Query 046293
Match_columns 695
No_of_seqs 288 out of 1232
Neff 8.3
Searched_HMMs 29240
Date Mon Mar 25 18:33:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046293.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/046293hhsearch_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 93.5 0.21 7.1E-06 39.5 6.7 57 50-127 16-73 (76)
2 1wj2_A Probable WRKY transcrip 92.8 0.17 5.9E-06 40.2 5.4 57 50-127 19-76 (78)
3 1a6b_B Momulv, zinc finger pro 89.3 0.19 6.6E-06 34.5 2.2 25 627-653 7-31 (40)
4 1nc8_A Nucleocapsid protein; H 87.6 0.22 7.5E-06 31.6 1.5 23 628-652 4-26 (29)
5 1dsq_A Nucleic acid binding pr 84.0 0.54 1.9E-05 28.9 1.9 21 631-653 3-23 (26)
6 2rpr_A Flywch-type zinc finger 79.9 2 6.8E-05 35.0 4.6 24 99-128 51-74 (87)
7 1u6p_A GAG polyprotein; MLV, A 78.1 0.87 3E-05 33.8 1.6 25 628-654 21-45 (56)
8 3kks_A Integrase, IN; beta-str 77.4 9.3 0.00032 33.5 8.9 65 208-282 3-67 (152)
9 2ec7_A GAG polyprotein (PR55GA 75.9 1.6 5.3E-05 31.4 2.4 22 628-651 4-25 (49)
10 2a51_A Nucleocapsid protein; s 72.5 1.9 6.6E-05 29.2 2.1 19 630-650 21-39 (39)
11 2bl6_A Nucleocapsid protein P1 63.4 3.5 0.00012 27.5 1.9 18 632-651 2-19 (37)
12 1a1t_A Nucleocapsid protein; s 61.6 2.8 9.4E-05 30.8 1.2 21 629-651 11-31 (55)
13 2ec7_A GAG polyprotein (PR55GA 60.7 3.2 0.00011 29.7 1.3 21 630-652 27-47 (49)
14 2a51_A Nucleocapsid protein; s 60.0 4.3 0.00015 27.4 1.8 18 632-651 2-19 (39)
15 3l3u_A POL polyprotein; DNA in 59.6 23 0.00078 31.5 7.5 65 207-281 9-73 (163)
16 2bl6_A Nucleocapsid protein P1 59.5 3.6 0.00012 27.4 1.4 18 631-650 20-37 (37)
17 3hph_A Integrase, IN; protein- 59.2 29 0.00099 32.7 8.5 65 208-282 61-125 (219)
18 2ysa_A Retinoblastoma-binding 58.2 5.6 0.00019 29.3 2.3 24 628-653 5-28 (55)
19 1a1t_A Nucleocapsid protein; s 58.1 3.4 0.00012 30.3 1.2 21 630-652 33-53 (55)
20 1cxq_A Avian sarcoma virus int 56.8 57 0.0019 28.9 9.7 71 207-282 11-81 (162)
21 1c0m_A Protein (integrase); HI 55.8 47 0.0016 31.9 9.5 71 207-282 10-80 (238)
22 3alr_A Nanos protein; zinc-fin 55.3 4.1 0.00014 33.7 1.3 24 629-654 70-96 (106)
23 2li8_A Protein LIN-28 homolog 55.2 6.5 0.00022 30.9 2.4 20 629-650 23-42 (74)
24 2cqf_A RNA-binding protein LIN 53.8 13 0.00044 28.0 3.8 21 630-652 29-49 (63)
25 3nyb_B Protein AIR2; polya RNA 51.1 5.5 0.00019 32.0 1.4 23 628-652 3-25 (83)
26 2cqf_A RNA-binding protein LIN 49.6 9.5 0.00033 28.8 2.5 21 629-651 6-26 (63)
27 1cl4_A Protein (GAG polyprotei 48.8 9.2 0.00031 28.5 2.3 23 629-653 29-51 (60)
28 2x78_A Integrase; viral protei 47.4 68 0.0023 29.4 8.9 70 207-282 13-83 (200)
29 2ihx_A Nucleocapsid (NC) prote 46.8 6.9 0.00024 29.3 1.3 23 630-654 30-52 (61)
30 2ihx_A Nucleocapsid (NC) prote 45.3 8.6 0.0003 28.8 1.6 22 629-652 3-24 (61)
31 2li8_A Protein LIN-28 homolog 41.3 13 0.00044 29.1 2.1 23 629-653 45-67 (74)
32 3av9_A Integrase, IN; protein- 40.9 87 0.003 28.4 8.4 66 207-282 29-94 (183)
33 3hot_A Transposable element ma 39.3 1.6E+02 0.0055 29.5 11.0 57 220-279 186-253 (345)
34 2l69_A Rossmann 2X3 fold prote 34.9 28 0.00095 28.1 3.1 30 31-60 6-35 (134)
35 3ts2_A Protein LIN-28 homolog 32.9 18 0.00061 32.5 2.0 18 631-650 98-115 (148)
36 3ts2_A Protein LIN-28 homolog 31.9 17 0.00059 32.6 1.6 23 630-654 119-141 (148)
37 1bco_A MUA domain II, bacterio 30.5 1.1E+02 0.0037 30.9 7.8 72 206-280 15-94 (327)
38 2lli_A Protein AIR2; RNA surve 29.6 27 0.00091 30.1 2.5 9 642-650 52-60 (124)
39 3oym_A PFV integrase, P42IN; p 28.1 3.8E+02 0.013 27.2 11.8 69 208-281 126-194 (395)
40 3f9k_A Integrase; protein-prot 27.9 1.1E+02 0.0038 28.3 6.8 63 208-280 60-122 (210)
41 1fme_A FSD-EY peptide; beta-BE 27.1 35 0.0012 20.2 1.8 20 27-46 6-25 (28)
42 1c6v_A Protein (SIV integrase) 26.6 1.7E+02 0.0057 25.3 7.5 63 208-280 10-72 (164)
43 1cl4_A Protein (GAG polyprotei 26.3 14 0.00048 27.4 0.0 20 631-652 2-21 (60)
44 1x9b_A Hypothetical membrane p 25.7 1.1E+02 0.0038 21.6 4.4 45 307-352 7-51 (53)
45 2lju_A Putative oxidoreductase 25.5 44 0.0015 28.1 2.9 30 26-59 59-88 (108)
46 2jya_A AGR_C_3324P, uncharacte 21.6 40 0.0014 28.3 1.9 28 28-59 53-80 (106)
47 1ex4_A Integrase; SH3-like dom 20.6 1.4E+02 0.0049 28.3 6.2 65 208-282 10-74 (239)
48 2lli_A Protein AIR2; RNA surve 20.5 47 0.0016 28.5 2.3 20 629-650 104-123 (124)
No 1
>2ayd_A WRKY transcription factor 1; beta strands, zinc finger; 1.60A {Arabidopsis thaliana}
