Query 048519
Match_columns 195
No_of_seqs 150 out of 298
Neff 6.8
Searched_HMMs 29240
Date Mon Mar 25 17:50:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048519.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/048519hhsearch_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 98.7 6.3E-09 2.1E-13 63.7 2.3 22 173-194 9-30 (40)
2 1u6p_A GAG polyprotein; MLV, A 98.6 1.6E-08 5.4E-13 66.3 2.0 23 172-194 21-43 (56)
3 1dsq_A Nucleic acid binding pr 98.5 1.7E-08 6E-13 56.1 1.1 20 175-194 3-22 (26)
4 1nc8_A Nucleocapsid protein; H 98.5 4.1E-08 1.4E-12 55.9 1.5 21 174-194 6-26 (29)
5 2ysa_A Retinoblastoma-binding 98.0 1.3E-06 4.4E-11 56.9 1.5 20 174-193 7-26 (55)
6 2ec7_A GAG polyprotein (PR55GA 97.5 2.4E-05 8.2E-10 49.5 1.2 20 175-194 28-47 (49)
7 1cl4_A Protein (GAG polyprotei 97.5 3.3E-05 1.1E-09 50.7 1.4 21 174-194 30-50 (60)
8 2a51_A Nucleocapsid protein; s 97.5 2.8E-05 9.7E-10 46.7 1.0 16 177-192 24-39 (39)
9 2a51_A Nucleocapsid protein; s 97.4 3.5E-05 1.2E-09 46.3 0.8 18 175-192 1-18 (39)
10 2ihx_A Nucleocapsid (NC) prote 97.4 3.8E-05 1.3E-09 50.7 0.9 21 174-194 30-50 (61)
11 2ec7_A GAG polyprotein (PR55GA 97.4 5.5E-05 1.9E-09 47.8 1.5 19 175-193 7-25 (49)
12 1a1t_A Nucleocapsid protein; s 97.4 5.1E-05 1.8E-09 48.9 1.3 21 174-194 33-53 (55)
13 2cqf_A RNA-binding protein LIN 97.3 4.8E-05 1.6E-09 50.6 1.0 21 174-194 29-49 (63)
14 2bl6_A Nucleocapsid protein P1 97.3 4.9E-05 1.7E-09 45.1 0.8 18 175-192 20-37 (37)
15 3nyb_B Protein AIR2; polya RNA 97.3 6.3E-05 2.2E-09 52.8 1.4 21 174-194 46-66 (83)
16 2ihx_A Nucleocapsid (NC) prote 97.3 7.8E-05 2.7E-09 49.2 1.7 20 174-193 4-23 (61)
17 2bl6_A Nucleocapsid protein P1 97.2 7.7E-05 2.6E-09 44.3 1.1 18 176-193 2-19 (37)
18 2cqf_A RNA-binding protein LIN 97.2 0.00016 5.6E-09 48.0 2.1 19 174-192 7-25 (63)
19 1cl4_A Protein (GAG polyprotei 97.1 7E-05 2.4E-09 49.1 0.0 18 176-193 3-20 (60)
20 2li8_A Protein LIN-28 homolog 97.1 0.00011 3.6E-09 50.6 0.9 21 174-194 46-66 (74)
21 1a1t_A Nucleocapsid protein; s 97.1 0.00012 4.1E-09 47.1 1.0 19 175-193 13-31 (55)
22 2li8_A Protein LIN-28 homolog 97.0 0.00025 8.7E-09 48.6 1.8 19 174-192 24-42 (74)
23 3ts2_A Protein LIN-28 homolog 96.7 0.00043 1.5E-08 53.5 1.1 20 175-194 120-139 (148)
24 3ts2_A Protein LIN-28 homolog 96.6 0.00083 2.8E-08 51.9 2.0 19 174-192 97-115 (148)
25 2lli_A Protein AIR2; RNA surve 95.9 0.0016 5.4E-08 48.4 0.6 19 174-192 105-123 (124)
26 2lli_A Protein AIR2; RNA surve 95.1 0.0071 2.4E-07 44.8 1.5 20 174-193 64-83 (124)
27 2hqh_E Restin; beta/BETA struc 90.2 0.058 2E-06 29.3 0.1 19 174-192 3-21 (26)
28 2pzo_E CAP-Gly domain-containi 86.7 0.14 4.7E-06 30.9 0.1 21 172-192 18-38 (42)
29 3e2u_E CAP-Gly domain-containi 83.3 0.24 8.3E-06 29.9 0.1 20 173-192 19-38 (42)
30 3nyb_B Protein AIR2; polya RNA 81.1 0.33 1.1E-05 33.6 0.2 17 176-192 26-42 (83)
31 3alr_A Nanos protein; zinc-fin 53.4 3.5 0.00012 29.6 0.5 19 175-193 72-93 (106)
32 2w0t_A Lethal(3)malignant brai 42.0 7.3 0.00025 23.6 0.6 15 175-189 7-21 (43)
