Query 015479
Match_columns 406
No_of_seqs 179 out of 249
Neff 3.6
Searched_HMMs 29240
Date Mon Mar 25 13:20:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015479.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/015479hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1nc8_A Nucleocapsid protein; H 97.3 6.9E-05 2.4E-09 49.5 1.6 22 114-135 6-27 (29)
2 1dsq_A Nucleic acid binding pr 97.2 0.00014 4.8E-09 47.1 2.1 21 115-135 3-23 (26)
3 1a6b_B Momulv, zinc finger pro 96.7 0.00082 2.8E-08 48.1 2.5 23 113-135 9-31 (40)
4 2a51_A Nucleocapsid protein; s 96.1 0.0023 7.7E-08 44.4 1.9 19 116-134 2-20 (39)
5 2ec7_A GAG polyprotein (PR55GA 96.1 0.0026 9E-08 46.2 2.3 21 114-134 6-26 (49)
6 1u6p_A GAG polyprotein; MLV, A 95.8 0.0032 1.1E-07 47.9 1.7 24 112-135 21-44 (56)
7 2bl6_A Nucleocapsid protein P1 95.6 0.0053 1.8E-07 42.0 2.2 18 116-133 2-19 (37)
8 2ihx_A Nucleocapsid (NC) prote 95.5 0.0049 1.7E-07 46.6 1.8 20 115-134 5-24 (61)
9 1a1t_A Nucleocapsid protein; s 95.3 0.0063 2.2E-07 44.7 1.8 20 114-133 12-31 (55)
10 2cqf_A RNA-binding protein LIN 95.1 0.011 3.7E-07 45.1 2.6 19 115-133 8-26 (63)
11 2ysa_A Retinoblastoma-binding 94.9 0.0077 2.6E-07 45.6 1.2 21 114-134 7-27 (55)
12 2a51_A Nucleocapsid protein; s 94.8 0.014 4.8E-07 40.3 2.2 19 114-132 21-39 (39)
13 1cl4_A Protein (GAG polyprotei 94.7 0.016 5.6E-07 43.2 2.6 22 114-135 30-51 (60)
14 1cl4_A Protein (GAG polyprotei 94.4 0.0072 2.5E-07 45.2 0.0 22 115-136 2-23 (60)
15 2li8_A Protein LIN-28 homolog 94.3 0.02 6.7E-07 45.3 2.4 21 114-134 24-44 (74)
16 2ihx_A Nucleocapsid (NC) prote 94.2 0.015 5E-07 43.9 1.4 23 114-136 30-52 (61)
17 3nyb_B Protein AIR2; polya RNA 94.1 0.017 5.6E-07 46.8 1.6 22 113-134 45-66 (83)
18 1a1t_A Nucleocapsid protein; s 93.9 0.021 7.3E-07 41.9 1.6 21 114-134 33-53 (55)
19 3ts2_A Protein LIN-28 homolog 93.4 0.028 9.4E-07 49.4 1.8 22 114-135 97-118 (148)
20 2ec7_A GAG polyprotein (PR55GA 93.3 0.031 1E-06 40.5 1.7 21 114-134 27-47 (49)
21 2cqf_A RNA-binding protein LIN 93.2 0.037 1.3E-06 42.1 2.0 21 114-134 29-49 (63)
22 2bl6_A Nucleocapsid protein P1 92.2 0.041 1.4E-06 37.6 1.0 18 115-132 20-37 (37)
23 2li8_A Protein LIN-28 homolog 91.2 0.084 2.9E-06 41.7 1.9 21 114-134 46-66 (74)
24 3ts2_A Protein LIN-28 homolog 91.1 0.081 2.8E-06 46.4 1.9 23 114-136 119-141 (148)
25 3nyb_B Protein AIR2; polya RNA 88.9 0.11 3.6E-06 42.1 0.7 21 113-133 4-24 (83)
26 2lli_A Protein AIR2; RNA surve 87.8 0.25 8.6E-06 41.3 2.4 20 113-132 104-123 (124)
27 2lli_A Protein AIR2; RNA surve 86.9 0.28 9.4E-06 41.0 2.1 19 115-133 5-23 (124)
28 1yfb_A Transition state regula 32.4 21 0.00073 26.8 2.0 16 178-193 25-40 (59)
29 2l66_A SSO7C4, transcriptional 31.2 25 0.00087 25.3 2.1 16 178-193 15-30 (53)
30 3a5y_A GENX, putative lysyl-tR 27.2 43 0.0015 32.7 3.7 26 183-208 288-313 (345)
31 2glw_A PHS018, 92AA long hypot 22.9 38 0.0013 27.4 2.0 17 178-194 63-79 (92)
