Query 004429
Match_columns 754
No_of_seqs 318 out of 1394
Neff 8.9
Searched_HMMs 29240
Date Tue Mar 26 00:57:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004429.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/004429hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2ayd_A WRKY transcription fact 95.4 0.049 1.7E-06 42.8 7.1 58 65-148 16-73 (76)
2 1wj2_A Probable WRKY transcrip 94.9 0.038 1.3E-06 43.6 5.3 58 65-148 19-76 (78)
3 1a6b_B Momulv, zinc finger pro 93.5 0.067 2.3E-06 36.5 3.5 23 723-745 11-33 (40)
4 1u6p_A GAG polyprotein; MLV, A 92.8 0.087 3E-06 38.9 3.4 24 722-745 23-46 (56)
5 1nc8_A Nucleocapsid protein; H 92.1 0.068 2.3E-06 33.7 1.9 22 721-742 5-26 (29)
6 1dsq_A Nucleic acid binding pr 92.1 0.078 2.7E-06 32.5 2.1 22 724-745 4-25 (26)
7 2ysa_A Retinoblastoma-binding 87.7 0.24 8.2E-06 36.3 2.0 26 721-746 6-31 (55)
8 2a51_A Nucleocapsid protein; s 83.9 0.63 2.1E-05 31.4 2.4 17 724-740 23-39 (39)
9 3alr_A Nanos protein; zinc-fin 81.9 0.46 1.6E-05 39.0 1.3 26 720-745 69-97 (106)
10 2ec7_A GAG polyprotein (PR55GA 81.1 0.79 2.7E-05 32.8 2.2 19 723-741 28-46 (49)
11 2ec7_A GAG polyprotein (PR55GA 79.9 0.83 2.8E-05 32.6 2.0 21 721-741 5-25 (49)
12 3u5c_N S27A, YS15, 40S ribosom 77.9 3.4 0.00012 36.6 5.6 85 158-242 23-142 (151)
13 2rpr_A Flywch-type zinc finger 77.9 3.6 0.00012 33.3 5.5 25 116-149 50-74 (87)
14 2xzm_O RPS13E; ribosome, trans 76.0 3.8 0.00013 36.4 5.3 85 158-242 25-144 (153)
15 3j20_Q 30S ribosomal protein S 75.8 2.8 9.7E-05 37.6 4.5 85 158-242 23-149 (158)
16 2a51_A Nucleocapsid protein; s 74.8 1.5 5.2E-05 29.5 2.0 18 724-741 2-19 (39)
17 2li8_A Protein LIN-28 homolog 74.2 2.5 8.4E-05 33.1 3.4 20 723-742 47-66 (74)
18 2bl6_A Nucleocapsid protein P1 73.2 1.7 5.9E-05 28.8 1.9 16 725-740 3-18 (37)
19 3kks_A Integrase, IN; beta-str 72.9 9.3 0.00032 33.7 7.7 67 269-345 2-68 (152)
20 1a1t_A Nucleocapsid protein; s 72.8 1.6 5.5E-05 31.9 1.9 19 724-742 35-53 (55)
21 1cl4_A Protein (GAG polyprotei 71.1 2.7 9.2E-05 31.3 2.8 22 723-744 31-52 (60)
22 2bl6_A Nucleocapsid protein P1 70.6 1.4 4.9E-05 29.2 1.1 17 724-740 21-37 (37)
23 1a1t_A Nucleocapsid protein; s 68.5 1.8 6.3E-05 31.6 1.4 22 720-741 10-31 (55)
24 3hot_A Transposable element ma 65.2 33 0.0011 35.2 11.0 57 281-340 185-252 (345)
25 2cqf_A RNA-binding protein LIN 64.4 3.2 0.00011 31.3 2.0 21 723-743 30-50 (63)
26 2cqf_A RNA-binding protein LIN 62.6 4.6 0.00016 30.4 2.6 20 722-741 7-26 (63)
27 1ex4_A Integrase; SH3-like dom 62.5 57 0.0019 31.4 11.5 64 270-343 10-73 (239)
28 2ihx_A Nucleocapsid (NC) prote 61.6 2.8 9.4E-05 31.4 1.2 21 723-743 31-51 (61)
29 3ts2_A Protein LIN-28 homolog 60.8 3.4 0.00012 37.2 1.9 24 723-746 120-143 (148)
30 2ihx_A Nucleocapsid (NC) prote 60.2 3.3 0.00011 31.0 1.4 21 723-743 5-25 (61)
31 2li8_A Protein LIN-28 homolog 56.6 4.6 0.00016 31.6 1.7 22 720-741 22-43 (74)
32 3nyb_B Protein AIR2; polya RNA 56.5 3.2 0.00011 33.2 0.9 19 723-741 6-24 (83)
33 1cxq_A Avian sarcoma virus int 51.8 45 0.0016 29.7 8.2 70 270-344 12-81 (162)
34 3hph_A Integrase, IN; protein- 51.8 31 0.0011 32.7 7.4 66 270-345 61-126 (219)
35 1je8_A Nitrate/nitrite respons 50.1 32 0.0011 27.0 5.9 74 143-230 4-77 (82)
36 3ts2_A Protein LIN-28 homolog 49.6 6.4 0.00022 35.4 1.7 20 722-741 97-116 (148)
37 2ezd_A High mobility group pro 48.3 12 0.00042 22.0 2.1 17 696-712 2-18 (26)
38 1x9b_A Hypothetical membrane p 47.4 20 0.00067 25.0 3.4 45 383-427 7-51 (53)
39 1c0m_A Protein (integrase); HI 45.4 57 0.0019 31.4 8.2 70 270-344 11-80 (238)
40 2hqh_E Restin; beta/BETA struc 39.8 7.4 0.00025 23.3 0.4 20 721-741 3-22 (26)
41 3l3u_A POL polyprotein; DNA in 39.7 47 0.0016 29.5 6.2 65 269-343 9-73 (163)
42 1cl4_A Protein (GAG polyprotei 35.9 7.7 0.00026 28.8 0.0 20 724-743 3-22 (60)
43 1bco_A MUA domain II, bacterio 35.2 64 0.0022 32.9 7.0 71 269-342 16-94 (327)
44 3f2k_A Histone-lysine N-methyl 34.3 2.1E+02 0.0071 27.1 10.2 62 278-342 64-135 (226)
45 2lli_A Protein AIR2; RNA surve 33.4 20 0.00069 30.9 2.3 21 723-743 65-85 (124)
46 3nyb_B Protein AIR2; polya RNA 32.7 20 0.00067 28.6 1.9 23 723-745 47-69 (83)
47 3av9_A Integrase, IN; protein- 31.7 84 0.0029 28.6 6.6 65 270-344 30-94 (183)
48 2x78_A Integrase; viral protei 31.4 1.2E+02 0.004 27.8 7.7 69 270-344 14-83 (200)
49 2l69_A Rossmann 2X3 fold prote 31.0 32 0.0011 27.5 2.8 28 47-74 7-34 (134)
50 2lju_A Putative oxidoreductase 30.6 48 0.0016 27.8 4.0 32 38-73 56-87 (108)
51 1tc3_C Protein (TC3 transposas 29.9 48 0.0016 22.2 3.6 42 161-213 4-45 (51)
52 2lli_A Protein AIR2; RNA surve 27.8 29 0.00098 29.9 2.3 20 722-741 105-124 (124)
53 3ulq_B Transcriptional regulat 23.4 1.2E+02 0.004 24.2 5.2 58 160-229 27-84 (90)
54 1p4w_A RCSB; solution structur 23.2 1.9E+02 0.0063 23.6 6.4 61 160-232 32-92 (99)
55 1c6v_A Protein (SIV integrase) 22.8 1.7E+02 0.0058 25.4 6.8 62 270-341 10-71 (164)
56 1fse_A GERE; helix-turn-helix 22.4 2.2E+02 0.0075 20.9 6.5 60 160-231 9-68 (74)
No 1
>2ayd_A WRKY transcription factor 1; beta strands, zinc finger; 1.60A {Arabidopsis thaliana}
Probab=95.36 E-value=0.049 Score=42.75 Aligned_cols=58 Identities=17% Similarity=0.417 Sum_probs=42.2
Q ss_pred cCCeEEEcceeccCCCCcceEEEEEeecCCCCCCCCCCCccccccCCCcccccccceEEEEEeeeCCCCcEEEEeecCCc
Q 004429 65 CGFSIRRHRTRGKDGVGRGVTRRDFTCHRGGFPQMKPSDDGKMQRNRKSSRCGCQAYMRIVKRVDFDVPEWHVTGFSNVH 144 (754)
Q Consensus 65 ~GF~ir~~~s~~~~~~~k~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~r~gCpa~i~v~~~~~~~~~~w~V~~~~~~H 144 (754)
-||.+|+--.+.-++. ..-+.+|.|+. .||||+=.|.+.. .+....++....+|
T Consensus 16 DGy~WRKYGQK~ikgs--~~PRsYYrCt~----------------------~gC~a~K~Ver~~--~d~~~~~~tY~G~H 69 (76)
