 ~~C~~C~~~gHn~~tC~~ 607 (608)
..|-+|++.||..+.||.
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 579999999999999985
No 6
>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=92.26 E-value=0.073 Score=37.32 Aligned_cols=20 Identities=40% Similarity=0.728 Sum_probs=17.9
Q ss_pred ceeecCCcCCCCcCccCCCC
Q 007308 588 RSLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 588 r~~~C~~C~~~gHn~~tC~~ 607 (608)
...+|-.||+.||..+.||.
T Consensus 22 ~~~~C~~Cge~GH~ardCp~ 41 (56)
T 1u6p_A 22 DRDQCAYCKEKGHWAKDCPK 41 (56)
T ss_dssp CTTBCSSSCCBSSCGGGCTT
T ss_pred CCCcceeCCCCCcccccCcC
Confidence 34689999999999999996
No 7
>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=90.29 E-value=0.14 Score=34.91 Aligned_cols=19 Identities=32% Similarity=0.683 Sum_probs=14.1
Q ss_pred eeecCCcCCCCcCccCCCC
Q 007308 589 SLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 589 ~~~C~~C~~~gHn~~tC~~ 607 (608)
...|-.|++.||-.+.||.
T Consensus 27 ~~~C~~Cg~~GH~~~~C~~ 45 (49)
T 2ec7_A 27 RQGCWKCGKTGHVMAKCPE 45 (49)
T ss_dssp CCSCSSSCCSSCCGGGCCS
T ss_pred CCeeCcCCCcCCccCCCcC
Confidence 4567778888888888775
No 8
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=88.75 E-value=0.18 Score=32.48 Aligned_cols=18 Identities=22% Similarity=0.503 Sum_probs=16.5
Q ss_pred eecCCcCCCCcCccCCCC
Q 007308 590 LQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 590 ~~C~~C~~~gHn~~tC~~ 607 (608)
..|-+|++.||-.+.||+
T Consensus 22 ~~C~~Cg~~GH~~~~C~~ 39 (39)
T 2a51_A 22 EGCWNCGSKEHRFAQCPK 39 (39)
T ss_dssp SSCTTTCCSSSCTTTSCC
T ss_pred CccccCCCCCCccCcCcC
Confidence 579999999999999985
No 9
>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=88.28 E-value=6.5 Score=38.87 Aligned_cols=58 Identities=10% Similarity=0.214 Sum_probs=39.5
Q ss_pred ccceeEEEEEEecCCCCeEEEEEEEee---cCCcccHHHHHHHHHHhc----CC----CCcEEEEecCcccH
Q 007308 246 KYQGTLLTATSADGDDGIFPVAFAVVD---AETEDNWHWFLQELKSAV----ST----SQQITFIADFQNGL 306 (608)
Q Consensus 246 ~y~~~l~~~~g~d~~~~~~~~a~a~~~---~E~~~~~~w~l~~l~~~~----~~----~~~~~iitD~~~~l 306 (608)
.+++.+++..+.+..| .+++.+++ .-+.+.|..+|+.+...+ +. ..+.+|+.|....-
T Consensus 186 ~~~~~~~v~~~~~~~g---~~~~~~~~~~~~~~~~~y~~~L~~~~~~~~~~~p~~~~~~~~~~~~~Dna~~h 254 (345)
T 3hot_A 186 RFGKKTMLCVWWDQSG---VIYYELLKPGETVNAARYQQQLINLNRALQRKRPEYQKRQHRVIFLHDNAPSH 254 (345)
T ss_dssp TTCCEEEEEEEEESSS---EEEEEEECSSCCCCHHHHHHHHHHHHHHHHHHSTTCC---CCCEEECCCCTTT
T ss_pred CcCCcEEEEEEEcccC---ceeeEecCCCCcccHHHHHHHHHHHHHHHHHhchhhhcCCCceEEEECCCCcc
Confidence 4556777777777777 57777776 567788888887765543 22 34678999997643
No 10
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=86.73 E-value=0.29 Score=31.04 Aligned_cols=15 Identities=53% Similarity=1.116 Sum_probs=7.8
Q ss_pred cCCcCCCCcCccCCC
Q 007308 592 CSKCKGLGHNKKTCK 606 (608)
Q Consensus 592 C~~C~~~gHn~~tC~ 606 (608)
|-+|++.||-.+.||
T Consensus 22 C~~Cg~~GH~a~~C~ 36 (37)
T 2bl6_A 22 CFKCKQPGHFSKQCR 36 (37)
T ss_dssp CSSCCCTTGGGGTTC
T ss_pred EccCCCcCCccCcCc
Confidence 444555555555554
No 11
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=86.68 E-value=0.27 Score=34.23 Aligned_cols=20 Identities=30% Similarity=0.705 Sum_probs=17.6
Q ss_pred ceeecCCcCCCCcCccCCCC
Q 007308 588 RSLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 588 r~~~C~~C~~~gHn~~tC~~ 607 (608)
+.+.|-+|++.||-.+.||.
T Consensus 6 ~~~~C~kCGk~GH~~k~Cp~ 25 (55)
T 2ysa_A 6 SGYTCFRCGKPGHYIKNCPT 25 (55)
T ss_dssp SSCCCTTTCCTTSCGGGCSG
T ss_pred CCCccccCCCcCcccccCCC
Confidence 34789999999999999993
No 12
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=85.87 E-value=0.34 Score=31.14 Aligned_cols=17 Identities=29% Similarity=0.909 Sum_probs=15.8
Q ss_pred ecCCcCCCCcCccCCCC
Q 007308 591 QCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 591 ~C~~C~~~gHn~~tC~~ 607 (608)
+|-+|++.||..+.||.
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 69999999999999985
No 13
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=84.37 E-value=0.42 Score=30.29 Aligned_cols=17 Identities=29% Similarity=0.806 Sum_probs=15.6
Q ss_pred ecCCcCCCCcCccCCCC
Q 007308 591 QCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 591 ~C~~C~~~gHn~~tC~~ 607 (608)
+|-+|++.||..+.||.
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 69999999999999984
No 14
>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=84.36 E-value=1.3 Score=34.30 Aligned_cols=46 Identities=24% Similarity=0.374 Sum_probs=34.0
Q ss_pred cCceEEEEeeCCeEEEEEEec---cCCCeEEEEEEcCCcceEEEEeccCccccccc
Q 007308 65 HGFAYRYKKNDSHRVTVKCKC---QGCPWRIYASRLSTTQLVCIKKMNSKHTCEGA 117 (608)
Q Consensus 65 ~gf~~~~~~s~~~r~~~~C~~---~gC~~~v~~~~~~~~~~~~V~~~~~~H~c~~~ 117 (608)
.||.|...+....+..+.|.. .+|++++.... . . +. ....|||++.
T Consensus 26 ~Gy~Y~~~~~~~~~~yWrC~~~~~~kCrARi~T~~--~--~--~~-~~~~HnH~p~ 74 (87)
T 2rpr_A 26 ESFLYRKEKAAGEKVYWMCRDQARLGCRSRAITQG--H--R--IM-VMRSHCHQPD 74 (87)
T ss_dssp TTEEEEEEEECSSCEEEEEGGGTTSCCCCEEEEET--T--E--EE-ECSCCSSCCC
T ss_pred CCEEEEeeecCCCcEEEEecCCCCCCCCEEEEEcC--C--C--EE-CCCCcCCCCc
Confidence 578888877777778899986 58999988764 2 2 22 4567999765
No 15
>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=83.09 E-value=0.45 Score=33.24 Aligned_cols=20 Identities=40% Similarity=0.816 Sum_probs=14.8
Q ss_pred ceeecCCcCCCCcCccCCCC
Q 007308 588 RSLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 588 r~~~C~~C~~~gHn~~tC~~ 607 (608)
+...|-.|++.||-.+.||.
T Consensus 32 ~~~~C~~Cg~~GH~~~~C~~ 51 (55)
T 1a1t_A 32 RKKGCWKCGKEGHQMKDCTE 51 (55)
T ss_dssp SCCBCTTTCCBSSCGGGCSS
T ss_pred CCCEeCCCCCcCCccCCCcC
Confidence 34678888888888888875
No 16
>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=80.80 E-value=0.63 Score=31.59 Aligned_cols=21 Identities=24% Similarity=0.855 Sum_probs=18.2
Q ss_pred cceeecCCcCCCCcCccCCCC
Q 007308 587 KRSLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 587 kr~~~C~~C~~~gHn~~tC~~ 607 (608)
++...|-+|++.||..+.||.