32 1qbj_A Protein (double-strande 22.0 30 0.001 27.2 1.2 33 173-205 21-55 (81)
No 1
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A
Probab=97.32 E-value=6.9e-05 Score=49.51 Aligned_cols=22 Identities=45% Similarity=1.081 Sum_probs=19.6
Q ss_pred CCccccCCCCCCCCCCCCCccC
Q 015479 114 ASRCFNCGSYSHSLKECPKPRD 135 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Prd 135 (406)
...|||||..+|..++||.|+-
T Consensus 6 ~~~C~nCgk~GH~ar~C~~prk 27 (29)
T 1nc8_A 6 VIRCWNCGKEGHSARQCRAPRR 27 (29)
T ss_dssp CCBCTTTSCBSSCGGGCCSSSS
T ss_pred CCEEEECCccccCHhHCccccc
Confidence 3679999999999999999973
No 2
>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=97.21 E-value=0.00014 Score=47.08 Aligned_cols=21 Identities=29% Similarity=0.854 Sum_probs=18.1
Q ss_pred CccccCCCCCCCCCCCCCccC
Q 015479 115 SRCFNCGSYSHSLKECPKPRD 135 (406)
Q Consensus 115 ~~CFNCG~~~HsLrdCP~Prd 135 (406)
..|||||..+|..++||.++.
T Consensus 3 ~~Cf~CG~~GH~ardC~~~~~ 23 (26)
T 1dsq_A 3 PVCFSCGKTGHIKRDCKEEXX 23 (26)
T ss_dssp CBCTTTCCBSSCTTTTTCC--
T ss_pred CeeEeCCCCCcccccCCCccc
Confidence 579999999999999999864
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=96.69 E-value=0.00082 Score=48.06 Aligned_cols=23 Identities=35% Similarity=0.735 Sum_probs=20.8
Q ss_pred CCCccccCCCCCCCCCCCCCccC
Q 015479 113 DASRCFNCGSYSHSLKECPKPRD 135 (406)
Q Consensus 113 ~~~~CFNCG~~~HsLrdCP~Prd 135 (406)
....|||||..+|-.++||.++.
T Consensus 9 ~~~~C~~Cgk~GH~ardCP~~~~ 31 (40)
T 1a6b_B 9 DRDQCAYCKEKGHWAKDCPKKPR 31 (40)
T ss_dssp CSSSCSSSCCTTCCTTSCSSSCC
T ss_pred CCCeeeECCCCCcchhhCcCCcc
Confidence 46899999999999999999874
No 4
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=96.10 E-value=0.0023 Score=44.39 Aligned_cols=19 Identities=47% Similarity=1.209 Sum_probs=16.2
Q ss_pred ccccCCCCCCCCCCCCCcc
Q 015479 116 RCFNCGSYSHSLKECPKPR 134 (406)
Q Consensus 116 ~CFNCG~~~HsLrdCP~Pr 134 (406)
.|||||..+|..++||.|+
T Consensus 2 ~C~~Cg~~GH~a~~C~~~~ 20 (39)
T 2a51_A 2 TCFNCGKPGHTARMCRQPR 20 (39)
T ss_dssp BCTTTCCBSSCTTTCCSCC
T ss_pred eeeccCCCCcccccCCCCC
Confidence 5899998899999998874
No 5
>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=96.09 E-value=0.0026 Score=46.17 Aligned_cols=21 Identities=48% Similarity=1.137 Sum_probs=16.3
Q ss_pred CCccccCCCCCCCCCCCCCcc
Q 015479 114 ASRCFNCGSYSHSLKECPKPR 134 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Pr 134 (406)
...|||||..+|..++||.|+
T Consensus 6 ~~~C~~Cg~~GH~a~~C~~~~ 26 (49)
T 2ec7_A 6 VIRCWNCGKEGHSARQCRAPR 26 (49)
T ss_dssp CCBCTTTCCBTCCTTTCCCSS
T ss_pred cCeeeecCCCCcChhhCcCCC
Confidence 357888888888888888774
No 6
>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A
Probab=95.79 E-value=0.0032 Score=47.89 Aligned_cols=24 Identities=33% Similarity=0.649 Sum_probs=21.1
Q ss_pred cCCCccccCCCCCCCCCCCCCccC
Q 015479 112 DDASRCFNCGSYSHSLKECPKPRD 135 (406)
Q Consensus 112 ~~~~~CFNCG~~~HsLrdCP~Prd 135 (406)
.....|||||..+|-.+|||.+..