T 2ayd_A 16 DGYRWRKYGQKSVKGS--PYPRSYYRCSS----------------------PGCPVKKHVERSS--HDTKLLITTYEGKH 69 (76)
T ss_dssp CSSCEEEEEEECCTTC--SSCEEEEEECS----------------------TTCCCEEEEEECS--SSTTEEEEEEESCC
T ss_pred CCchhhhCcccccCCC--CCceeEeEcCC----------------------CCCCceeeEEEEC--CCCCEEEEEEccCc
Confidence 4788887655443332 23466788852 3799999898864 45788899999999
Q ss_pred cCCC
Q 004429 145 NHEL 148 (754)
Q Consensus 145 NH~l 148 (754)
||++
T Consensus 70 ~H~~ 73 (76)
T 2ayd_A 70 DHDM 73 (76)
T ss_dssp SSCC
T ss_pred CCCC
Confidence 9987
No 2
>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=94.93 E-value=0.038 Score=43.60 Aligned_cols=58 Identities=24% Similarity=0.433 Sum_probs=41.7
Q ss_pred cCCeEEEcceeccCCCCcceEEEEEeecCCCCCCCCCCCccccccCCCcccccccceEEEEEeeeCCCCcEEEEeecCCc
Q 004429 65 CGFSIRRHRTRGKDGVGRGVTRRDFTCHRGGFPQMKPSDDGKMQRNRKSSRCGCQAYMRIVKRVDFDVPEWHVTGFSNVH 144 (754)
Q Consensus 65 ~GF~ir~~~s~~~~~~~k~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~r~gCpa~i~v~~~~~~~~~~w~V~~~~~~H 144 (754)
-||.+|+--.+.-++. ..-+.+|.|+. .||||+=.|.+.. .+....++.+..+|
T Consensus 19 DGy~WRKYGQK~ikgs--~~PRsYYrCt~----------------------~gC~a~K~Ver~~--~d~~~~~~tY~G~H 72 (78)
T 1wj2_A 19 DGYRWRKYGQKVVKGN--PYPRSYYKCTT----------------------PGCGVRKHVERAA--TDPKAVVTTYEGKH 72 (78)
T ss_dssp SSSCBCCCEEECCTTC--SSCEEEEEEEC----------------------SSCEEEEEEEEET--TTTSEEEEEEESCC
T ss_pred CCchhhhCcccccCCC--cCeeEEeecCc----------------------CCCCcEeeEEEEc--CCCCEEEEEEeeEc
Confidence 4777777655443332 23466788954 3799999998864 45778888999999
Q ss_pred cCCC
Q 004429 145 NHEL 148 (754)
Q Consensus 145 NH~l 148 (754)
||++
T Consensus 73 ~H~~ 76 (78)
T 1wj2_A 73 NHDL 76 (78)
T ss_dssp SSCC
T ss_pred CCCC
Confidence 9987
No 3
>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=93.51 E-value=0.067 Score=36.45 Aligned_cols=23 Identities=26% Similarity=0.429 Sum_probs=19.9
Q ss_pred ccCCccCCCCCCCCCCCCcCcCC
Q 004429 723 CSEPCCRHFGHDASSCPIMGSDT 745 (754)
Q Consensus 723 ~~C~~C~~~gHn~~tCp~~~~~~ 745 (754)
..|-+|++.||-++.||....+.
T Consensus 11 ~~C~~Cgk~GH~ardCP~~~~~~ 33 (40)
T 1a6b_B 11 DQCAYCKEKGHWAKDCPKKPRGP 33 (40)
T ss_dssp SSCSSSCCTTCCTTSCSSSCCCT
T ss_pred CeeeECCCCCcchhhCcCCcccC
Confidence 45999999999999999987654
No 4
>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=92.77 E-value=0.087 Score=38.85 Aligned_cols=24 Identities=25% Similarity=0.419 Sum_probs=20.3
Q ss_pred cccCCccCCCCCCCCCCCCcCcCC
Q 004429 722 HCSEPCCRHFGHDASSCPIMGSDT 745 (754)
Q Consensus 722 ~~~C~~C~~~gHn~~tCp~~~~~~ 745 (754)
...|-+|++.||-.+.||....+.
T Consensus 23 ~~~C~~Cge~GH~ardCp~~~~~~ 46 (56)
T 1u6p_A 23 RDQCAYCKEKGHWAKDCPKKPRGP 46 (56)
T ss_dssp TTBCSSSCCBSSCGGGCTTCCCSS
T ss_pred CCcceeCCCCCcccccCcCCcccc
Confidence 345999999999999999987654
No 5
>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=92.13 E-value=0.068 Score=33.67 Aligned_cols=22 Identities=23% Similarity=0.285 Sum_probs=18.4
Q ss_pred ccccCCccCCCCCCCCCCCCcC
Q 004429 721 RHCSEPCCRHFGHDASSCPIMG 742 (754)
Q Consensus 721 r~~~C~~C~~~gHn~~tCp~~~ 742 (754)
+...|-+|++.||-.+.||.-.
T Consensus 5 ~~~~C~nCgk~GH~ar~C~~pr 26 (29)
T 1nc8_A 5 KVIRCWNCGKEGHSARQCRAPR 26 (29)
T ss_dssp CCCBCTTTSCBSSCGGGCCSSS
T ss_pred CCCEEEECCccccCHhHCcccc
Confidence 4456999999999999998653
No 6
>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=92.08 E-value=0.078 Score=32.45 Aligned_cols=22 Identities=18% Similarity=0.196 Sum_probs=16.7
Q ss_pred cCCccCCCCCCCCCCCCcCcCC
Q 004429 724 SEPCCRHFGHDASSCPIMGSDT 745 (754)
Q Consensus 724 ~C~~C~~~gHn~~tCp~~~~~~ 745 (754)
.|-.|++.||..+.||..+..+
T Consensus 4 ~Cf~CG~~GH~ardC~~~~~~~ 25 (26)
T 1dsq_A 4 VCFSCGKTGHIKRDCKEEXXXX 25 (26)
T ss_dssp BCTTTCCBSSCTTTTTCC----
T ss_pred eeEeCCCCCcccccCCCccccc
Confidence 4889999999999999876543
No 7
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=87.75 E-value=0.24 Score=36.34 Aligned_cols=26 Identities=23% Similarity=0.438 Sum_probs=21.0
Q ss_pred ccccCCccCCCCCCCCCCCCcCcCCc
Q 004429 721 RHCSEPCCRHFGHDASSCPIMGSDTL 746 (754)
Q Consensus 721 r~~~C~~C~~~gHn~~tCp~~~~~~~ 746 (754)
+.+.|=+|++.||-++.||.....+.
T Consensus 6 ~~~~C~kCGk~GH~~k~Cp~~~~~~f 31 (55)
T 2ysa_A 6 SGYTCFRCGKPGHYIKNCPTNGDKNF 31 (55)
T ss_dssp SSCCCTTTCCTTSCGGGCSGGGCSSC
T ss_pred CCCccccCCCcCcccccCCCCCCCCc
Confidence 44569999999999999997765544
No 8
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=83.90 E-value=0.63 Score=31.45 Aligned_cols=17 Identities=24% Similarity=0.364 Sum_probs=15.2
Q ss_pred cCCccCCCCCCCCCCCC
Q 004429 724 SEPCCRHFGHDASSCPI 740 (754)
Q Consensus 724 ~C~~C~~~gHn~~tCp~ 740 (754)
.|-+|++.||-.+.||+
T Consensus 23 ~C~~Cg~~GH~~~~C~~ 39 (39)
T 2a51_A 23 GCWNCGSKEHRFAQCPK 39 (39)
T ss_dssp SCTTTCCSSSCTTTSCC
T ss_pred ccccCCCCCCccCcCcC
Confidence 58899999999999985
No 9
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=81.93 E-value=0.46 Score=38.96 Aligned_cols=26 Identities=27% Similarity=0.600 Sum_probs=21.4
Q ss_pred cccccCCccCCCC---CCCCCCCCcCcCC
Q 004429 720 RRHCSEPCCRHFG---HDASSCPIMGSDT 745 (754)
Q Consensus 720 ~r~~~C~~C~~~g---Hn~~tCp~~~~~~ 745 (754)
=|.+.|..|+..| |+++-||+....+
T Consensus 69 LR~Y~CpiCGATGd~AHT~kYCP~~~~~~ 97 (106)
T 3alr_A 69 LRQYKCPLCGATGAKAHTKRFCPMVDKNY 97 (106)
T ss_dssp GGGCCCTTTCCCGGGCCCGGGCTTCGGGG
T ss_pred cccccCCCCCCcCCcccceecCCCCCCcc
Confidence 3568899999888 9999999987543
No 10
>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=81.06 E-value=0.79 Score=32.77 Aligned_cols=19 Identities=26% Similarity=0.370 Sum_probs=10.9
Q ss_pred ccCCccCCCCCCCCCCCCc
Q 004429 723 CSEPCCRHFGHDASSCPIM 741 (754)
Q Consensus 723 ~~C~~C~~~gHn~~tCp~~ 741 (754)
..|-.|++.||-.+.||..