Probab=93.45 E-value=0.21 Score=39.52 Aligned_cols=57 Identities=23% Similarity=0.397 Sum_probs=40.2
Q ss_pred cCcEEEEecccccccCCceeEEEEEEccCCcccccccccccccccccccCceeEEEEEEee-CceEEEEEEeecccCCC
Q 046293 50 GGFSIQINSSKICKESNDIIRKEYVCFKEGQARQSKVVNRKRRRGIIRGGCSANLVVVKYE-FGKYMVRIFVEEHNHTL 127 (695)
Q Consensus 50 ~GF~i~~~~s~~~k~~g~~~~~~~~C~r~G~~~~~~~~~~~r~~~~~r~gC~a~i~~~~~~-~~~w~v~~~~~~HNH~l 127 (695)
-||..|+---+..+.+ .--+.+|.|+.. ||||+=.+.+.. +....++.+..+|||++
T Consensus 16 DGy~WRKYGQK~ikgs-~~PRsYYrCt~~--------------------gC~a~K~Ver~~~d~~~~~~tY~G~H~H~~ 73 (76)
T 2ayd_A 16 DGYRWRKYGQKSVKGS-PYPRSYYRCSSP--------------------GCPVKKHVERSSHDTKLLITTYEGKHDHDM 73 (76)
T ss_dssp CSSCEEEEEEECCTTC-SSCEEEEEECST--------------------TCCCEEEEEECSSSTTEEEEEEESCCSSCC
T ss_pred CCchhhhCcccccCCC-CCceeEeEcCCC--------------------CCCceeeEEEECCCCCEEEEEEccCcCCCC
Confidence 4777776444333322 223567888742 799999998865 77888999999999976
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=92.78 E-value=0.17 Score=40.16 Aligned_cols=57 Identities=26% Similarity=0.413 Sum_probs=39.2
Q ss_pred cCcEEEEecccccccCCceeEEEEEEccCCcccccccccccccccccccCceeEEEEEEee-CceEEEEEEeecccCCC
Q 046293 50 GGFSIQINSSKICKESNDIIRKEYVCFKEGQARQSKVVNRKRRRGIIRGGCSANLVVVKYE-FGKYMVRIFVEEHNHTL 127 (695)
Q Consensus 50 ~GF~i~~~~s~~~k~~g~~~~~~~~C~r~G~~~~~~~~~~~r~~~~~r~gC~a~i~~~~~~-~~~w~v~~~~~~HNH~l 127 (695)
-||..|+---+..+.+ .--+.+|.|+.. ||+|+=.+.+.. ++.-.++.+..+|||++
T Consensus 19 DGy~WRKYGQK~ikgs-~~PRsYYrCt~~--------------------gC~a~K~Ver~~~d~~~~~~tY~G~H~H~~ 76 (78)
T 1wj2_A 19 DGYRWRKYGQKVVKGN-PYPRSYYKCTTP--------------------GCGVRKHVERAATDPKAVVTTYEGKHNHDL 76 (78)
T ss_dssp SSSCBCCCEEECCTTC-SSCEEEEEEECS--------------------SCEEEEEEEEETTTTSEEEEEEESCCSSCC
T ss_pred CCchhhhCcccccCCC-cCeeEEeecCcC--------------------CCCcEeeEEEEcCCCCEEEEEEeeEcCCCC
Confidence 4566654433222222 234667888752 799999998865 77888899999999976
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=89.27 E-value=0.19 Score=34.52 Aligned_cols=25 Identities=20% Similarity=0.497 Sum_probs=21.1
Q ss_pred CCCcccCCCCCCCCCCCCCCCCcchhh
Q 046293 627 KDKGRRCNGCGLVGQSHDKRNCPLLIK 653 (695)
Q Consensus 627 ~kr~~~C~~C~~~~~GHn~~tCp~~~~ 653 (695)
.+....|-.|+ ..||-.+.||....
T Consensus 7 ~~~~~~C~~Cg--k~GH~ardCP~~~~ 31 (40)
T 1a6b_B 7 QLDRDQCAYCK--EKGHWAKDCPKKPR 31 (40)
T ss_dssp SCCSSSCSSSC--CTTCCTTSCSSSCC
T ss_pred CCCCCeeeECC--CCCcchhhCcCCcc
Confidence 35568999999 67999999999765
No 4
>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=87.55 E-value=0.22 Score=31.60 Aligned_cols=23 Identities=35% Similarity=0.660 Sum_probs=19.2
Q ss_pred CCcccCCCCCCCCCCCCCCCCcchh
Q 046293 628 DKGRRCNGCGLVGQSHDKRNCPLLI 652 (695)
Q Consensus 628 kr~~~C~~C~~~~~GHn~~tCp~~~ 652 (695)
++...|-+|+ ..||-.+.||...
T Consensus 4 r~~~~C~nCg--k~GH~ar~C~~pr 26 (29)
T 1nc8_A 4 RKVIRCWNCG--KEGHSARQCRAPR 26 (29)
T ss_dssp CCCCBCTTTS--CBSSCGGGCCSSS
T ss_pred CCCCEEEECC--ccccCHhHCcccc
Confidence 4567899999 6899999999753
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=83.99 E-value=0.54 Score=28.93 Aligned_cols=21 Identities=33% Similarity=0.620 Sum_probs=17.0
Q ss_pred ccCCCCCCCCCCCCCCCCcchhh
Q 046293 631 RRCNGCGLVGQSHDKRNCPLLIK 653 (695)
Q Consensus 631 ~~C~~C~~~~~GHn~~tCp~~~~ 653 (695)
..|-+|+ ..||..+.||..+.
T Consensus 3 ~~Cf~CG--~~GH~ardC~~~~~ 23 (26)
T 1dsq_A 3 PVCFSCG--KTGHIKRDCKEEXX 23 (26)
T ss_dssp CBCTTTC--CBSSCTTTTTCC--
T ss_pred CeeEeCC--CCCcccccCCCccc
Confidence 5799999 68999999997643
No 6
>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=79.91 E-value=2 Score=34.95 Aligned_cols=24 Identities=17% Similarity=0.470 Sum_probs=17.1
Q ss_pred CceeEEEEEEeeCceEEEEEEeecccCCCC
Q 046293 99 GCSANLVVVKYEFGKYMVRIFVEEHNHTLS 128 (695)
Q Consensus 99 gC~a~i~~~~~~~~~w~v~~~~~~HNH~l~ 128 (695)
+|+|++.... ++ + .....||||+.
T Consensus 51 kCrARi~T~~--~~---~-~~~~~HnH~p~ 74 (87)
T 2rpr_A 51 GCRSRAITQG--HR---I-MVMRSHCHQPD 74 (87)
T ss_dssp CCCCEEEEET--TE---E-EECSCCSSCCC
T ss_pred CCCEEEEEcC--CC---E-ECCCCcCCCCc
Confidence 7999988753 22 2 35678999774
No 7
>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=78.12 E-value=0.87 Score=33.78 Aligned_cols=25 Identities=20% Similarity=0.464 Sum_probs=20.9
Q ss_pred CCcccCCCCCCCCCCCCCCCCcchhhh
Q 046293 628 DKGRRCNGCGLVGQSHDKRNCPLLIKR 654 (695)
Q Consensus 628 kr~~~C~~C~~~~~GHn~~tCp~~~~~ 654 (695)
.....|-.|| ..||-.+.||.....