T Consensus 21 ~~~~~C~~Cge~GH~ardCp~~~~ 44 (56)
T 1u6p_A 21 LDRDQCAYCKEKGHWAKDCPKKPR 44 (56)
T ss_dssp CCTTBCSSSCCBSSCGGGCTTCCC
T ss_pred CCCCcceeCCCCCcccccCcCCcc
Confidence 346899999999999999999864
No 7
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=95.63 E-value=0.0053 Score=42.05 Aligned_cols=18 Identities=39% Similarity=1.056 Sum_probs=13.4
Q ss_pred ccccCCCCCCCCCCCCCc
Q 015479 116 RCFNCGSYSHSLKECPKP 133 (406)
Q Consensus 116 ~CFNCG~~~HsLrdCP~P 133 (406)
.|||||..+|..++||.|
T Consensus 2 ~C~~Cg~~GH~~~~C~~~ 19 (37)
T 2bl6_A 2 TCYNCGKPGHLSSQCRAP 19 (37)
T ss_dssp CBSSSCCSSCCTTTSSCB
T ss_pred cccccCCCCcchhhCcCc
Confidence 477777777777777765
No 8
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=95.51 E-value=0.0049 Score=46.56 Aligned_cols=20 Identities=45% Similarity=1.050 Sum_probs=10.6
Q ss_pred CccccCCCCCCCCCCCCCcc
Q 015479 115 SRCFNCGSYSHSLKECPKPR 134 (406)
Q Consensus 115 ~~CFNCG~~~HsLrdCP~Pr 134 (406)
..||||+...|..++||.++
T Consensus 5 ~~C~~Cg~~GH~a~~C~~~~ 24 (61)
T 2ihx_A 5 GLCYTCGSPGHYQAQCPKKR 24 (61)
T ss_dssp TBCSSSCCBTCCGGGCTTTT
T ss_pred CcccccCCCCeehhhCcCCc
Confidence 34555555555555555544
No 9
>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=95.32 E-value=0.0063 Score=44.72 Aligned_cols=20 Identities=45% Similarity=1.089 Sum_probs=14.2
Q ss_pred CCccccCCCCCCCCCCCCCc
Q 015479 114 ASRCFNCGSYSHSLKECPKP 133 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~P 133 (406)
...|||||..+|..++||.|
T Consensus 12 ~~~C~~Cg~~GH~a~~C~~~ 31 (55)
T 1a1t_A 12 TVKCFNCGKEGHIAKNCRAP 31 (55)
T ss_dssp TCBCTTTCCBSSCGGGCSSC
T ss_pred CcceeeeCCCCcChhhcCCC
Confidence 35677777777777777766
No 10
>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=95.10 E-value=0.011 Score=45.08 Aligned_cols=19 Identities=53% Similarity=1.268 Sum_probs=12.5
Q ss_pred CccccCCCCCCCCCCCCCc
Q 015479 115 SRCFNCGSYSHSLKECPKP 133 (406)
Q Consensus 115 ~~CFNCG~~~HsLrdCP~P 133 (406)
..|||||..+|..++||.+
T Consensus 8 ~~C~~Cg~~GH~a~~C~~~ 26 (63)
T 2cqf_A 8 DRCYNCGGLDHHAKECKLP 26 (63)
T ss_dssp CCCSSSCCSSSCTTTCCSC
T ss_pred CcccccCCCCcChhhCCCC
Confidence 4566666666666666655
No 11
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=94.85 E-value=0.0077 Score=45.63 Aligned_cols=21 Identities=38% Similarity=0.967 Sum_probs=18.1
Q ss_pred CCccccCCCCCCCCCCCCCcc
Q 015479 114 ASRCFNCGSYSHSLKECPKPR 134 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Pr 134 (406)
...||.||..+|.+++||...