33 1ef4_A Subunit N, DNA-directed 31.4 12 0.00042 23.7 0.4 9 175-183 4-12 (55)
34 3a1y_A 50S ribosomal protein P 30.7 83 0.0029 19.7 4.4 54 65-119 2-56 (58)
35 4ayb_N DNA-directed RNA polyme 29.5 12 0.0004 24.7 0.1 9 175-183 5-13 (66)
36 3a4c_A DNA replication factor 27.0 47 0.0016 23.8 2.9 41 82-122 4-45 (106)
37 2odb_B Serine/threonine-protei 24.8 13 0.00045 21.0 -0.3 12 90-101 23-34 (35)
38 1twf_J DNA-directed RNA polyme 23.5 18 0.00061 24.1 0.1 9 175-183 5-13 (70)
39 2qme_I CRIB domain of the seri 22.7 14 0.00049 21.1 -0.4 13 90-102 23-35 (36)
40 2lnh_A N-WAsp, neural wiskott- 21.1 40 0.0014 21.9 1.4 15 90-104 20-34 (65)
41 2wsc_J PSAJ, PSI-J, photosyste 20.7 46 0.0016 20.1 1.5 15 1-15 1-15 (44)
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=98.69 E-value=6.3e-09 Score=63.72 Aligned_cols=22 Identities=27% Similarity=0.697 Sum_probs=19.3
Q ss_pred CccceeecCCcceecccCCCcc
Q 048519 173 KKGNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 173 ~k~~C~~CgK~GH~ar~C~~rK 194 (195)
.+..||+||+.|||+++||+++
T Consensus 9 ~~~~C~~Cgk~GH~ardCP~~~ 30 (40)
T 1a6b_B 9 DRDQCAYCKEKGHWAKDCPKKP 30 (40)
T ss_dssp CSSSCSSSCCTTCCTTSCSSSC
T ss_pred CCCeeeECCCCCcchhhCcCCc
Confidence 3568999999999999999865
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=98.58 E-value=1.6e-08 Score=66.33 Aligned_cols=23 Identities=26% Similarity=0.624 Sum_probs=19.9
Q ss_pred CCccceeecCCcceecccCCCcc
Q 048519 172 NKKGNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 172 k~k~~C~~CgK~GH~ar~C~~rK 194 (195)
..+..||+||+.|||+++||+++
T Consensus 21 ~~~~~C~~Cge~GH~ardCp~~~ 43 (56)
T 1u6p_A 21 LDRDQCAYCKEKGHWAKDCPKKP 43 (56)
T ss_dssp CCTTBCSSSCCBSSCGGGCTTCC
T ss_pred CCCCcceeCCCCCcccccCcCCc
Confidence 34578999999999999999865
No 3
>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=98.53 E-value=1.7e-08 Score=56.08 Aligned_cols=20 Identities=35% Similarity=0.853 Sum_probs=17.6
Q ss_pred cceeecCCcceecccCCCcc
Q 048519 175 GNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 175 ~~C~~CgK~GH~ar~C~~rK 194 (195)
..||.||+.||++++|+.++
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 47999999999999999875
No 4
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A
Probab=98.47 E-value=4.1e-08 Score=55.88 Aligned_cols=21 Identities=43% Similarity=0.711 Sum_probs=18.2
Q ss_pred ccceeecCCcceecccCCCcc
Q 048519 174 KGNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~rK 194 (195)
...||+||+.||++++|+..+
T Consensus 6 ~~~C~nCgk~GH~ar~C~~pr 26 (29)
T 1nc8_A 6 VIRCWNCGKEGHSARQCRAPR 26 (29)
T ss_dssp CCBCTTTSCBSSCGGGCCSSS
T ss_pred CCEEEECCccccCHhHCcccc
Confidence 367999999999999998654
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=98.03 E-value=1.3e-06 Score=56.94 Aligned_cols=20 Identities=40% Similarity=0.861 Sum_probs=17.3
Q ss_pred ccceeecCCcceecccCCCc
Q 048519 174 KGNCFVCGKIIHYANQCRHK 193 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~r 193 (195)
...||.||++|||+++|+..