T Consensus 21 ~~~~~C~~Cg--e~GH~ardCp~~~~~ 45 (56)
T 1u6p_A 21 LDRDQCAYCK--EKGHWAKDCPKKPRG 45 (56)
T ss_dssp CCTTBCSSSC--CBSSCGGGCTTCCCS
T ss_pred CCCCcceeCC--CCCcccccCcCCccc
Confidence 4557999999 689999999997653
No 8
>3kks_A Integrase, IN; beta-strands flanked by alpha-helices, DNA binding protein; 2.20A {Bovine immunodeficiency virus} PDB: 3kkr_A
Probab=77.41 E-value=9.3 Score=33.54 Aligned_cols=65 Identities=14% Similarity=0.119 Sum_probs=47.4
Q ss_pred cEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh
Q 046293 208 DVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL 282 (695)
Q Consensus 208 dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~ 282 (695)
++..+|.|+..++ +.++.+|..-+.+ +++.+ .+++.+...-++..+....+ |.+|.||+......
T Consensus 3 ~~w~~D~t~~~~~-----y~~~~iD~~sr~~-~~~~~-~~~~~~~~~~~l~~~~~~~g---p~~i~sDnG~~f~s 67 (152)
T 3kks_A 3 HLWQMDNTHWNKT-----IIWVAVETNSGLV-EAQVI-PEETALQVALCILQLIQRYT---VLHLHSDNGPCFTA 67 (152)
T ss_dssp CEEEEEEEEETTE-----EEEEEEETTTCCE-EEEEE-SSSCHHHHHHHHHHHHHHSC---CSEEEECSCHHHHS
T ss_pred cEEEEeeeeeCCE-----EEEEEEEcCCCcE-EEEEe-CCcCHHHHHHHHHHHHHHhC---CcEEecCCchHhhH
Confidence 5778999987433 5666778776655 55544 57888877777777766665 99999999988654
No 9
>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=75.87 E-value=1.6 Score=31.38 Aligned_cols=22 Identities=36% Similarity=0.726 Sum_probs=15.8
Q ss_pred CCcccCCCCCCCCCCCCCCCCcch
Q 046293 628 DKGRRCNGCGLVGQSHDKRNCPLL 651 (695)
Q Consensus 628 kr~~~C~~C~~~~~GHn~~tCp~~ 651 (695)
++...|-+|+ ..||..+.||..
T Consensus 4 ~r~~~C~~Cg--~~GH~a~~C~~~ 25 (49)
T 2ec7_A 4 RKVIRCWNCG--KEGHSARQCRAP 25 (49)
T ss_dssp CCCCBCTTTC--CBTCCTTTCCCS
T ss_pred CCcCeeeecC--CCCcChhhCcCC
Confidence 4556788888 568888888764
No 10
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=72.52 E-value=1.9 Score=29.17 Aligned_cols=19 Identities=32% Similarity=0.814 Sum_probs=15.8
Q ss_pred cccCCCCCCCCCCCCCCCCcc
Q 046293 630 GRRCNGCGLVGQSHDKRNCPL 650 (695)
Q Consensus 630 ~~~C~~C~~~~~GHn~~tCp~ 650 (695)
...|-+|+ ..||-.+.||+
T Consensus 21 ~~~C~~Cg--~~GH~~~~C~~ 39 (39)
T 2a51_A 21 QEGCWNCG--SKEHRFAQCPK 39 (39)
T ss_dssp CSSCTTTC--CSSSCTTTSCC
T ss_pred CCccccCC--CCCCccCcCcC
Confidence 35899999 67999999985
No 11
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=63.44 E-value=3.5 Score=27.51 Aligned_cols=18 Identities=28% Similarity=0.689 Sum_probs=14.5
Q ss_pred cCCCCCCCCCCCCCCCCcch
Q 046293 632 RCNGCGLVGQSHDKRNCPLL 651 (695)
Q Consensus 632 ~C~~C~~~~~GHn~~tCp~~ 651 (695)
.|-+|+ ..||..+.||..
T Consensus 2 ~C~~Cg--~~GH~~~~C~~~ 19 (37)
T 2bl6_A 2 TCYNCG--KPGHLSSQCRAP 19 (37)
T ss_dssp CBSSSC--CSSCCTTTSSCB
T ss_pred cccccC--CCCcchhhCcCc
Confidence 588888 679988888864
No 12
>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=61.59 E-value=2.8 Score=30.79 Aligned_cols=21 Identities=33% Similarity=0.732 Sum_probs=13.7
Q ss_pred CcccCCCCCCCCCCCCCCCCcch
Q 046293 629 KGRRCNGCGLVGQSHDKRNCPLL 651 (695)
Q Consensus 629 r~~~C~~C~~~~~GHn~~tCp~~ 651 (695)
+...|-+|+ ..||-.+.||..
T Consensus 11 ~~~~C~~Cg--~~GH~a~~C~~~ 31 (55)
T 1a1t_A 11 KTVKCFNCG--KEGHIAKNCRAP 31 (55)
T ss_dssp GTCBCTTTC--CBSSCGGGCSSC
T ss_pred CCcceeeeC--CCCcChhhcCCC
Confidence 445677777 557777777654
No 13
>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=60.67 E-value=3.2 Score=29.72 Aligned_cols=21 Identities=29% Similarity=0.601 Sum_probs=17.9
Q ss_pred cccCCCCCCCCCCCCCCCCcchh
Q 046293 630 GRRCNGCGLVGQSHDKRNCPLLI 652 (695)
Q Consensus 630 ~~~C~~C~~~~~GHn~~tCp~~~ 652 (695)
...|-.|+ ..||-.+.||...
T Consensus 27 ~~~C~~Cg--~~GH~~~~C~~~~ 47 (49)
T 2ec7_A 27 RQGCWKCG--KTGHVMAKCPERQ 47 (49)
T ss_dssp CCSCSSSC--CSSCCGGGCCSSC
T ss_pred CCeeCcCC--CcCCccCCCcCCC
Confidence 35799999 6899999999754
No 14
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=60.05 E-value=4.3 Score=27.42 Aligned_cols=18 Identities=33% Similarity=0.752 Sum_probs=16.1
Q ss_pred cCCCCCCCCCCCCCCCCcch
Q 046293 632 RCNGCGLVGQSHDKRNCPLL 651 (695)
Q Consensus 632 ~C~~C~~~~~GHn~~tCp~~ 651 (695)
.|-+|+ ..||..+.||..