T Consensus 28 ~~C~~Cg~~GH~~~~C~~~ 46 (49)
T 2ec7_A 28 QGCWKCGKTGHVMAKCPER 46 (49)
T ss_dssp CSCSSSCCSSCCGGGCCSS
T ss_pred CeeCcCCCcCCccCCCcCC
Confidence 3455666666666666554
No 11
>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=79.88 E-value=0.83 Score=32.64 Aligned_cols=21 Identities=24% Similarity=0.314 Sum_probs=18.1
Q ss_pred ccccCCccCCCCCCCCCCCCc
Q 004429 721 RHCSEPCCRHFGHDASSCPIM 741 (754)
Q Consensus 721 r~~~C~~C~~~gHn~~tCp~~ 741 (754)
|...|-+|++.||..+.||..
T Consensus 5 r~~~C~~Cg~~GH~a~~C~~~ 25 (49)
T 2ec7_A 5 KVIRCWNCGKEGHSARQCRAP 25 (49)
T ss_dssp CCCBCTTTCCBTCCTTTCCCS
T ss_pred CcCeeeecCCCCcChhhCcCC
Confidence 445699999999999999975
No 12
>3u5c_N S27A, YS15, 40S ribosomal protein S13; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_O 3o30_G 3o2z_G 3u5g_N 3iz6_O 3jyv_O* 1ysh_E 1s1h_O
Probab=77.94 E-value=3.4 Score=36.60 Aligned_cols=85 Identities=21% Similarity=0.316 Sum_probs=55.9
Q ss_pred cccCCCCc-chhhHHHHhhhcCCcHHHHHHHHHHhcCcc----------------CCCCCcchhhhhhhHHHhhhc----
Q 004429 158 PAYCSITP-DDKTRICMFAKAGMSVRQMLRLMELEKGVK----------------LGCLPFTEIDVRNLLQSFRNV---- 216 (754)
Q Consensus 158 ~s~R~l~~-~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~----------------~~~~~~~~~Di~N~~~~~r~~---- 216 (754)
|++-+++. +..+.|..|.+.|.+|++|--+|+.++|+. .+..+-.+.|++|++.+.-..
T Consensus 23 P~W~~~~~eeVe~~I~klakkG~tpSqIG~iLRD~~GIp~Vk~vtG~kI~rILk~~glapeiPEDL~~LikKAv~lrkHL 102 (151)
T 3u5c_N 23 PAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHL 102 (151)
T ss_dssp CSSCCSCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCSCHHHHSSSCHHHHHHHTTCCCSSCHHHHHHHHHHHHHHHHH
T ss_pred CCCcCCCHHHHHHHHHHHHHCCCCHHHhhhHHhccCCCCCeeeecccHHHHHHHhCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 34444444 456778899999999999999999999873 112233557888876653211
Q ss_pred --------------cCcccHHHHHHHHHHhhcCCCCcEEE
Q 004429 217 --------------NRDYDAIDLIAMCKKMKDKNPNFQYD 242 (754)
Q Consensus 217 --------------~~~~d~~~l~~~~~~~~~~np~~~~~ 242 (754)
..+.-.-.|..|.+....--|+|.|+
T Consensus 103 e~n~kD~~sK~~L~liESkI~RL~rYYk~~~~LP~~WkY~ 142 (151)
T 3u5c_N 103 ERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYE 142 (151)
T ss_dssp HHCTTCHHHHHHHHHHHHHHHHHHHHHHHTTSSCTTCCCC
T ss_pred HHccccHHHHHHHHHHHHHHHHHHHHHHhcCcCCCCCcCC
Confidence 01223345667887777777777765
No 13
>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=77.90 E-value=3.6 Score=33.27 Aligned_cols=25 Identities=16% Similarity=0.183 Sum_probs=16.7
Q ss_pred ccccceEEEEEeeeCCCCcEEEEeecCCccCCCC
Q 004429 116 CGCQAYMRIVKRVDFDVPEWHVTGFSNVHNHELL 149 (754)
Q Consensus 116 ~gCpa~i~v~~~~~~~~~~w~V~~~~~~HNH~l~ 149 (754)
.+|+|++.... +. | .....||||+.
T Consensus 50 ~kCrARi~T~~------~~--~-~~~~~HnH~p~ 74 (87)
T 2rpr_A 50 LGCRSRAITQG------HR--I-MVMRSHCHQPD 74 (87)
T ss_dssp SCCCCEEEEET------TE--E-EECSCCSSCCC
T ss_pred CCCCEEEEEcC------CC--E-ECCCCcCCCCc
Confidence 37999986542 22 3 25678999874
No 14
>2xzm_O RPS13E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_O 1ysh_E 3jyv_O* 1s1h_O
Probab=75.97 E-value=3.8 Score=36.36 Aligned_cols=85 Identities=21% Similarity=0.341 Sum_probs=55.8
Q ss_pred cccCCCCc-chhhHHHHhhhcCCcHHHHHHHHHHhcCcc----------------CCCCCcchhhhhhhHHHh---hhc-
Q 004429 158 PAYCSITP-DDKTRICMFAKAGMSVRQMLRLMELEKGVK----------------LGCLPFTEIDVRNLLQSF---RNV- 216 (754)
Q Consensus 158 ~s~R~l~~-~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~----------------~~~~~~~~~Di~N~~~~~---r~~- 216 (754)
|++-+++. +..+.|..|.+.|.+|++|--+|+.++|+. .+..+-.+.|++|++.+. |+-
T Consensus 25 P~W~~~~~eeVe~~I~klakkG~tpSqIG~iLRD~~GIp~Vk~vtG~kI~rILk~~glapeiPEDL~~LikKAv~lRkHL 104 (153)
T 2xzm_O 25 PKWLHMTPSTVVDLSVKLAKKGLTPSQIGVILRDQHGIPQVRFLTGQKILRILKKNGCAPQLPEDLYFLIKKALSIRKHL 104 (153)
T ss_dssp CSSCCCCHHHHHHHHHHHHHTTCCHHHHHHHHHHSSCCSCHHHHHSSCHHHHHHHTTCCCSSCHHHHHHHHHHHHHHHHH
T ss_pred CccccCCHHHHHHHHHHHHHCCCCHHHhhhHHhhcCCCCCeeeeccchHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 33334444 456778899999999999999999999873 122234567888887663 221
Q ss_pred -cC-------------cccHHHHHHHHHHhhcCCCCcEEE
Q 004429 217 -NR-------------DYDAIDLIAMCKKMKDKNPNFQYD 242 (754)
Q Consensus 217 -~~-------------~~d~~~l~~~~~~~~~~np~~~~~ 242 (754)
.. +.-...|..|.+....--|+|.|+
T Consensus 105 e~n~kD~~sK~~L~LiESkI~RL~rYYk~~~~LP~~WkY~ 144 (153)
T 2xzm_O 105 EKNRKDKDSKYRLILVESRIHRLSRYYKLNQKLPPKWKYN 144 (153)
T ss_dssp HHTTTCHHHHHHHHHHHHHHHHHHHHHHHTTSSCTTCCCS
T ss_pred HHcccchhhHHHHHHHHHHHHHHHHHHHhcCcCCCCCcCC
Confidence 11 223335667777777777777765
No 15
>3j20_Q 30S ribosomal protein S15P/S13E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=75.79 E-value=2.8 Score=37.56 Aligned_cols=85 Identities=19% Similarity=0.254 Sum_probs=56.2
Q ss_pred cccCCCCc-chhhHHHHhhhcCCcHHHHHHHHHHhcCccC-----------------------CCCCcchhhhhhhHHHh
Q 004429 158 PAYCSITP-DDKTRICMFAKAGMSVRQMLRLMELEKGVKL-----------------------GCLPFTEIDVRNLLQSF 213 (754)
Q Consensus 158 ~s~R~l~~-~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~~-----------------------~~~~~~~~Di~N~~~~~ 213 (754)
|++-+++. +..+.|..|.+.|.+|++|--+|+.++|+.. +..+-.+-|++++..++
T Consensus 23 P~W~~~~~eev~~~i~klakkG~~pSqIG~~LRD~~gip~Vk~vt~~~~~~~G~ki~~iLk~~gl~p~iPEDL~~Lt~RI 102 (158)
T 3j20_Q 23 PIWVEYTVEEIENLVVKLRKEGYSTAMIGTILRDQYGIPSVKLFKDPDNPNRNLTITRILEKHGLAPEIPEDLMFLIRRA 102 (158)
T ss_dssp CSSSCCCHHHHHHHHHHHHHHTCCHHHHHHHHHHTTCCSCHHHHHCSSSTTSCCCTHHHHHHHTCSCSSCHHHHHHHHHH
T ss_pred CCCcCCCHHHHHHHHHHHHHCCCCHHHhhHHHhccCCCCCeeeccccccccCcCcHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 34444444 4566788999999999999999999999721 01122345777776665
Q ss_pred hhc------------------cCcccHHHHHHHHHHhhcCCCCcEEE
Q 004429 214 RNV------------------NRDYDAIDLIAMCKKMKDKNPNFQYD 242 (754)
Q Consensus 214 r~~------------------~~~~d~~~l~~~~~~~~~~np~~~~~ 242 (754)
... ...+.-..|++|+++...--|+|.|+
T Consensus 103 ~~Lt~HLk~hkKD~hSrRgL~~lv~kRrrLL~YLk~kd~lp~~w~Y~ 149 (158)
T 3j20_Q 103 VNLRKHLEQHPKDLHSMRGLQLIESKIRRLVKYYKRKGKLPKNWRYD 149 (158)
T ss_dssp HHHHHHHHHCCCCSHHHHHHHHHHHHHHHHHHHHHHHTSSCTTCCCC
T ss_pred HHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCceEC
Confidence 432 11234556888888877667777765
No 16
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=74.76 E-value=1.5 Score=29.51 Aligned_cols=18 Identities=28% Similarity=0.370 Sum_probs=16.4
Q ss_pred cCCccCCCCCCCCCCCCc
Q 004429 724 SEPCCRHFGHDASSCPIM 741 (754)
Q Consensus 724 ~C~~C~~~gHn~~tCp~~ 741 (754)
.|-+|++.||-++.||..
