Query 043997
Match_columns 222
No_of_seqs 152 out of 946
Neff 8.5
Searched_HMMs 29240
Date Mon Mar 25 18:06:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043997.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/043997hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1a6b_B Momulv, zinc finger pro 98.2 5.9E-07 2E-11 52.2 2.5 25 195-219 8-33 (40)
2 1u6p_A GAG polyprotein; MLV, A 98.1 8.4E-07 2.9E-11 55.4 2.3 25 195-219 21-46 (56)
3 1nc8_A Nucleocapsid protein; H 97.9 4E-06 1.4E-10 45.2 1.9 19 197-215 6-25 (29)
4 1dsq_A Nucleic acid binding pr 97.9 4.4E-06 1.5E-10 43.9 1.8 19 198-216 3-22 (26)
5 2ysa_A Retinoblastoma-binding 97.6 2.4E-05 8.2E-10 48.6 2.1 22 196-217 6-28 (55)
6 2a51_A Nucleocapsid protein; s 97.0 0.00035 1.2E-08 40.1 2.3 16 198-213 22-38 (39)
7 2ec7_A GAG polyprotein (PR55GA 97.0 0.00038 1.3E-08 42.2 2.5 18 198-215 28-46 (49)
8 2bl6_A Nucleocapsid protein P1 96.7 0.00086 2.9E-08 38.0 2.1 16 198-213 20-36 (37)
9 2ec7_A GAG polyprotein (PR55GA 96.6 0.00091 3.1E-08 40.4 2.2 18 197-214 6-24 (49)
10 2a51_A Nucleocapsid protein; s 96.6 0.00087 3E-08 38.4 1.9 16 198-213 1-17 (39)
11 1cl4_A Protein (GAG polyprotei 96.6 0.0013 4.4E-08 41.4 2.7 23 196-218 29-52 (60)
12 1a1t_A Nucleocapsid protein; s 96.6 0.0013 4.5E-08 40.6 2.6 16 199-214 35-51 (55)
13 2bl6_A Nucleocapsid protein P1 96.5 0.001 3.6E-08 37.6 1.8 16 199-214 2-18 (37)
14 3nyb_B Protein AIR2; polya RNA 96.5 0.0012 4.2E-08 44.5 2.2 20 196-215 45-65 (83)
15 2ihx_A Nucleocapsid (NC) prote 96.4 0.002 6.7E-08 40.8 2.5 18 198-215 31-49 (61)
16 1a1t_A Nucleocapsid protein; s 96.3 0.0014 4.9E-08 40.5 1.8 20 196-215 11-31 (55)
17 2cqf_A RNA-binding protein LIN 96.2 0.002 6.9E-08 41.0 2.1 20 197-216 29-49 (63)
18 2ihx_A Nucleocapsid (NC) prote 96.2 0.0017 5.8E-08 41.1 1.6 18 197-214 4-22 (61)
19 1cl4_A Protein (GAG polyprotei 96.1 0.0013 4.3E-08 41.5 0.7 18 198-215 2-20 (60)
20 2cqf_A RNA-binding protein LIN 96.0 0.0039 1.3E-07 39.7 2.8 19 197-215 7-26 (63)
21 2li8_A Protein LIN-28 homolog 96.0 0.0036 1.2E-07 41.2 2.3 17 198-214 25-42 (74)
22 2li8_A Protein LIN-28 homolog 95.7 0.0046 1.6E-07 40.7 2.0 21 196-216 45-66 (74)
23 3ts2_A Protein LIN-28 homolog 95.6 0.0048 1.6E-07 46.2 2.1 19 198-216 98-117 (148)
24 3ts2_A Protein LIN-28 homolog 95.6 0.0047 1.6E-07 46.3 2.0 21 197-217 119-140 (148)
25 3nyb_B Protein AIR2; polya RNA 95.4 0.0063 2.2E-07 40.9 1.9 20 196-215 4-24 (83)
26 2lli_A Protein AIR2; RNA surve 93.8 0.026 8.9E-07 40.7 2.0 18 197-214 105-123 (124)
27 2lli_A Protein AIR2; RNA surve 91.5 0.096 3.3E-06 37.6 2.4 19 197-215 64-83 (124)
28 2hqh_E Restin; beta/BETA struc 85.8 0.14 4.6E-06 26.1 -0.2 19 196-214 2-21 (26)
29 2pzo_E CAP-Gly domain-containi 66.8 1.1 3.9E-05 25.4 -0.1 20 195-214 18-38 (42)