T Consensus 7 ~~~C~kCGk~GH~~k~Cp~~~ 27 (55)
T 2ysa_A 7 GYTCFRCGKPGHYIKNCPTNG 27 (55)
T ss_dssp SCCCTTTCCTTSCGGGCSGGG
T ss_pred CCccccCCCcCcccccCCCCC
Confidence 467999999999999998543
No 12
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=94.76 E-value=0.014 Score=40.32 Aligned_cols=19 Identities=47% Similarity=1.186 Sum_probs=17.4
Q ss_pred CCccccCCCCCCCCCCCCC
Q 015479 114 ASRCFNCGSYSHSLKECPK 132 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~ 132 (406)
...|||||..+|..++||+
T Consensus 21 ~~~C~~Cg~~GH~~~~C~~ 39 (39)
T 2a51_A 21 QEGCWNCGSKEHRFAQCPK 39 (39)
T ss_dssp CSSCTTTCCSSSCTTTSCC
T ss_pred CCccccCCCCCCccCcCcC
Confidence 4689999999999999995
No 13
>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=94.68 E-value=0.016 Score=43.20 Aligned_cols=22 Identities=27% Similarity=0.510 Sum_probs=19.9
Q ss_pred CCccccCCCCCCCCCCCCCccC
Q 015479 114 ASRCFNCGSYSHSLKECPKPRD 135 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Prd 135 (406)
...||+||..+|..++||.+.+
T Consensus 30 ~~~C~~Cg~~GH~ar~C~~~~~ 51 (60)
T 1cl4_A 30 PGLCPRCKRGKHWANECKSKTD 51 (60)
T ss_dssp CCSCSSCSSCSSCSTTCCCTTS
T ss_pred CcceeECCCCCCccCcCCCccc
Confidence 4789999999999999999865
No 14
>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=94.38 E-value=0.0072 Score=45.15 Aligned_cols=22 Identities=32% Similarity=0.806 Sum_probs=0.0
Q ss_pred CccccCCCCCCCCCCCCCccCH
Q 015479 115 SRCFNCGSYSHSLKECPKPRDK 136 (406)
Q Consensus 115 ~~CFNCG~~~HsLrdCP~Prd~ 136 (406)
..|||||..+|..++||.+++.
T Consensus 2 ~~Cf~Cg~~GH~a~~C~~~~~~ 23 (60)
T 1cl4_A 2 GSCFKCGKKGHFAKNCHEHAHN 23 (60)
T ss_dssp ----------------------
T ss_pred CccccCCCCCcCHhhCcCCCCC
Confidence 3699999999999999988653
No 15
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=94.35 E-value=0.02 Score=45.33 Aligned_cols=21 Identities=48% Similarity=1.141 Sum_probs=16.2
Q ss_pred CCccccCCCCCCCCCCCCCcc
Q 015479 114 ASRCFNCGSYSHSLKECPKPR 134 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Pr 134 (406)
...|||||..+|..++||.+.
T Consensus 24 ~~~C~~Cg~~GH~a~~C~~~~ 44 (74)
T 2li8_A 24 GDRCYNCGGLDHHAKECKLPP 44 (74)
T ss_dssp TSCCTTTCCSSSCTTTCSSCC
T ss_pred CCcccccCCcCcCcccCCCCC
Confidence 467888888888888888654
No 16
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=94.22 E-value=0.015 Score=43.93 Aligned_cols=23 Identities=30% Similarity=0.679 Sum_probs=19.3
Q ss_pred CCccccCCCCCCCCCCCCCccCH
Q 015479 114 ASRCFNCGSYSHSLKECPKPRDK 136 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Prd~ 136 (406)
...|||||...|..++||.++..