T Consensus 7 ~~~C~kCGk~GH~~k~Cp~~ 26 (55)
T 2ysa_A 7 GYTCFRCGKPGHYIKNCPTN 26 (55)
T ss_dssp SCCCTTTCCTTSCGGGCSGG
T ss_pred CCccccCCCcCcccccCCCC
Confidence 34799999999999999843
No 6
>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=97.52 E-value=2.4e-05 Score=49.45 Aligned_cols=20 Identities=30% Similarity=0.798 Sum_probs=17.9
Q ss_pred cceeecCCcceecccCCCcc
Q 048519 175 GNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 175 ~~C~~CgK~GH~ar~C~~rK 194 (195)
..||.||+.||++++|+.++
T Consensus 28 ~~C~~Cg~~GH~~~~C~~~~ 47 (49)
T 2ec7_A 28 QGCWKCGKTGHVMAKCPERQ 47 (49)
T ss_dssp CSCSSSCCSSCCGGGCCSSC
T ss_pred CeeCcCCCcCCccCCCcCCC
Confidence 57999999999999999875
No 7
>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=97.46 E-value=3.3e-05 Score=50.70 Aligned_cols=21 Identities=38% Similarity=0.809 Sum_probs=18.4
Q ss_pred ccceeecCCcceecccCCCcc
Q 048519 174 KGNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~rK 194 (195)
...||.||+.||++++|+.+.
T Consensus 30 ~~~C~~Cg~~GH~ar~C~~~~ 50 (60)
T 1cl4_A 30 PGLCPRCKRGKHWANECKSKT 50 (60)
T ss_dssp CCSCSSCSSCSSCSTTCCCTT
T ss_pred CcceeECCCCCCccCcCCCcc
Confidence 457999999999999998754
No 8
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=97.46 E-value=2.8e-05 Score=46.74 Aligned_cols=16 Identities=38% Similarity=0.870 Sum_probs=12.0
Q ss_pred eeecCCcceecccCCC
Q 048519 177 CFVCGKIIHYANQCRH 192 (195)
Q Consensus 177 C~~CgK~GH~ar~C~~ 192 (195)
||.||+.||++++||+
T Consensus 24 C~~Cg~~GH~~~~C~~ 39 (39)
T 2a51_A 24 CWNCGSKEHRFAQCPK 39 (39)
T ss_dssp CTTTCCSSSCTTTSCC
T ss_pred cccCCCCCCccCcCcC
Confidence 7777777777777764
No 9
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=97.39 E-value=3.5e-05 Score=46.32 Aligned_cols=18 Identities=50% Similarity=0.921 Sum_probs=16.1
Q ss_pred cceeecCCcceecccCCC
Q 048519 175 GNCFVCGKIIHYANQCRH 192 (195)
Q Consensus 175 ~~C~~CgK~GH~ar~C~~ 192 (195)
+.||+||+.||++++|+.
T Consensus 1 i~C~~Cg~~GH~a~~C~~ 18 (39)
T 2a51_A 1 LTCFNCGKPGHTARMCRQ 18 (39)
T ss_dssp CBCTTTCCBSSCTTTCCS
T ss_pred CeeeccCCCCcccccCCC
Confidence 369999999999999974
No 10
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=97.38 E-value=3.8e-05 Score=50.73 Aligned_cols=21 Identities=33% Similarity=0.816 Sum_probs=18.4
Q ss_pred ccceeecCCcceecccCCCcc
Q 048519 174 KGNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~rK 194 (195)
...||+||+.||++++|+.++
T Consensus 30 ~~~C~~Cg~~GH~ar~C~~~~ 50 (61)
T 2ihx_A 30 RERCQLCNGMGHNAKQCRKRD 50 (61)
T ss_dssp CSBCTTTCCBSSCGGGCCCCC
T ss_pred CCeeCCCCCCCCCcCCCcCCC
Confidence 357999999999999998764
No 11
>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=97.37 E-value=5.5e-05 Score=47.76 Aligned_cols=19 Identities=47% Similarity=0.826 Sum_probs=17.3
Q ss_pred cceeecCCcceecccCCCc
Q 048519 175 GNCFVCGKIIHYANQCRHK 193 (195)
Q Consensus 175 ~~C~~CgK~GH~ar~C~~r 193 (195)
..||+||+.||++++|+..