T Consensus 2 ~C~~Cg~~GH~a~~C~~~ 19 (39)
T 2a51_A 2 TCFNCGKPGHTARMCRQP 19 (39)
T ss_dssp BCTTTCCBSSCTTTCCSC
T ss_pred eeeccCCCCcccccCCCC
Confidence 588999999999999975
No 17
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=74.21 E-value=2.5 Score=33.15 Aligned_cols=20 Identities=25% Similarity=0.567 Sum_probs=13.7
Q ss_pred ccCCccCCCCCCCCCCCCcC
Q 004429 723 CSEPCCRHFGHDASSCPIMG 742 (754)
Q Consensus 723 ~~C~~C~~~gHn~~tCp~~~ 742 (754)
..|-+|++.||-.+.||...
T Consensus 47 ~~C~~Cg~~GH~ar~Cp~~~ 66 (74)
T 2li8_A 47 KKCHFCQSISHMVASCPLKA 66 (74)
T ss_dssp CCCTTTCCTTSCGGGCTTGG
T ss_pred CccCCcCCcCCccCcCcCCc
Confidence 34667777777777777655
No 18
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=73.24 E-value=1.7 Score=28.84 Aligned_cols=16 Identities=31% Similarity=0.445 Sum_probs=11.3
Q ss_pred CCccCCCCCCCCCCCC
Q 004429 725 EPCCRHFGHDASSCPI 740 (754)
Q Consensus 725 C~~C~~~gHn~~tCp~ 740 (754)
|-+|++.||..+.||.
T Consensus 3 C~~Cg~~GH~~~~C~~ 18 (37)
T 2bl6_A 3 CYNCGKPGHLSSQCRA 18 (37)
T ss_dssp BSSSCCSSCCTTTSSC
T ss_pred ccccCCCCcchhhCcC
Confidence 6677777777777765
No 19
>3kks_A Integrase, IN; beta-strands flanked by alpha-helices, DNA binding protein; 2.20A {Bovine immunodeficiency virus} PDB: 3kkr_A
Probab=72.93 E-value=9.3 Score=33.72 Aligned_cols=67 Identities=16% Similarity=0.208 Sum_probs=47.0
Q ss_pred CCEEEEcCccccCcCCceeeEEEEeecCCceeEEeeecccCCchhhHHHHHHHHHHHhCCCCCeEeeccccHHHHHH
Q 004429 269 GDALVFDTTHRLDSYDMLFGIWVGLDNHGMACFFGCVLLRDENMQSFSWSLKTLLGFMNGKAPQTLLTDQNIWLKEA 345 (754)
Q Consensus 269 ~dvl~~D~Ty~~n~y~~~l~~~~g~d~~~~~~~~a~al~~~E~~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~A 345 (754)
.+++.+|.|+..++ +.++.+|..-+.+ +++.+ .+++.+...-+|..+....+ |..|.||+.......
T Consensus 2 n~~w~~D~t~~~~~-----y~~~~iD~~sr~~-~~~~~-~~~~~~~~~~~l~~~~~~~g---p~~i~sDnG~~f~s~ 68 (152)
T 3kks_A 2 SHLWQMDNTHWNKT-----IIWVAVETNSGLV-EAQVI-PEETALQVALCILQLIQRYT---VLHLHSDNGPCFTAH 68 (152)
T ss_dssp CCEEEEEEEEETTE-----EEEEEEETTTCCE-EEEEE-SSSCHHHHHHHHHHHHHHSC---CSEEEECSCHHHHSH
T ss_pred CcEEEEeeeeeCCE-----EEEEEEEcCCCcE-EEEEe-CCcCHHHHHHHHHHHHHHhC---CcEEecCCchHhhHH
Confidence 36788999987432 5667778766554 55554 47777777766666666555 999999999887643
No 20
>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=72.79 E-value=1.6 Score=31.95 Aligned_cols=19 Identities=21% Similarity=0.289 Sum_probs=15.3
Q ss_pred cCCccCCCCCCCCCCCCcC
Q 004429 724 SEPCCRHFGHDASSCPIMG 742 (754)
Q Consensus 724 ~C~~C~~~gHn~~tCp~~~ 742 (754)
.|-.|++.||-.+.||...
T Consensus 35 ~C~~Cg~~GH~~~~C~~~~ 53 (55)
T 1a1t_A 35 GCWKCGKEGHQMKDCTERQ 53 (55)
T ss_dssp BCTTTCCBSSCGGGCSSSC
T ss_pred EeCCCCCcCCccCCCcCcC
Confidence 4888888888888888754
No 21
>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=71.09 E-value=2.7 Score=31.35 Aligned_cols=22 Identities=23% Similarity=0.311 Sum_probs=19.0
Q ss_pred ccCCccCCCCCCCCCCCCcCcC
Q 004429 723 CSEPCCRHFGHDASSCPIMGSD 744 (754)
Q Consensus 723 ~~C~~C~~~gHn~~tCp~~~~~ 744 (754)
..|-+|++.||-.+.||.....
T Consensus 31 ~~C~~Cg~~GH~ar~C~~~~~~ 52 (60)
T 1cl4_A 31 GLCPRCKRGKHWANECKSKTDN 52 (60)
T ss_dssp CSCSSCSSCSSCSTTCCCTTSS
T ss_pred cceeECCCCCCccCcCCCcccc
Confidence 3599999999999999987653
No 22
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=70.59 E-value=1.4 Score=29.23 Aligned_cols=17 Identities=24% Similarity=0.380 Sum_probs=15.6
Q ss_pred cCCccCCCCCCCCCCCC
Q 004429 724 SEPCCRHFGHDASSCPI 740 (754)
Q Consensus 724 ~C~~C~~~gHn~~tCp~ 740 (754)
.|-+|++.||-.+.||.
T Consensus 21 ~C~~Cg~~GH~a~~C~~ 37 (37)
T 2bl6_A 21 VCFKCKQPGHFSKQCRS 37 (37)
T ss_dssp TCSSCCCTTGGGGTTCC
T ss_pred eEccCCCcCCccCcCcC
Confidence 59999999999999984
No 23
>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=68.54 E-value=1.8 Score=31.61 Aligned_cols=22 Identities=27% Similarity=0.386 Sum_probs=18.4
Q ss_pred cccccCCccCCCCCCCCCCCCc
Q 004429 720 RRHCSEPCCRHFGHDASSCPIM 741 (754)
Q Consensus 720 ~r~~~C~~C~~~gHn~~tCp~~ 741 (754)
++...|-+|++.||-.+.||..
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 3445699999999999999975
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=65.20 E-value=33 Score=35.17 Aligned_cols=57 Identities=18% Similarity=0.156 Sum_probs=37.3
Q ss_pred CcCCceeeEEEEeecCCceeEEeeeccc---CCchhhHHHHHHHHHHHh----CC----CCCeEeeccccH
Q 004429 281 DSYDMLFGIWVGLDNHGMACFFGCVLLR---DENMQSFSWSLKTLLGFM----NG----KAPQTLLTDQNI 340 (754)
Q Consensus 281 n~y~~~l~~~~g~d~~~~~~~~a~al~~---~E~~es~~w~l~~~~~~~----~~----~~p~~iitD~~~ 340 (754)
+.++..++.+.+++..| ++++.++. .-+.+.|.-+|+.++..+ +. ..+.+|+.|...
T Consensus 185 ~~~~~~~~v~~~~~~~g---~~~~~~~~~~~~~~~~~y~~~L~~~~~~~~~~~p~~~~~~~~~~~~~Dna~ 252 (345)
T 3hot_A 185 NRFGKKTMLCVWWDQSG---VIYYELLKPGETVNAARYQQQLINLNRALQRKRPEYQKRQHRVIFLHDNAP 252 (345)
T ss_dssp CTTCCEEEEEEEEESSS---EEEEEEECSSCCCCHHHHHHHHHHHHHHHHHHSTTCC---CCCEEECCCCT
T ss_pred cCcCCcEEEEEEEcccC---ceeeEecCCCCcccHHHHHHHHHHHHHHHHHhchhhhcCCCceEEEECCCC
Confidence 34556667777777777 45666665 457778887787766544 22 235688899865
No 25
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=64.37 E-value=3.2 Score=31.32 Aligned_cols=21 Identities=24% Similarity=0.543 Sum_probs=17.9
Q ss_pred ccCCccCCCCCCCCCCCCcCc
Q 004429 723 CSEPCCRHFGHDASSCPIMGS 743 (754)
Q Consensus 723 ~~C~~C~~~gHn~~tCp~~~~ 743 (754)
..|-+|++.||-.+.||....