30 3e2u_E CAP-Gly domain-containi 49.5 3.7 0.00013 23.4 0.1 20 195-214 18-38 (42)
31 3ljm_A Coil Ser L9C; de novo d 49.0 25 0.00087 17.8 3.4 26 96-125 3-28 (31)
32 1ef4_A Subunit N, DNA-directed 34.9 14 0.00048 22.3 1.1 9 198-206 4-12 (55)
33 4ayb_N DNA-directed RNA polyme 34.2 12 0.00043 23.5 0.8 9 198-206 5-13 (66)
34 2yqp_A Probable ATP-dependent 29.5 23 0.00077 21.6 1.3 17 196-212 18-35 (60)
35 1twf_J DNA-directed RNA polyme 26.1 21 0.00071 22.7 0.8 9 198-206 5-13 (70)
36 2ds5_A CLPX, ATP-dependent CLP 25.2 23 0.00077 21.0 0.8 11 198-208 12-22 (51)
37 3a4c_A DNA replication factor 23.8 70 0.0024 22.0 3.2 43 131-174 3-45 (106)
38 3t72_q RNA polymerase sigma fa 21.7 1.6E+02 0.0055 19.5 4.8 40 134-173 11-50 (99)
39 1ovx_A ATP-dependent CLP prote 21.4 39 0.0013 21.2 1.4 12 197-208 18-29 (67)
40 2w0t_A Lethal(3)malignant brai 21.4 19 0.00064 20.6 -0.1 13 198-210 7-19 (43)
No 1
>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=98.23 E-value=5.9e-07 Score=52.18 Aligned_cols=25 Identities=16% Similarity=0.177 Sum_probs=20.6
Q ss_pred ccCCCCCCCCCCCccc-ccccCcccc
Q 043997 195 TSRKGSSNCHSTWKAQ-DVSFRERVD 219 (222)
Q Consensus 195 ~~~~~C~~C~k~GH~~-dC~~~~~~~ 219 (222)
..+.+||+||+.||++ |||.....+
T Consensus 8 ~~~~~C~~Cgk~GH~ardCP~~~~~~ 33 (40)
T 1a6b_B 8 LDRDQCAYCKEKGHWAKDCPKKPRGP 33 (40)
T ss_dssp CCSSSCSSSCCTTCCTTSCSSSCCCT
T ss_pred CCCCeeeECCCCCcchhhCcCCcccC
Confidence 3567899999999999 999885543
No 2
>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=98.15 E-value=8.4e-07 Score=55.44 Aligned_cols=25 Identities=16% Similarity=0.177 Sum_probs=21.0
Q ss_pred ccCCCCCCCCCCCccc-ccccCcccc
Q 043997 195 TSRKGSSNCHSTWKAQ-DVSFRERVD 219 (222)
Q Consensus 195 ~~~~~C~~C~k~GH~~-dC~~~~~~~ 219 (222)
..+.+||+||+.||++ |||..++.+
T Consensus 21 ~~~~~C~~Cge~GH~ardCp~~~~~~ 46 (56)
T 1u6p_A 21 LDRDQCAYCKEKGHWAKDCPKKPRGP 46 (56)
T ss_dssp CCTTBCSSSCCBSSCGGGCTTCCCSS
T ss_pred CCCCcceeCCCCCcccccCcCCcccc
Confidence 4567799999999999 999986543
No 3
>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=97.92 E-value=4e-06 Score=45.24 Aligned_cols=19 Identities=11% Similarity=0.013 Sum_probs=16.7
Q ss_pred CCCCCCCCCCCccc-ccccC
Q 043997 197 RKGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 197 ~~~C~~C~k~GH~~-dC~~~ 215 (222)
...||+||+.||++ ||+..
T Consensus 6 ~~~C~nCgk~GH~ar~C~~p 25 (29)
T 1nc8_A 6 VIRCWNCGKEGHSARQCRAP 25 (29)
T ss_dssp CCBCTTTSCBSSCGGGCCSS
T ss_pred CCEEEECCccccCHhHCccc
Confidence 46799999999999 99864
No 4
>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1
Probab=97.90 E-value=4.4e-06 Score=43.89 Aligned_cols=19 Identities=16% Similarity=0.109 Sum_probs=16.5
Q ss_pred CCCCCCCCCCccc-ccccCc
Q 043997 198 KGSSNCHSTWKAQ-DVSFRE 216 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~~~ 216 (222)
..||+||+.||++ ||+...