T Consensus 4 ~r~~~C~~Cg~~GH~a~~C~~ 24 (49)
T 2ec7_A 4 RKVIRCWNCGKEGHSARQCRA 24 (49)
T ss_dssp CCCCBCTTTCCBTCCTTTCCC
T ss_pred CCcCeeeecCCCCcChhhCcC
Confidence 355789999999999999984
No 17
>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=79.79 E-value=0.69 Score=32.28 Aligned_cols=21 Identities=29% Similarity=0.844 Sum_probs=18.1
Q ss_pred cceeecCCcCCCCcCccCCCC
Q 007308 587 KRSLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 587 kr~~~C~~C~~~gHn~~tC~~ 607 (608)
++...|-+|++.||..+.||.
T Consensus 10 ~~~~~C~~Cg~~GH~a~~C~~ 30 (55)
T 1a1t_A 10 RKTVKCFNCGKEGHIAKNCRA 30 (55)
T ss_dssp GGTCBCTTTCCBSSCGGGCSS
T ss_pred CCCcceeeeCCCCcChhhcCC
Confidence 455789999999999999974
No 18
>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=79.57 E-value=7.4 Score=36.21 Aligned_cols=69 Identities=10% Similarity=-0.090 Sum_probs=46.7
Q ss_pred ccEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccH
Q 007308 233 RPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGL 306 (608)
Q Consensus 233 ~~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l 306 (608)
..++.+|.|+.... ++-.+.++.+|...+ +++++.+- +++.+....+|+.+....+ .|.+|.||+....
T Consensus 10 ~~~w~~D~~~~~~~-~g~~yl~~~iD~~Sr-~i~~~~~~-~~~~~~v~~~l~~~~~~~g--~p~~i~sDnG~~f 78 (238)
T 1c0m_A 10 LQIWQTDFTLEPRM-APRSWLAVTVDTASS-AIVVTQHG-RVTSVAVQHHWATAIAVLG--RPKAIKTDNGSCF 78 (238)
T ss_dssp TSEEEEEEEECGGG-CSSCEEEEEEETTTC-CEEEEEES-SCCHHHHHHHHHHHHHHHC--CCSEEEECSCHHH
T ss_pred CCEEEEeecccccc-CCCEEEEEEEECCCC-CEEEEEcc-CCCHHHHHHHHHHHHHHhC--CCcEEEECCCCcc
Confidence 35889999986543 233555666776554 45677765 7777777777776666655 3779999997754
No 19
>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=78.39 E-value=8.7 Score=33.05 Aligned_cols=69 Identities=10% Similarity=-0.087 Sum_probs=44.4
Q ss_pred ccEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccH
Q 007308 233 RPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGL 306 (608)
Q Consensus 233 ~~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l 306 (608)
..++.+|.|+.... ++-.+.++.+|...+. ++++.+- +.+.+.-..+|+.+....+ .|..|.||+....
T Consensus 11 ~~~~~~D~~~~~~~-~g~~yl~~~iD~~Sr~-i~~~~~~-~~~~~~v~~~l~~~~~~~g--~p~~i~sDnG~~f 79 (162)
T 1cxq_A 11 LQIWQTDFTLEPRM-APRSWLAVTVDTASSA-IVVTQHG-RVTSVAAQHHWATAIAVLG--RPKAIKTDNGSCF 79 (162)
T ss_dssp CCEEEEEEEECGGG-TTSCEEEEEEETTTCC-EEEEEES-SCCHHHHHHHHHHHHHHHC--CCSEEECCSCHHH
T ss_pred CCEEEeeeeecccC-CCCEEEEEEEEcCCCe-EEEEECC-CccHHHHHHHHHHHHHHHC--CCeEEEeCCchhh
Confidence 45788998886432 2345556667766554 4667665 5666665556665555554 3679999997754
No 20
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=77.98 E-value=1.3 Score=32.96 Aligned_cols=19 Identities=21% Similarity=0.606 Sum_probs=14.3
Q ss_pred eeecCCcCCCCcCccCCCC
Q 007308 589 SLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 589 ~~~C~~C~~~gHn~~tC~~ 607 (608)
...|-.|++.||-.+.||.
T Consensus 46 ~~~C~~Cg~~GH~ar~Cp~ 64 (74)
T 2li8_A 46 PKKCHFCQSISHMVASCPL 64 (74)
T ss_dssp CCCCTTTCCTTSCGGGCTT
T ss_pred CCccCCcCCcCCccCcCcC
Confidence 4677788888888888874
No 21
>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=75.95 E-value=1.2 Score=32.00 Aligned_cols=17 Identities=24% Similarity=0.747 Sum_probs=9.1
Q ss_pred eecCCcCCCCcCccCCC
Q 007308 590 LQCSKCKGLGHNKKTCK 606 (608)
Q Consensus 590 ~~C~~C~~~gHn~~tC~ 606 (608)
..|-+|++.||-.+.||
T Consensus 30 ~~C~~Cg~~GH~ar~Cp 46 (63)
T 2cqf_A 30 KKCHFCQSISHMVASCP 46 (63)
T ss_dssp SCCTTTCCSSSCTTTCT
T ss_pred CccCCcCCcCCccCcCC
Confidence 34555555555555555
No 22
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=75.72 E-value=1 Score=32.23 Aligned_cols=18 Identities=44% Similarity=1.182 Sum_probs=13.9
Q ss_pred eecCCcCCCCcCccCCCC
Q 007308 590 LQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 590 ~~C~~C~~~gHn~~tC~~ 607 (608)
..|-.|++.||-.+.||.
T Consensus 31 ~~C~~Cg~~GH~ar~C~~ 48 (61)
T 2ihx_A 31 ERCQLCNGMGHNAKQCRK 48 (61)
T ss_dssp SBCTTTCCBSSCGGGCCC
T ss_pred CeeCCCCCCCCCcCCCcC
Confidence 458888888888888875
No 23
>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=74.37 E-value=1.4 Score=31.24 Aligned_cols=20 Identities=30% Similarity=0.552 Sum_probs=17.7
Q ss_pred ceeecCCcCCCCcCccCCCC
Q 007308 588 RSLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 588 r~~~C~~C~~~gHn~~tC~~ 607 (608)
+...|-+|++.||-.+.||.
T Consensus 29 ~~~~C~~Cg~~GH~ar~C~~ 48 (60)
T 1cl4_A 29 VPGLCPRCKRGKHWANECKS 48 (60)
T ss_dssp CCCSCSSCSSCSSCSTTCCC
T ss_pred CCcceeECCCCCCccCcCCC
Confidence 34689999999999999986
No 24
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=74.19 E-value=1.2 Score=31.75 Aligned_cols=19 Identities=26% Similarity=0.627 Sum_probs=16.8
Q ss_pred eeecCCcCCCCcCccCCCC
Q 007308 589 SLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 589 ~~~C~~C~~~gHn~~tC~~ 607 (608)
...|-+|++.||..+.||.
T Consensus 4 ~~~C~~Cg~~GH~a~~C~~ 22 (61)
T 2ihx_A 4 RGLCYTCGSPGHYQAQCPK 22 (61)
T ss_dssp TTBCSSSCCBTCCGGGCTT
T ss_pred CCcccccCCCCeehhhCcC
Confidence 3579999999999999984
No 25
>3kks_A Integrase, IN; beta-strands flanked by alpha-helices, DNA binding protein; 2.20A {Bovine immunodeficiency virus} PDB: 3kkr_A
Probab=70.42 E-value=9.2 Score=32.18 Aligned_cols=64 Identities=16% Similarity=0.164 Sum_probs=44.5
Q ss_pred cEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccHH
Q 007308 234 PLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGLN 307 (608)
Q Consensus 234 ~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l~ 307 (608)
.++.+|.|+..++ ++++.+|...+.. +++.+ .+++.+....+|..+....| |..|.||+.....
T Consensus 3 ~~w~~D~t~~~~~-----y~~~~iD~~sr~~-~~~~~-~~~~~~~~~~~l~~~~~~~g---p~~i~sDnG~~f~ 66 (152)
T 3kks_A 3 HLWQMDNTHWNKT-----IIWVAVETNSGLV-EAQVI-PEETALQVALCILQLIQRYT---VLHLHSDNGPCFT 66 (152)
T ss_dssp CEEEEEEEEETTE-----EEEEEEETTTCCE-EEEEE-SSSCHHHHHHHHHHHHHHSC---CSEEEECSCHHHH
T ss_pred cEEEEeeeeeCCE-----EEEEEEEcCCCcE-EEEEe-CCcCHHHHHHHHHHHHHHhC---CcEEecCCchHhh
Confidence 5788999988433 4556677666544 56555 46777777777766666655 8999999987654
No 26
>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=69.84 E-value=1.7 Score=31.26 Aligned_cols=20 Identities=40% Similarity=0.830 Sum_probs=17.3
Q ss_pred ceeecCCcCCCCcCccCCCC
Q 007308 588 RSLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 588 r~~~C~~C~~~gHn~~tC~~ 607 (608)
+...|-+|++.||..+.||.