T Consensus 30 ~~C~~Cg~~GH~ar~Cp~~~~ 50 (63)
T 2cqf_A 30 KKCHFCQSISHMVASCPLKAQ 50 (63)
T ss_dssp SCCTTTCCSSSCTTTCTGGGC
T ss_pred CccCCcCCcCCccCcCCCccc
Confidence 359999999999999998653
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=62.64 E-value=4.6 Score=30.43 Aligned_cols=20 Identities=20% Similarity=0.316 Sum_probs=17.2
Q ss_pred cccCCccCCCCCCCCCCCCc
Q 004429 722 HCSEPCCRHFGHDASSCPIM 741 (754)
Q Consensus 722 ~~~C~~C~~~gHn~~tCp~~ 741 (754)
...|-+|++.||..+.||..
T Consensus 7 ~~~C~~Cg~~GH~a~~C~~~ 26 (63)
T 2cqf_A 7 GDRCYNCGGLDHHAKECKLP 26 (63)
T ss_dssp CCCCSSSCCSSSCTTTCCSC
T ss_pred CCcccccCCCCcChhhCCCC
Confidence 34599999999999999964
No 27
>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=62.47 E-value=57 Score=31.39 Aligned_cols=64 Identities=22% Similarity=0.127 Sum_probs=36.8
Q ss_pred CEEEEcCccccCcCCceeeEEEEeecCCceeEEeeecccCCchhhHHHHHHHHHHHhCCCCCeEeeccccHHHH
Q 004429 270 DALVFDTTHRLDSYDMLFGIWVGLDNHGMACFFGCVLLRDENMQSFSWSLKTLLGFMNGKAPQTLLTDQNIWLK 343 (754)
Q Consensus 270 dvl~~D~Ty~~n~y~~~l~~~~g~d~~~~~~~~a~al~~~E~~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~ 343 (754)
.++.+|.|+..++ +.++.+|..-. +++++.+- .++.....-++..+.... .|.+|.||+...+.
T Consensus 10 ~~w~~D~t~~~g~-----~~l~~vD~~Sr-~i~~~~~~-~~~~~~~~~~~~~~~~~~---~~~~i~sDnG~eF~ 73 (239)
T 1ex4_A 10 GIWQLDCTHLEGK-----VILVAVHVASG-YIEAEVIP-AETGQETAYFLLKLAGRW---PVKTIHTDNGSNFT 73 (239)
T ss_dssp GEEEEEEEEETTE-----EEEEEECTTTC-CEEEECCS-SSSTTHHHHHHHHHHHHS---CCCEEEECCCHHHH
T ss_pred CEEEEeccccCCe-----EEEEEEECCCC-eEEEEEeC-CCCHHHHHHHHHHHHHhc---CCcEEEecCcHHHH
Confidence 5788899887332 24444565443 45666544 455555443333333322 46899999887764
No 28
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=61.61 E-value=2.8 Score=31.44 Aligned_cols=21 Identities=24% Similarity=0.460 Sum_probs=17.9
Q ss_pred ccCCccCCCCCCCCCCCCcCc
Q 004429 723 CSEPCCRHFGHDASSCPIMGS 743 (754)
Q Consensus 723 ~~C~~C~~~gHn~~tCp~~~~ 743 (754)
..|-+|++.||-.+.||....
T Consensus 31 ~~C~~Cg~~GH~ar~C~~~~~ 51 (61)
T 2ihx_A 31 ERCQLCNGMGHNAKQCRKRDG 51 (61)
T ss_dssp SBCTTTCCBSSCGGGCCCCC-
T ss_pred CeeCCCCCCCCCcCCCcCCCc
Confidence 359999999999999998764
No 29
>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=60.77 E-value=3.4 Score=37.23 Aligned_cols=24 Identities=21% Similarity=0.441 Sum_probs=16.9
Q ss_pred ccCCccCCCCCCCCCCCCcCcCCc
Q 004429 723 CSEPCCRHFGHDASSCPIMGSDTL 746 (754)
Q Consensus 723 ~~C~~C~~~gHn~~tCp~~~~~~~ 746 (754)
..|-+|++.||-.+.||.....+.
T Consensus 120 ~~C~~Cg~~GH~~r~Cp~~~~~~~ 143 (148)
T 3ts2_A 120 KKCHFCQSINHMVASCPLKAQQGP 143 (148)
T ss_dssp CCCTTTCCSSCCGGGCTTTTC---
T ss_pred CcccccCCcCCEeccCcCCCCCCC
Confidence 458888888888888888765543
No 30
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=60.19 E-value=3.3 Score=31.03 Aligned_cols=21 Identities=24% Similarity=0.341 Sum_probs=18.0
Q ss_pred ccCCccCCCCCCCCCCCCcCc
Q 004429 723 CSEPCCRHFGHDASSCPIMGS 743 (754)
Q Consensus 723 ~~C~~C~~~gHn~~tCp~~~~ 743 (754)
..|-+|++.||-++.||....
T Consensus 5 ~~C~~Cg~~GH~a~~C~~~~~ 25 (61)
T 2ihx_A 5 GLCYTCGSPGHYQAQCPKKRK 25 (61)
T ss_dssp TBCSSSCCBTCCGGGCTTTTS
T ss_pred CcccccCCCCeehhhCcCCcC
Confidence 359999999999999998643
No 31
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=56.60 E-value=4.6 Score=31.57 Aligned_cols=22 Identities=18% Similarity=0.326 Sum_probs=18.4
Q ss_pred cccccCCccCCCCCCCCCCCCc
Q 004429 720 RRHCSEPCCRHFGHDASSCPIM 741 (754)
Q Consensus 720 ~r~~~C~~C~~~gHn~~tCp~~ 741 (754)
.+...|-+|++.||..+.||..
T Consensus 22 ~r~~~C~~Cg~~GH~a~~C~~~ 43 (74)
T 2li8_A 22 SKGDRCYNCGGLDHHAKECKLP 43 (74)
T ss_dssp STTSCCTTTCCSSSCTTTCSSC
T ss_pred CCCCcccccCCcCcCcccCCCC
Confidence 3445699999999999999964
No 32
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=56.54 E-value=3.2 Score=33.25 Aligned_cols=19 Identities=21% Similarity=0.550 Sum_probs=16.6
Q ss_pred ccCCccCCCCCCCCCCCCc
Q 004429 723 CSEPCCRHFGHDASSCPIM 741 (754)
Q Consensus 723 ~~C~~C~~~gHn~~tCp~~ 741 (754)
..|-.|++.||-.+.||..
T Consensus 6 ~~C~~Cg~~GH~~~~Cp~~ 24 (83)
T 3nyb_B 6 VQCTLCKSKKHSKERCPSI 24 (83)
T ss_dssp -CCSSSCCSSSCGGGCGGG
T ss_pred CCCCCCCCCCCccccCCCc
Confidence 3599999999999999975
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=51.79 E-value=45 Score=29.68 Aligned_cols=70 Identities=13% Similarity=-0.007 Sum_probs=46.7
Q ss_pred CEEEEcCccccCcCCceeeEEEEeecCCceeEEeeecccCCchhhHHHHHHHHHHHhCCCCCeEeeccccHHHHH
Q 004429 270 DALVFDTTHRLDSYDMLFGIWVGLDNHGMACFFGCVLLRDENMQSFSWSLKTLLGFMNGKAPQTLLTDQNIWLKE 344 (754)
Q Consensus 270 dvl~~D~Ty~~n~y~~~l~~~~g~d~~~~~~~~a~al~~~E~~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~ 344 (754)
+++.+|.|+..... +-.+.++.+|..-+. ++|+.+- +.+.+...-+|+.+....+ .|..|.||+......
T Consensus 12 ~~~~~D~~~~~~~~-g~~yl~~~iD~~Sr~-i~~~~~~-~~~~~~v~~~l~~~~~~~g--~p~~i~sDnG~~f~s 81 (162)
T 1cxq_A 12 QIWQTDFTLEPRMA-PRSWLAVTVDTASSA-IVVTQHG-RVTSVAAQHHWATAIAVLG--RPKAIKTDNGSCFTS 81 (162)
T ss_dssp CEEEEEEEECGGGT-TSCEEEEEEETTTCC-EEEEEES-SCCHHHHHHHHHHHHHHHC--CCSEEECCSCHHHHS
T ss_pred CEEEeeeeecccCC-CCEEEEEEEEcCCCe-EEEEECC-CccHHHHHHHHHHHHHHHC--CCeEEEeCCchhhhh
Confidence 57788888765432 345667778876554 4456554 6777776666666555554 478999999988754
No 34
>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=51.75 E-value=31 Score=32.66 Aligned_cols=66 Identities=20% Similarity=0.203 Sum_probs=44.8
Q ss_pred CEEEEcCccccCcCCceeeEEEEeecCCceeEEeeecccCCchhhHHHHHHHHHHHhCCCCCeEeeccccHHHHHH
Q 004429 270 DALVFDTTHRLDSYDMLFGIWVGLDNHGMACFFGCVLLRDENMQSFSWSLKTLLGFMNGKAPQTLLTDQNIWLKEA 345 (754)
Q Consensus 270 dvl~~D~Ty~~n~y~~~l~~~~g~d~~~~~~~~a~al~~~E~~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~A 345 (754)
+++.+|.|+..++ +.++.+|..-..+ +++. +.+++.....-+|..+....| |.+|.||+......+
T Consensus 61 ~~w~~D~t~~~~~-----y~~~~iD~~Sr~~-~~~~-~~~~~~~~~~~~l~~~~~~~g---p~~i~sDnG~~F~s~ 126 (219)
T 3hph_A 61 DHWQVDYTHYEDK-----IILVWVETNSGLI-YAER-VKGETGQEFRVQTMKWYAMFA---PKSLQSDNGPAFVAE 126 (219)
T ss_dssp CEEEEEEEEETTE-----EEEEEEETTTCCE-EEEE-ESCCCHHHHHHHHHHHHHHHC---CCEEEECCCHHHHSH
T ss_pred ceEEEEEecCCCE-----EEEEEEeCCCCcE-EEEE-eCCCCHHHHHHHHHHHHHHhC---CcEEEeCCCchhhhH
Confidence 5667888865443 5667778776655 4544 456677666666666655555 899999999987643
No 35
>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A
Probab=50.11 E-value=32 Score=27.00 Aligned_cols=74 Identities=12% Similarity=0.180 Sum_probs=39.7
Q ss_pred CccCCCCCccccccccccCCCCcchhhHHHHhhhcCCcHHHHHHHHHHhcCccCCCCCcchhhhhhhHHHhhhccCcccH
Q 004429 143 VHNHELLKLNEVRLLPAYCSITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNVNRDYDA 222 (754)
Q Consensus 143 ~HNH~l~~~~~~~~l~s~R~l~~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~~~~~d~ 222 (754)
.|+|++..+.. ....-..|++.+++.+.. ...|.+..+|.+.+. ++...|++.+.+.++.+.....