T Consensus 3 ~~Cf~CG~~GH~ardC~~~~ 22 (26)
T 1dsq_A 3 PVCFSCGKTGHIKRDCKEEX 22 (26)
T ss_dssp CBCTTTCCBSSCTTTTTCC-
T ss_pred CeeEeCCCCCcccccCCCcc
Confidence 5699999999999 999763
No 5
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=97.61 E-value=2.4e-05 Score=48.60 Aligned_cols=22 Identities=9% Similarity=-0.028 Sum_probs=18.1
Q ss_pred cCCCCCCCCCCCccc-ccccCcc
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFRER 217 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~~~ 217 (222)
....||.||++||++ ||+...+
T Consensus 6 ~~~~C~kCGk~GH~~k~Cp~~~~ 28 (55)
T 2ysa_A 6 SGYTCFRCGKPGHYIKNCPTNGD 28 (55)
T ss_dssp SSCCCTTTCCTTSCGGGCSGGGC
T ss_pred CCCccccCCCcCcccccCCCCCC
Confidence 345799999999999 9996643
No 6
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=97.01 E-value=0.00035 Score=40.15 Aligned_cols=16 Identities=25% Similarity=0.318 Sum_probs=10.7
Q ss_pred CCCCCCCCCCccc-ccc
Q 043997 198 KGSSNCHSTWKAQ-DVS 213 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~ 213 (222)
..|+.||+.||++ |||
T Consensus 22 ~~C~~Cg~~GH~~~~C~ 38 (39)
T 2a51_A 22 EGCWNCGSKEHRFAQCP 38 (39)
T ss_dssp SSCTTTCCSSSCTTTSC
T ss_pred CccccCCCCCCccCcCc
Confidence 4567777777766 665
No 7
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1
Probab=97.01 E-value=0.00038 Score=42.15 Aligned_cols=18 Identities=22% Similarity=0.294 Sum_probs=10.3
Q ss_pred CCCCCCCCCCccc-ccccC
Q 043997 198 KGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~~ 215 (222)
..||.||+.||++ ||+.+
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 3466666666666 66543
No 8
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=96.66 E-value=0.00086 Score=37.97 Aligned_cols=16 Identities=13% Similarity=0.119 Sum_probs=10.1
Q ss_pred CCCCCCCCCCccc-ccc
Q 043997 198 KGSSNCHSTWKAQ-DVS 213 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~ 213 (222)
..|+.|++.||++ ||+
T Consensus 20 ~~C~~Cg~~GH~a~~C~ 36 (37)
T 2bl6_A 20 KVCFKCKQPGHFSKQCR 36 (37)
T ss_dssp TTCSSCCCTTGGGGTTC
T ss_pred CeEccCCCcCCccCcCc
Confidence 4566666666666 665
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=96.63 E-value=0.00091 Score=40.41 Aligned_cols=18 Identities=11% Similarity=0.030 Sum_probs=16.1
Q ss_pred CCCCCCCCCCCccc-cccc
Q 043997 197 RKGSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 197 ~~~C~~C~k~GH~~-dC~~ 214 (222)
...||+||+.||++ +|+.
T Consensus 6 ~~~C~~Cg~~GH~a~~C~~ 24 (49)
T 2ec7_A 6 VIRCWNCGKEGHSARQCRA 24 (49)
T ss_dssp CCBCTTTCCBTCCTTTCCC
T ss_pred cCeeeecCCCCcChhhCcC
Confidence 35799999999999 9986
No 10
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=96.61 E-value=0.00087 Score=38.43 Aligned_cols=16 Identities=13% Similarity=0.044 Sum_probs=14.5
Q ss_pred CCCCCCCCCCccc-ccc
Q 043997 198 KGSSNCHSTWKAQ-DVS 213 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~ 213 (222)
.+||+|++.||++ +|+
T Consensus 1 i~C~~Cg~~GH~a~~C~ 17 (39)
T 2a51_A 1 LTCFNCGKPGHTARMCR 17 (39)
T ss_dssp CBCTTTCCBSSCTTTCC
T ss_pred CeeeccCCCCcccccCC
Confidence 3699999999999 996
No 11
>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=96.58 E-value=0.0013 Score=41.45 Aligned_cols=23 Identities=4% Similarity=-0.032 Sum_probs=19.1
Q ss_pred cCCCCCCCCCCCccc-ccccCccc
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFRERV 218 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~~~~ 218 (222)
....||.|++.||++ ||+...+-
T Consensus 29 ~~~~C~~Cg~~GH~ar~C~~~~~~ 52 (60)
T 1cl4_A 29 VPGLCPRCKRGKHWANECKSKTDN 52 (60)
T ss_dssp CCCSCSSCSSCSSCSTTCCCTTSS
T ss_pred CCcceeECCCCCCccCcCCCcccc
Confidence 356799999999999 99987543
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=96.57 E-value=0.0013 Score=40.64 Aligned_cols=16 Identities=19% Similarity=0.252 Sum_probs=8.4
Q ss_pred CCCCCCCCCccc-cccc
Q 043997 199 GSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 199 ~C~~C~k~GH~~-dC~~ 214 (222)
.||.||+.||++ ||+.