T Consensus 30 ~~~C~~Cg~~GH~ar~C~~~~~~ 52 (61)
T 2ihx_A 30 RERCQLCNGMGHNAKQCRKRDGN 52 (61)
T ss_dssp CSBCTTTCCBSSCGGGCCCCC--
T ss_pred CCeeCCCCCCCCCcCCCcCCCcC
Confidence 36799999999999999998754
No 17
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=94.10 E-value=0.017 Score=46.78 Aligned_cols=22 Identities=32% Similarity=0.800 Sum_probs=20.2
Q ss_pred CCCccccCCCCCCCCCCCCCcc
Q 015479 113 DASRCFNCGSYSHSLKECPKPR 134 (406)
Q Consensus 113 ~~~~CFNCG~~~HsLrdCP~Pr 134 (406)
....|+|||..+|.-+|||++|
T Consensus 45 ~~~~CYnCG~~GH~~rdC~~~r 66 (83)
T 3nyb_B 45 HTIYCYNCGGKGHFGDDCKEKR 66 (83)
T ss_dssp CCCBCSSSSCBSSCGGGCSSCC
T ss_pred CCCeecccCCCCcCcccCCccc
Confidence 3578999999999999999988
No 18
>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=93.86 E-value=0.021 Score=41.88 Aligned_cols=21 Identities=29% Similarity=0.933 Sum_probs=19.0
Q ss_pred CCccccCCCCCCCCCCCCCcc
Q 015479 114 ASRCFNCGSYSHSLKECPKPR 134 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Pr 134 (406)
...||+||..+|..++||..+
T Consensus 33 ~~~C~~Cg~~GH~~~~C~~~~ 53 (55)
T 1a1t_A 33 KKGCWKCGKEGHQMKDCTERQ 53 (55)
T ss_dssp CCBCTTTCCBSSCGGGCSSSC
T ss_pred CCEeCCCCCcCCccCCCcCcC
Confidence 468999999999999999865
No 19
>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=93.37 E-value=0.028 Score=49.41 Aligned_cols=22 Identities=45% Similarity=1.103 Sum_probs=18.4
Q ss_pred CCccccCCCCCCCCCCCCCccC
Q 015479 114 ASRCFNCGSYSHSLKECPKPRD 135 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Prd 135 (406)
..+|||||..+|..++||.|..
T Consensus 97 ~~~C~~Cg~~GH~a~~C~~~~~ 118 (148)
T 3ts2_A 97 GDRCYNCGGLDHHAKECKLPPQ 118 (148)
T ss_dssp SCCCTTTCCSSCCGGGCCSCCC
T ss_pred CCcccEeCCccchhhhCCCCCC
Confidence 3579999999999999998654
No 20
>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=93.33 E-value=0.031 Score=40.49 Aligned_cols=21 Identities=29% Similarity=0.963 Sum_probs=18.5
Q ss_pred CCccccCCCCCCCCCCCCCcc
Q 015479 114 ASRCFNCGSYSHSLKECPKPR 134 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Pr 134 (406)
...||+||..+|..++||...
T Consensus 27 ~~~C~~Cg~~GH~~~~C~~~~ 47 (49)
T 2ec7_A 27 RQGCWKCGKTGHVMAKCPERQ 47 (49)
T ss_dssp CCSCSSSCCSSCCGGGCCSSC
T ss_pred CCeeCcCCCcCCccCCCcCCC
Confidence 367999999999999999754
No 21
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=93.17 E-value=0.037 Score=42.12 Aligned_cols=21 Identities=33% Similarity=0.755 Sum_probs=19.0
Q ss_pred CCccccCCCCCCCCCCCCCcc
Q 015479 114 ASRCFNCGSYSHSLKECPKPR 134 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Pr 134 (406)
...||||+..+|..++||...
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 478999999999999999764
No 22
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=92.24 E-value=0.041 Score=37.55 Aligned_cols=18 Identities=33% Similarity=0.778 Sum_probs=16.7
Q ss_pred CccccCCCCCCCCCCCCC
Q 015479 115 SRCFNCGSYSHSLKECPK 132 (406)
Q Consensus 115 ~~CFNCG~~~HsLrdCP~ 132 (406)
..||+||..+|..++||.