T Consensus 6 r~~~C~~Cg~~GH~a~~C~~ 25 (63)
T 2cqf_A 6 SGDRCYNCGGLDHHAKECKL 25 (63)
T ss_dssp SCCCCSSSCCSSSCTTTCCS
T ss_pred CCCcccccCCCCcChhhCCC
Confidence 34679999999999999983
No 27
>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=69.61 E-value=22 Score=32.02 Aligned_cols=64 Identities=20% Similarity=0.144 Sum_probs=41.2
Q ss_pred ccEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccH
Q 007308 233 RPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGL 306 (608)
Q Consensus 233 ~~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l 306 (608)
..++.+|-|+..++| +++.+|..-+ +++++.+- +++.+....+|..+....| +..|.||+....
T Consensus 59 ~~~w~~D~~~~~~~y-----~l~~vD~~sr-~~~~~~~~-~~~~~~~~~~l~~~~~~~g---~~~i~sDnG~~F 122 (210)
T 3f9k_A 59 LGTWQMDCTHLEGKI-----IIVAVHVASG-FIEAEVIP-QESGRQTALFLLKLASRWP---ITHLHTDNGANF 122 (210)
T ss_dssp TTEEEEEEEEETTEE-----EEEEEETTTT-EEEEEEES-SCCHHHHHHHHHHHHTTSC---CSEEEECCCTTT
T ss_pred CCeEeEeecccCCeE-----EEEEEEcCCC-cEEEEEeC-CcchHHHHHHHHHHHHHcC---CCEEEeCCCchh
Confidence 347889988885543 5566676665 55666554 4666666666665555544 345999998754
No 28
>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=68.59 E-value=14 Score=34.19 Aligned_cols=64 Identities=25% Similarity=0.258 Sum_probs=37.0
Q ss_pred ccEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccH
Q 007308 233 RPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGL 306 (608)
Q Consensus 233 ~~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l 306 (608)
..++.+|.|+..++| +++ .+|..-+ +++++.+- .++......++..+.... .+..|.||+....
T Consensus 9 ~~~w~~D~t~~~g~~---~l~--~vD~~Sr-~i~~~~~~-~~~~~~~~~~~~~~~~~~---~~~~i~sDnG~eF 72 (239)
T 1ex4_A 9 PGIWQLDCTHLEGKV---ILV--AVHVASG-YIEAEVIP-AETGQETAYFLLKLAGRW---PVKTIHTDNGSNF 72 (239)
T ss_dssp GGEEEEEEEEETTEE---EEE--EECTTTC-CEEEECCS-SSSTTHHHHHHHHHHHHS---CCCEEEECCCHHH
T ss_pred CCEEEEeccccCCeE---EEE--EEECCCC-eEEEEEeC-CCCHHHHHHHHHHHHHhc---CCcEEEecCcHHH
Confidence 348899999983332 333 3355444 45666554 445444444444343333 3589999997754
No 29
>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=66.42 E-value=4.8 Score=22.45 Aligned_cols=14 Identities=50% Similarity=1.001 Sum_probs=9.6
Q ss_pred CCCCCCCCCCCCCC
Q 007308 566 PPTRRPPGRPKMKQ 579 (608)
Q Consensus 566 p~~~r~~GRPk~~r 579 (608)
|.-+|++||||-..
T Consensus 2 ptpKrpRgRpkGSK 15 (26)
T 2ezd_A 2 PTPKRPRGRPKGSK 15 (26)
T ss_dssp CSCCCCSSCCTTCC
T ss_pred CCCcCCCCCcCccc
Confidence 34478899997543
No 30
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=66.35 E-value=2.1 Score=33.47 Aligned_cols=20 Identities=35% Similarity=0.841 Sum_probs=18.0
Q ss_pred ceeecCCcCCCC---cCccCCCC
Q 007308 588 RSLQCSKCKGLG---HNKKTCKD 607 (608)
Q Consensus 588 r~~~C~~C~~~g---Hn~~tC~~ 607 (608)
|.+.|..||..| |+.+-||+
T Consensus 70 R~Y~CpiCGATGd~AHT~kYCP~ 92 (106)
T 3alr_A 70 RQYKCPLCGATGAKAHTKRFCPM 92 (106)
T ss_dssp GGCCCTTTCCCGGGCCCGGGCTT
T ss_pred ccccCCCCCCcCCcccceecCCC
Confidence 569999999988 99999996
No 31
>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=66.15 E-value=2.7 Score=36.11 Aligned_cols=19 Identities=21% Similarity=0.606 Sum_probs=15.0
Q ss_pred eeecCCcCCCCcCccCCCC
Q 007308 589 SLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 589 ~~~C~~C~~~gHn~~tC~~ 607 (608)
..+|-+|++.||-.+.||.
T Consensus 119 ~~~C~~Cg~~GH~~r~Cp~ 137 (148)
T 3ts2_A 119 PKKCHFCQSINHMVASCPL 137 (148)
T ss_dssp CCCCTTTCCSSCCGGGCTT
T ss_pred CCcccccCCcCCEeccCcC
Confidence 4678888888888888885
No 32
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=66.13 E-value=2.5 Score=31.45 Aligned_cols=20 Identities=40% Similarity=0.878 Sum_probs=17.5
Q ss_pred ceeecCCcCCCCcCccCCCC
Q 007308 588 RSLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 588 r~~~C~~C~~~gHn~~tC~~ 607 (608)
+...|-+|++.||..+.||.
T Consensus 23 r~~~C~~Cg~~GH~a~~C~~ 42 (74)
T 2li8_A 23 KGDRCYNCGGLDHHAKECKL 42 (74)
T ss_dssp TTSCCTTTCCSSSCTTTCSS
T ss_pred CCCcccccCCcCcCcccCCC
Confidence 44689999999999999984
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=62.03 E-value=1.6 Score=30.94 Aligned_cols=18 Identities=39% Similarity=0.787 Sum_probs=0.0
Q ss_pred eecCCcCCCCcCccCCCC
Q 007308 590 LQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 590 ~~C~~C~~~gHn~~tC~~ 607 (608)
..|-+|++.||-.+.||.
T Consensus 2 ~~Cf~Cg~~GH~a~~C~~ 19 (60)
T 1cl4_A 2 GSCFKCGKKGHFAKNCHE 19 (60)
T ss_dssp ------------------
T ss_pred CccccCCCCCcCHhhCcC
Confidence 369999999999999985
No 34
>1k6y_A Integrase; HIV-1, domain organization, transferase; 2.40A {Human immunodeficiency virus 1} SCOP: a.4.10.1 c.55.3.2 PDB: 1wjb_A 1wjd_A 1wjf_A 1wja_A 1wjc_A 1wje_A
Probab=57.84 E-value=57 Score=29.14 Aligned_cols=64 Identities=23% Similarity=0.242 Sum_probs=36.0
Q ss_pred ccEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccH
Q 007308 233 RPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGL 306 (608)
Q Consensus 233 ~~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l 306 (608)
..++.+|.|+..++| ++ +.+|..-+ +++++.+-. .+.+....++..+....+ +..|.||+....
T Consensus 58 ~~~w~~D~~~~~~~~---~l--~~vD~~Sr-~~~~~~~~~-~~~~~~~~~~~~~~~~~~---~~~i~sDnG~~f 121 (212)
T 1k6y_A 58 PGIWQLDCTHLEGKV---IL--VAVHVASG-YIEAEVIPA-ETGQETAYFLLKLAGRWP---VKTVHTDNGSNF 121 (212)
T ss_dssp TTEEEEEEEEETTEE---EE--EEEETTTT-EEEEEEESS-CCHHHHHHHHHHHHHHSC---CCEEECCCSTTT
T ss_pred CCeeeEEEecCCCeE---EE--EEEEccCC-cEEEEEecC-cchHHHHHHHHHHHHhcC---CeEEEcCCCccc
Confidence 457888988873322 33 33365444 445565544 444444444444444333 489999998754
No 35
>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=56.14 E-value=4.6 Score=34.65 Aligned_cols=19 Identities=42% Similarity=0.877 Sum_probs=17.4
Q ss_pred eeecCCcCCCCcCccCCCC
Q 007308 589 SLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 589 ~~~C~~C~~~gHn~~tC~~ 607 (608)
..+|-+|++.||-.+.||.