T Consensus 2 ~C~~Cg--~~GH~a~~C~~~ 19 (39)
T 2a51_A 2 TCFNCG--KPGHTARMCRQP 19 (39)
T ss_dssp BCTTTC--CBSSCTTTCCSC
T ss_pred eeeccC--CCCcccccCCCC
Confidence 699999 689999999975
No 15
>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=59.55 E-value=23 Score=31.55 Aligned_cols=65 Identities=17% Similarity=0.159 Sum_probs=46.1
Q ss_pred CcEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHH
Q 046293 207 GDVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMI 281 (695)
Q Consensus 207 ~dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~ 281 (695)
.+++.+|.|+..++ +.++.+|.....+ +++.+ .+++.+...-++..+....+ +.+|.||+.....
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 36888999998653 4667778877654 55555 56677777777776666654 4799999988753
No 16
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=59.54 E-value=3.6 Score=27.40 Aligned_cols=18 Identities=22% Similarity=0.577 Sum_probs=16.0
Q ss_pred ccCCCCCCCCCCCCCCCCcc
Q 046293 631 RRCNGCGLVGQSHDKRNCPL 650 (695)
Q Consensus 631 ~~C~~C~~~~~GHn~~tCp~ 650 (695)
..|-+|+ ..||-.+.||+
T Consensus 20 ~~C~~Cg--~~GH~a~~C~~ 37 (37)
T 2bl6_A 20 KVCFKCK--QPGHFSKQCRS 37 (37)
T ss_dssp TTCSSCC--CTTGGGGTTCC
T ss_pred CeEccCC--CcCCccCcCcC
Confidence 5899999 67999999985
No 17
>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=59.18 E-value=29 Score=32.73 Aligned_cols=65 Identities=22% Similarity=0.279 Sum_probs=45.0
Q ss_pred cEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh
Q 046293 208 DVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL 282 (695)
Q Consensus 208 dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~ 282 (695)
+++.+|.|+..++ +.++.+|..-..+ +++. +.+.+.+...-++..+....| |.+|+||+......
T Consensus 61 ~~w~~D~t~~~~~-----y~~~~iD~~Sr~~-~~~~-~~~~~~~~~~~~l~~~~~~~g---p~~i~sDnG~~F~s 125 (219)
T 3hph_A 61 DHWQVDYTHYEDK-----IILVWVETNSGLI-YAER-VKGETGQEFRVQTMKWYAMFA---PKSLQSDNGPAFVA 125 (219)
T ss_dssp CEEEEEEEEETTE-----EEEEEEETTTCCE-EEEE-ESCCCHHHHHHHHHHHHHHHC---CCEEEECCCHHHHS
T ss_pred ceEEEEEecCCCE-----EEEEEEeCCCCcE-EEEE-eCCCCHHHHHHHHHHHHHHhC---CcEEEeCCCchhhh
Confidence 5777888876543 4567778777655 4444 556677666666666555554 89999999998654
No 18
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=58.22 E-value=5.6 Score=29.26 Aligned_cols=24 Identities=33% Similarity=0.670 Sum_probs=19.6
Q ss_pred CCcccCCCCCCCCCCCCCCCCcchhh
Q 046293 628 DKGRRCNGCGLVGQSHDKRNCPLLIK 653 (695)
Q Consensus 628 kr~~~C~~C~~~~~GHn~~tCp~~~~ 653 (695)
...+.|=+|+ ..||-.+.||....
T Consensus 5 p~~~~C~kCG--k~GH~~k~Cp~~~~ 28 (55)
T 2ysa_A 5 SSGYTCFRCG--KPGHYIKNCPTNGD 28 (55)
T ss_dssp SSSCCCTTTC--CTTSCGGGCSGGGC
T ss_pred CCCCccccCC--CcCcccccCCCCCC
Confidence 3557899999 67999999996554
No 19
>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=58.14 E-value=3.4 Score=30.27 Aligned_cols=21 Identities=24% Similarity=0.661 Sum_probs=18.0
Q ss_pred cccCCCCCCCCCCCCCCCCcchh
Q 046293 630 GRRCNGCGLVGQSHDKRNCPLLI 652 (695)
Q Consensus 630 ~~~C~~C~~~~~GHn~~tCp~~~ 652 (695)
...|-.|+ ..||-.+.||...
T Consensus 33 ~~~C~~Cg--~~GH~~~~C~~~~ 53 (55)
T 1a1t_A 33 KKGCWKCG--KEGHQMKDCTERQ 53 (55)
T ss_dssp CCBCTTTC--CBSSCGGGCSSSC
T ss_pred CCEeCCCC--CcCCccCCCcCcC
Confidence 46899999 6899999999754
No 20
>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=56.84 E-value=57 Score=28.87 Aligned_cols=71 Identities=15% Similarity=-0.004 Sum_probs=47.5
Q ss_pred CcEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh
Q 046293 207 GDVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL 282 (695)
Q Consensus 207 ~dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~ 282 (695)
.+++.+|.|+..... +-.+.++.+|..-..+ +|+.+- +.+.+...-+|+.+....+ .|.+|.||+......
T Consensus 11 ~~~~~~D~~~~~~~~-g~~yl~~~iD~~Sr~i-~~~~~~-~~~~~~v~~~l~~~~~~~g--~p~~i~sDnG~~f~s 81 (162)
T 1cxq_A 11 LQIWQTDFTLEPRMA-PRSWLAVTVDTASSAI-VVTQHG-RVTSVAAQHHWATAIAVLG--RPKAIKTDNGSCFTS 81 (162)
T ss_dssp CCEEEEEEEECGGGT-TSCEEEEEEETTTCCE-EEEEES-SCCHHHHHHHHHHHHHHHC--CCSEEECCSCHHHHS
T ss_pred CCEEEeeeeecccCC-CCEEEEEEEEcCCCeE-EEEECC-CccHHHHHHHHHHHHHHHC--CCeEEEeCCchhhhh
Confidence 357888888865432 3355667788776544 566655 6777776666666555544 478999999988654
No 21
>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=55.78 E-value=47 Score=31.89 Aligned_cols=71 Identities=15% Similarity=0.008 Sum_probs=49.9
Q ss_pred CcEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh
Q 046293 207 GDVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL 282 (695)
Q Consensus 207 ~dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~ 282 (695)
.+++.+|.|+..... +-.+.++.+|..-.. ++|+.+- +++.+...-+|.......+ .|.+|.||+......
T Consensus 10 ~~~w~~D~~~~~~~~-g~~yl~~~iD~~Sr~-i~~~~~~-~~~~~~v~~~l~~~~~~~g--~p~~i~sDnG~~f~s 80 (238)
T 1c0m_A 10 LQIWQTDFTLEPRMA-PRSWLAVTVDTASSA-IVVTQHG-RVTSVAVQHHWATAIAVLG--RPKAIKTDNGSCFTS 80 (238)
T ss_dssp TSEEEEEEEECGGGC-SSCEEEEEEETTTCC-EEEEEES-SCCHHHHHHHHHHHHHHHC--CCSEEEECSCHHHHS
T ss_pred CCEEEEeeccccccC-CCEEEEEEEECCCCC-EEEEEcc-CCCHHHHHHHHHHHHHHhC--CCcEEEECCCCcccc
Confidence 357889998865433 335566777776554 4566665 8888887777776666655 488999999998754
No 22
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=55.35 E-value=4.1 Score=33.70 Aligned_cols=24 Identities=38% Similarity=0.861 Sum_probs=21.1
Q ss_pred CcccCCCCCCCCCC---CCCCCCcchhhh
Q 046293 629 KGRRCNGCGLVGQS---HDKRNCPLLIKR 654 (695)
Q Consensus 629 r~~~C~~C~~~~~G---Hn~~tCp~~~~~ 654 (695)
|.+.|..|| ..| |+++-||+....
