Query 014840
Match_columns 417
No_of_seqs 182 out of 239
Neff 3.5
Searched_HMMs 29240
Date Mon Mar 25 18:46:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014840.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/014840hhsearch_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 49.7 1.5 22 125-146 6-27 (29)
2 1dsq_A Nucleic acid binding pr 97.2 0.00014 4.9E-09 47.2 2.1 21 126-146 3-23 (26)
3 1a6b_B Momulv, zinc finger pro 96.7 0.00082 2.8E-08 48.2 2.5 23 124-146 9-31 (40)
4 2a51_A Nucleocapsid protein; s 96.1 0.0023 7.7E-08 44.5 1.9 19 127-145 2-20 (39)
5 2ec7_A GAG polyprotein (PR55GA 96.0 0.0027 9.2E-08 46.3 2.2 21 125-145 6-26 (49)
6 1u6p_A GAG polyprotein; MLV, A 95.8 0.0032 1.1E-07 48.1 1.8 24 123-146 21-44 (56)
7 2bl6_A Nucleocapsid protein P1 95.6 0.0055 1.9E-07 42.1 2.1 18 127-144 2-19 (37)
8 2ihx_A Nucleocapsid (NC) prote 95.5 0.005 1.7E-07 46.6 1.8 20 126-145 5-24 (61)
9 1a1t_A Nucleocapsid protein; s 95.3 0.0062 2.1E-07 44.9 1.7 20 125-144 12-31 (55)
10 2cqf_A RNA-binding protein LIN 95.1 0.011 3.7E-07 45.2 2.6 19 126-144 8-26 (63)
11 2ysa_A Retinoblastoma-binding 94.7 0.0084 2.9E-07 45.6 1.1 21 125-145 7-27 (55)
12 2a51_A Nucleocapsid protein; s 94.7 0.015 5.1E-07 40.3 2.1 19 125-143 21-39 (39)
13 1cl4_A Protein (GAG polyprotei 94.6 0.017 5.9E-07 43.2 2.6 22 125-146 30-51 (60)
14 1cl4_A Protein (GAG polyprotei 94.3 0.0075 2.6E-07 45.2 0.0 22 126-147 2-23 (60)
15 2li8_A Protein LIN-28 homolog 94.3 0.02 6.7E-07 45.5 2.3 21 125-145 24-44 (74)
16 2ihx_A Nucleocapsid (NC) prote 94.1 0.015 5.2E-07 43.9 1.3 23 125-147 30-52 (61)
17 3nyb_B Protein AIR2; polya RNA 94.0 0.018 6E-07 46.8 1.6 22 124-145 45-66 (83)
18 1a1t_A Nucleocapsid protein; s 93.7 0.022 7.6E-07 41.9 1.6 21 125-145 33-53 (55)
19 3ts2_A Protein LIN-28 homolog 93.3 0.027 9.3E-07 49.5 1.6 22 125-146 97-118 (148)
20 2ec7_A GAG polyprotein (PR55GA 93.2 0.032 1.1E-06 40.5 1.6 21 125-145 27-47 (49)
21 2cqf_A RNA-binding protein LIN 93.0 0.038 1.3E-06 42.1 1.9 21 125-145 29-49 (63)
22 2bl6_A Nucleocapsid protein P1 92.2 0.043 1.5E-06 37.6 1.1 18 126-143 20-37 (37)
23 2li8_A Protein LIN-28 homolog 90.9 0.088 3E-06 41.7 1.8 21 125-145 46-66 (74)
24 3ts2_A Protein LIN-28 homolog 90.8 0.085 2.9E-06 46.4 1.8 23 125-147 119-141 (148)
25 3nyb_B Protein AIR2; polya RNA 88.9 0.1 3.6E-06 42.2 0.8 21 124-144 4-24 (83)
26 2lli_A Protein AIR2; RNA surve 87.3 0.25 8.6E-06 41.4 2.1 19 125-143 105-123 (124)
27 2lli_A Protein AIR2; RNA surve 86.6 0.29 9.8E-06 41.0 2.1 19 126-144 5-23 (124)
