Query 007230
Match_columns 612
No_of_seqs 180 out of 238
Neff 3.0
Searched_HMMs 29240
Date Mon Mar 25 20:31:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007230.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/007230hhsearch_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 97.1 0.00016 5.6E-09 50.1 1.5 22 320-341 6-27 (29)
2 1dsq_A Nucleic acid binding pr 96.9 0.00034 1.1E-08 47.5 2.0 22 320-341 2-23 (26)
3 1a6b_B Momulv, zinc finger pro 96.3 0.0017 5.9E-08 48.7 2.4 23 319-341 9-31 (40)
4 2a51_A Nucleocapsid protein; s 95.6 0.0045 1.5E-07 45.0 1.9 19 322-340 2-20 (39)
5 2ec7_A GAG polyprotein (PR55GA 95.5 0.0059 2E-07 46.4 2.2 21 320-340 6-26 (49)
6 1u6p_A GAG polyprotein; MLV, A 95.3 0.0059 2E-07 48.7 1.7 24 318-341 21-44 (56)
7 2bl6_A Nucleocapsid protein P1 95.0 0.01 3.5E-07 42.6 2.1 18 322-339 2-19 (37)
8 2ihx_A Nucleocapsid (NC) prote 94.8 0.01 3.6E-07 46.8 1.8 20 321-340 5-24 (61)
9 1a1t_A Nucleocapsid protein; s 94.6 0.013 4.4E-07 45.1 1.8 20 320-339 12-31 (55)
10 2cqf_A RNA-binding protein LIN 94.1 0.024 8.2E-07 45.2 2.6 19 321-339 8-26 (63)
11 2ysa_A Retinoblastoma-binding 93.8 0.017 5.7E-07 46.0 1.0 19 320-338 7-25 (55)
12 1cl4_A Protein (GAG polyprotei 93.7 0.033 1.1E-06 43.5 2.6 22 320-341 30-51 (60)
13 2a51_A Nucleocapsid protein; s 93.6 0.031 1.1E-06 40.5 2.1 19 320-338 21-39 (39)
14 1cl4_A Protein (GAG polyprotei 93.3 0.015 5.2E-07 45.4 0.0 22 321-342 2-23 (60)
15 2ihx_A Nucleocapsid (NC) prote 93.1 0.029 9.8E-07 44.3 1.3 23 320-342 30-52 (61)
16 2li8_A Protein LIN-28 homolog 93.0 0.042 1.4E-06 45.5 2.3 21 320-340 24-44 (74)
17 3nyb_B Protein AIR2; polya RNA 93.0 0.032 1.1E-06 47.2 1.6 22 319-340 45-66 (83)
18 1a1t_A Nucleocapsid protein; s 92.5 0.043 1.5E-06 42.1 1.5 21 320-340 33-53 (55)
19 3ts2_A Protein LIN-28 homolog 92.0 0.05 1.7E-06 49.8 1.6 22 320-341 97-118 (148)
20 2ec7_A GAG polyprotein (PR55GA 91.8 0.061 2.1E-06 40.8 1.6 21 320-340 27-47 (49)
21 2cqf_A RNA-binding protein LIN 91.5 0.072 2.5E-06 42.4 1.8 21 320-340 29-49 (63)
22 2bl6_A Nucleocapsid protein P1 90.2 0.089 3E-06 37.7 1.1 18 321-338 20-37 (37)
23 3ts2_A Protein LIN-28 homolog 88.7 0.15 5.1E-06 46.7 1.7 23 320-342 119-141 (148)
24 2li8_A Protein LIN-28 homolog 88.4 0.17 5.8E-06 41.8 1.7 20 320-339 46-65 (74)
25 3nyb_B Protein AIR2; polya RNA 86.3 0.18 6.1E-06 42.6 0.7 21 319-339 4-24 (83)
26 2lli_A Protein AIR2; RNA surve 83.9 0.45 1.5E-05 41.5 2.1 20 319-338 104-123 (124)
27 2lli_A Protein AIR2; RNA surve 82.3 0.55 1.9E-05 40.9 2.0 18 321-338 5-22 (124)
28 1yfb_A Transition state regula 21.5 41 0.0014 26.6 1.8 16 384-399 25-40 (59)
29 3a5y_A GENX, putative lysyl-tR 21.3 62 0.0021 33.1 3.6 27 388-414 287-313 (345)
30 2l66_A SSO7C4, transcriptional 21.3 47 0.0016 25.2 2.1 16 384-399 15-30 (53)
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=97.08 E-value=0.00016 Score=50.06 Aligned_cols=22 Identities=45% Similarity=1.081 Sum_probs=19.7
Q ss_pred CCceecCCCCCCCCCCCCCccC
Q 007230 320 ASRCFNCGSYSHSLKECPKPRD 341 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PRD 341 (612)
...|||||.++|..++||.|+-
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 4679999999999999999973
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=96.94 E-value=0.00034 Score=47.54 Aligned_cols=22 Identities=27% Similarity=0.822 Sum_probs=18.4
Q ss_pred CCceecCCCCCCCCCCCCCccC
Q 007230 320 ASRCFNCGSYSHSLKECPKPRD 341 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PRD 341 (612)
...|||||..+|..++||.|+.