T Consensus 70 R~Y~CpiCG--ATGd~AHT~kYCP~~~~~ 96 (106)
T 3alr_A 70 RQYKCPLCG--ATGAKAHTKRFCPMVDKN 96 (106)
T ss_dssp GGCCCTTTC--CCGGGCCCGGGCTTCGGG
T ss_pred ccccCCCCC--CcCCcccceecCCCCCCc
Confidence 568999999 889 999999998764
No 23
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=55.17 E-value=6.5 Score=30.86 Aligned_cols=20 Identities=50% Similarity=1.212 Sum_probs=13.5
Q ss_pred CcccCCCCCCCCCCCCCCCCcc
Q 046293 629 KGRRCNGCGLVGQSHDKRNCPL 650 (695)
Q Consensus 629 r~~~C~~C~~~~~GHn~~tCp~ 650 (695)
+...|-+|+ ..||..+.||.
T Consensus 23 r~~~C~~Cg--~~GH~a~~C~~ 42 (74)
T 2li8_A 23 KGDRCYNCG--GLDHHAKECKL 42 (74)
T ss_dssp TTSCCTTTC--CSSSCTTTCSS
T ss_pred CCCcccccC--CcCcCcccCCC
Confidence 445677777 56777777775
No 24
>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=53.79 E-value=13 Score=28.04 Aligned_cols=21 Identities=33% Similarity=0.703 Sum_probs=13.6
Q ss_pred cccCCCCCCCCCCCCCCCCcchh
Q 046293 630 GRRCNGCGLVGQSHDKRNCPLLI 652 (695)
Q Consensus 630 ~~~C~~C~~~~~GHn~~tCp~~~ 652 (695)
...|-+|+ ..||-.+.||...
T Consensus 29 ~~~C~~Cg--~~GH~ar~Cp~~~ 49 (63)
T 2cqf_A 29 PKKCHFCQ--SISHMVASCPLKA 49 (63)
T ss_dssp SSCCTTTC--CSSSCTTTCTGGG
T ss_pred CCccCCcC--CcCCccCcCCCcc
Confidence 45677777 4577777777654
No 25
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=51.05 E-value=5.5 Score=32.04 Aligned_cols=23 Identities=30% Similarity=0.650 Sum_probs=16.9
Q ss_pred CCcccCCCCCCCCCCCCCCCCcchh
Q 046293 628 DKGRRCNGCGLVGQSHDKRNCPLLI 652 (695)
Q Consensus 628 kr~~~C~~C~~~~~GHn~~tCp~~~ 652 (695)
-+...|-+|+ ..||-.+.||...
T Consensus 3 ~k~~~C~~Cg--~~GH~~~~Cp~~~ 25 (83)
T 3nyb_B 3 WKKVQCTLCK--SKKHSKERCPSIW 25 (83)
T ss_dssp ----CCSSSC--CSSSCGGGCGGGT
T ss_pred cccCCCCCCC--CCCCccccCCCcc
Confidence 3557899999 6799999999853
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=49.57 E-value=9.5 Score=28.79 Aligned_cols=21 Identities=43% Similarity=1.069 Sum_probs=18.1
Q ss_pred CcccCCCCCCCCCCCCCCCCcch
Q 046293 629 KGRRCNGCGLVGQSHDKRNCPLL 651 (695)
Q Consensus 629 r~~~C~~C~~~~~GHn~~tCp~~ 651 (695)
+...|-+|+ ..||..+.||..
T Consensus 6 r~~~C~~Cg--~~GH~a~~C~~~ 26 (63)
T 2cqf_A 6 SGDRCYNCG--GLDHHAKECKLP 26 (63)
T ss_dssp SCCCCSSSC--CSSSCTTTCCSC
T ss_pred CCCcccccC--CCCcChhhCCCC
Confidence 456899999 689999999974
No 27
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A
Probab=48.83 E-value=9.2 Score=28.46 Aligned_cols=23 Identities=17% Similarity=0.289 Sum_probs=19.4
Q ss_pred CcccCCCCCCCCCCCCCCCCcchhh
Q 046293 629 KGRRCNGCGLVGQSHDKRNCPLLIK 653 (695)
Q Consensus 629 r~~~C~~C~~~~~GHn~~tCp~~~~ 653 (695)
+...|-+|+ ..||-.+.||....
T Consensus 29 ~~~~C~~Cg--~~GH~ar~C~~~~~ 51 (60)
T 1cl4_A 29 VPGLCPRCK--RGKHWANECKSKTD 51 (60)
T ss_dssp CCCSCSSCS--SCSSCSTTCCCTTS
T ss_pred CCcceeECC--CCCCccCcCCCccc
Confidence 457899999 68999999998654
No 28
>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=47.42 E-value=68 Score=29.40 Aligned_cols=70 Identities=14% Similarity=0.001 Sum_probs=45.7
Q ss_pred CcEEEEec-ccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh
Q 046293 207 GDVIVFDT-TYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL 282 (695)
Q Consensus 207 ~dVl~iD~-Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~ 282 (695)
.+++.+|- ++.... ++..+.++.+|..-..+ +++.+ .+.+.+...-+| ..++....|.+|.||+......
T Consensus 13 ~~~~~~D~~~~~~~~-~g~~y~~~~iD~~Sr~~-~~~~~-~~~~~~~~~~~l---~~~~~~g~p~~i~sDnG~~f~s 83 (200)
T 2x78_A 13 FDKFFIDYIGPLPPS-QGYLYVLVVVDGMTGFT-WLYPT-KAPSTSATVKSL---NVLTSIAIPRVIHSDQGAAFTS 83 (200)
T ss_dssp TSEEEEEEECCCSCB-TTBCEEEEEEETTTCCE-EEEEE-SSSCHHHHHHHH---HHHTTTCCCSEEEECSCHHHHS
T ss_pred ccEEEEEEeCCCccC-CCCeEEEEEEeCCCCcE-EEEEC-CCCCHHHHHHHH---HHHHHhCCCcEEEecCCcceeh
Confidence 35788886 554433 44566777788776644 56665 666666654444 3444446789999999987654
No 29
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=46.78 E-value=6.9 Score=29.34 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=17.0
Q ss_pred cccCCCCCCCCCCCCCCCCcchhhh
Q 046293 630 GRRCNGCGLVGQSHDKRNCPLLIKR 654 (695)
Q Consensus 630 ~~~C~~C~~~~~GHn~~tCp~~~~~ 654 (695)
...|-+|+ ..||-.+.||.....