T Consensus 35 ~C~~Cg~~GH~~~~C~~ 51 (55)
T 1a1t_A 35 GCWKCGKEGHQMKDCTE 51 (55)
T ss_dssp BCTTTCCBSSCGGGCSS
T ss_pred EeCCCCCcCCccCCCcC
Confidence 455555555555 5544
No 13
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=96.53 E-value=0.001 Score=37.62 Aligned_cols=16 Identities=13% Similarity=0.110 Sum_probs=14.7
Q ss_pred CCCCCCCCCccc-cccc
Q 043997 199 GSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 199 ~C~~C~k~GH~~-dC~~ 214 (222)
.||+|++.||++ +|+.
T Consensus 2 ~C~~Cg~~GH~~~~C~~ 18 (37)
T 2bl6_A 2 TCYNCGKPGHLSSQCRA 18 (37)
T ss_dssp CBSSSCCSSCCTTTSSC
T ss_pred cccccCCCCcchhhCcC
Confidence 599999999999 9975
No 14
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=96.49 E-value=0.0012 Score=44.47 Aligned_cols=20 Identities=15% Similarity=0.052 Sum_probs=17.5
Q ss_pred cCCCCCCCCCCCccc-ccccC
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~ 215 (222)
....|++||+.||+. ||+..
T Consensus 45 ~~~~CYnCG~~GH~~rdC~~~ 65 (83)
T 3nyb_B 45 HTIYCYNCGGKGHFGDDCKEK 65 (83)
T ss_dssp CCCBCSSSSCBSSCGGGCSSC
T ss_pred CCCeecccCCCCcCcccCCcc
Confidence 346799999999999 99876
No 15
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=96.36 E-value=0.002 Score=40.80 Aligned_cols=18 Identities=11% Similarity=0.154 Sum_probs=14.7
Q ss_pred CCCCCCCCCCccc-ccccC
Q 043997 198 KGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~~ 215 (222)
..||.|++.||++ ||+..
T Consensus 31 ~~C~~Cg~~GH~ar~C~~~ 49 (61)
T 2ihx_A 31 ERCQLCNGMGHNAKQCRKR 49 (61)
T ss_dssp SBCTTTCCBSSCGGGCCCC
T ss_pred CeeCCCCCCCCCcCCCcCC
Confidence 5688888888888 88875
No 16
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A
Probab=96.34 E-value=0.0014 Score=40.49 Aligned_cols=20 Identities=10% Similarity=0.047 Sum_probs=17.0
Q ss_pred cCCCCCCCCCCCccc-ccccC
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~ 215 (222)
....||+|++.||++ +|+..
T Consensus 11 ~~~~C~~Cg~~GH~a~~C~~~ 31 (55)
T 1a1t_A 11 KTVKCFNCGKEGHIAKNCRAP 31 (55)
T ss_dssp GTCBCTTTCCBSSCGGGCSSC
T ss_pred CCcceeeeCCCCcChhhcCCC
Confidence 346799999999999 99864
No 17
>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=96.23 E-value=0.002 Score=41.03 Aligned_cols=20 Identities=15% Similarity=0.218 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCccc-ccccCc
Q 043997 197 RKGSSNCHSTWKAQ-DVSFRE 216 (222)
Q Consensus 197 ~~~C~~C~k~GH~~-dC~~~~ 216 (222)
...||.|++.||++ ||+...
T Consensus 29 ~~~C~~Cg~~GH~ar~Cp~~~ 49 (63)
T 2cqf_A 29 PKKCHFCQSISHMVASCPLKA 49 (63)
T ss_dssp SSCCTTTCCSSSCTTTCTGGG
T ss_pred CCccCCcCCcCCccCcCCCcc
Confidence 45688888888888 887653
No 18
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=96.20 E-value=0.0017 Score=41.08 Aligned_cols=18 Identities=22% Similarity=0.102 Sum_probs=16.1
Q ss_pred CCCCCCCCCCCccc-cccc
Q 043997 197 RKGSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 197 ~~~C~~C~k~GH~~-dC~~ 214 (222)
...||+|++.||++ ||+.