T Consensus 2 ~~~Cf~CG~~GH~ardC~~~~~ 23 (26)
T 1dsq_A 2 GPVCFSCGKTGHIKRDCKEEXX 23 (26)
T ss_dssp CCBCTTTCCBSSCTTTTTCC--
T ss_pred CCeeEeCCCCCcccccCCCccc
Confidence 3579999999999999999864
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=96.32 E-value=0.0017 Score=48.68 Aligned_cols=23 Identities=35% Similarity=0.735 Sum_probs=20.7
Q ss_pred CCCceecCCCCCCCCCCCCCccC
Q 007230 319 DASRCFNCGSYSHSLKECPKPRD 341 (612)
Q Consensus 319 ~~~rCFNCGs~eHsLrDCP~PRD 341 (612)
....|||||..+|-.++||.++.
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 46899999999999999999764
No 4
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=95.62 E-value=0.0045 Score=44.95 Aligned_cols=19 Identities=47% Similarity=1.209 Sum_probs=16.4
Q ss_pred ceecCCCCCCCCCCCCCcc
Q 007230 322 RCFNCGSYSHSLKECPKPR 340 (612)
Q Consensus 322 rCFNCGs~eHsLrDCP~PR 340 (612)
.|||||..+|..++||.|+
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 6999999999999999874
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=95.48 E-value=0.0059 Score=46.40 Aligned_cols=21 Identities=48% Similarity=1.137 Sum_probs=15.9
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 007230 320 ASRCFNCGSYSHSLKECPKPR 340 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PR 340 (612)
...|||||..+|..++||.|+
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 456888888888888888764
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=95.31 E-value=0.0059 Score=48.70 Aligned_cols=24 Identities=33% Similarity=0.649 Sum_probs=21.0
Q ss_pred cCCCceecCCCCCCCCCCCCCccC
Q 007230 318 DDASRCFNCGSYSHSLKECPKPRD 341 (612)
Q Consensus 318 ~~~~rCFNCGs~eHsLrDCP~PRD 341 (612)
.....|||||..+|-.+|||.+..
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 346889999999999999999764
No 7
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=95.00 E-value=0.01 Score=42.62 Aligned_cols=18 Identities=39% Similarity=1.056 Sum_probs=13.6
Q ss_pred ceecCCCCCCCCCCCCCc
Q 007230 322 RCFNCGSYSHSLKECPKP 339 (612)
Q Consensus 322 rCFNCGs~eHsLrDCP~P 339 (612)
.|||||..+|..++||.|
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 577777777777777765
No 8
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=94.77 E-value=0.01 Score=46.81 Aligned_cols=20 Identities=45% Similarity=1.050 Sum_probs=10.9
Q ss_pred CceecCCCCCCCCCCCCCcc
Q 007230 321 SRCFNCGSYSHSLKECPKPR 340 (612)
Q Consensus 321 ~rCFNCGs~eHsLrDCP~PR 340 (612)
..|||||.+.|..++||.++
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 34555555555555555543
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=94.59 E-value=0.013 Score=45.06 Aligned_cols=20 Identities=45% Similarity=1.089 Sum_probs=14.2
Q ss_pred CCceecCCCCCCCCCCCCCc
Q 007230 320 ASRCFNCGSYSHSLKECPKP 339 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~P 339 (612)
...|||||..+|..++||.|
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=94.14 E-value=0.024 Score=45.16 Aligned_cols=19 Identities=53% Similarity=1.268 Sum_probs=12.3
Q ss_pred CceecCCCCCCCCCCCCCc
Q 007230 321 SRCFNCGSYSHSLKECPKP 339 (612)
Q Consensus 321 ~rCFNCGs~eHsLrDCP~P 339 (612)
..|||||..+|..++||.|
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 4566666666666666654
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=93.77 E-value=0.017 Score=45.95 Aligned_cols=19 Identities=42% Similarity=1.102 Sum_probs=17.4
Q ss_pred CCceecCCCCCCCCCCCCC
Q 007230 320 ASRCFNCGSYSHSLKECPK 338 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~ 338 (612)
...||.||.++|.+++||.