T Consensus 20 ~~C~~Cg~~GH~a~~C~~ 37 (37)
T 2bl6_A 20 KVCFKCKQPGHFSKQCRS 37 (37)
T ss_dssp TTCSSCCCTTGGGGTTCC
T ss_pred CeEccCCCcCCccCcCcC
Confidence 689999999999999984
No 23
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=91.18 E-value=0.084 Score=41.67 Aligned_cols=21 Identities=33% Similarity=0.755 Sum_probs=18.8
Q ss_pred CCccccCCCCCCCCCCCCCcc
Q 015479 114 ASRCFNCGSYSHSLKECPKPR 134 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Pr 134 (406)
...||+||..+|..++||...
T Consensus 46 ~~~C~~Cg~~GH~ar~Cp~~~ 66 (74)
T 2li8_A 46 PKKCHFCQSISHMVASCPLKA 66 (74)
T ss_dssp CCCCTTTCCTTSCGGGCTTGG
T ss_pred CCccCCcCCcCCccCcCcCCc
Confidence 478999999999999999764
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=91.08 E-value=0.081 Score=46.41 Aligned_cols=23 Identities=26% Similarity=0.706 Sum_probs=19.4
Q ss_pred CCccccCCCCCCCCCCCCCccCH
Q 015479 114 ASRCFNCGSYSHSLKECPKPRDK 136 (406)
Q Consensus 114 ~~~CFNCG~~~HsLrdCP~Prd~ 136 (406)
...||+||..+|..++||...-.
T Consensus 119 ~~~C~~Cg~~GH~~r~Cp~~~~~ 141 (148)
T 3ts2_A 119 PKKCHFCQSINHMVASCPLKAQQ 141 (148)
T ss_dssp CCCCTTTCCSSCCGGGCTTTTC-
T ss_pred CCcccccCCcCCEeccCcCCCCC
Confidence 46899999999999999976544
No 25
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=88.86 E-value=0.11 Score=42.05 Aligned_cols=21 Identities=33% Similarity=0.664 Sum_probs=17.2
Q ss_pred CCCccccCCCCCCCCCCCCCc
Q 015479 113 DASRCFNCGSYSHSLKECPKP 133 (406)
Q Consensus 113 ~~~~CFNCG~~~HsLrdCP~P 133 (406)
+...||||++.+|..++||..
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 357899999999999999986
No 26
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=87.80 E-value=0.25 Score=41.27 Aligned_cols=20 Identities=30% Similarity=0.811 Sum_probs=18.2
Q ss_pred CCCccccCCCCCCCCCCCCC
Q 015479 113 DASRCFNCGSYSHSLKECPK 132 (406)
Q Consensus 113 ~~~~CFNCG~~~HsLrdCP~ 132 (406)
....|||||+.+|..+|||+
T Consensus 104 ~~~~Cy~Cg~~GH~a~dCp~ 123 (124)
T 2lli_A 104 HTIYCYNCGGKGHFGDDCKE 123 (124)
T ss_dssp CCCCTTTTSSSCTTTTTSCC
T ss_pred CCCCcCCCCCCCcCcccCcC
Confidence 35799999999999999997
No 27
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=86.87 E-value=0.28 Score=41.04 Aligned_cols=19 Identities=37% Similarity=0.891 Sum_probs=13.0
Q ss_pred CccccCCCCCCCCCCCCCc
Q 015479 115 SRCFNCGSYSHSLKECPKP 133 (406)
Q Consensus 115 ~~CFNCG~~~HsLrdCP~P 133 (406)
..||||+..+|..++||.+
T Consensus 5 ~~C~~C~~~GH~~~~Cp~~ 23 (124)
T 2lli_A 5 PKCNNCSQRGHLKKDCPHI 23 (124)
T ss_dssp SCCSSCSSSSCCTTTTTSC
T ss_pred CcccCCCCCCcCcccCcCC
Confidence 4577777777777777763
No 28
>1yfb_A Transition state regulatory protein ABRB; , homodimer, bioinformatics, swapped-hairpin barrel, transcription; NMR {Bacillus subtilis} SCOP: b.129.1.3 PDB: 1ysf_A 2k1n_A* 1z0r_A 2ro4_A 2fy9_A 2ro3_A