T Consensus 4 ~~~C~~Cg~~GH~a~~C~~ 22 (61)
T 2ihx_A 4 RGLCYTCGSPGHYQAQCPK 22 (61)
T ss_dssp TTBCSSSCCBTCCGGGCTT
T ss_pred CCcccccCCCCeehhhCcC
Confidence 35699999999999 9986
No 19
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A
Probab=96.13 E-value=0.0013 Score=41.51 Aligned_cols=18 Identities=6% Similarity=0.012 Sum_probs=0.0
Q ss_pred CCCCCCCCCCccc-ccccC
Q 043997 198 KGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~~ 215 (222)
+.||+|++.||++ ||+..
T Consensus 2 ~~Cf~Cg~~GH~a~~C~~~ 20 (60)
T 1cl4_A 2 GSCFKCGKKGHFAKNCHEH 20 (60)
T ss_dssp -------------------
T ss_pred CccccCCCCCcCHhhCcCC
Confidence 3599999999999 99986
No 20
>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=96.05 E-value=0.0039 Score=39.66 Aligned_cols=19 Identities=11% Similarity=0.143 Sum_probs=16.7
Q ss_pred CCCCCCCCCCCccc-ccccC
Q 043997 197 RKGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 197 ~~~C~~C~k~GH~~-dC~~~ 215 (222)
...||+|++.||++ ||+..
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 35799999999999 99964
No 21
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=95.96 E-value=0.0036 Score=41.20 Aligned_cols=17 Identities=12% Similarity=0.196 Sum_probs=9.9
Q ss_pred CCCCCCCCCCccc-cccc
Q 043997 198 KGSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~ 214 (222)
..||+|++.||+. +|+.
T Consensus 25 ~~C~~Cg~~GH~a~~C~~ 42 (74)
T 2li8_A 25 DRCYNCGGLDHHAKECKL 42 (74)
T ss_dssp SCCTTTCCSSSCTTTCSS
T ss_pred CcccccCCcCcCcccCCC
Confidence 3466666666666 6654
No 22
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=95.69 E-value=0.0046 Score=40.69 Aligned_cols=21 Identities=14% Similarity=0.211 Sum_probs=18.1
Q ss_pred cCCCCCCCCCCCccc-ccccCc
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFRE 216 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~~ 216 (222)
....||.|++.||++ ||+...
T Consensus 45 ~~~~C~~Cg~~GH~ar~Cp~~~ 66 (74)
T 2li8_A 45 QPKKCHFCQSISHMVASCPLKA 66 (74)
T ss_dssp CCCCCTTTCCTTSCGGGCTTGG
T ss_pred CCCccCCcCCcCCccCcCcCCc
Confidence 346899999999999 999763
No 23
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*
Probab=95.62 E-value=0.0048 Score=46.20 Aligned_cols=19 Identities=11% Similarity=0.151 Sum_probs=16.0
Q ss_pred CCCCCCCCCCccc-ccccCc
Q 043997 198 KGSSNCHSTWKAQ-DVSFRE 216 (222)
Q Consensus 198 ~~C~~C~k~GH~~-dC~~~~ 216 (222)
.+||+||+.||++ +|+..|
T Consensus 98 ~~C~~Cg~~GH~a~~C~~~~ 117 (148)
T 3ts2_A 98 DRCYNCGGLDHHAKECKLPP 117 (148)
T ss_dssp CCCTTTCCSSCCGGGCCSCC
T ss_pred CcccEeCCccchhhhCCCCC
Confidence 4699999999999 998743
No 24
>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=95.60 E-value=0.0047 Score=46.28 Aligned_cols=21 Identities=14% Similarity=0.227 Sum_probs=18.3
Q ss_pred CCCCCCCCCCCccc-ccccCcc
Q 043997 197 RKGSSNCHSTWKAQ-DVSFRER 217 (222)
Q Consensus 197 ~~~C~~C~k~GH~~-dC~~~~~ 217 (222)
...|+.|++.||++ |||.++.
T Consensus 119 ~~~C~~Cg~~GH~~r~Cp~~~~ 140 (148)
T 3ts2_A 119 PKKCHFCQSINHMVASCPLKAQ 140 (148)
T ss_dssp CCCCTTTCCSSCCGGGCTTTTC
T ss_pred CCcccccCCcCCEeccCcCCCC
Confidence 46799999999999 9998843
No 25
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=95.41 E-value=0.0063 Score=40.93 Aligned_cols=20 Identities=10% Similarity=0.131 Sum_probs=15.0
Q ss_pred cCCCCCCCCCCCccc-ccccC
Q 043997 196 SRKGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~~ 215 (222)
++..|++|++.||.+ +||..