T Consensus 7 ~~~C~kCGk~GH~~k~Cp~ 25 (55)
T 2ysa_A 7 GYTCFRCGKPGHYIKNCPT 25 (55)
T ss_dssp SCCCTTTCCTTSCGGGCSG
T ss_pred CCccccCCCcCcccccCCC
Confidence 4679999999999999996
No 12
>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=93.72 E-value=0.033 Score=43.47 Aligned_cols=22 Identities=27% Similarity=0.510 Sum_probs=19.7
Q ss_pred CCceecCCCCCCCCCCCCCccC
Q 007230 320 ASRCFNCGSYSHSLKECPKPRD 341 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PRD 341 (612)
...||+||..+|..++||.+++
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 5789999999999999999754
No 13
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=93.59 E-value=0.031 Score=40.48 Aligned_cols=19 Identities=47% Similarity=1.186 Sum_probs=17.4
Q ss_pred CCceecCCCCCCCCCCCCC
Q 007230 320 ASRCFNCGSYSHSLKECPK 338 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~ 338 (612)
...|||||..+|..++||+
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 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=93.28 E-value=0.015 Score=45.38 Aligned_cols=22 Identities=32% Similarity=0.806 Sum_probs=0.0
Q ss_pred CceecCCCCCCCCCCCCCccCH
Q 007230 321 SRCFNCGSYSHSLKECPKPRDK 342 (612)
Q Consensus 321 ~rCFNCGs~eHsLrDCP~PRD~ 342 (612)
..|||||.++|..++||.+++.
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 3699999999999999997653
No 15
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=93.09 E-value=0.029 Score=44.30 Aligned_cols=23 Identities=30% Similarity=0.679 Sum_probs=19.2
Q ss_pred CCceecCCCCCCCCCCCCCccCH
Q 007230 320 ASRCFNCGSYSHSLKECPKPRDK 342 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PRD~ 342 (612)
...|||||...|..++||.++..
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 46799999999999999997653
No 16
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=93.02 E-value=0.042 Score=45.45 Aligned_cols=21 Identities=48% Similarity=1.141 Sum_probs=15.0
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 007230 320 ASRCFNCGSYSHSLKECPKPR 340 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PR 340 (612)
...|||||..+|..++||.+.
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 356777777777777777653
No 17
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=93.01 E-value=0.032 Score=47.20 Aligned_cols=22 Identities=32% Similarity=0.800 Sum_probs=20.1
Q ss_pred CCCceecCCCCCCCCCCCCCcc
Q 007230 319 DASRCFNCGSYSHSLKECPKPR 340 (612)
Q Consensus 319 ~~~rCFNCGs~eHsLrDCP~PR 340 (612)
....|+|||..+|.-+|||++|
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 3578999999999999999977
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=92.49 E-value=0.043 Score=42.11 Aligned_cols=21 Identities=29% Similarity=0.933 Sum_probs=18.9
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 007230 320 ASRCFNCGSYSHSLKECPKPR 340 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PR 340 (612)
...||+||..+|..++||.++
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=91.96 E-value=0.05 Score=49.82 Aligned_cols=22 Identities=45% Similarity=1.103 Sum_probs=17.0
Q ss_pred CCceecCCCCCCCCCCCCCccC
Q 007230 320 ASRCFNCGSYSHSLKECPKPRD 341 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PRD 341 (612)
..+|||||..+|..++||.|..
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 3568888888888888887543
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=91.78 E-value=0.061 Score=40.79 Aligned_cols=21 Identities=29% Similarity=0.963 Sum_probs=18.5
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 007230 320 ASRCFNCGSYSHSLKECPKPR 340 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PR 340 (612)
...||+||..+|..++||...
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 467999999999999999854
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=91.48 E-value=0.072 Score=42.41 Aligned_cols=21 Identities=33% Similarity=0.755 Sum_probs=18.8
Q ss_pred CCceecCCCCCCCCCCCCCcc
Q 007230 320 ASRCFNCGSYSHSLKECPKPR 340 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PR 340 (612)
...|||||..+|..++||..+
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 578999999999999999853
No 22
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=90.18 E-value=0.089 Score=37.67 Aligned_cols=18 Identities=33% Similarity=0.778 Sum_probs=16.7
Q ss_pred CceecCCCCCCCCCCCCC
Q 007230 321 SRCFNCGSYSHSLKECPK 338 (612)
Q Consensus 321 ~rCFNCGs~eHsLrDCP~ 338 (612)
..||+||..+|..++||.
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
>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=88.74 E-value=0.15 Score=46.73 Aligned_cols=23 Identities=26% Similarity=0.706 Sum_probs=19.2
Q ss_pred CCceecCCCCCCCCCCCCCccCH
Q 007230 320 ASRCFNCGSYSHSLKECPKPRDK 342 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~PRD~ 342 (612)
...||+||..+|..++||...-.