28 1yfb_A Transition state regula 30.6 24 0.00081 26.7 2.0 16 189-204 25-40 (59)
29 2l66_A SSO7C4, transcriptional 29.6 28 0.00096 25.1 2.1 16 189-204 15-30 (53)
30 3m20_A 4-oxalocrotonate tautom 26.1 69 0.0024 23.1 3.8 26 8-33 1-26 (62)
31 3a5y_A GENX, putative lysyl-tR 25.7 48 0.0016 32.5 3.7 26 194-219 288-313 (345)
32 2glw_A PHS018, 92AA long hypot 21.7 41 0.0014 27.3 2.0 17 189-205 63-79 (92)
33 2fhd_A RAD9 homolog, DNA repai 21.6 25 0.00085 31.8 0.7 17 55-71 21-37 (153)
34 1otf_A 4-oxalocrotonate tautom 20.8 1.1E+02 0.0039 21.1 4.0 27 8-34 1-28 (62)
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=97.31 E-value=6.9e-05 Score=49.69 Aligned_cols=22 Identities=45% Similarity=1.081 Sum_probs=19.6
Q ss_pred CCceecCCCCCCCCCCCCCccC
Q 014840 125 ASRCFNCGSYSHSLKECPKPRD 146 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PRd 146 (417)
...|||||.++|..++||.|+-
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=97.19 E-value=0.00014 Score=47.17 Aligned_cols=21 Identities=29% Similarity=0.854 Sum_probs=18.1
Q ss_pred CceecCCCCCCCCCCCCCccC
Q 014840 126 SRCFNCGSYSHSLKECPKPRD 146 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~PRd 146 (417)
..|||||..+|..++||.++.
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=96.68 E-value=0.00082 Score=48.23 Aligned_cols=23 Identities=35% Similarity=0.735 Sum_probs=20.8
Q ss_pred CCCceecCCCCCCCCCCCCCccC
Q 014840 124 DASRCFNCGSYSHSLKECPKPRD 146 (417)
Q Consensus 124 ~~~~CFNCG~~~HsLrdCP~PRd 146 (417)
....|||||..+|-.++||.++.
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 46899999999999999999875
No 4
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=96.08 E-value=0.0023 Score=44.53 Aligned_cols=19 Identities=47% Similarity=1.209 Sum_probs=16.3
Q ss_pred ceecCCCCCCCCCCCCCcc
Q 014840 127 RCFNCGSYSHSLKECPKPR 145 (417)
Q Consensus 127 ~CFNCG~~~HsLrdCP~PR 145 (417)
.|||||..+|..++||.|+
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=96.04 E-value=0.0027 Score=46.27 Aligned_cols=21 Identities=48% Similarity=1.137 Sum_probs=16.2
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 014840 125 ASRCFNCGSYSHSLKECPKPR 145 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PR 145 (417)
...|||||..+|..++||.|+
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=95.80 E-value=0.0032 Score=48.08 Aligned_cols=24 Identities=33% Similarity=0.649 Sum_probs=21.1
Q ss_pred cCCCceecCCCCCCCCCCCCCccC
Q 014840 123 DDASRCFNCGSYSHSLKECPKPRD 146 (417)
Q Consensus 123 ~~~~~CFNCG~~~HsLrdCP~PRd 146 (417)
.....|||||..+|-.+|||.+..