T Consensus 30 ~~~C~~Cg--~~GH~ar~C~~~~~~ 52 (61)
T 2ihx_A 30 RERCQLCN--GMGHNAKQCRKRDGN 52 (61)
T ss_dssp CSBCTTTC--CBSSCGGGCCCCC--
T ss_pred CCeeCCCC--CCCCCcCCCcCCCcC
Confidence 35799999 679999999886553
No 30
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=45.34 E-value=8.6 Score=28.80 Aligned_cols=22 Identities=27% Similarity=0.613 Sum_probs=18.7
Q ss_pred CcccCCCCCCCCCCCCCCCCcchh
Q 046293 629 KGRRCNGCGLVGQSHDKRNCPLLI 652 (695)
Q Consensus 629 r~~~C~~C~~~~~GHn~~tCp~~~ 652 (695)
....|-+|+ ..||-.+.||...
T Consensus 3 ~~~~C~~Cg--~~GH~a~~C~~~~ 24 (61)
T 2ihx_A 3 ARGLCYTCG--SPGHYQAQCPKKR 24 (61)
T ss_dssp CTTBCSSSC--CBTCCGGGCTTTT
T ss_pred CCCcccccC--CCCeehhhCcCCc
Confidence 346899999 6899999999874
No 31
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=41.26 E-value=13 Score=29.14 Aligned_cols=23 Identities=30% Similarity=0.686 Sum_probs=19.6
Q ss_pred CcccCCCCCCCCCCCCCCCCcchhh
Q 046293 629 KGRRCNGCGLVGQSHDKRNCPLLIK 653 (695)
Q Consensus 629 r~~~C~~C~~~~~GHn~~tCp~~~~ 653 (695)
+...|-+|+ ..||-.+.||....
T Consensus 45 ~~~~C~~Cg--~~GH~ar~Cp~~~~ 67 (74)
T 2li8_A 45 QPKKCHFCQ--SISHMVASCPLKAQ 67 (74)
T ss_dssp CCCCCTTTC--CTTSCGGGCTTGGG
T ss_pred CCCccCCcC--CcCCccCcCcCCcC
Confidence 457899999 68999999998764
No 32
>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=40.89 E-value=87 Score=28.37 Aligned_cols=66 Identities=17% Similarity=0.140 Sum_probs=39.2
Q ss_pred CcEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh
Q 046293 207 GDVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL 282 (695)
Q Consensus 207 ~dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~ 282 (695)
.+++.+|.|+..++| .++.+|..-..+ +++.+ .+.+.+...-++..+....+ +.+|.||+......
T Consensus 29 ~~~w~~D~~~~~g~~-----~l~~vD~~Sr~~-~~~~~-~~~~~~~~~~~~~~~~~~~~---~~~i~sDnG~ef~s 94 (183)
T 3av9_A 29 PGIWQLDCTHLEGKV-----ILVAVHVASGYI-EAEVI-PAETGQETAYFLLKLAGRWP---VKTVHTDNGSNFTS 94 (183)
T ss_dssp TTEEEEEEEEETTEE-----EEEEEETTTTEE-EEEEE-SSCCHHHHHHHHHHHHHHSC---CCEEECSSHHHHHC
T ss_pred CCEEEEeccccCCcE-----EEEEEECCCCCE-EEEEe-CCccchHHHHHHHHHHHHcC---CcEEEecCchhcch
Confidence 356777777763332 344456665544 56654 45555555544444444442 48999999988654
No 33
>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=39.32 E-value=1.6e+02 Score=29.55 Aligned_cols=57 Identities=14% Similarity=0.257 Sum_probs=37.6
Q ss_pred CCCCceeeEeEEecCCceEEEEEEecc---CCChhhHHHHHHHHHHHC----CC----CCCceeecCChHH
Q 046293 220 RYNMIFAPFVGVNNHGQTIIFGCGFLS---DETTESFLWLFEQFKEAM----PG----DDPKMIITDQDPA 279 (695)
Q Consensus 220 ~y~~pL~~~~g~d~~~~~~~~~~al~~---~E~~es~~W~l~~f~~~~----~~----~~p~~iitD~~~a 279 (695)
..+.-+....+++..| ++++.++. .-+.+.|.-+|+.++..+ +. ..+.+|+.|....
T Consensus 186 ~~~~~~~v~~~~~~~g---~~~~~~~~~~~~~~~~~y~~~L~~~~~~~~~~~p~~~~~~~~~~~~~Dna~~ 253 (345)
T 3hot_A 186 RFGKKTMLCVWWDQSG---VIYYELLKPGETVNAARYQQQLINLNRALQRKRPEYQKRQHRVIFLHDNAPS 253 (345)
T ss_dssp TTCCEEEEEEEEESSS---EEEEEEECSSCCCCHHHHHHHHHHHHHHHHHHSTTCC---CCCEEECCCCTT
T ss_pred CcCCcEEEEEEEcccC---ceeeEecCCCCcccHHHHHHHHHHHHHHHHHhchhhhcCCCceEEEECCCCc
Confidence 4455556666677666 56677766 457888888888776554 22 2366899999664
No 34
>2l69_A Rossmann 2X3 fold protein; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Artificial gene}
Probab=34.94 E-value=28 Score=28.09 Aligned_cols=30 Identities=23% Similarity=0.387 Sum_probs=24.5
Q ss_pred CccCCHHHHHHHHHHHhhhcCcEEEEeccc
Q 046293 31 KKFDTLDDAYEFYKKYAKEGGFSIQINSSK 60 (695)
Q Consensus 31 ~~F~S~eea~~~y~~yA~~~GF~i~~~~s~ 60 (695)
.+|.+.||...-+.+.-+++||.||.-+|.
T Consensus 6 vvfstdeetlrkfkdiikkngfkvrtvrsp 35 (134)
T 2l69_A 6 VVFSTDEETLRKFKDIIKKNGFKVRTVRSP 35 (134)
T ss_dssp EECCCCHHHHHHHHHHHHHTTCEEEEECSH
T ss_pred EEEeCCHHHHHHHHHHHHhcCceEEEecCH
Confidence 368888888888888888999999887773
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=32.91 E-value=18 Score=32.47 Aligned_cols=18 Identities=44% Similarity=1.165 Sum_probs=9.2
Q ss_pred ccCCCCCCCCCCCCCCCCcc
Q 046293 631 RRCNGCGLVGQSHDKRNCPL 650 (695)
Q Consensus 631 ~~C~~C~~~~~GHn~~tCp~ 650 (695)
.+|-+|+ ..||-.+.||.
T Consensus 98 ~~C~~Cg--~~GH~a~~C~~ 115 (148)
T 3ts2_A 98 DRCYNCG--GLDHHAKECKL 115 (148)
T ss_dssp CCCTTTC--CSSCCGGGCCS
T ss_pred CcccEeC--CccchhhhCCC
Confidence 3455555 34555555554
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=31.93 E-value=17 Score=32.61 Aligned_cols=23 Identities=26% Similarity=0.667 Sum_probs=19.2
Q ss_pred cccCCCCCCCCCCCCCCCCcchhhh
Q 046293 630 GRRCNGCGLVGQSHDKRNCPLLIKR 654 (695)
Q Consensus 630 ~~~C~~C~~~~~GHn~~tCp~~~~~ 654 (695)
...|-+|+ ..||-.+.||.....