T Consensus 7 ~~C~~Cg~~GH~a~~C~~~ 25 (49)
T 2ec7_A 7 IRCWNCGKEGHSARQCRAP 25 (49)
T ss_dssp CBCTTTCCBTCCTTTCCCS
T ss_pred CeeeecCCCCcChhhCcCC
Confidence 5799999999999999864
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=97.36 E-value=5.1e-05 Score=48.88 Aligned_cols=21 Identities=33% Similarity=0.786 Sum_probs=17.8
Q ss_pred ccceeecCCcceecccCCCcc
Q 048519 174 KGNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~rK 194 (195)
...||.||+.||++++|+.++
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 357999999999999998764
No 13
>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=97.34 E-value=4.8e-05 Score=50.60 Aligned_cols=21 Identities=33% Similarity=0.691 Sum_probs=18.0
Q ss_pred ccceeecCCcceecccCCCcc
Q 048519 174 KGNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~rK 194 (195)
...||+||+.||++++|+.++
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 457999999999999998754
No 14
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=97.31 E-value=4.9e-05 Score=45.14 Aligned_cols=18 Identities=39% Similarity=0.925 Sum_probs=16.1
Q ss_pred cceeecCCcceecccCCC
Q 048519 175 GNCFVCGKIIHYANQCRH 192 (195)
Q Consensus 175 ~~C~~CgK~GH~ar~C~~ 192 (195)
..||+||+.||++++|+.
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 579999999999999984
No 15
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=97.30 E-value=6.3e-05 Score=52.85 Aligned_cols=21 Identities=29% Similarity=0.808 Sum_probs=18.5
Q ss_pred ccceeecCCcceecccCCCcc
Q 048519 174 KGNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~rK 194 (195)
...||+||+.||++++|++++
T Consensus 46 ~~~CYnCG~~GH~~rdC~~~r 66 (83)
T 3nyb_B 46 TIYCYNCGGKGHFGDDCKEKR 66 (83)
T ss_dssp CCBCSSSSCBSSCGGGCSSCC
T ss_pred CCeecccCCCCcCcccCCccc
Confidence 467999999999999998764
No 16
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=97.30 E-value=7.8e-05 Score=49.17 Aligned_cols=20 Identities=45% Similarity=1.072 Sum_probs=17.7
Q ss_pred ccceeecCCcceecccCCCc
Q 048519 174 KGNCFVCGKIIHYANQCRHK 193 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~r 193 (195)
...||+||+.||++++|+..
T Consensus 4 ~~~C~~Cg~~GH~a~~C~~~ 23 (61)
T 2ihx_A 4 RGLCYTCGSPGHYQAQCPKK 23 (61)
T ss_dssp TTBCSSSCCBTCCGGGCTTT
T ss_pred CCcccccCCCCeehhhCcCC
Confidence 35799999999999999874
No 17
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=97.24 E-value=7.7e-05 Score=44.27 Aligned_cols=18 Identities=44% Similarity=1.010 Sum_probs=16.4
Q ss_pred ceeecCCcceecccCCCc
Q 048519 176 NCFVCGKIIHYANQCRHK 193 (195)
Q Consensus 176 ~C~~CgK~GH~ar~C~~r 193 (195)
.||+||+.||++++|+..
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 599999999999999864
No 18
>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=97.15 E-value=0.00016 Score=47.95 Aligned_cols=19 Identities=32% Similarity=0.889 Sum_probs=17.1
Q ss_pred ccceeecCCcceecccCCC
Q 048519 174 KGNCFVCGKIIHYANQCRH 192 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~ 192 (195)
...||+||+.||++++|+.