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 46899999999999999985443
No 24
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=88.44 E-value=0.17 Score=41.84 Aligned_cols=20 Identities=35% Similarity=0.803 Sum_probs=18.3
Q ss_pred CCceecCCCCCCCCCCCCCc
Q 007230 320 ASRCFNCGSYSHSLKECPKP 339 (612)
Q Consensus 320 ~~rCFNCGs~eHsLrDCP~P 339 (612)
...||+||..+|..++||..
T Consensus 46 ~~~C~~Cg~~GH~ar~Cp~~ 65 (74)
T 2li8_A 46 PKKCHFCQSISHMVASCPLK 65 (74)
T ss_dssp CCCCTTTCCTTSCGGGCTTG
T ss_pred CCccCCcCCcCCccCcCcCC
Confidence 47899999999999999984
No 25
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=86.32 E-value=0.18 Score=42.65 Aligned_cols=21 Identities=33% Similarity=0.664 Sum_probs=17.1
Q ss_pred CCCceecCCCCCCCCCCCCCc
Q 007230 319 DASRCFNCGSYSHSLKECPKP 339 (612)
Q Consensus 319 ~~~rCFNCGs~eHsLrDCP~P 339 (612)
+...||||++.+|..++||..
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 467899999999999999985
No 26
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=83.86 E-value=0.45 Score=41.52 Aligned_cols=20 Identities=30% Similarity=0.811 Sum_probs=18.3
Q ss_pred CCCceecCCCCCCCCCCCCC
Q 007230 319 DASRCFNCGSYSHSLKECPK 338 (612)
Q Consensus 319 ~~~rCFNCGs~eHsLrDCP~ 338 (612)
....|||||+.+|..+|||+
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 35789999999999999997
No 27
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=82.29 E-value=0.55 Score=40.93 Aligned_cols=18 Identities=39% Similarity=0.988 Sum_probs=13.4
Q ss_pred CceecCCCCCCCCCCCCC
Q 007230 321 SRCFNCGSYSHSLKECPK 338 (612)
Q Consensus 321 ~rCFNCGs~eHsLrDCP~ 338 (612)
..||||+..+|..++||.
T Consensus 5 ~~C~~C~~~GH~~~~Cp~ 22 (124)
T 2lli_A 5 PKCNNCSQRGHLKKDCPH 22 (124)
T ss_dssp SCCSSCSSSSCCTTTTTS
T ss_pred CcccCCCCCCcCcccCcC
Confidence 457777777777777776
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=21.46 E-value=41 Score=26.63 Aligned_cols=16 Identities=38% Similarity=0.599 Sum_probs=14.4
Q ss_pred CCCHHHHHHhCCCCCC
Q 007230 384 ALDAETRQLLGLGELD 399 (612)
Q Consensus 384 kLS~ELReALGm~~nd 399 (612)
.|-+++|++|||.+++
T Consensus 25 tIPkeiR~~Lgi~~Gd 40 (59)
T 1yfb_A 25 VIPIELRRTLGIAEKD 40 (59)
T ss_dssp ECCHHHHHHTTCCTTC
T ss_pred EeCHHHHHHcCCCCCC
Confidence 5889999999999877
No 29
>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=21.28 E-value=62 Score=33.09 Aligned_cols=27 Identities=22% Similarity=0.227 Sum_probs=22.8
Q ss_pred HHHHHhCCCCCCChHHHHHHHhcCCCC
Q 007230 388 ETRQLLGLGELDPPPWLHRMRELGYPP 414 (612)
Q Consensus 388 ELReALGm~~ndpPPWLyrMrrlGyPP 414 (612)
+.|+++|+.+.....|+..+.++|.||
T Consensus 287 ~~~~~~g~~~~~~d~~yl~al~yG~PP 313 (345)
T 3a5y_A 287 RKRAARGLPQHPIDQNLIEALKVGMPD 313 (345)
T ss_dssp HHHHHTTCCCCCCCHHHHHHHHHCCCS
T ss_pred HHHHhcCCChhhHHHHHHHHHhcCCCC
Confidence 456778998887778999999999997
No 30
>2l66_A SSO7C4, transcriptional regulator, ABRB family; DNA binding protein, transcription regulator; NMR {Sulfolobus solfataricus}
Probab=21.26 E-value=47 Score=25.15 Aligned_cols=16 Identities=31% Similarity=0.380 Sum_probs=14.0
Q ss_pred CCCHHHHHHhCCCCCC
Q 007230 384 ALDAETRQLLGLGELD 399 (612)
Q Consensus 384 kLS~ELReALGm~~nd 399 (612)
.|-.++|++|||.+++
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
Done!