T Consensus 119 ~~~C~~Cg--~~GH~~r~Cp~~~~~ 141 (148)
T 3ts2_A 119 PKKCHFCQ--SINHMVASCPLKAQQ 141 (148)
T ss_dssp CCCCTTTC--CSSCCGGGCTTTTC-
T ss_pred CCcccccC--CcCCEeccCcCCCCC
Confidence 57899999 679999999987553
No 37
>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=30.52 E-value=1.1e+02 Score=30.91 Aligned_cols=72 Identities=14% Similarity=-0.016 Sum_probs=49.5
Q ss_pred CCcEEEEecccccCC----CCC--ceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCc--eeecCCh
Q 046293 206 YGDVIVFDTTYNTNR----YNM--IFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPK--MIITDQD 277 (695)
Q Consensus 206 f~dVl~iD~Ty~tn~----y~~--pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~--~iitD~~ 277 (695)
-.+++.+|.|+..-. .+. -....+.+|..-. .++|+.+...++.++..-+|.......+ .|. .|.+|+.
T Consensus 15 p~~~w~~D~t~~d~~~~~~~g~~~r~~l~~~iD~~SR-~ivg~~~~~~~~~~~v~~aL~~a~~~~G--~P~~~~i~sDnG 91 (327)
T 1bco_A 15 AMQWINGDGYLHNVFVRWFNGDVIRPKTWFWQDVKTR-KILGWRCDVSENIDSIRLSFMDVVTRYG--IPEDFHITIDNT 91 (327)
T ss_dssp TTTEEEEEEEECSBCEECTTSCEECCEEEEEEETTTC-CEEEEEEESSCCHHHHHHHHHHHHHHHC--EESSCEEECCCT
T ss_pred CCcEEEecCCEEEEEEECCCCccceeEEEEEEECCCC-cEEEEEEECCCCHHHHHHHHHHHHHhcC--CCCCcEEEeeCc
Confidence 346888998875432 121 2445566777655 4578999889998888777776665544 567 9999997
Q ss_pred HHH
Q 046293 278 PAM 280 (695)
Q Consensus 278 ~al 280 (695)
.+.
T Consensus 92 ~~f 94 (327)
T 1bco_A 92 RGA 94 (327)
T ss_dssp TST
T ss_pred hhh
Confidence 664
No 38
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=29.63 E-value=27 Score=30.14 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=3.8
Q ss_pred CCCCCCCcc
Q 046293 642 SHDKRNCPL 650 (695)
Q Consensus 642 GHn~~tCp~ 650 (695)
||..+.||.
T Consensus 52 GH~~~~C~~ 60 (124)
T 2lli_A 52 GHYRSQCPH 60 (124)
T ss_dssp SSSTTTSCC
T ss_pred CCccccCcC
Confidence 444444443
No 39
>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=28.15 E-value=3.8e+02 Score=27.24 Aligned_cols=69 Identities=16% Similarity=0.034 Sum_probs=41.5
Q ss_pred cEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHH
Q 046293 208 DVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMI 281 (695)
Q Consensus 208 dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~ 281 (695)
.++.+|-+.---.-++-.+.++.+|..-.. +.++.+ .+.+.+...-++ .+.. ....|..|+||+.....
T Consensus 126 ~~~~~D~~~~~~~~~g~~y~l~~vD~~sr~-~~~~~~-~~~~~~~~~~~l-~~~~--~~g~p~~i~sDnG~~f~ 194 (395)
T 3oym_A 126 DKFFIDYIGPLPPSQGYLYVLVVVDGMTGF-TWLYPT-KAPSTSATVKSL-NVLT--SIAIPKVIHSDQGAAFT 194 (395)
T ss_dssp SEEEEEEECCCSCBTTBCEEEEEEETTTCC-EEEEEE-SSSCHHHHHHHH-HHHT--TTCCCSEEEECSCHHHH
T ss_pred eEEEEEEecccCCCCCccEEEEEEecCCce-EEEEEe-cCCcHHHHHHHh-hHhh--ccCCceEEEeCCCCcee
Confidence 578888654222224556677778877654 445554 445555555555 2222 22568999999987653
No 40
>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=27.90 E-value=1.1e+02 Score=28.34 Aligned_cols=63 Identities=14% Similarity=0.120 Sum_probs=41.3
Q ss_pred cEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHH
Q 046293 208 DVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAM 280 (695)
Q Consensus 208 dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al 280 (695)
.++.+|.|+..++| .++.+|..-. ++.++. +.+++.+...-++..+....+ +.+|+||+....
T Consensus 60 ~~w~~D~~~~~~~y-----~l~~vD~~sr-~~~~~~-~~~~~~~~~~~~l~~~~~~~g---~~~i~sDnG~~F 122 (210)
T 3f9k_A 60 GTWQMDCTHLEGKI-----IIVAVHVASG-FIEAEV-IPQESGRQTALFLLKLASRWP---ITHLHTDNGANF 122 (210)
T ss_dssp TEEEEEEEEETTEE-----EEEEEETTTT-EEEEEE-ESSCCHHHHHHHHHHHHTTSC---CSEEEECCCTTT
T ss_pred CeEeEeecccCCeE-----EEEEEEcCCC-cEEEEE-eCCcchHHHHHHHHHHHHHcC---CCEEEeCCCchh
Confidence 47788988876543 5666777766 455554 455777777766665444443 346999997754
No 41
>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=27.10 E-value=35 Score=20.22 Aligned_cols=20 Identities=25% Similarity=0.549 Sum_probs=17.3
Q ss_pred CCCCCccCCHHHHHHHHHHH
Q 046293 27 PHKGKKFDTLDDAYEFYKKY 46 (695)
Q Consensus 27 p~~g~~F~S~eea~~~y~~y 46 (695)
-+-|..|..+.|+.+|+..|
T Consensus 6 kykgrtfrnekelrdfiekf 25 (28)
T 1fme_A 6 KYKGRTFRNEKELRDFIEKF 25 (28)
T ss_dssp ESSSCEECCHHHHHHHHHHC
T ss_pred hhcccccccHHHHHHHHHHh
Confidence 35689999999999999875
No 42
>1c6v_A Protein (SIV integrase); DNA integration, DNA binding protein; 3.00A {Simian immunodeficiency virus} SCOP: c.55.3.2
Probab=26.55 E-value=1.7e+02 Score=25.30 Aligned_cols=63 Identities=14% Similarity=0.038 Sum_probs=38.1
Q ss_pred cEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHH
Q 046293 208 DVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAM 280 (695)
Q Consensus 208 dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al 280 (695)
.++.+|.|+..+ . +.++.+|..-.. ++++. +.+.+.+.+.-++..+.... .|.+|.+|+....