T Consensus 97 ~~~C~~Cg~~GH~a~~C~~ 115 (148)
T 3ts2_A 97 GDRCYNCGGLDHHAKECKL 115 (148)
T ss_dssp SCCCTTTCCSSCCGGGCCS
T ss_pred CCcccEeCCccchhhhCCC
Confidence 4789999999999999986
No 36
>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=55.97 E-value=24 Score=30.05 Aligned_cols=65 Identities=23% Similarity=0.220 Sum_probs=44.6
Q ss_pred ccEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccHH
Q 007308 233 RPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGLN 307 (608)
Q Consensus 233 ~~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l~ 307 (608)
..++.+|.|+..++ ++++.+|...+.. +++.+ .+++.+....+|..+....+ +..|.||+.....
T Consensus 9 ~~~w~~D~t~~~g~-----y~~~~iD~~sr~~-~~~~~-~~~~~~~~~~~l~~~~~~~~---~~~i~sD~G~~f~ 73 (163)
T 3l3u_A 9 PGIWQLDCTHLEGK-----VILVAVHVASGYI-EAEVI-PAETGQETAYFLLKLAGRWP---VKTVHTDNGSNFT 73 (163)
T ss_dssp TTEEEEEEEEETTE-----EEEEEEETTTCCE-EEEEE-SSCCHHHHHHHHHHHHHHSC---CCEEEECCCGGGG
T ss_pred CCEEEEEecccCCc-----EEEEEEecCCCcE-EEEEe-CCCcHHHHHHHHHHHHHHcC---CcEEeecChHhhh
Confidence 45889999998653 4666777766644 56655 45566666666666655554 4789999988654
No 37
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=50.36 E-value=6.1 Score=30.09 Aligned_cols=19 Identities=37% Similarity=0.950 Sum_probs=17.3
Q ss_pred eeecCCcCCCCcCccCCCC
Q 007308 589 SLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 589 ~~~C~~C~~~gHn~~tC~~ 607 (608)
...|-+|++.||-.+-||.
T Consensus 46 ~~~CYnCG~~GH~~rdC~~ 64 (83)
T 3nyb_B 46 TIYCYNCGGKGHFGDDCKE 64 (83)
T ss_dssp CCBCSSSSCBSSCGGGCSS
T ss_pred CCeecccCCCCcCcccCCc
Confidence 3689999999999999985
No 38
>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=50.03 E-value=30 Score=31.25 Aligned_cols=64 Identities=14% Similarity=0.120 Sum_probs=42.7
Q ss_pred cEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccHH
Q 007308 234 PLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGLN 307 (608)
Q Consensus 234 ~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l~ 307 (608)
.++.+|.|+..++ ++++.+|..-+.. .++. +.+++.+....+|..+....| |..|.||+.....
T Consensus 61 ~~w~~D~t~~~~~-----y~~~~iD~~Sr~~-~~~~-~~~~~~~~~~~~l~~~~~~~g---p~~i~sDnG~~F~ 124 (219)
T 3hph_A 61 DHWQVDYTHYEDK-----IILVWVETNSGLI-YAER-VKGETGQEFRVQTMKWYAMFA---PKSLQSDNGPAFV 124 (219)
T ss_dssp CEEEEEEEEETTE-----EEEEEEETTTCCE-EEEE-ESCCCHHHHHHHHHHHHHHHC---CCEEEECCCHHHH
T ss_pred ceEEEEEecCCCE-----EEEEEEeCCCCcE-EEEE-eCCCCHHHHHHHHHHHHHHhC---CcEEEeCCCchhh
Confidence 4778898876443 4566677766654 5555 455566666666666655555 8899999988654
No 39
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=44.73 E-value=9.4 Score=31.49 Aligned_cols=18 Identities=39% Similarity=0.922 Sum_probs=16.6
Q ss_pred eecCCcCCCCcCccCCCC
Q 007308 590 LQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 590 ~~C~~C~~~gHn~~tC~~ 607 (608)
..|-+|++.||..+.||.
T Consensus 65 ~~C~~Cg~~GH~~~~Cp~ 82 (124)
T 2lli_A 65 VQCTLCKSKKHSKERCPS 82 (124)
T ss_dssp CSSSSSCSSCCCTTTCCC
T ss_pred ccCCCCCcCCcchhhCCC
Confidence 679999999999999995
No 40
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=44.40 E-value=24 Score=28.96 Aligned_cols=20 Identities=35% Similarity=0.913 Sum_probs=18.1
Q ss_pred ceeecCCcCCCCcCccCCCC
Q 007308 588 RSLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 588 r~~~C~~C~~~gHn~~tC~~ 607 (608)
....|-+|++.||..+.||+
T Consensus 104 ~~~~Cy~Cg~~GH~a~dCp~ 123 (124)
T 2lli_A 104 HTIYCYNCGGKGHFGDDCKE 123 (124)
T ss_dssp CCCCTTTTSSSCTTTTTSCC
T ss_pred CCCCcCCCCCCCcCcccCcC
Confidence 35789999999999999996
No 41
>2qh9_A UPF0215 protein AF_1433; structural genomics, PSI-2, MCSG, PR structure initiative; 1.80A {Archaeoglobus fulgidus}
Probab=39.91 E-value=1e+02 Score=27.14 Aligned_cols=67 Identities=7% Similarity=-0.019 Sum_probs=48.5
Q ss_pred cEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcc
Q 007308 234 PLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQN 304 (608)
Q Consensus 234 ~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~ 304 (608)
.|+.+|-.|.. +...++.+..+ +....=++|+.+.-...++..-+++.+++.-....+.+||.|+..
T Consensus 8 rv~GiDds~~~---~~~~l~gvv~~-~~~v~g~~~~~~~vdG~dat~~i~~~~~~l~~~p~~~vvllDG~g 74 (184)
T 2qh9_A 8 RFLGIDDSFDD---RKCCVVGCVTC-GGYVEGFLYTEIDIDGLDATDKLISMVRRSKFREQIKCIFLPGIT 74 (184)
T ss_dssp EEEEEEEEECS---SCEEEEEEEEE-TTEEEEEEEEEECTTCSCHHHHHHHHHTTCTTTTTEEEEEESSSE
T ss_pred EEEEEEcccCC---CceEEEEEEEE-CCEEEEEEEEEEEECChhHHHHHHHHHHhcCCCCCCcEEEECCEe
Confidence 48999999972 33444444555 777888999999999999999777776554221226999999975
No 42
>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=39.63 E-value=47 Score=32.37 Aligned_cols=72 Identities=11% Similarity=-0.114 Sum_probs=48.1
Q ss_pred ccEEEeecccccCc----cc--eeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcE--EEEecCcc
Q 007308 233 RPLLFLDTTPLNSK----YQ--GTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQI--TFIADFQN 304 (608)
Q Consensus 233 ~~vi~~D~T~~~~~----y~--~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~--~iitD~~~ 304 (608)
..++.+|+|+.... .+ +...+.+.+|...+ .++|+.+...|+.+.....|.......| .|. .|.+|+..
T Consensus 16 ~~~w~~D~t~~d~~~~~~~g~~~r~~l~~~iD~~SR-~ivg~~~~~~~~~~~v~~aL~~a~~~~G--~P~~~~i~sDnG~ 92 (327)
T 1bco_A 16 MQWINGDGYLHNVFVRWFNGDVIRPKTWFWQDVKTR-KILGWRCDVSENIDSIRLSFMDVVTRYG--IPEDFHITIDNTR 92 (327)
T ss_dssp TTEEEEEEEECSBCEECTTSCEECCEEEEEEETTTC-CEEEEEEESSCCHHHHHHHHHHHHHHHC--EESSCEEECCCTT
T ss_pred CcEEEecCCEEEEEEECCCCccceeEEEEEEECCCC-cEEEEEEECCCCHHHHHHHHHHHHHhcC--CCCCcEEEeeCch
Confidence 45889999876432 12 13455566676554 4589999888877777666666555544 456 99999987
Q ss_pred cHH
Q 007308 305 GLN 307 (608)
Q Consensus 305 ~l~ 307 (608)
...
T Consensus 93 ~f~ 95 (327)
T 1bco_A 93 GAA 95 (327)
T ss_dssp STT
T ss_pred hhc
Confidence 654
No 43
>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=39.47 E-value=38 Score=29.63 Aligned_cols=66 Identities=24% Similarity=0.240 Sum_probs=38.2
Q ss_pred CccEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccHH
Q 007308 232 CRPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGLN 307 (608)
Q Consensus 232 ~~~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l~ 307 (608)
-..++.+|.|+..++| +++ .+|..-+.. +++.+- +++.+....++..+....+ +..|.+|+.....