T Consensus 7 ~~~C~~Cg~~GH~a~~C~~ 25 (63)
T 2cqf_A 7 GDRCYNCGGLDHHAKECKL 25 (63)
T ss_dssp CCCCSSSCCSSSCTTTCCS
T ss_pred CCcccccCCCCcChhhCCC
Confidence 3579999999999999985
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=97.12 E-value=7e-05 Score=49.08 Aligned_cols=18 Identities=44% Similarity=1.119 Sum_probs=0.0
Q ss_pred ceeecCCcceecccCCCc
Q 048519 176 NCFVCGKIIHYANQCRHK 193 (195)
Q Consensus 176 ~C~~CgK~GH~ar~C~~r 193 (195)
.||.||+.||++++|+..
T Consensus 3 ~Cf~Cg~~GH~a~~C~~~ 20 (60)
T 1cl4_A 3 SCFKCGKKGHFAKNCHEH 20 (60)
T ss_dssp ------------------
T ss_pred ccccCCCCCcCHhhCcCC
Confidence 599999999999999864
No 20
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=97.11 E-value=0.00011 Score=50.57 Aligned_cols=21 Identities=33% Similarity=0.691 Sum_probs=17.2
Q ss_pred ccceeecCCcceecccCCCcc
Q 048519 174 KGNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~rK 194 (195)
...||+||+.||++++|+.++
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 357999999999999998754
No 21
>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=97.11 E-value=0.00012 Score=47.11 Aligned_cols=19 Identities=47% Similarity=0.910 Sum_probs=17.2
Q ss_pred cceeecCCcceecccCCCc
Q 048519 175 GNCFVCGKIIHYANQCRHK 193 (195)
Q Consensus 175 ~~C~~CgK~GH~ar~C~~r 193 (195)
..||.||+.||++++|+..
T Consensus 13 ~~C~~Cg~~GH~a~~C~~~ 31 (55)
T 1a1t_A 13 VKCFNCGKEGHIAKNCRAP 31 (55)
T ss_dssp CBCTTTCCBSSCGGGCSSC
T ss_pred cceeeeCCCCcChhhcCCC
Confidence 5799999999999999864
No 22
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=96.99 E-value=0.00025 Score=48.64 Aligned_cols=19 Identities=32% Similarity=0.889 Sum_probs=17.0
Q ss_pred ccceeecCCcceecccCCC
Q 048519 174 KGNCFVCGKIIHYANQCRH 192 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~ 192 (195)
...||+||+.||++++|+.
T Consensus 24 ~~~C~~Cg~~GH~a~~C~~ 42 (74)
T 2li8_A 24 GDRCYNCGGLDHHAKECKL 42 (74)
T ss_dssp TSCCTTTCCSSSCTTTCSS
T ss_pred CCcccccCCcCcCcccCCC
Confidence 3579999999999999985
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=96.67 E-value=0.00043 Score=53.51 Aligned_cols=20 Identities=35% Similarity=0.718 Sum_probs=15.7
Q ss_pred cceeecCCcceecccCCCcc
Q 048519 175 GNCFVCGKIIHYANQCRHKA 194 (195)
Q Consensus 175 ~~C~~CgK~GH~ar~C~~rK 194 (195)
..||.||+.||++++||++.
T Consensus 120 ~~C~~Cg~~GH~~r~Cp~~~ 139 (148)
T 3ts2_A 120 KKCHFCQSINHMVASCPLKA 139 (148)
T ss_dssp CCCTTTCCSSCCGGGCTTTT
T ss_pred CcccccCCcCCEeccCcCCC
Confidence 46888888888888888653
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=96.55 E-value=0.00083 Score=51.86 Aligned_cols=19 Identities=32% Similarity=0.889 Sum_probs=17.2
Q ss_pred ccceeecCCcceecccCCC
Q 048519 174 KGNCFVCGKIIHYANQCRH 192 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~ 192 (195)
...||+||+.||++++|+.