T Consensus 10 ~~w~~D~~~~~g----~-~~l~~iD~~Sr~-~~~~~-~~~~~~~~~~~~~~~~~~~~---~~~~i~sDnG~~f 72 (164)
T 1c6v_A 10 GTWQMDCTHLEG----K-IVIVAVHVASGF-IEAEV-IPQETGRQTALFLLKLAGRW---PITHLHTDNGANF 72 (164)
T ss_dssp TEEEEEEEEETT----E-EEEEEECTTSCC-EEEEE-CSSCSHHHHHHHHHHHHTTS---CCCEEECCCCSST
T ss_pred CEEEEeecccCC----E-EEEEEEEccCCE-EEEEE-cCCCchHHHHHHHHHHHHhc---CCCEEEeCCchhh
Confidence 577888888722 2 344447776653 45554 44566666555544433333 3799999997653
No 43
>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=26.26 E-value=14 Score=27.43 Aligned_cols=20 Identities=30% Similarity=0.625 Sum_probs=0.0
Q ss_pred ccCCCCCCCCCCCCCCCCcchh
Q 046293 631 RRCNGCGLVGQSHDKRNCPLLI 652 (695)
Q Consensus 631 ~~C~~C~~~~~GHn~~tCp~~~ 652 (695)
..|-+|+ ..||-.+.||...
T Consensus 2 ~~Cf~Cg--~~GH~a~~C~~~~ 21 (60)
T 1cl4_A 2 GSCFKCG--KKGHFAKNCHEHA 21 (60)
T ss_dssp ----------------------
T ss_pred CccccCC--CCCcCHhhCcCCC
Confidence 3699999 6799999999864
No 44
>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=25.71 E-value=1.1e+02 Score=21.56 Aligned_cols=45 Identities=16% Similarity=0.231 Sum_probs=31.6
Q ss_pred HHHHHHHhhcCChHHHHHHHHHHHHHhccchhHHHHHHHHhhccch
Q 046293 307 RHFQKCIWESNTIEKFDALWKDVIDKAKLIENEWLQGVYEIRSKWV 352 (695)
Q Consensus 307 ~~~~~~v~~~~t~~eFe~~w~~l~~~~~~~~~~~l~~l~~~re~Wa 352 (695)
..|...| ++++..+|-....+|...-.--+..|...+-+.+++|-
T Consensus 7 ~~Fe~~I-nS~SK~~Fv~nL~ELE~is~rlg~~Y~~~LeeaK~kWk 51 (53)
T 1x9b_A 7 AKFESMI-NSPSKSVFVRNLNELEALAVRLGKSYRIQLDQAKEKWK 51 (53)
T ss_dssp HHHHHHH-HSCCHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHC
T ss_pred HHHHHHh-CCccHHHHHHhHHHHHHHHHHHchHHHHHHHHHHHhhc
Confidence 4566655 48899999988888754322224678877888889983
No 45
>2lju_A Putative oxidoreductase; structural genomics, seattle structural GENO center for infectious disease, ssgcid; NMR {Ehrlichia chaffeensis}
Probab=25.51 E-value=44 Score=28.10 Aligned_cols=30 Identities=20% Similarity=0.155 Sum_probs=24.4
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhhcCcEEEEecc
Q 046293 26 KPHKGKKFDTLDDAYEFYKKYAKEGGFSIQINSS 59 (695)
Q Consensus 26 ~p~~g~~F~S~eea~~~y~~yA~~~GF~i~~~~s 59 (695)
.-.+.+.|+|.|+|.. ||.++|....+...
T Consensus 59 ~~qv~L~F~skE~Aia----yAek~G~~y~V~ep 88 (108)
T 2lju_A 59 KQQVCLSFTTRELAIA----YAVAHKIDYTVLQD 88 (108)
T ss_dssp CCCSCEEESSHHHHHH----HHHHTTCEEEEECS
T ss_pred cccceEecCCHHHHHH----HHHHcCCEEEEecC
Confidence 3456889999999975 78999999887754
No 46
>2jya_A AGR_C_3324P, uncharacterized protein ATU1810; protein with unknown function ATU1810, ontario centre for ST proteomics, OCSP; NMR {Agrobacterium tumefaciens str}
Probab=21.63 E-value=40 Score=28.27 Aligned_cols=28 Identities=21% Similarity=0.341 Sum_probs=22.9
Q ss_pred CCCCccCCHHHHHHHHHHHhhhcCcEEEEecc
Q 046293 28 HKGKKFDTLDDAYEFYKKYAKEGGFSIQINSS 59 (695)
Q Consensus 28 ~~g~~F~S~eea~~~y~~yA~~~GF~i~~~~s 59 (695)
.+.+.|+|.|+|.. ||.++|....+...
T Consensus 53 qv~L~F~skE~Aia----yAek~G~~y~V~ep 80 (106)
T 2jya_A 53 QVKLTFETQEQAEA----YAQRKGIEYRVILP 80 (106)
T ss_dssp EEEEEESSHHHHHH----HHHHHTCEEEECCC
T ss_pred cceEecCCHHHHHH----HHHHcCCEEEEeCC
Confidence 35689999999975 78899999887755
No 47
>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=20.62 E-value=1.4e+02 Score=28.25 Aligned_cols=65 Identities=17% Similarity=0.113 Sum_probs=38.7
Q ss_pred cEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh
Q 046293 208 DVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL 282 (695)
Q Consensus 208 dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~ 282 (695)
.++.+|.|+..++ +.++.+|..-. +++++.+ .+++.....-++..+.... .|.+|.||+......
T Consensus 10 ~~w~~D~t~~~g~-----~~l~~vD~~Sr-~i~~~~~-~~~~~~~~~~~~~~~~~~~---~~~~i~sDnG~eF~s 74 (239)
T 1ex4_A 10 GIWQLDCTHLEGK-----VILVAVHVASG-YIEAEVI-PAETGQETAYFLLKLAGRW---PVKTIHTDNGSNFTG 74 (239)
T ss_dssp GEEEEEEEEETTE-----EEEEEECTTTC-CEEEECC-SSSSTTHHHHHHHHHHHHS---CCCEEEECCCHHHHC
T ss_pred CEEEEeccccCCe-----EEEEEEECCCC-eEEEEEe-CCCCHHHHHHHHHHHHHhc---CCcEEEecCcHHHHH
Confidence 4788999988333 23444565544 4456644 4555555444443333333 369999999988654
No 48
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=20.51 E-value=47 Score=28.49 Aligned_cols=20 Identities=30% Similarity=0.713 Sum_probs=17.8
Q ss_pred CcccCCCCCCCCCCCCCCCCcc
Q 046293 629 KGRRCNGCGLVGQSHDKRNCPL 650 (695)
Q Consensus 629 r~~~C~~C~~~~~GHn~~tCp~ 650 (695)
....|-+|+ +.||..+.||.
T Consensus 104 ~~~~Cy~Cg--~~GH~a~dCp~ 123 (124)
T 2lli_A 104 HTIYCYNCG--GKGHFGDDCKE 123 (124)
T ss_dssp CCCCTTTTS--SSCTTTTTSCC
T ss_pred CCCCcCCCC--CCCcCcccCcC
Confidence 457999999 78999999996
Done!