T Consensus 28 p~~~w~~D~~~~~g~~---~l~--~vD~~Sr~~-~~~~~~-~~~~~~~~~~~~~~~~~~~---~~~i~sDnG~ef~ 93 (183)
T 3av9_A 28 SPGIWQLDCTHLEGKV---ILV--AVHVASGYI-EAEVIP-AETGQETAYFLLKLAGRWP---VKTVHTDNGSNFT 93 (183)
T ss_dssp CTTEEEEEEEEETTEE---EEE--EEETTTTEE-EEEEES-SCCHHHHHHHHHHHHHHSC---CCEEECSSHHHHH
T ss_pred CCCEEEEeccccCCcE---EEE--EEECCCCCE-EEEEeC-CccchHHHHHHHHHHHHcC---CcEEEecCchhcc
Confidence 3458889999874432 333 346555544 676554 4444444444444444433 4899999977653
No 44
>2zjr_Z 50S ribosomal protein L32; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: g.41.8.5 PDB: 1j5a_M* 1jzy_M* 1jzz_M* 1k01_M* 1nkw_Z 1ond_Z* 1sm1_Z* 1yl3_5 2b66_5 2b9n_5 2b9p_5 2zjp_Y* 2zjq_Z 1jzx_M 3cf5_Y* 3dll_Y* 3pio_Z* 3pip_Z* 1nwy_Z* 1nwx_Z* ...
Probab=38.58 E-value=10 Score=26.83 Aligned_cols=42 Identities=17% Similarity=0.469 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCCCCCCccccccceeecCCcCCCCcCccCCCC
Q 007308 566 PPTRRPPGRPKMKQPESAEIIKRSLQCSKCKGLGHNKKTCKD 607 (608)
Q Consensus 566 p~~~r~~GRPk~~r~~~~~~~kr~~~C~~C~~~gHn~~tC~~ 607 (608)
|+.+.++.|..++|..-.-.......|+.||+.----+-||.
T Consensus 7 PKrK~Sksrr~~RRsh~kl~~p~l~~c~~cG~~~~pH~vc~~ 48 (60)
T 2zjr_Z 7 PKKKTSKSKRDMRRSHHALTAPNLTECPQCHGKKLSHHICPN 48 (60)
T ss_dssp CSSCCCTTHHHHHTTTCCCCCCCCEECTTTCCEECTTBCCTT
T ss_pred CCCCCChHHhhhhcccccccCCCceECCCCCCEeCCceEcCC
Confidence 555555665555553322233456889999886322234444
No 45
>2nrr_A Uvrabc system protein C; UVRC, endonuclase, NER, hydrolase; 1.20A {Thermotoga maritima}
Probab=37.62 E-value=47 Score=28.52 Aligned_cols=62 Identities=16% Similarity=0.234 Sum_probs=43.5
Q ss_pred cEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCC-CCcEEEEecCcccHHHHHhh
Q 007308 234 PLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVST-SQQITFIADFQNGLNKSLAE 312 (608)
Q Consensus 234 ~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~-~~~~~iitD~~~~l~~Ai~~ 312 (608)
=|++.|+-..+..|+- |-|-. +..+.|.-+=+.+.+.... .-|-.|+.|+.+|..+|..+
T Consensus 37 mVVf~~g~p~K~~YRr------------------f~I~~-~g~DDya~M~Evl~RR~~r~~~PDLilIDGGkgQl~aA~~ 97 (159)
T 2nrr_A 37 LVVFEDGFPKKGDYRR------------------YKIEQ-DHPDDYESIRTVVKRRYSKHPLPNLLFVDGGIGQVNAAIE 97 (159)
T ss_dssp EEEEETTEECGGGCEE------------------EEC------CHHHHHHHHHHHHHTTSCCCSEEEESSCHHHHHHHHH
T ss_pred EEEEeCCccChhhCce------------------eecCC-CCCCHHHHHHHHHHHHhccCCCCCEEEEeCCHHHHHHHHH
Confidence 3788888888887763 12222 2347788887877777543 45889999999999999888
Q ss_pred hc
Q 007308 313 VF 314 (608)
Q Consensus 313 vf 314 (608)
++
T Consensus 98 vl 99 (159)
T 2nrr_A 98 AL 99 (159)
T ss_dssp HH
T ss_pred HH
Confidence 76
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=36.09 E-value=23 Score=19.53 Aligned_cols=18 Identities=22% Similarity=0.479 Sum_probs=15.8
Q ss_pred ccceeCCHHHHHHHHHHH
Q 007308 44 VDQRFSSFSEFREALHKY 61 (608)
Q Consensus 44 vG~~F~s~~e~~~~~~~y 61 (608)
.|.+|.+..|+++++..|
T Consensus 8 kgrtfrnekelrdfiekf 25 (28)
T 1fme_A 8 KGRTFRNEKELRDFIEKF 25 (28)
T ss_dssp SSCEECCHHHHHHHHHHC
T ss_pred cccccccHHHHHHHHHHh
Confidence 588999999999998764
No 47
>2bw3_A Transposase; DNA recombination, transposition; 2.0A {Musca domestica} SCOP: a.270.1.1 c.55.3.12 PDB: 2bw3_B
Probab=36.02 E-value=1e+02 Score=32.23 Aligned_cols=67 Identities=22% Similarity=0.265 Sum_probs=46.4
Q ss_pred eEEEEEEEeec--CCcccHHHHHHHHHHhcCCCC--cEEEEecCcccHHHHHhhhcCCccccchHHHHHHHHHhh
Q 007308 263 IFPVAFAVVDA--ETEDNWHWFLQELKSAVSTSQ--QITFIADFQNGLNKSLAEVFDNCYHSYCLRHLAEKLNRD 333 (608)
Q Consensus 263 ~~~~a~a~~~~--E~~~~~~w~l~~l~~~~~~~~--~~~iitD~~~~l~~Ai~~vfP~a~~~~C~~Hi~~n~~~~ 333 (608)
..++++.-++. .+.++....+..+.+..+... ...++||....+..|++.. .|..|.-|+...+.+.
T Consensus 131 ~~~L~~~~~~~~~~t~~~i~~~i~~~l~~~~l~~~~~v~~vtDnasn~~~~~~~~----~~i~C~~H~lnLi~~~ 201 (534)
T 2bw3_A 131 DLILGLKSLDFERSTAENIYKKLKAIFSQFNVEDLSSIKFVTDRGANVVKSLANN----IRINCSSHLLSNVLEN 201 (534)
T ss_dssp EEEEEEEEECGGGCSHHHHHHHHHHHHHTTTCCCCTTCEEEECCCHHHHHHTTTS----EEEECHHHHHHHHHHH
T ss_pred EEEEeEeecCCCCCCHHHHHHHHHHHHHHcCCCcccceeEECCCHHHHHHHHhcC----cccccHHHHHHHHHHH
Confidence 34566766663 455665555555555555443 6679999999988888753 5889999998877665
No 48
>2l0z_A Glycoprotein G2; zinc-binding domain, virus envelope glycoprotein, GPC, junin arenavirus, viral protein; NMR {Junin virus}
Probab=35.81 E-value=12 Score=23.72 Aligned_cols=15 Identities=20% Similarity=0.419 Sum_probs=12.9
Q ss_pred ceeeecCCcccCCCC
Q 007308 492 RWDCTCKTWHLTGLP 506 (608)
Q Consensus 492 ~~~CsC~~~~~~giP 506 (608)
...|+|++|...|.|
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 468999999998876
No 49
>2lju_A Putative oxidoreductase; structural genomics, seattle structural GENO center for infectious disease, ssgcid; NMR {Ehrlichia chaffeensis}
Probab=35.60 E-value=45 Score=26.57 Aligned_cols=28 Identities=21% Similarity=0.268 Sum_probs=23.4
Q ss_pred ccccceeCCHHHHHHHHHHHHHhcCceEEEEe
Q 007308 42 TGVDQRFSSFSEFREALHKYSIAHGFAYRYKK 73 (608)
Q Consensus 42 ~~vG~~F~s~~e~~~~~~~ya~~~gf~~~~~~ 73 (608)
-.|...|+|+|++. .||.++|..|.+..