T Consensus 97 ~~~C~~Cg~~GH~a~~C~~ 115 (148)
T 3ts2_A 97 GDRCYNCGGLDHHAKECKL 115 (148)
T ss_dssp SCCCTTTCCSSCCGGGCCS
T ss_pred CCcccEeCCccchhhhCCC
Confidence 3579999999999999987
No 25
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=95.93 E-value=0.0016 Score=48.42 Aligned_cols=19 Identities=26% Similarity=0.847 Sum_probs=17.4
Q ss_pred ccceeecCCcceecccCCC
Q 048519 174 KGNCFVCGKIIHYANQCRH 192 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~ 192 (195)
.+.||+||+.||++++||+
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 4689999999999999986
No 26
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=95.07 E-value=0.0071 Score=44.81 Aligned_cols=20 Identities=25% Similarity=0.541 Sum_probs=17.1
Q ss_pred ccceeecCCcceecccCCCc
Q 048519 174 KGNCFVCGKIIHYANQCRHK 193 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~r 193 (195)
...||+||+.||++++||..
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 35799999999999999864
No 27
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=90.20 E-value=0.058 Score=29.31 Aligned_cols=19 Identities=26% Similarity=0.738 Sum_probs=16.2
Q ss_pred ccceeecCCcceecccCCC
Q 048519 174 KGNCFVCGKIIHYANQCRH 192 (195)
Q Consensus 174 k~~C~~CgK~GH~ar~C~~ 192 (195)
++-|-+|...||+..+|..
T Consensus 3 RpYCe~CE~FGH~t~~C~d 21 (26)
T 2hqh_E 3 RPYCEICEMFGHWATNCND 21 (26)
T ss_dssp -CEETTTTEESSCGGGCCT
T ss_pred CccchHHHHhCcccccCCc
Confidence 4679999999999999964
No 28
>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=86.69 E-value=0.14 Score=30.93 Aligned_cols=21 Identities=24% Similarity=0.702 Sum_probs=16.5
Q ss_pred CCccceeecCCcceecccCCC
Q 048519 172 NKKGNCFVCGKIIHYANQCRH 192 (195)
Q Consensus 172 k~k~~C~~CgK~GH~ar~C~~ 192 (195)
..++-|-+|...|||..+|..
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 345679999999999999964
No 29
>3e2u_E CAP-Gly domain-containing linker protein 1; structural protein microtubule binding, dynactin, cytoskelet associated protein, P150glued; 2.60A {Homo sapiens}
Probab=83.30 E-value=0.24 Score=29.92 Aligned_cols=20 Identities=25% Similarity=0.722 Sum_probs=17.1
Q ss_pred CccceeecCCcceecccCCC
Q 048519 173 KKGNCFVCGKIIHYANQCRH 192 (195)
Q Consensus 173 ~k~~C~~CgK~GH~ar~C~~ 192 (195)
.++-|-+|-..|||..+|..
T Consensus 19 eRpYCe~CEVFGH~t~eC~d 38 (42)
T 3e2u_E 19 ERPYCEICEMFGHWATNCND 38 (42)
T ss_dssp -CCEETTTTEESSCGGGCCT
T ss_pred cCcccccceecccccccCCc
Confidence 35679999999999999964
No 30
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=81.11 E-value=0.33 Score=33.58 Aligned_cols=17 Identities=6% Similarity=-0.140 Sum_probs=4.8
Q ss_pred ceeecCCcceecccCCC
Q 048519 176 NCFVCGKIIHYANQCRH 192 (195)
Q Consensus 176 ~C~~CgK~GH~ar~C~~ 192 (195)
.||+|+..||.+++|..
T Consensus 26 rcY~c~~~gh~~~~c~~ 42 (83)
T 3nyb_B 26 RAYILVDDNEKAKPKVL 42 (83)
T ss_dssp CCCCBC-----------
T ss_pred cccccccCCcccccccC
Confidence 58888888888887754
No 31
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=53.37 E-value=3.5 Score=29.64 Aligned_cols=19 Identities=26% Similarity=0.490 Sum_probs=16.6
Q ss_pred cceeecCCcc---eecccCCCc
Q 048519 175 GNCFVCGKII---HYANQCRHK 193 (195)
Q Consensus 175 ~~C~~CgK~G---H~ar~C~~r 193 (195)
-+|-+||-.| |..+.||..