T Consensus 4 k~~~C~~Cg~~GH~~~~Cp~~ 24 (83)
T 3nyb_B 4 KKVQCTLCKSKKHSKERCPSI 24 (83)
T ss_dssp ---CCSSSCCSSSCGGGCGGG
T ss_pred ccCCCCCCCCCCCccccCCCc
Confidence 456799999999999 99864
No 26
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=93.79 E-value=0.026 Score=40.71 Aligned_cols=18 Identities=17% Similarity=0.012 Sum_probs=16.2
Q ss_pred CCCCCCCCCCCccc-cccc
Q 043997 197 RKGSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 197 ~~~C~~C~k~GH~~-dC~~ 214 (222)
...|++|++.||++ |||.
T Consensus 105 ~~~Cy~Cg~~GH~a~dCp~ 123 (124)
T 2lli_A 105 TIYCYNCGGKGHFGDDCKE 123 (124)
T ss_dssp CCCTTTTSSSCTTTTTSCC
T ss_pred CCCcCCCCCCCcCcccCcC
Confidence 46799999999999 9985
No 27
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=91.47 E-value=0.096 Score=37.64 Aligned_cols=19 Identities=11% Similarity=0.135 Sum_probs=15.3
Q ss_pred CCCCCCCCCCCccc-ccccC
Q 043997 197 RKGSSNCHSTWKAQ-DVSFR 215 (222)
Q Consensus 197 ~~~C~~C~k~GH~~-dC~~~ 215 (222)
...|+.|++.||++ |||..
T Consensus 64 ~~~C~~Cg~~GH~~~~Cp~~ 83 (124)
T 2lli_A 64 KVQCTLCKSKKHSKERCPSI 83 (124)
T ss_dssp CCSSSSSCSSCCCTTTCCCS
T ss_pred CccCCCCCcCCcchhhCCCc
Confidence 35788888888888 88865
No 28
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=85.83 E-value=0.14 Score=26.13 Aligned_cols=19 Identities=16% Similarity=-0.006 Sum_probs=15.0
Q ss_pred cCCCCCCCCCCCccc-cccc
Q 043997 196 SRKGSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC~~ 214 (222)
.++-|.+|...||.. +|..
T Consensus 2 ~RpYCe~CE~FGH~t~~C~d 21 (26)
T 2hqh_E 2 SRPYCEICEMFGHWATNCND 21 (26)
T ss_dssp --CEETTTTEESSCGGGCCT
T ss_pred CCccchHHHHhCcccccCCc
Confidence 355699999999999 9953
No 29
>2pzo_E CAP-Gly domain-containing linker protein 1; structural protein microtubule binding, dynactin, cytoskeleton associated protein, P150glued; 2.60A {Homo sapiens} PDB: 3e2u_E
Probab=66.78 E-value=1.1 Score=25.39 Aligned_cols=20 Identities=10% Similarity=-0.041 Sum_probs=15.2
Q ss_pred ccCCCCCCCCCCCccc-cccc
Q 043997 195 TSRKGSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 195 ~~~~~C~~C~k~GH~~-dC~~ 214 (222)
..+.-|..|.-.||.. +|.-
T Consensus 18 ~eRpYCd~CEvFGH~t~~Cnd 38 (42)
T 2pzo_E 18 EERPYCEICEMFGHWATNCND 38 (42)
T ss_dssp ---CEETTTTEESSCGGGCCT
T ss_pred cCCcccccccccCcccccCCc
Confidence 4566799999999999 9953
No 30
>3e2u_E CAP-Gly domain-containing linker protein 1; structural protein microtubule binding, dynactin, cytoskelet associated protein, P150glued; 2.60A {Homo sapiens}
Probab=49.50 E-value=3.7 Score=23.36 Aligned_cols=20 Identities=10% Similarity=-0.041 Sum_probs=15.9
Q ss_pred ccCCCCCCCCCCCccc-cccc
Q 043997 195 TSRKGSSNCHSTWKAQ-DVSF 214 (222)
Q Consensus 195 ~~~~~C~~C~k~GH~~-dC~~ 214 (222)
..++-|..|--+||.. +|.-
T Consensus 18 ~eRpYCe~CEVFGH~t~eC~d 38 (42)
T 3e2u_E 18 EERPYCEICEMFGHWATNCND 38 (42)
T ss_dssp --CCEETTTTEESSCGGGCCT
T ss_pred ccCcccccceecccccccCCc
Confidence 3466799999999999 9964
No 31
>3ljm_A Coil Ser L9C; de novo design, three stranded coiled coil, APO, de novo Pro; 1.36A {Synthetic} PDB: 2jgo_A 1cos_A 3h5g_A 3h5f_A 3pbj_A 2x6p_C 1coi_A
Probab=48.99 E-value=25 Score=17.77 Aligned_cols=26 Identities=46% Similarity=0.801 Sum_probs=18.0
Q ss_pred HHHHHHHhhchhHHHHHHHHHHHHHHHHhh
Q 043997 96 WDAMKKKFEGNARVKKSQLQALRREFETLE 125 (222)
Q Consensus 96 W~~L~~~y~~~~~~~~~~l~~l~~~~~~~~ 125 (222)
|++|.+....- ..++|.|.+.++.+.