T Consensus 4 ~~~~~~~~~~~--~~~~~~~Lt~~e~~vl~l-~~~g~s~~eIA~~l~-----------is~~tV~~~l~r~~~kL~~~~~ 69 (82)
T 1je8_A 4 SHHHHHHGSAT--TERDVNQLTPRERDILKL-IAQGLPNKMIARRLD-----------ITESTVKVHVKHMLKKMKLKSR 69 (82)
T ss_dssp ---------------CCGGGSCHHHHHHHHH-HTTTCCHHHHHHHHT-----------SCHHHHHHHHHHHHHHTTCSSH
T ss_pred ccCCCCCCchH--HHHHHccCCHHHHHHHHH-HHcCCCHHHHHHHHC-----------cCHHHHHHHHHHHHHHHcCCCH
Confidence 46666644332 223345688888766655 478999999988763 3556777777776655444444
Q ss_pred HHHHHHHH
Q 004429 223 IDLIAMCK 230 (754)
Q Consensus 223 ~~l~~~~~ 230 (754)
..+..+..
T Consensus 70 ~~l~~~a~ 77 (82)
T 1je8_A 70 VEAAVWVH 77 (82)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 44544443
No 36
>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=49.65 E-value=6.4 Score=35.44 Aligned_cols=20 Identities=20% Similarity=0.316 Sum_probs=17.4
Q ss_pred cccCCccCCCCCCCCCCCCc
Q 004429 722 HCSEPCCRHFGHDASSCPIM 741 (754)
Q Consensus 722 ~~~C~~C~~~gHn~~tCp~~ 741 (754)
..+|-+|++.||-++.||..
T Consensus 97 ~~~C~~Cg~~GH~a~~C~~~ 116 (148)
T 3ts2_A 97 GDRCYNCGGLDHHAKECKLP 116 (148)
T ss_dssp SCCCTTTCCSSCCGGGCCSC
T ss_pred CCcccEeCCccchhhhCCCC
Confidence 44699999999999999973
No 37
>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=48.28 E-value=12 Score=22.02 Aligned_cols=17 Identities=12% Similarity=0.163 Sum_probs=11.7
Q ss_pred CCcccccCCccccCCCC
Q 004429 696 SHESFTLGKLKERRPRD 712 (754)
Q Consensus 696 P~~~~~kGrpk~~r~r~ 712 (754)
|.-+++.||||....|+
T Consensus 2 ptpKrpRgRpkGSKNk~ 18 (26)
T 2ezd_A 2 PTPKRPRGRPKGSKNKG 18 (26)
T ss_dssp CSCCCCSSCCTTCCCCS
T ss_pred CCCcCCCCCcCcccccC
Confidence 44467889998765543
No 38
>1x9b_A Hypothetical membrane protein TA0354_69_121; alpha protein, structural genomics, protein structure initiative, PSI; NMR {Thermoplasma acidophilum} SCOP: a.10.2.1
Probab=47.40 E-value=20 Score=24.99 Aligned_cols=45 Identities=13% Similarity=0.068 Sum_probs=34.1
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHhccCchhHHHHHHHHhhcccc
Q 004429 383 AEFYRLYNLELEEDFEEEWSKMVNKYGLREYKHITSLYALRTFWA 427 (754)
Q Consensus 383 ~~~~~~~~~~~~~eFe~~w~~l~~~~~~~~~~~l~~l~~~r~~W~ 427 (754)
..|..++++++..+|-..+.+|-..-.--+..|...+-+-+++|-
T Consensus 7 ~~Fe~~InS~SK~~Fv~nL~ELE~is~rlg~~Y~~~LeeaK~kWk 51 (53)
T 1x9b_A 7 AKFESMINSPSKSVFVRNLNELEALAVRLGKSYRIQLDQAKEKWK 51 (53)
T ss_dssp HHHHHHHHSCCHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHC
T ss_pred HHHHHHhCCccHHHHHHhHHHHHHHHHHHchHHHHHHHHHHHhhc
Confidence 368889999999999999988854333234568888877888884
No 39
>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=45.39 E-value=57 Score=31.42 Aligned_cols=70 Identities=11% Similarity=-0.005 Sum_probs=48.8
Q ss_pred CEEEEcCccccCcCCceeeEEEEeecCCceeEEeeecccCCchhhHHHHHHHHHHHhCCCCCeEeeccccHHHHH
Q 004429 270 DALVFDTTHRLDSYDMLFGIWVGLDNHGMACFFGCVLLRDENMQSFSWSLKTLLGFMNGKAPQTLLTDQNIWLKE 344 (754)
Q Consensus 270 dvl~~D~Ty~~n~y~~~l~~~~g~d~~~~~~~~a~al~~~E~~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~ 344 (754)
+++.+|.|+..... +-.+.++.+|..-. .++|+.+- .++.+...-+|.......+ .|.+|.||+...+..
T Consensus 11 ~~w~~D~~~~~~~~-g~~yl~~~iD~~Sr-~i~~~~~~-~~~~~~v~~~l~~~~~~~g--~p~~i~sDnG~~f~s 80 (238)
T 1c0m_A 11 QIWQTDFTLEPRMA-PRSWLAVTVDTASS-AIVVTQHG-RVTSVAVQHHWATAIAVLG--RPKAIKTDNGSCFTS 80 (238)
T ss_dssp SEEEEEEEECGGGC-SSCEEEEEEETTTC-CEEEEEES-SCCHHHHHHHHHHHHHHHC--CCSEEEECSCHHHHS
T ss_pred CEEEEeeccccccC-CCEEEEEEEECCCC-CEEEEEcc-CCCHHHHHHHHHHHHHHhC--CCcEEEECCCCcccc
Confidence 57888988765433 33566777776654 44466655 7888887777777666665 478999999988754
No 40
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=39.77 E-value=7.4 Score=23.29 Aligned_cols=20 Identities=35% Similarity=0.536 Sum_probs=16.4
Q ss_pred ccccCCccCCCCCCCCCCCCc
Q 004429 721 RHCSEPCCRHFGHDASSCPIM 741 (754)
Q Consensus 721 r~~~C~~C~~~gHn~~tCp~~ 741 (754)
|++ |-.|-..||....|+..
T Consensus 3 RpY-Ce~CE~FGH~t~~C~d~ 22 (26)
T 2hqh_E 3 RPY-CEICEMFGHWATNCNDD 22 (26)
T ss_dssp -CE-ETTTTEESSCGGGCCTT
T ss_pred Ccc-chHHHHhCcccccCCcc
Confidence 454 99999999999999754
No 41
>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=39.65 E-value=47 Score=29.49 Aligned_cols=65 Identities=22% Similarity=0.094 Sum_probs=44.2
Q ss_pred CCEEEEcCccccCcCCceeeEEEEeecCCceeEEeeecccCCchhhHHHHHHHHHHHhCCCCCeEeeccccHHHH
Q 004429 269 GDALVFDTTHRLDSYDMLFGIWVGLDNHGMACFFGCVLLRDENMQSFSWSLKTLLGFMNGKAPQTLLTDQNIWLK 343 (754)
Q Consensus 269 ~dvl~~D~Ty~~n~y~~~l~~~~g~d~~~~~~~~a~al~~~E~~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~ 343 (754)
.+++.+|.|+..++ +.++.+|...+.+ +++.+ .+++.+...-+|..+...++ +..|.||+.....
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 36788999987543 5677788776644 55554 56677777666666555543 4799999987653
No 42
>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=35.87 E-value=7.7 Score=28.78 Aligned_cols=20 Identities=30% Similarity=0.311 Sum_probs=0.0
Q ss_pred cCCccCCCCCCCCCCCCcCc
Q 004429 724 SEPCCRHFGHDASSCPIMGS 743 (754)
Q Consensus 724 ~C~~C~~~gHn~~tCp~~~~ 743 (754)
.|-+|++.||-++.||....