T Consensus 72 Y~CpiCGATGd~AHT~kYCP~~ 93 (106)
T 3alr_A 72 YKCPLCGATGAKAHTKRFCPMV 93 (106)
T ss_dssp CCCTTTCCCGGGCCCGGGCTTC
T ss_pred ccCCCCCCcCCcccceecCCCC
Confidence 4699999999 999999864
No 32
>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=42.02 E-value=7.3 Score=23.55 Aligned_cols=15 Identities=20% Similarity=0.381 Sum_probs=12.3
Q ss_pred cceeecCCcceeccc
Q 048519 175 GNCFVCGKIIHYANQ 189 (195)
Q Consensus 175 ~~C~~CgK~GH~ar~ 189 (195)
.+|-.||+.||...-
T Consensus 7 ~~CE~CG~~g~~~~F 21 (43)
T 2w0t_A 7 AVCEMCGIVGTREAF 21 (43)
T ss_dssp EECTTTCCEEETTTS
T ss_pred ehhhhhcCcchhhhh
Confidence 579999999987654
No 33
>1ef4_A Subunit N, DNA-directed RNA polymerase; three helix bundle, zinc binding, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: a.4.11.1
Probab=31.37 E-value=12 Score=23.75 Aligned_cols=9 Identities=44% Similarity=1.043 Sum_probs=7.7
Q ss_pred cceeecCCc
Q 048519 175 GNCFVCGKI 183 (195)
Q Consensus 175 ~~C~~CgK~ 183 (195)
..||-|||.
T Consensus 4 VRCFTCGkv 12 (55)
T 1ef4_A 4 VRCLSCGKP 12 (55)
T ss_dssp SSCSCTTSC
T ss_pred eecCCCCCC
Confidence 579999996
No 34
>3a1y_A 50S ribosomal protein P1 (L12P); stalk, helix SPIN, ribonucleoprotein; 2.13A {Pyrococcus horikoshii}
Probab=30.69 E-value=83 Score=19.70 Aligned_cols=54 Identities=15% Similarity=-0.061 Sum_probs=35.4
Q ss_pred HHHHHHHHHhhcCCCCCchhhHHHHHhhcccchHHHHHhhhcC-CcccCHHHHHHH
Q 048519 65 HVYNLADYLQSSLLEEGTEDYDKKLQTWNAESWGDYIKTSKHK-KKQVSLKDAIIH 119 (195)
Q Consensus 65 ~~~~L~~~L~~~~~~~~~~~~~~~IL~sLP~S~~~f~~~i~~~-~~~~sleeli~~ 119 (195)
.|..-++-|++.|. .++++.+..||.+-.-+-+++.-.+-.+ -+..+++|||..
T Consensus 2 ~~~yAallL~~~g~-~~t~~~I~~il~aaGveve~~~~~~~~~~L~gk~i~elI~~ 56 (58)
T 3a1y_A 2 EYVYAALLLHSVGK-EINEENLKAVLQAAGVEPEEARIKALVAALEGVNIDEVIEK 56 (58)
T ss_dssp HHHHHHHHHHHTTC-CCCHHHHHHHHHHTTCCCCHHHHHHHHHHHSSCCHHHHHHH
T ss_pred HHHHHHHHHHhCCC-CCCHHHHHHHHHHcCCCccHHHHHHHHHHHCCCCHHHHHHc
Confidence 34555677888885 5567777888888877776665544332 134478888764
No 35
>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=29.51 E-value=12 Score=24.70 Aligned_cols=9 Identities=44% Similarity=1.305 Sum_probs=7.7
Q ss_pred cceeecCCc
Q 048519 175 GNCFVCGKI 183 (195)
Q Consensus 175 ~~C~~CgK~ 183 (195)
++||.|||.
T Consensus 5 VRCFTCGkv 13 (66)
T 4ayb_N 5 IRCFTCGSL 13 (66)
T ss_dssp SBCTTTCCB
T ss_pred cccCCCcHh
Confidence 579999985
No 36
>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=27.01 E-value=47 Score=23.77 Aligned_cols=41 Identities=5% Similarity=-0.095 Sum_probs=29.5
Q ss_pred chhhHHHHHhhcccchHHHHHhhhc-CCcccCHHHHHHHHHH
Q 048519 82 TEDYDKKLQTWNAESWGDYIKTSKH-KKKQVSLKDAIIHIRI 122 (195)
Q Consensus 82 ~~~~~~~IL~sLP~S~~~f~~~i~~-~~~~~sleeli~~L~~ 122 (195)
++++-...++.||+=..-++..+.. ++..+++++++.++..