T Consensus 3 wealekkcaal----esklqalekkleale 28 (31)
T 3ljm_A 3 WEALEKKCAAL----ESKLQALEKKLEALE 28 (31)
T ss_dssp HHHHHHHHHHH----HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHH----HHHHHHHHHHHHHHH
Confidence 88888766543 457888887777653
No 32
>1ef4_A Subunit N, DNA-directed RNA polymerase; three helix bundle, zinc binding, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: a.4.11.1
Probab=34.85 E-value=14 Score=22.35 Aligned_cols=9 Identities=11% Similarity=0.242 Sum_probs=7.6
Q ss_pred CCCCCCCCC
Q 043997 198 KGSSNCHST 206 (222)
Q Consensus 198 ~~C~~C~k~ 206 (222)
.+||-|||+
T Consensus 4 VRCFTCGkv 12 (55)
T 1ef4_A 4 VRCLSCGKP 12 (55)
T ss_dssp SSCSCTTSC
T ss_pred eecCCCCCC
Confidence 479999996
No 33
>4ayb_N DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_N 2y0s_N 2waq_N 4b1o_N 4b1p_O 2pmz_N 3hkz_N
Probab=34.18 E-value=12 Score=23.46 Aligned_cols=9 Identities=22% Similarity=0.213 Sum_probs=7.6
Q ss_pred CCCCCCCCC
Q 043997 198 KGSSNCHST 206 (222)
Q Consensus 198 ~~C~~C~k~ 206 (222)
.+||-|||+
T Consensus 5 VRCFTCGkv 13 (66)
T 4ayb_N 5 IRCFTCGSL 13 (66)
T ss_dssp SBCTTTCCB
T ss_pred cccCCCcHh
Confidence 479999986
No 34
>2yqp_A Probable ATP-dependent RNA helicase DDX59; structure genomics, ZF-HIT domain, DEAD box polypeptide 59 isoform 2, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=29.48 E-value=23 Score=21.58 Aligned_cols=17 Identities=12% Similarity=-0.062 Sum_probs=13.8
Q ss_pred cCCCCCCCCCCCccc-cc
Q 043997 196 SRKGSSNCHSTWKAQ-DV 212 (222)
Q Consensus 196 ~~~~C~~C~k~GH~~-dC 212 (222)
..+.|-.||+.|-++ |=
T Consensus 18 gePvCvvCGryGeYICd~ 35 (60)
T 2yqp_A 18 GEPICVVCGRYGEYICDK 35 (60)
T ss_dssp TSCCCSSSSSCCSEECSS
T ss_pred CCceEEEecCccceeecC
Confidence 446699999999998 63
No 35
>1twf_J DNA-directed RNA polymerases I, II, and III 8.3 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.11.1 PDB: 1i3q_J 1i6h_J 1k83_J* 1nik_J 1nt9_J 1pqv_J 1r5u_J 1r9s_J* 1r9t_J* 1sfo_J* 1twa_J* 1twc_J* 1i50_J* 1twg_J* 1twh_J* 1wcm_J 1y1v_J 1y1w_J 1y1y_J 1y77_J* ...