T Consensus 60 ~qv~L~F~skE~Ai----ayAek~G~~y~V~e 87 (108)
T 2lju_A 60 QQVCLSFTTRELAI----AYAVAHKIDYTVLQ 87 (108)
T ss_dssp CCSCEEESSHHHHH----HHHHHTTCEEEEEC
T ss_pred ccceEecCCHHHHH----HHHHHcCCEEEEec
Confidence 46788999988875 58999999999864
No 50
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A
Probab=34.86 E-value=73 Score=29.03 Aligned_cols=62 Identities=16% Similarity=0.234 Sum_probs=46.2
Q ss_pred cEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCC-CCcEEEEecCcccHHHHHhh
Q 007308 234 PLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVST-SQQITFIADFQNGLNKSLAE 312 (608)
Q Consensus 234 ~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~-~~~~~iitD~~~~l~~Ai~~ 312 (608)
=|++.|+-..++.|+- |-|-. +..+.|.-+=+.+.+.... .-|-.|+.|+.+|..+|..+
T Consensus 42 mVvf~~g~p~k~~YRr------------------f~i~~-~g~DDya~m~Evl~RR~~r~~~PDLiliDGGkgQl~~a~~ 102 (220)
T 2nrt_A 42 LVVFEDGFPKKGDYRR------------------YKIEQ-DHPDDYESIRTVVKRRYSKHPLPNLLFVDGGIGQVNAAIE 102 (220)
T ss_dssp EEEEETTEECGGGCEE------------------EEEEC-SSCCHHHHHHHHHHHHHTTSCCCSEEEESSSHHHHHHHHH
T ss_pred EEEEeCCccChhhCce------------------eeCCC-CCCCHHHHHHHHHHHHhccCCCCCEEEEeCCHHHHHHHHH
Confidence 3788888888887763 22322 3457888888888777643 45889999999999999888
Q ss_pred hc
Q 007308 313 VF 314 (608)
Q Consensus 313 vf 314 (608)
++
T Consensus 103 vl 104 (220)
T 2nrt_A 103 AL 104 (220)
T ss_dssp HH
T ss_pred HH
Confidence 76
No 51
>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=34.19 E-value=77 Score=27.83 Aligned_cols=69 Identities=22% Similarity=0.226 Sum_probs=43.0
Q ss_pred ccEEEeec-ccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccHH
Q 007308 233 RPLLFLDT-TPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGLN 307 (608)
Q Consensus 233 ~~vi~~D~-T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l~ 307 (608)
..++.+|- ++.... +|..++++.+|..-+. ++++.+ .+.+.+....+|+.+ +....|..|.||+.....
T Consensus 13 ~~~~~~D~~~~~~~~-~g~~y~~~~iD~~Sr~-~~~~~~-~~~~~~~~~~~l~~~---~~~g~p~~i~sDnG~~f~ 82 (200)
T 2x78_A 13 FDKFFIDYIGPLPPS-QGYLYVLVVVDGMTGF-TWLYPT-KAPSTSATVKSLNVL---TSIAIPRVIHSDQGAAFT 82 (200)
T ss_dssp TSEEEEEEECCCSCB-TTBCEEEEEEETTTCC-EEEEEE-SSSCHHHHHHHHHHH---TTTCCCSEEEECSCHHHH
T ss_pred ccEEEEEEeCCCccC-CCCeEEEEEEeCCCCc-EEEEEC-CCCCHHHHHHHHHHH---HHhCCCcEEEecCCccee
Confidence 35788887 555433 4556677777766554 456665 555555554444433 333468899999987654
No 52
>3f2k_A Histone-lysine N-methyltransferase setmar; histone-lysine N-methyltransferase setmar, SET domain and mariner transposase fusion; 1.85A {Homo sapiens} PDB: 3k9k_A 3k9j_A
Probab=33.55 E-value=82 Score=28.67 Aligned_cols=123 Identities=10% Similarity=0.082 Sum_probs=64.3
Q ss_pred ccCccceeEEEEEEecCCCCeEEEEEEEee---cCCcccHHHHHHHHHHhc-------CCCCcEEEEecCcccHH-----
Q 007308 243 LNSKYQGTLLTATSADGDDGIFPVAFAVVD---AETEDNWHWFLQELKSAV-------STSQQITFIADFQNGLN----- 307 (608)
Q Consensus 243 ~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~---~E~~~~~~w~l~~l~~~~-------~~~~~~~iitD~~~~l~----- 307 (608)
.++++++.+++.++.+.+|.+ ++.+++ .-+.+.|..+|+.+...+ ......+++.|..+.-.
T Consensus 65 ~~~~~~~~vmv~~~~s~~G~~---~~~~l~~~~tinse~Y~~~l~~l~~~l~~~~~~~~~~~~~i~~~Dna~~H~~~~~~ 141 (226)
T 3f2k_A 65 KPILHPKKVMVTIWWSAAGLI---HYSFLNPGETITSEKYAQEIDEMNQKLQRLQLALVNRKGPILLHDNARPHVAQPTL 141 (226)
T ss_dssp ----CCCEEEEEEEEETTEEE---EEEECCTTCCCSHHHHHHHHHHHHHHHHHHTC----CCCCEEECCCCHHHHSTTHH
T ss_pred ccccCCcceEEEEEeecCCcE---EEEEecCCcccCHHHHHHHHHHHHHHHhhhhhHhhccCCcEEEeCCCccchhhhHH
Confidence 355677788888999888864 455664 566788888887764332 12346788899876432
Q ss_pred HHHhhh----c---CCccccchHH-HHHHHHHhhhcccccHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Q 007308 308 KSLAEV----F---DNCYHSYCLR-HLAEKLNRDIKGQFSHEARRFMINDLYAAAYAPKFEGFQCSIESI 369 (608)
Q Consensus 308 ~Ai~~v----f---P~a~~~~C~~-Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~f~~~~~~l 369 (608)
..+.+. + |.+.-+.-+- |+.+.++..+.+..- ...+++.+.+.....+.+.+.+....+.|
T Consensus 142 ~~l~~~~~~~~~~P~ySPdlnpie~~~w~~lk~~l~~~~~-~~~~~l~~~i~~~~~~~~~~~~~~~i~~~ 210 (226)
T 3f2k_A 142 QKLNELGYEVLPHPPYSPDLLPTNYHVFKHLNNFLQGKRF-HNQQDAENAFQEFVESQSTDFYATGINQL 210 (226)
T ss_dssp HHHHHHTCEECCCCTTCGGGCHHHHTHHHHHHHHHTTCBC-SSHHHHHHHHHHHHHTSCTTHHHHHHHHH
T ss_pred HHHHhhcceeecCCCCCCCcchHHHHHHHHHHHHHHhcCC-ccHHHHHHHHHhHHhhcCcHHHHHHHHHH
Confidence 223221 1 2343333333 555555554443211 11223444444444455555555555444
No 53
>2jya_A AGR_C_3324P, uncharacterized protein ATU1810; protein with unknown function ATU1810, ontario centre for ST proteomics, OCSP; NMR {Agrobacterium tumefaciens str}
Probab=32.25 E-value=40 Score=26.79 Aligned_cols=29 Identities=21% Similarity=0.320 Sum_probs=23.8
Q ss_pred ccccceeCCHHHHHHHHHHHHHhcCceEEEEee
Q 007308 42 TGVDQRFSSFSEFREALHKYSIAHGFAYRYKKN 74 (608)
Q Consensus 42 ~~vG~~F~s~~e~~~~~~~ya~~~gf~~~~~~s 74 (608)
-.|...|+|+|++. .||.++|..|.+..-
T Consensus 52 ~qv~L~F~skE~Ai----ayAek~G~~y~V~ep 80 (106)
T 2jya_A 52 QQVKLTFETQEQAE----AYAQRKGIEYRVILP 80 (106)
T ss_dssp EEEEEEESSHHHHH----HHHHHHTCEEEECCC
T ss_pred ccceEecCCHHHHH----HHHHHcCCEEEEeCC
Confidence 46788999988875 589999999998653
No 54
>1c6v_A Protein (SIV integrase); DNA integration, DNA binding protein; 3.00A {Simian immunodeficiency virus} SCOP: c.55.3.2
Probab=30.42 E-value=95 Score=25.87 Aligned_cols=64 Identities=19% Similarity=0.148 Sum_probs=38.4
Q ss_pred ccEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccH
Q 007308 233 RPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGL 306 (608)
Q Consensus 233 ~~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l 306 (608)
..++.+|.|+..+ . +.++.+|..-+ +++++.+ .+.+.+....++..+.... +|.+|.+|+....