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=95.57 E-value=0.0055 Score=42.08 Aligned_cols=18 Identities=39% Similarity=1.056 Sum_probs=13.1
Q ss_pred ceecCCCCCCCCCCCCCc
Q 014840 127 RCFNCGSYSHSLKECPKP 144 (417)
Q Consensus 127 ~CFNCG~~~HsLrdCP~P 144 (417)
.|||||..+|..++||.|
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=95.48 E-value=0.005 Score=46.64 Aligned_cols=20 Identities=45% Similarity=1.050 Sum_probs=11.0
Q ss_pred CceecCCCCCCCCCCCCCcc
Q 014840 126 SRCFNCGSYSHSLKECPKPR 145 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~PR 145 (417)
..|||||...|..++||.++
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 34555555555555555554
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=95.30 E-value=0.0062 Score=44.87 Aligned_cols=20 Identities=45% Similarity=1.089 Sum_probs=14.3
Q ss_pred CCceecCCCCCCCCCCCCCc
Q 014840 125 ASRCFNCGSYSHSLKECPKP 144 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~P 144 (417)
...|||||..+|..++||.|
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 35677777777777777776
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=45.19 Aligned_cols=19 Identities=53% Similarity=1.268 Sum_probs=13.1
Q ss_pred CceecCCCCCCCCCCCCCc
Q 014840 126 SRCFNCGSYSHSLKECPKP 144 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~P 144 (417)
..|||||..+|..++||.+
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 4577777777777777765
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=94.73 E-value=0.0084 Score=45.61 Aligned_cols=21 Identities=38% Similarity=0.967 Sum_probs=18.1
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 014840 125 ASRCFNCGSYSHSLKECPKPR 145 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PR 145 (417)
...||.||..+|.+++||...
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 467999999999999998533
No 12
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=94.66 E-value=0.015 Score=40.34 Aligned_cols=19 Identities=47% Similarity=1.186 Sum_probs=17.4
Q ss_pred CCceecCCCCCCCCCCCCC
Q 014840 125 ASRCFNCGSYSHSLKECPK 143 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~ 143 (417)
...|||||..+|..++||+
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=94.63 E-value=0.017 Score=43.18 Aligned_cols=22 Identities=27% Similarity=0.510 Sum_probs=19.9
Q ss_pred CCceecCCCCCCCCCCCCCccC
Q 014840 125 ASRCFNCGSYSHSLKECPKPRD 146 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PRd 146 (417)
...||+||..+|..++||.+.+
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=94.33 E-value=0.0075 Score=45.18 Aligned_cols=22 Identities=32% Similarity=0.806 Sum_probs=0.0
Q ss_pred CceecCCCCCCCCCCCCCccCH
Q 014840 126 SRCFNCGSYSHSLKECPKPRDK 147 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~PRd~ 147 (417)
..|||||..+|..++||.+.+.
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=94.30 E-value=0.02 Score=45.45 Aligned_cols=21 Identities=48% Similarity=1.141 Sum_probs=16.1
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 014840 125 ASRCFNCGSYSHSLKECPKPR 145 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PR 145 (417)
...|||||..+|..++||.+.
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 457888888888888888653
No 16
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=94.12 E-value=0.015 Score=43.94 Aligned_cols=23 Identities=30% Similarity=0.679 Sum_probs=19.3
Q ss_pred CCceecCCCCCCCCCCCCCccCH
Q 014840 125 ASRCFNCGSYSHSLKECPKPRDK 147 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PRd~ 147 (417)
...|||||...|..++||.++..
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=94.03 E-value=0.018 Score=46.77 Aligned_cols=22 Identities=32% Similarity=0.800 Sum_probs=20.2
Q ss_pred CCCceecCCCCCCCCCCCCCcc
Q 014840 124 DASRCFNCGSYSHSLKECPKPR 145 (417)
Q Consensus 124 ~~~~CFNCG~~~HsLrdCP~PR 145 (417)
....|+|||..+|.-+|||++|
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=93.74 E-value=0.022 Score=41.88 Aligned_cols=21 Identities=29% Similarity=0.933 Sum_probs=19.0
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 014840 125 ASRCFNCGSYSHSLKECPKPR 145 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PR 145 (417)
...||+||..+|..++||..+
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=93.28 E-value=0.027 Score=49.55 Aligned_cols=22 Identities=45% Similarity=1.103 Sum_probs=18.2
Q ss_pred CCceecCCCCCCCCCCCCCccC
Q 014840 125 ASRCFNCGSYSHSLKECPKPRD 146 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PRd 146 (417)
..+|||||..+|..++||.|..