Probab=26.11 E-value=21 Score=22.73 Aligned_cols=9 Identities=11% Similarity=0.213 Sum_probs=7.6
Q ss_pred CCCCCCCCC
Q 043997 198 KGSSNCHST 206 (222)
Q Consensus 198 ~~C~~C~k~ 206 (222)
.+||-|||+
T Consensus 5 VRCFTCGkv 13 (70)
T 1twf_J 5 VRCFSCGKV 13 (70)
T ss_dssp SBCTTTCCB
T ss_pred eecCCCCCC
Confidence 469999996
No 36
>2ds5_A CLPX, ATP-dependent CLP protease ATP-binding subunit CLPX; treble cleft zinc finger, metal binding protein, protein binding; HET: PG4; 1.50A {Escherichia coli} SCOP: g.39.1.11 PDB: 2ds6_A 2ds8_A 2ds7_A
Probab=25.22 E-value=23 Score=21.02 Aligned_cols=11 Identities=18% Similarity=0.084 Sum_probs=9.1
Q ss_pred CCCCCCCCCCc
Q 043997 198 KGSSNCHSTWK 208 (222)
Q Consensus 198 ~~C~~C~k~GH 208 (222)
..|++|||..+
T Consensus 12 ~~CSFCGk~~~ 22 (51)
T 2ds5_A 12 LYCSFCGKSQH 22 (51)
T ss_dssp CBCTTTCCBTT
T ss_pred cEecCCCCCHH
Confidence 57999999764
No 37
>3a4c_A DNA replication factor CDT1; alpha-beta structure, cell cycle, DNA- binding, nucleus, phosphoprotein, proto-oncogene, UBL conjugation; HET: DNA; 1.89A {Mus musculus} PDB: 2rqq_A*
Probab=23.84 E-value=70 Score=21.99 Aligned_cols=43 Identities=12% Similarity=0.002 Sum_probs=31.8
Q ss_pred hhHHHHHHHHhhcccchhHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 043997 131 EDVKIVEKILRTLTEKFNDIVCSIEESKDIDSLSEEAEVKEDEV 174 (222)
Q Consensus 131 ~d~~~v~~lL~~Lp~~~~~~~~~i~~~~~~~~lt~~ev~~~l~~ 174 (222)
++++.-...+..||+=...++.....-+ -+.++++.++.++..
T Consensus 3 p~qeke~~~~srLPelArilR~vFvaEk-K~vl~~e~~~~ki~~ 45 (106)
T 3a4c_A 3 PEQELRLQRLERLPELARVLRNVFVSER-KPALTMEVVCARMVD 45 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTCS-SSEEEHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHhcc-cCCccHHHHHHHHHh
Confidence 3455566778888888888887766554 367888888888887
No 38
>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B
Probab=21.66 E-value=1.6e+02 Score=19.54 Aligned_cols=40 Identities=13% Similarity=-0.011 Sum_probs=23.3
Q ss_pred HHHHHHHhhcccchhHHHHHHhhcCCCCCCCHHHHHHHHH
Q 043997 134 KIVEKILRTLTEKFNDIVCSIEESKDIDSLSEEAEVKEDE 173 (222)
Q Consensus 134 ~~v~~lL~~Lp~~~~~~~~~i~~~~~~~~lt~~ev~~~l~ 173 (222)
..+...|..||+....++.---...+...+|++|+-..+-
T Consensus 11 ~~l~~aL~~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lg 50 (99)
T 3t72_q 11 AATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFD 50 (99)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC
Confidence 4566677788887777665432222223567777655543
No 39
>1ovx_A ATP-dependent CLP protease ATP-binding subunit CL; treble CLEF zinc finger, homodimer, metal binding protein; NMR {Escherichia coli} SCOP: g.39.1.11
Probab=21.43 E-value=39 Score=21.23 Aligned_cols=12 Identities=17% Similarity=0.016 Sum_probs=9.4
Q ss_pred CCCCCCCCCCCc
Q 043997 197 RKGSSNCHSTWK 208 (222)
Q Consensus 197 ~~~C~~C~k~GH 208 (222)
...|++|||...
T Consensus 18 ~~~CSFCGK~e~ 29 (67)
T 1ovx_A 18 LLYCSFCGKSQH 29 (67)
T ss_dssp CCCCTTTCCCTT
T ss_pred CcEecCCCCCHH
Confidence 357999999764
No 40
>2w0t_A Lethal(3)malignant brain tumor-like 2 protein; zinc, YACG, LMBL2, nucleus, zinc-finger, RNA binding, MBT repeats, PCG proteins, polymorphism; NMR {Homo sapiens}
Probab=21.39 E-value=19 Score=20.63 Aligned_cols=13 Identities=8% Similarity=0.000 Sum_probs=10.5
Q ss_pred CCCCCCCCCCccc
Q 043997 198 KGSSNCHSTWKAQ 210 (222)
Q Consensus 198 ~~C~~C~k~GH~~ 210 (222)
.+|-.||+.||..
T Consensus 7 ~~CE~CG~~g~~~ 19 (43)
T 2w0t_A 7 AVCEMCGIVGTRE 19 (43)
T ss_dssp EECTTTCCEEETT
T ss_pred ehhhhhcCcchhh
Confidence 4699999998754
Done!