Probab=32.39 E-value=21 Score=26.81 Aligned_cols=16 Identities=38% Similarity=0.599 Sum_probs=14.5
Q ss_pred cCCHHHHHHhCCCCCC
Q 015479 178 ALDAETRQLLGLGELD 193 (406)
Q Consensus 178 ~LS~eLReALGm~~~d 193 (406)
+|-.++|++|||.+++
T Consensus 25 tIPkeiR~~Lgi~~Gd 40 (59)
T 1yfb_A 25 VIPIELRRTLGIAEKD 40 (59)
T ss_dssp ECCHHHHHHTTCCTTC
T ss_pred EeCHHHHHHcCCCCCC
Confidence 5889999999999887
No 29
>2l66_A SSO7C4, transcriptional regulator, ABRB family; DNA binding protein, transcription regulator; NMR {Sulfolobus solfataricus}
Probab=31.18 E-value=25 Score=25.27 Aligned_cols=16 Identities=31% Similarity=0.380 Sum_probs=14.1
Q ss_pred cCCHHHHHHhCCCCCC
Q 015479 178 ALDAETRQLLGLGELD 193 (406)
Q Consensus 178 ~LS~eLReALGm~~~d 193 (406)
.|-.++|++|||.+++
T Consensus 15 ~IPk~ir~~lgi~~Gd 30 (53)
T 2l66_A 15 TIPAKVRQKFQIKEGD 30 (53)
T ss_dssp CCCHHHHHHSCCCTTC
T ss_pred EeCHHHHHHcCcCCCC
Confidence 5789999999999876
No 30
>3a5y_A GENX, putative lysyl-tRNA synthetase; aminoacyl-tRNA synthetase paralog, translation, lysyl- synthetase, lysyladenylate analog; HET: KAA; 1.90A {Escherichia coli} PDB: 3a5z_A* 3g1z_A*
Probab=27.18 E-value=43 Score=32.74 Aligned_cols=26 Identities=23% Similarity=0.230 Sum_probs=21.9
Q ss_pred HHHHhCCCCCCChHHHHHHHhcCCCC
Q 015479 183 TRQLLGLGELDPPPWLHRMRELGYPP 208 (406)
Q Consensus 183 LReALGm~~~dpPPWL~rMr~~GyPP 208 (406)
.++++|+.......|+..+.++|.||
T Consensus 288 ~~~~~g~~~~~~d~~yl~al~yG~PP 313 (345)
T 3a5y_A 288 KRAARGLPQHPIDQNLIEALKVGMPD 313 (345)
T ss_dssp HHHHTTCCCCCCCHHHHHHHHHCCCS
T ss_pred HHHhcCCChhhHHHHHHHHHhcCCCC
Confidence 45567998887778999999999997
No 31
>2glw_A PHS018, 92AA long hypothetical protein; RIFT barrel, bioinformatics, transcription; NMR {Pyrococcus horikoshii}
Probab=22.87 E-value=38 Score=27.44 Aligned_cols=17 Identities=12% Similarity=0.278 Sum_probs=14.7
Q ss_pred cCCHHHHHHhCCCCCCC
Q 015479 178 ALDAETRQLLGLGELDP 194 (406)
Q Consensus 178 ~LS~eLReALGm~~~dp 194 (406)
+|-.++|++|||.+++.
T Consensus 63 tIPkeiR~~lgi~~Gd~ 79 (92)
T 2glw_A 63 IIPKALRDVIGIKPGEV 79 (92)
T ss_dssp ECCHHHHHHHTCCTTCE
T ss_pred ECcHHHHHHcCCCCCCE
Confidence 47899999999999873
No 32
>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A
Probab=21.97 E-value=30 Score=27.21 Aligned_cols=33 Identities=18% Similarity=0.163 Sum_probs=27.2
Q ss_pred CCCCCc-CC-HHHHHHhCCCCCCChHHHHHHHhcC
Q 015479 173 GLRPGA-LD-AETRQLLGLGELDPPPWLHRMRELG 205 (406)
Q Consensus 173 ~~kPG~-LS-~eLReALGm~~~dpPPWL~rMr~~G 205 (406)
+..||+ ++ .+|-++|||+....=-.|++|++-|
T Consensus 21 ~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G 55 (81)
T 1qbj_A 21 ELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKG 55 (81)
T ss_dssp HHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred HcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 445665 56 6799999999988999999999875
Done!