T Consensus 4 ~qeke~~~~srLPelArilR~vFvaEkK~vl~~e~~~~ki~~ 45 (106)
T 3a4c_A 4 EQELRLQRLERLPELARVLRNVFVSERKPALTMEVVCARMVD 45 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTCSSSEEEHHHHHHHHHH
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHhcccCCccHHHHHHHHHh
Confidence 4566677788888888877777665 4566788888877754
No 37
>2odb_B Serine/threonine-protein kinase PAK 6; small GTPase, CRIB, protein-protein complex, structu genomics, structural genomics consortium, SGC; HET: GCP; 2.40A {Homo sapiens}
Probab=24.80 E-value=13 Score=21.03 Aligned_cols=12 Identities=8% Similarity=0.221 Sum_probs=9.5
Q ss_pred HhhcccchHHHH
Q 048519 90 QTWNAESWGDYI 101 (195)
Q Consensus 90 L~sLP~S~~~f~ 101 (195)
+.+||++|+.+.
T Consensus 23 f~Glp~eW~~ll 34 (35)
T 2odb_B 23 FVGLPPQWQNIL 34 (35)
T ss_dssp EESCCHHHHHHH
T ss_pred ccCCCHHHHHHh
Confidence 469999998764
No 38
>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=23.47 E-value=18 Score=24.11 Aligned_cols=9 Identities=56% Similarity=1.438 Sum_probs=7.7
Q ss_pred cceeecCCc
Q 048519 175 GNCFVCGKI 183 (195)
Q Consensus 175 ~~C~~CgK~ 183 (195)
..||-|||.
T Consensus 5 VRCFTCGkv 13 (70)
T 1twf_J 5 VRCFSCGKV 13 (70)
T ss_dssp SBCTTTCCB
T ss_pred eecCCCCCC
Confidence 579999986
No 39
>2qme_I CRIB domain of the serine/threonine-protein kinas; GTPase RAC3, small GTP binding protein, P21 RAC, RAS-related botulinum toxin substrate 3; HET: GCP; 1.75A {Homo sapiens}
Probab=22.69 E-value=14 Score=21.05 Aligned_cols=13 Identities=23% Similarity=0.424 Sum_probs=1.2
Q ss_pred HhhcccchHHHHH
Q 048519 90 QTWNAESWGDYIK 102 (195)
Q Consensus 90 L~sLP~S~~~f~~ 102 (195)
+.+||++|+.+..
T Consensus 23 ~~glp~~W~~ll~ 35 (36)
T 2qme_I 23 FTGMPEQWARLLQ 35 (36)
T ss_dssp CC-----------
T ss_pred ccCCCHHHHHHHh
Confidence 4789999987753
No 40
>2lnh_A N-WAsp, neural wiskott-aldrich syndrome protein; protein complex, signaling protein-protein binding complex; NMR {Homo sapiens}
Probab=21.10 E-value=40 Score=21.90 Aligned_cols=15 Identities=0% Similarity=-0.150 Sum_probs=12.3
Q ss_pred HhhcccchHHHHHhh
Q 048519 90 QTWNAESWGDYIKTS 104 (195)
Q Consensus 90 L~sLP~S~~~f~~~i 104 (195)
+.+||++|+.+-...
T Consensus 20 ~~glp~eW~~ll~~s 34 (65)
T 2lnh_A 20 LNNLDPELKNLFDMC 34 (65)
T ss_dssp GGGCCTTHHHHHHHH
T ss_pred CcCCCHHHHHHHHHc
Confidence 578999999987655
No 41
>2wsc_J PSAJ, PSI-J, photosystem I reaction center subunit IX; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Spinacia oleracea} PDB: 2wse_J* 2wsf_J* 2o01_J* 3lw5_J*
Probab=20.74 E-value=46 Score=20.06 Aligned_cols=15 Identities=33% Similarity=0.518 Sum_probs=12.6
Q ss_pred CCCCCCCcccccccc
Q 048519 1 MSDLPPSLATAPIAL 15 (195)
Q Consensus 1 ~~~~~~~~~~~~~~~ 15 (195)
|.|+-.-++|||..+
T Consensus 1 m~~f~kyLStAPVla 15 (44)
T 2wsc_J 1 MRDFKTYLSVAPVLS 15 (44)
T ss_dssp CCCSSCCCCCCTTSG
T ss_pred CchHHHHHhhhhHHH
Confidence 778888899999874
Done!