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=93.19 E-value=0.032 Score=40.48 Aligned_cols=21 Identities=29% Similarity=0.963 Sum_probs=18.5
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 014840 125 ASRCFNCGSYSHSLKECPKPR 145 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PR 145 (417)
...||+||..+|..++||...
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=93.04 E-value=0.038 Score=42.14 Aligned_cols=21 Identities=33% Similarity=0.755 Sum_probs=19.0
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 014840 125 ASRCFNCGSYSHSLKECPKPR 145 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PR 145 (417)
...|||||..+|..++||...
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=92.23 E-value=0.043 Score=37.56 Aligned_cols=18 Identities=33% Similarity=0.778 Sum_probs=16.7
Q ss_pred CceecCCCCCCCCCCCCC
Q 014840 126 SRCFNCGSYSHSLKECPK 143 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~ 143 (417)
..||+||..+|..++||.
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=90.95 E-value=0.088 Score=41.68 Aligned_cols=21 Identities=33% Similarity=0.755 Sum_probs=18.8
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 014840 125 ASRCFNCGSYSHSLKECPKPR 145 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PR 145 (417)
...||+||..+|..++||...
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=90.80 E-value=0.085 Score=46.41 Aligned_cols=23 Identities=26% Similarity=0.706 Sum_probs=19.4
Q ss_pred CCceecCCCCCCCCCCCCCccCH
Q 014840 125 ASRCFNCGSYSHSLKECPKPRDK 147 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~PRd~ 147 (417)
...||+||..+|..++||...-.
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=88.92 E-value=0.1 Score=42.19 Aligned_cols=21 Identities=33% Similarity=0.664 Sum_probs=17.2
Q ss_pred CCCceecCCCCCCCCCCCCCc
Q 014840 124 DASRCFNCGSYSHSLKECPKP 144 (417)
Q Consensus 124 ~~~~CFNCG~~~HsLrdCP~P 144 (417)
+...||||++.+|..++||..
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 457899999999999999986
No 26
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=87.32 E-value=0.25 Score=41.37 Aligned_cols=19 Identities=32% Similarity=0.847 Sum_probs=17.8
Q ss_pred CCceecCCCCCCCCCCCCC
Q 014840 125 ASRCFNCGSYSHSLKECPK 143 (417)
Q Consensus 125 ~~~CFNCG~~~HsLrdCP~ 143 (417)
...|||||+.+|..+|||+
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 5789999999999999997
No 27
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=86.59 E-value=0.29 Score=41.04 Aligned_cols=19 Identities=37% Similarity=0.891 Sum_probs=13.7
Q ss_pred CceecCCCCCCCCCCCCCc
Q 014840 126 SRCFNCGSYSHSLKECPKP 144 (417)
Q Consensus 126 ~~CFNCG~~~HsLrdCP~P 144 (417)
..||||+..+|..++||.+
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=30.63 E-value=24 Score=26.66 Aligned_cols=16 Identities=38% Similarity=0.599 Sum_probs=14.4
Q ss_pred cCCHHHHHHhCCCCCC
Q 014840 189 ALDAETRQLLGLGELD 204 (417)
Q Consensus 189 ~LS~eLReALGm~~~~ 204 (417)
.|-.++|++|||.+++