T Consensus 9 ~~~w~~D~~~~~g----~-~~l~~iD~~Sr-~~~~~~~-~~~~~~~~~~~~~~~~~~~---~~~~i~sDnG~~f 72 (164)
T 1c6v_A 9 LGTWQMDCTHLEG----K-IVIVAVHVASG-FIEAEVI-PQETGRQTALFLLKLAGRW---PITHLHTDNGANF 72 (164)
T ss_dssp TTEEEEEEEEETT----E-EEEEEECTTSC-CEEEEEC-SSCSHHHHHHHHHHHHTTS---CCCEEECCCCSST
T ss_pred CCEEEEeecccCC----E-EEEEEEEccCC-EEEEEEc-CCCchHHHHHHHHHHHHhc---CCCEEEeCCchhh
Confidence 3578899988832 2 23333776555 4456644 4555555555544444333 3789999998765
No 55
>2aus_D NOP10, ribosome biogenesis protein NOP10; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_B 3lwo_B* 3lwq_B* 3lwp_B 3lwv_B 3hax_C* 2hvy_C* 3hay_C* 2ey4_E 3hjw_B* 2rfk_B* 3hjy_B 3mqk_B
Probab=27.04 E-value=25 Score=24.71 Aligned_cols=20 Identities=35% Similarity=0.645 Sum_probs=14.3
Q ss_pred ceeecCCcCCCCcCccCCCCC
Q 007308 588 RSLQCSKCKGLGHNKKTCKDS 608 (608)
Q Consensus 588 r~~~C~~C~~~gHn~~tC~~~ 608 (608)
+.++|+.||...= +..||.|
T Consensus 4 ~mr~C~~Cg~YTL-k~~CP~C 23 (60)
T 2aus_D 4 RIRKCPKCGRYTL-KETCPVC 23 (60)
T ss_dssp CCEECTTTCCEES-SSBCTTT
T ss_pred cceECCCCCCEEc-cccCcCC
Confidence 5688999987655 6667753
No 56
>3v2d_5 50S ribosomal protein L32; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_4 2hgj_4 2hgu_4 2j03_5 2jl6_5 2jl8_5 2v47_5 2v49_5 2wdi_5 2wdj_5 2wdl_5 2wdn_5 2wh2_5 2wh4_5 2wrj_5 2wrl_5 2wro_5 2wrr_5 2x9s_5 2x9u_5 ...
Probab=26.41 E-value=8 Score=27.33 Aligned_cols=43 Identities=16% Similarity=0.434 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCCCCCCccccccceeecCCcCCCCcCccCCCCC
Q 007308 566 PPTRRPPGRPKMKQPESAEIIKRSLQCSKCKGLGHNKKTCKDS 608 (608)
Q Consensus 566 p~~~r~~GRPk~~r~~~~~~~kr~~~C~~C~~~gHn~~tC~~~ 608 (608)
|+.+.++.|..++|..-.-.......|+.||+.--.=+-||.|
T Consensus 7 PKrK~Sksr~~~RRsh~kl~~p~l~~c~~cGe~~~~H~vc~~C 49 (60)
T 3v2d_5 7 PKKKTSKARRDARRSHHALTPPTLVPCPECKAMKPPHTVCPEC 49 (60)
T ss_dssp CSSCCCHHHHHHHGGGCCCCCCCCEECTTTCCEECTTSCCTTT
T ss_pred CcCcCChhhcchhhccccccCCceeECCCCCCeecceEEcCCC
Confidence 4444444444444322111233468999998852222336653
No 57
>4fcy_A Transposase; rnaseh, DDE transposase, DNA binding protein-DNA complex; HET: DNA; 3.71A {Enterobacteria phage MU} PDB: 2ezk_A 2ezl_A 2ezh_A 2ezi_A
Probab=26.31 E-value=5.5e+02 Score=26.39 Aligned_cols=73 Identities=10% Similarity=-0.032 Sum_probs=37.9
Q ss_pred cEEEeeccccc-------CccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccH
Q 007308 234 PLLFLDTTPLN-------SKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGL 306 (608)
Q Consensus 234 ~vi~~D~T~~~-------~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l 306 (608)
.++.+|+|.+. ++-+-|.+ .+.+|..-+ .++||.+...++.++-.-.|.......|...+..|.+|...+.
T Consensus 188 e~~~~D~t~~dv~~~~~~g~~~Rp~l-~~~iD~~SR-~i~g~~~~~~~~~~~~~~~l~~a~~~~g~p~~~~i~~Dng~~~ 265 (529)
T 4fcy_A 188 QWINGDGYLHNVFVRWFNGDVIRPKT-WFWQDVKTR-KILGWRCDVSENIDSIRLSFMDVVTRYGIPEDFHITIDNTRGA 265 (529)
T ss_dssp TEEEEEEEECCSCEECTTSCEECCEE-EEEEETTTC-CEEEEEEESSCCHHHHHHHHHHHHHHHCEESSEEEECCCC---
T ss_pred CEEEeCeEEecceeECCCCCeeeEEE-EEEEEccCC-cEEEEEecCCCCHHHHHHHHHHHHHHhCCCCeeEEEeeCchhh
Confidence 46777776542 22222333 344554444 3678888877776655554444333334334567889987765
Q ss_pred HH
Q 007308 307 NK 308 (608)
Q Consensus 307 ~~ 308 (608)
..
T Consensus 266 ~s 267 (529)
T 4fcy_A 266 AN 267 (529)
T ss_dssp --
T ss_pred cc
Confidence 43
No 58
>3oym_A PFV integrase, P42IN; protein-DNA complex; HET: DNA; 2.02A {Human spumaretrovirus} PDB: 3oyn_A* 3s3o_A* 4be2_A* 3l2q_A 3l2s_A 3l2r_A* 3l2u_A* 3l2v_A* 3l2w_A* 3l2t_A* 3os1_A* 3os2_A* 3os0_A* 3oya_A* 3oy9_A* 3oyc_A* 3oyd_A* 3oye_A* 3oyb_A* 3oyg_A* ...
Probab=25.38 E-value=1.9e+02 Score=28.49 Aligned_cols=69 Identities=16% Similarity=0.120 Sum_probs=40.1
Q ss_pred ccEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcCCCCcEEEEecCcccH
Q 007308 233 RPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGL 306 (608)
Q Consensus 233 ~~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~iitD~~~~l 306 (608)
-.++.+|-+.....-++..++++.+|..-+. ++++.+-. .+.+....+|..+. .. ..|..|+||+....
T Consensus 125 ~~~~~~D~~~~~~~~~g~~y~l~~vD~~sr~-~~~~~~~~-~~~~~~~~~l~~~~-~~--g~p~~i~sDnG~~f 193 (395)
T 3oym_A 125 FDKFFIDYIGPLPPSQGYLYVLVVVDGMTGF-TWLYPTKA-PSTSATVKSLNVLT-SI--AIPKVIHSDQGAAF 193 (395)
T ss_dssp TSEEEEEEECCCSCBTTBCEEEEEEETTTCC-EEEEEESS-SCHHHHHHHHHHHT-TT--CCCSEEEECSCHHH
T ss_pred ceEEEEEEecccCCCCCccEEEEEEecCCce-EEEEEecC-CcHHHHHHHhhHhh-cc--CCceEEEeCCCCce
Confidence 3578888664322224556677777766654 45665544 44444444443322 22 35789999998754
No 59
>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A
Probab=24.38 E-value=29 Score=24.42 Aligned_cols=20 Identities=30% Similarity=0.602 Sum_probs=13.5
Q ss_pred ceeecCCcCCCCcCccCCCCC
Q 007308 588 RSLQCSKCKGLGHNKKTCKDS 608 (608)
Q Consensus 588 r~~~C~~C~~~gHn~~tC~~~ 608 (608)
+.++|+.|+...= +..||.|
T Consensus 5 ~mr~C~~CgvYTL-k~~CP~C 24 (60)
T 2apo_B 5 RMKKCPKCGLYTL-KEICPKC 24 (60)
T ss_dssp CCEECTTTCCEES-SSBCSSS
T ss_pred hceeCCCCCCEec-cccCcCC
Confidence 4678888877544 5667753
No 60
>2ahq_A Sigma-54, RNA polymerase sigma factor RPON; sigma-54,sigma factors, solution structure, transcription; NMR {Aquifex aeolicus} PDB: 2o8k_A 2o9l_A
Probab=23.66 E-value=1.5e+02 Score=21.86 Aligned_cols=47 Identities=23% Similarity=0.393 Sum_probs=35.8
Q ss_pred cchhhHHHHHHHHhhhC-C--CCCHHHHHHHHHHHhCCcccHHHHHHHHHH
Q 007308 125 ATRGWVGNIIKEKLKAS-P--NYKPKDIADDIKREYGIQLNYSQAWRAKEI 172 (608)
Q Consensus 125 ~s~~~i~~~~~~~l~~~-~--~~~~~~i~~~v~~~~g~~~s~~~~~~~k~~ 172 (608)
.+..-|-..++++|..+ + -++-.+|.+.|+++ |+.++..++-+.|+.