T Consensus 3 ~Cf~Cg~~GH~a~~C~~~~~ 22 (60)
T 1cl4_A 3 SCFKCGKKGHFAKNCHEHAH 22 (60)
T ss_dssp --------------------
T ss_pred ccccCCCCCcCHhhCcCCCC
Confidence 37899999999999998754
No 43
>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=35.23 E-value=64 Score=32.87 Aligned_cols=71 Identities=14% Similarity=-0.009 Sum_probs=47.8
Q ss_pred CCEEEEcCccccCc----CCc--eeeEEEEeecCCceeEEeeecccCCchhhHHHHHHHHHHHhCCCCCe--EeeccccH
Q 004429 269 GDALVFDTTHRLDS----YDM--LFGIWVGLDNHGMACFFGCVLLRDENMQSFSWSLKTLLGFMNGKAPQ--TLLTDQNI 340 (754)
Q Consensus 269 ~dvl~~D~Ty~~n~----y~~--~l~~~~g~d~~~~~~~~a~al~~~E~~es~~w~l~~~~~~~~~~~p~--~iitD~~~ 340 (754)
++++.+|.|+..-. .+. -.++.+.+|..-. .++|+.+...++.++..-+|.......+ .|. .|.+|+-.
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 46788888864322 121 3455666776555 4578888888998888877776665554 466 89999876
Q ss_pred HH
Q 004429 341 WL 342 (754)
Q Consensus 341 ~l 342 (754)
..
T Consensus 93 ~f 94 (327)
T 1bco_A 93 GA 94 (327)
T ss_dssp ST
T ss_pred hh
Confidence 54
No 44
>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=34.25 E-value=2.1e+02 Score=27.14 Aligned_cols=62 Identities=8% Similarity=0.018 Sum_probs=36.4
Q ss_pred cccCcCCceeeEEEEeecCCceeEEeeeccc---CCchhhHHHHHHHHHHHh----C---CCCCeEeeccccHHH
Q 004429 278 HRLDSYDMLFGIWVGLDNHGMACFFGCVLLR---DENMQSFSWSLKTLLGFM----N---GKAPQTLLTDQNIWL 342 (754)
Q Consensus 278 y~~n~y~~~l~~~~g~d~~~~~~~~a~al~~---~E~~es~~w~l~~~~~~~----~---~~~p~~iitD~~~~l 342 (754)
-.+++++..+.+.++++..|...+ .++. .=|.+.|.-+|+.+...+ + ...+.+++-|....-
T Consensus 64 ~~~~~~~~~vmv~~~~s~~G~~~~---~~l~~~~tinse~Y~~~l~~l~~~l~~~~~~~~~~~~~i~~~Dna~~H 135 (226)
T 3f2k_A 64 PKPILHPKKVMVTIWWSAAGLIHY---SFLNPGETITSEKYAQEIDEMNQKLQRLQLALVNRKGPILLHDNARPH 135 (226)
T ss_dssp -----CCCEEEEEEEEETTEEEEE---EECCTTCCCSHHHHHHHHHHHHHHHHHHTC----CCCCEEECCCCHHH
T ss_pred cccccCCcceEEEEEeecCCcEEE---EEecCCcccCHHHHHHHHHHHHHHHhhhhhHhhccCCcEEEeCCCccc
Confidence 345677778888888888876543 4443 456677777776654332 1 234567888987754
No 45
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=33.40 E-value=20 Score=30.90 Aligned_cols=21 Identities=19% Similarity=0.431 Sum_probs=18.2
Q ss_pred ccCCccCCCCCCCCCCCCcCc
Q 004429 723 CSEPCCRHFGHDASSCPIMGS 743 (754)
Q Consensus 723 ~~C~~C~~~gHn~~tCp~~~~ 743 (754)
..|-+|++.||..+.||....
T Consensus 65 ~~C~~Cg~~GH~~~~Cp~~~~ 85 (124)
T 2lli_A 65 VQCTLCKSKKHSKERCPSIWR 85 (124)
T ss_dssp CSSSSSCSSCCCTTTCCCSTT
T ss_pred ccCCCCCcCCcchhhCCCccc
Confidence 459999999999999998643
No 46
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=32.72 E-value=20 Score=28.64 Aligned_cols=23 Identities=22% Similarity=0.187 Sum_probs=19.5
Q ss_pred ccCCccCCCCCCCCCCCCcCcCC
Q 004429 723 CSEPCCRHFGHDASSCPIMGSDT 745 (754)
Q Consensus 723 ~~C~~C~~~gHn~~tCp~~~~~~ 745 (754)
..|-+|++.||-.+-||......
T Consensus 47 ~~CYnCG~~GH~~rdC~~~r~s~ 69 (83)
T 3nyb_B 47 IYCYNCGGKGHFGDDCKEKRSSR 69 (83)
T ss_dssp CBCSSSSCBSSCGGGCSSCCSCS
T ss_pred CeecccCCCCcCcccCCccccCc
Confidence 46999999999999999876543
No 47
>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=31.71 E-value=84 Score=28.60 Aligned_cols=65 Identities=22% Similarity=0.113 Sum_probs=37.2
Q ss_pred CEEEEcCccccCcCCceeeEEEEeecCCceeEEeeecccCCchhhHHHHHHHHHHHhCCCCCeEeeccccHHHHH
Q 004429 270 DALVFDTTHRLDSYDMLFGIWVGLDNHGMACFFGCVLLRDENMQSFSWSLKTLLGFMNGKAPQTLLTDQNIWLKE 344 (754)
Q Consensus 270 dvl~~D~Ty~~n~y~~~l~~~~g~d~~~~~~~~a~al~~~E~~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~ 344 (754)
+++.+|.|+..++| .++.+|..-+.+ +|+.+- +++.....-++..+.... .+.+|.||+.....+
T Consensus 30 ~~w~~D~~~~~g~~-----~l~~vD~~Sr~~-~~~~~~-~~~~~~~~~~~~~~~~~~---~~~~i~sDnG~ef~s 94 (183)
T 3av9_A 30 GIWQLDCTHLEGKV-----ILVAVHVASGYI-EAEVIP-AETGQETAYFLLKLAGRW---PVKTVHTDNGSNFTS 94 (183)
T ss_dssp TEEEEEEEEETTEE-----EEEEEETTTTEE-EEEEES-SCCHHHHHHHHHHHHHHS---CCCEEECSSHHHHHC
T ss_pred CEEEEeccccCCcE-----EEEEEECCCCCE-EEEEeC-CccchHHHHHHHHHHHHc---CCcEEEecCchhcch
Confidence 56777777763322 344456555544 666544 455555544443333333 348999999888753
No 48
>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=31.42 E-value=1.2e+02 Score=27.83 Aligned_cols=69 Identities=14% Similarity=0.055 Sum_probs=44.3
Q ss_pred CEEEEcC-ccccCcCCceeeEEEEeecCCceeEEeeecccCCchhhHHHHHHHHHHHhCCCCCeEeeccccHHHHH
Q 004429 270 DALVFDT-THRLDSYDMLFGIWVGLDNHGMACFFGCVLLRDENMQSFSWSLKTLLGFMNGKAPQTLLTDQNIWLKE 344 (754)
Q Consensus 270 dvl~~D~-Ty~~n~y~~~l~~~~g~d~~~~~~~~a~al~~~E~~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~ 344 (754)
+++.+|- ++.... ++..+.++.+|..-..+ +++.+ .+.+.+...-+|+ .++....|..|.||+.....+
T Consensus 14 ~~~~~D~~~~~~~~-~g~~y~~~~iD~~Sr~~-~~~~~-~~~~~~~~~~~l~---~~~~~g~p~~i~sDnG~~f~s 83 (200)
T 2x78_A 14 DKFFIDYIGPLPPS-QGYLYVLVVVDGMTGFT-WLYPT-KAPSTSATVKSLN---VLTSIAIPRVIHSDQGAAFTS 83 (200)
T ss_dssp SEEEEEEECCCSCB-TTBCEEEEEEETTTCCE-EEEEE-SSSCHHHHHHHHH---HHTTTCCCSEEEECSCHHHHS
T ss_pred cEEEEEEeCCCccC-CCCeEEEEEEeCCCCcE-EEEEC-CCCCHHHHHHHHH---HHHHhCCCcEEEecCCcceeh
Confidence 5778886 454433 45677778888765544 45555 6666666554443 333335789999999987754
No 49
>2l69_A Rossmann 2X3 fold protein; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Artificial gene}
Probab=31.02 E-value=32 Score=27.47 Aligned_cols=28 Identities=21% Similarity=0.456 Sum_probs=25.2
Q ss_pred ccCCHHHHHHHHHHHHhhcCCeEEEcce
Q 004429 47 RFVSQDAAYEFYCSFAKQCGFSIRRHRT 74 (754)
Q Consensus 47 ~F~S~eea~~~y~~yA~~~GF~ir~~~s 74 (754)
+|.+.||-..-+...-+++||.+|.-+|
T Consensus 7 vfstdeetlrkfkdiikkngfkvrtvrs 34 (134)
T 2l69_A 7 VFSTDEETLRKFKDIIKKNGFKVRTVRS 34 (134)
T ss_dssp ECCCCHHHHHHHHHHHHHTTCEEEEECS
T ss_pred EEeCCHHHHHHHHHHHHhcCceEEEecC
Confidence 6899999999999999999999998776
No 50
>2lju_A Putative oxidoreductase; structural genomics, seattle structural GENO center for infectious disease, ssgcid; NMR {Ehrlichia chaffeensis}
Probab=30.63 E-value=48 Score=27.76 Aligned_cols=32 Identities=9% Similarity=0.100 Sum_probs=25.3
Q ss_pred CCCCCCCCCccCCHHHHHHHHHHHHhhcCCeEEEcc
Q 004429 38 VNLVPFIGQRFVSQDAAYEFYCSFAKQCGFSIRRHR 73 (754)
Q Consensus 38 ~~~~P~vg~~F~S~eea~~~y~~yA~~~GF~ir~~~ 73 (754)
.+..-.|.+.|+|.|+|. +||+++|....+.-
T Consensus 56 ~D~~~qv~L~F~skE~Ai----ayAek~G~~y~V~e 87 (108)
T 2lju_A 56 HDTKQQVCLSFTTRELAI----AYAVAHKIDYTVLQ 87 (108)
T ss_dssp CCCCCCSCEEESSHHHHH----HHHHHTTCEEEEEC
T ss_pred CCccccceEecCCHHHHH----HHHHHcCCEEEEec
Confidence 444556789999999996 57999998887654
No 51
>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2
Probab=29.89 E-value=48 Score=22.21 Aligned_cols=42 Identities=12% Similarity=0.226 Sum_probs=29.1
Q ss_pred CCCCcchhhHHHHhhhcCCcHHHHHHHHHHhcCccCCCCCcchhhhhhhHHHh
Q 004429 161 CSITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSF 213 (754)
Q Consensus 161 R~l~~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~~~~~~~~~~Di~N~~~~~ 213 (754)
+.++++++..|..+...|++..+|...+. +....|++++...