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=29.55 E-value=28 Score=25.13 Aligned_cols=16 Identities=31% Similarity=0.380 Sum_probs=14.0
Q ss_pred cCCHHHHHHhCCCCCC
Q 014840 189 ALDAETRQLLGLGELD 204 (417)
Q Consensus 189 ~LS~eLReALGm~~~~ 204 (417)
.|-.++|++|||.+++
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 4789999999999876
No 30
>3m20_A 4-oxalocrotonate tautomerase, putative; DMPI, thermophIle, beta-alpha-beta, catalytic proline, isomerase; 2.37A {Archaeoglobus fulgidus}
Probab=26.09 E-value=69 Score=23.06 Aligned_cols=26 Identities=23% Similarity=0.217 Sum_probs=21.8
Q ss_pred CeEEEEecccCHHHHHHHHHHHHHHH
Q 014840 8 PSVHVIYNSLTRASKQKLEELLQQWS 33 (417)
Q Consensus 8 psv~v~y~~l~r~sk~kl~e~lq~Ws 33 (417)
|-|+|+...+|.+.|++|-+.|-+=-
T Consensus 1 P~I~I~~~grt~eqK~~L~~~it~~~ 26 (62)
T 3m20_A 1 PVLIVYGPKLDVGKKREFVERLTSVA 26 (62)
T ss_dssp CEEEEECSCCCHHHHHHHHHHHHHHH
T ss_pred CEEEEEECCCCHHHHHHHHHHHHHHH
Confidence 66888888999999999999886543
No 31
>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=25.66 E-value=48 Score=32.51 Aligned_cols=26 Identities=23% Similarity=0.230 Sum_probs=21.9
Q ss_pred HHHHhCCCCCCChHHHHHHHhcCCCC
Q 014840 194 TRQLLGLGELDPPPWLHRMRELGYPP 219 (417)
Q Consensus 194 LReALGm~~~~pPPWL~~Mr~~GyPP 219 (417)
.++++|+.+.....|+..+.++|.||
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 32
>2glw_A PHS018, 92AA long hypothetical protein; RIFT barrel, bioinformatics, transcription; NMR {Pyrococcus horikoshii}
Probab=21.67 E-value=41 Score=27.31 Aligned_cols=17 Identities=12% Similarity=0.278 Sum_probs=14.7
Q ss_pred cCCHHHHHHhCCCCCCC
Q 014840 189 ALDAETRQLLGLGELDP 205 (417)
Q Consensus 189 ~LS~eLReALGm~~~~p 205 (417)
.|-.++|++|||.+++.
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 33
>2fhd_A RAD9 homolog, DNA repair protein RHP9/CRB2; tamdem tudor domains, cell cycle; HET: DNA MSE PO4; 2.40A {Schizosaccharomyces pombe}
Probab=21.63 E-value=25 Score=31.76 Aligned_cols=17 Identities=18% Similarity=0.397 Sum_probs=12.9
Q ss_pred eeeecceeccCCCCCce
Q 014840 55 QTFFPAIRVGKAKGPAV 71 (417)
Q Consensus 55 ~~~fpa~~v~~~~~~a~ 71 (417)
-.||||+|||..-++++
T Consensus 21 ~~YYPATcvg~~~~~~~ 37 (153)
T 2fhd_A 21 SFYYPATLVAPVHSAVT 37 (153)
T ss_dssp CCEEEEEEEEEECCSSC
T ss_pred ccccceEEEccCCCccc
Confidence 46999999998755433
No 34
>1otf_A 4-oxalocrotonate tautomerase; isomerase; 1.90A {Pseudomonas SP} SCOP: d.80.1.1 PDB: 4otc_A 4ota_A 4otb_A 1bjp_A 2fm7_A
Probab=20.82 E-value=1.1e+02 Score=21.10 Aligned_cols=27 Identities=15% Similarity=0.160 Sum_probs=21.6
Q ss_pred CeEEEE-ecccCHHHHHHHHHHHHHHHH
Q 014840 8 PSVHVI-YNSLTRASKQKLEELLQQWSE 34 (417)
Q Consensus 8 psv~v~-y~~l~r~sk~kl~e~lq~Wse 34 (417)
|-|+|. ....|.+.|++|-+.|.+--.
T Consensus 1 P~i~I~~~~grs~e~k~~l~~~i~~~l~ 28 (62)
T 1otf_A 1 PIAQLYIIEGRTDEQKETLIRQVSEAMA 28 (62)
T ss_dssp CEEEEEEESCCCHHHHHHHHHHHHHHHH
T ss_pred CEEEEEEcCCCCHHHHHHHHHHHHHHHH
Confidence 668887 578899999999998876543
Done!