T Consensus 16 ~S~~~Ik~~Ik~lI~~Ed~~kPlSD~~I~~~L~~~-Gi~IaRRTVaKYRe~ 65 (76)
T 2ahq_A 16 LTQGELMKLIKEIVENEDKRKPYSDQEIANILKEK-GFKVARRTVAKYREM 65 (76)
T ss_dssp CCHHHHHHHHHHHGGGCCSSSCCCHHHHHHHHTTT-SSCCCHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHc-CCCccHHHHHHHHHH
Confidence 35556777888888864 3 26788999988776 999999988877764
No 61
>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus}
Probab=23.31 E-value=2.1e+02 Score=24.62 Aligned_cols=74 Identities=8% Similarity=0.026 Sum_probs=41.4
Q ss_pred CccEEEeecccccCccc-----eeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHH----HHhcCCCCcEEEEecC
Q 007308 232 CRPLLFLDTTPLNSKYQ-----GTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQEL----KSAVSTSQQITFIADF 302 (608)
Q Consensus 232 ~~~vi~~D~T~~~~~y~-----~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l----~~~~~~~~~~~iitD~ 302 (608)
+.=||+.||..+-|... +=..++++.++....+.-++........+.. -.+..| ..++....++.|.||-
T Consensus 6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~-Aei~Al~~al~~al~~~~~v~I~TDS 84 (165)
T 2lsn_A 6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQM-AEIAAVEFACKKALKIPGPVLVITDS 84 (165)
T ss_dssp CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHH-HHHHHHHHHHHHHHHSSSCEEEEESC
T ss_pred ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHH-HHHHHHHHHHHHHhcCCCeEEEEeCh
Confidence 34478999998866432 2344455555544444555555544444433 333333 3444444579999998
Q ss_pred cccH
Q 007308 303 QNGL 306 (608)
Q Consensus 303 ~~~l 306 (608)
.-.+
T Consensus 85 ~Yvi 88 (165)
T 2lsn_A 85 FYVA 88 (165)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 6543
No 62
>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*
Probab=21.76 E-value=1.5e+02 Score=20.26 Aligned_cols=37 Identities=16% Similarity=0.262 Sum_probs=28.0
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHHhCCcccHHHHHHHHH
Q 007308 134 IKEKLKASPNYKPKDIADDIKREYGIQLNYSQAWRAKE 171 (608)
Q Consensus 134 ~~~~l~~~~~~~~~~i~~~v~~~~g~~~s~~~~~~~k~ 171 (608)
+...+..+..++..+|.+.+.+ .|..+|..+++|.-.
T Consensus 10 i~~ll~~~~~~t~~el~~~l~~-~~~~vs~~Tv~R~L~ 46 (64)
T 2p5k_A 10 IREIITSNEIETQDELVDMLKQ-DGYKVTQATVSRDIK 46 (64)
T ss_dssp HHHHHHHSCCCSHHHHHHHHHH-TTCCCCHHHHHHHHH
T ss_pred HHHHHHcCCCCCHHHHHHHHHH-hCCCcCHHHHHHHHH
Confidence 3445556677899999999975 477899999988644
No 63
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus}
Probab=21.41 E-value=89 Score=28.62 Aligned_cols=63 Identities=16% Similarity=0.289 Sum_probs=41.8
Q ss_pred cEEEeecccccCccceeEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHHhcC-----C-CCcEEEEecCcccHH
Q 007308 234 PLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVS-----T-SQQITFIADFQNGLN 307 (608)
Q Consensus 234 ~vi~~D~T~~~~~y~~~l~~~~g~d~~~~~~~~a~a~~~~E~~~~~~w~l~~l~~~~~-----~-~~~~~iitD~~~~l~ 307 (608)
=|++.|+-..+..|+- |-|-..+..+.|.-+=+.+.+... . .-|-.|+.|+.+|..
T Consensus 34 mVvf~~g~p~k~~YR~------------------f~i~~~~g~DDya~m~Evl~RR~~r~~~e~~~~PDLiliDGGkgQl 95 (226)
T 3c65_A 34 LVVFLDGKPAKKEYRK------------------YKVKTVAGPNDYETMREVVRRRYTRVLKEGLPLPDLIIIDGGKGHL 95 (226)
T ss_dssp EEEEETTEECGGGCEE------------------EECCCCCTTCHHHHHHHHHHHHHHHHHHHTCCCCSEEEESSCHHHH
T ss_pred EEEEeCCccChhhCce------------------eecCCCCCCcHHHHHHHHHHHHHhhhhcccCCCCCEEEEeCCHHHH
Confidence 3778888888887763 111111234666666665554432 1 358899999999999
Q ss_pred HHHhhhc
Q 007308 308 KSLAEVF 314 (608)
Q Consensus 308 ~Ai~~vf 314 (608)
+|..+++
T Consensus 96 ~~a~~vl 102 (226)
T 3c65_A 96 SAVRDVL 102 (226)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 9998887
No 64
>1q1v_A DEK protein; winged-helix motif, DNA binding protein; NMR {Homo sapiens} SCOP: a.159.4.1
Probab=21.13 E-value=2.4e+02 Score=20.36 Aligned_cols=42 Identities=19% Similarity=0.198 Sum_probs=34.5
Q ss_pred cccchhhHHHHHHHHhhh-C-CCCCHHHHHHHHHHHh-CCcccHH
Q 007308 123 YRATRGWVGNIIKEKLKA-S-PNYKPKDIADDIKREY-GIQLNYS 164 (608)
Q Consensus 123 ~~~s~~~i~~~~~~~l~~-~-~~~~~~~i~~~v~~~~-g~~~s~~ 164 (608)
..++...+...+.++|+. + .+++.++|...+.+.+ |..++-.
T Consensus 10 ~~Psd~ei~~~I~~IL~~aDL~tvT~K~VR~~Le~~~pg~dLs~k 54 (70)
T 1q1v_A 10 KPPTDEELKETIKKLLASANLEEVTMKQICKKVYENYPTYDLTER 54 (70)
T ss_dssp CCCCHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHCSSSCCSHH
T ss_pred CCcCHHHHHHHHHHHHHhCCHHHHhHHHHHHHHHHHccCCCChHH
Confidence 356777788888998885 3 4789999999999999 9999854
No 65
>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5
Probab=20.63 E-value=1.2e+02 Score=24.02 Aligned_cols=37 Identities=30% Similarity=0.363 Sum_probs=29.2
Q ss_pred HHHHHHhhhCCCCCHHHHHHHHHHHhCC-----cccHHHHHHH
Q 007308 132 NIIKEKLKASPNYKPKDIADDIKREYGI-----QLNYSQAWRA 169 (608)
Q Consensus 132 ~~~~~~l~~~~~~~~~~i~~~v~~~~g~-----~~s~~~~~~~ 169 (608)
..+.+.+..+|.+++.+|...+.+. |+ .+|++++++.
T Consensus 82 ~~i~~~~~~~~~~s~~~i~~~l~~~-g~~~~~~~~s~~tv~r~ 123 (128)
T 1pdn_C 82 NRIEEYKRSSPGMFSWEIREKLIRE-GVCDRSTAPSVSAISRL 123 (128)
T ss_dssp HHHHHTTTTCTTCCHHHHHHHHHHT-SSSCSTTCCCHHHHHHH
T ss_pred HHHHHHHHhCcchHHHHHHHHHHHc-CCccccCCcCHHHHHHH
Confidence 3455566678899999999998765 87 6899998875
No 66
>1mus_A TN5 transposase; hairpin, DNA binding, transcription/DNA complex; HET: DNA; 1.90A {Escherichia coli} SCOP: c.55.3.4 PDB: 1mur_A* 4dm0_A* 1mm8_A 1muh_A* 3ecp_A* 1b7e_A*
Probab=20.16 E-value=4.9e+02 Score=26.65 Aligned_cols=63 Identities=8% Similarity=0.070 Sum_probs=40.2
Q ss_pred ccceeEEEEEEecC-CCCeEEEEEEE--ee--------cCCcccHHHH--HHHHHHhcCCCC-cEEEEecCcccHHHHH
Q 007308 246 KYQGTLLTATSADG-DDGIFPVAFAV--VD--------AETEDNWHWF--LQELKSAVSTSQ-QITFIADFQNGLNKSL 310 (608)
Q Consensus 246 ~y~~~l~~~~g~d~-~~~~~~~a~a~--~~--------~E~~~~~~w~--l~~l~~~~~~~~-~~~iitD~~~~l~~Ai 310 (608)
..++.|-..+.+++ .|. |||..- .. -|..|++.|+ ++...+.++... ..+.|.|+...+..-+
T Consensus 121 ~~G~~lHstLavtp~~g~--pLGl~~~~~W~R~~~~~pieeKES~rWle~~~~~~~~~~~~~~rvV~V~DRE~Di~elf 197 (477)
T 1mus_A 121 SRGWWVHSVLLLEATTFR--TVGLLHQEWWMRPDDPADADEKESGKWLAAAATSRLRMGSMMSNVIAVCDREADIHAYL 197 (477)
T ss_dssp CEEEEEEEEEEEETTTCC--EEEEEEEEEECCCSSGGGCSSCGGGHHHHHHHHHHHHHGGGGGGEEEEECGGGCCHHHH
T ss_pred ccceEEEEEEEEcCCCCc--eeeeeeeeEeecccccCCcccchhHHHHHHHHHHHHhcCCCcceEEEEechhhhHHHHH
Confidence 35677777888887 554 555432 21 3567888765 445555555555 7889999998665443
Done!