T Consensus 4 ~~l~~~~~~~i~~~~~~g~s~~~IA~~lg-----------is~~Tv~~~~~~~ 45 (51)
T 1tc3_C 4 SALSDTERAQLDVMKLLNVSLHEMSRKIS-----------RSRHCIRVYLKDP 45 (51)
T ss_dssp CCCCHHHHHHHHHHHHTTCCHHHHHHHHT-----------CCHHHHHHHHHCS
T ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHHC-----------cCHHHHHHHHhhH
Confidence 35677788788777788999888876552 3445666665544
No 52
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=27.77 E-value=29 Score=29.92 Aligned_cols=20 Identities=20% Similarity=0.185 Sum_probs=17.4
Q ss_pred cccCCccCCCCCCCCCCCCc
Q 004429 722 HCSEPCCRHFGHDASSCPIM 741 (754)
Q Consensus 722 ~~~C~~C~~~gHn~~tCp~~ 741 (754)
...|-+|++.||-.+.||+.
T Consensus 105 ~~~Cy~Cg~~GH~a~dCp~~ 124 (124)
T 2lli_A 105 TIYCYNCGGKGHFGDDCKEK 124 (124)
T ss_dssp CCCTTTTSSSCTTTTTSCCC
T ss_pred CCCcCCCCCCCcCcccCcCC
Confidence 34699999999999999973
No 53
>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A
Probab=23.45 E-value=1.2e+02 Score=24.24 Aligned_cols=58 Identities=10% Similarity=0.122 Sum_probs=38.3
Q ss_pred cCCCCcchhhHHHHhhhcCCcHHHHHHHHHHhcCccCCCCCcchhhhhhhHHHhhhccCcccHHHHHHHH
Q 004429 160 YCSITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNVNRDYDAIDLIAMC 229 (754)
Q Consensus 160 ~R~l~~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~~~~~d~~~l~~~~ 229 (754)
...|++.+++.+..+ ..|.+..+|...|. ++.+.|++++....+.+.-.....++.+.
T Consensus 27 ~~~Lt~rE~~Vl~l~-~~G~s~~eIA~~L~-----------iS~~TV~~~~~~i~~Klgv~~r~~lv~~a 84 (90)
T 3ulq_B 27 QDVLTPRECLILQEV-EKGFTNQEIADALH-----------LSKRSIEYSLTSIFNKLNVGSRTEAVLIA 84 (90)
T ss_dssp --CCCHHHHHHHHHH-HTTCCHHHHHHHHT-----------CCHHHHHHHHHHHHHHTTCSSHHHHHHHH
T ss_pred ccCCCHHHHHHHHHH-HcCCCHHHHHHHHC-----------cCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 345777666655444 48999999987663 46678888888877665555555555554
No 54
>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2
Probab=23.25 E-value=1.9e+02 Score=23.57 Aligned_cols=61 Identities=10% Similarity=0.092 Sum_probs=40.9
Q ss_pred cCCCCcchhhHHHHhhhcCCcHHHHHHHHHHhcCccCCCCCcchhhhhhhHHHhhhccCcccHHHHHHHHHHh
Q 004429 160 YCSITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNVNRDYDAIDLIAMCKKM 232 (754)
Q Consensus 160 ~R~l~~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~~~~~d~~~l~~~~~~~ 232 (754)
...|++.+++.+.. ...|.+..+|.+.+. ++...|++.+...++.+...+-..+..+..+.
T Consensus 32 ~~~Lt~re~~Vl~l-~~~G~s~~EIA~~L~-----------iS~~TV~~~l~ri~~KLgv~~r~elv~~a~~~ 92 (99)
T 1p4w_A 32 DKRLSPKESEVLRL-FAEGFLVTEIAKKLN-----------RSIKTISSQKKSAMMKLGVDNDIALLNYLSSV 92 (99)
T ss_dssp SSSCCHHHHHHHHH-HHHTCCHHHHHHHHT-----------SCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHH-HHcCCCHHHHHHHHC-----------cCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHc
Confidence 45678777765544 458999999987663 46677888887777665455455555555443
No 55
>1c6v_A Protein (SIV integrase); DNA integration, DNA binding protein; 3.00A {Simian immunodeficiency virus} SCOP: c.55.3.2
Probab=22.82 E-value=1.7e+02 Score=25.40 Aligned_cols=62 Identities=18% Similarity=0.010 Sum_probs=35.6
Q ss_pred CEEEEcCccccCcCCceeeEEEEeecCCceeEEeeecccCCchhhHHHHHHHHHHHhCCCCCeEeeccccHH
Q 004429 270 DALVFDTTHRLDSYDMLFGIWVGLDNHGMACFFGCVLLRDENMQSFSWSLKTLLGFMNGKAPQTLLTDQNIW 341 (754)
Q Consensus 270 dvl~~D~Ty~~n~y~~~l~~~~g~d~~~~~~~~a~al~~~E~~es~~w~l~~~~~~~~~~~p~~iitD~~~~ 341 (754)
+++.+|.|+.. +. +.++.+|..-+ .++++.+ .+.+.+.+.-++..+ +....|.+|.+|+...
T Consensus 10 ~~w~~D~~~~~----g~-~~l~~iD~~Sr-~~~~~~~-~~~~~~~~~~~~~~~---~~~~~~~~i~sDnG~~ 71 (164)
T 1c6v_A 10 GTWQMDCTHLE----GK-IVIVAVHVASG-FIEAEVI-PQETGRQTALFLLKL---AGRWPITHLHTDNGAN 71 (164)
T ss_dssp TEEEEEEEEET----TE-EEEEEECTTSC-CEEEEEC-SSCSHHHHHHHHHHH---HTTSCCCEEECCCCSS
T ss_pred CEEEEeecccC----CE-EEEEEEEccCC-EEEEEEc-CCCchHHHHHHHHHH---HHhcCCCEEEeCCchh
Confidence 56778888772 22 34444776655 3455544 455555554444333 3333478999998654
No 56
>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2
Probab=22.43 E-value=2.2e+02 Score=20.94 Aligned_cols=60 Identities=8% Similarity=0.011 Sum_probs=37.2
Q ss_pred cCCCCcchhhHHHHhhhcCCcHHHHHHHHHHhcCccCCCCCcchhhhhhhHHHhhhccCcccHHHHHHHHHH
Q 004429 160 YCSITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNVNRDYDAIDLIAMCKK 231 (754)
Q Consensus 160 ~R~l~~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~~~~~d~~~l~~~~~~ 231 (754)
...|++.++..+.. ...|.+..+|.+.+. .+...|++.+.+.++......-..++.+..+
T Consensus 9 ~~~L~~~e~~il~~-~~~g~s~~eIA~~l~-----------is~~tV~~~~~~~~~kl~~~~~~~~~~~~~~ 68 (74)
T 1fse_A 9 KPLLTKREREVFEL-LVQDKTTKEIASELF-----------ISEKTVRNHISNAMQKLGVKGRSQAVVELLR 68 (74)
T ss_dssp CCCCCHHHHHHHHH-HTTTCCHHHHHHHHT-----------SCHHHHHHHHHHHHHHHTCSSHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHH-HHcCCCHHHHHHHHC-----------CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 35677777766655 478999999887663 3556677777766655433333444444433
Done!