Query 013098
Match_columns 449
No_of_seqs 153 out of 220
Neff 4.4
Searched_HMMs 29240
Date Mon Mar 25 04:10:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013098.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/013098hhsearch_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 95.5 0.0065 2.2E-07 40.3 2.1 24 46-70 6-29 (29)
2 1u6p_A GAG polyprotein; MLV, A 93.1 0.05 1.7E-06 41.7 2.6 26 46-71 23-48 (56)
3 1dsq_A Nucleic acid binding pr 92.1 0.055 1.9E-06 35.0 1.5 21 47-67 3-23 (26)
4 1a6b_B Momulv, zinc finger pro 88.3 0.19 6.5E-06 36.0 1.7 25 46-70 10-34 (40)
5 1cl4_A Protein (GAG polyprotei 87.9 0.22 7.7E-06 37.6 2.0 27 45-71 29-55 (60)
6 2ec7_A GAG polyprotein (PR55GA 87.5 0.22 7.6E-06 36.4 1.7 21 45-65 26-46 (49)
7 1a1t_A Nucleocapsid protein; s 87.2 0.25 8.5E-06 36.7 1.9 21 45-65 32-52 (55)
8 2cqf_A RNA-binding protein LIN 86.6 0.29 1E-05 37.6 2.0 23 45-67 28-50 (63)
9 3nyb_B Protein AIR2; polya RNA 86.3 0.37 1.3E-05 39.4 2.5 20 46-65 46-65 (83)
10 2cqf_A RNA-binding protein LIN 85.6 0.31 1.1E-05 37.5 1.7 24 45-68 6-29 (63)
11 2a51_A Nucleocapsid protein; s 84.9 0.35 1.2E-05 33.6 1.5 20 45-64 20-39 (39)
12 3nyb_B Protein AIR2; polya RNA 82.1 0.49 1.7E-05 38.7 1.5 24 43-66 2-25 (83)
13 3ts2_A Protein LIN-28 homolog 82.1 0.51 1.7E-05 42.1 1.8 23 47-69 98-120 (148)
14 2ihx_A Nucleocapsid (NC) prote 81.6 0.56 1.9E-05 35.7 1.7 22 47-68 31-52 (61)
15 2li8_A Protein LIN-28 homolog 81.2 0.69 2.4E-05 36.9 2.1 23 44-66 22-44 (74)
16 2a51_A Nucleocapsid protein; s 78.2 0.92 3.2E-05 31.5 1.7 17 48-64 2-18 (39)
17 2ysa_A Retinoblastoma-binding 77.9 1.5 5.1E-05 33.4 2.9 20 45-64 6-25 (55)
18 2li8_A Protein LIN-28 homolog 76.1 1 3.5E-05 35.9 1.6 23 45-67 45-67 (74)
19 2ec7_A GAG polyprotein (PR55GA 75.9 0.96 3.3E-05 33.0 1.3 21 45-65 5-25 (49)
20 2ihx_A Nucleocapsid (NC) prote 75.2 1.2 4E-05 33.9 1.7 21 46-66 4-24 (61)
21 3ts2_A Protein LIN-28 homolog 71.1 1.7 5.9E-05 38.6 2.0 24 46-69 119-142 (148)
22 2bl6_A Nucleocapsid protein P1 66.7 2 7E-05 29.3 1.2 17 48-64 2-18 (37)
23 1a1t_A Nucleocapsid protein; s 66.3 2.2 7.5E-05 31.5 1.4 20 45-64 11-30 (55)
24 2bl6_A Nucleocapsid protein P1 64.9 2.2 7.4E-05 29.2 1.1 17 47-63 20-36 (37)
25 1cl4_A Protein (GAG polyprotei 62.3 1.6 5.5E-05 32.8 0.0 20 47-66 2-21 (60)
26 2lli_A Protein AIR2; RNA surve 58.1 4 0.00014 34.6 1.8 23 45-67 63-85 (124)
27 2hqh_E Restin; beta/BETA struc 56.7 3.1 0.00011 27.4 0.6 17 48-64 5-21 (26)
28 2lli_A Protein AIR2; RNA surve 44.4 8.2 0.00028 32.6 1.5 20 45-64 104-123 (124)
29 3fac_A Putative uncharacterize 43.8 7.2 0.00025 32.6 1.1 53 45-100 66-118 (118)
30 3eop_A Thymocyte nuclear prote 41.3 11 0.00037 35.0 1.9 43 204-256 86-129 (176)
31 2ar1_A Hypothetical protein; s 39.9 11 0.00039 34.7 1.8 18 204-223 93-110 (172)
32 2eve_A Hypothetical protein ps 39.7 12 0.0004 34.2 1.8 18 204-223 75-92 (157)
33 1kil_E Complexin I snare-compl 24.4 1.1E+02 0.0039 22.7 4.5 18 285-302 31-48 (49)
34 2e6i_A Tyrosine-protein kinase 24.2 23 0.0008 27.7 0.9 31 342-378 5-35 (64)
35 2pzo_E CAP-Gly domain-containi 22.8 25 0.00086 25.5 0.8 18 47-64 21-38 (42)
36 1q42_A MTR2, mRNA transport re 22.2 21 0.00071 33.7 0.3 43 317-361 121-164 (201)
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=95.46 E-value=0.0065 Score=40.31 Aligned_cols=24 Identities=42% Similarity=0.857 Sum_probs=20.2
Q ss_pred cccccccccCCCCcccccccccccc
Q 013098 46 KGACANCGAMTHDAKSCMERPRKMG 70 (449)
Q Consensus 46 KGACeNCGAmtHk~KDClERPRK~G 70 (449)
...|-|||..+|-.++|-. |||+|
T Consensus 6 ~~~C~nCgk~GH~ar~C~~-prkkg 29 (29)
T 1nc8_A 6 VIRCWNCGKEGHSARQCRA-PRRQG 29 (29)
T ss_dssp CCBCTTTSCBSSCGGGCCS-SSSCC
T ss_pred CCEEEECCccccCHhHCcc-cccCC
Confidence 4679999999999999975 67765
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=93.09 E-value=0.05 Score=41.70 Aligned_cols=26 Identities=35% Similarity=0.657 Sum_probs=23.2
Q ss_pred cccccccccCCCCccccccccccccc
Q 013098 46 KGACANCGAMTHDAKSCMERPRKMGA 71 (449)
Q Consensus 46 KGACeNCGAmtHk~KDClERPRK~GA 71 (449)
+..|-|||..+|-.+||-.+||+...
T Consensus 23 ~~~C~~Cge~GH~ardCp~~~~~~~~ 48 (56)
T 1u6p_A 23 RDQCAYCKEKGHWAKDCPKKPRGPRG 48 (56)
T ss_dssp TTBCSSSCCBSSCGGGCTTCCCSSCS
T ss_pred CCcceeCCCCCcccccCcCCccccCC
Confidence 67899999999999999999987654
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=92.11 E-value=0.055 Score=34.99 Aligned_cols=21 Identities=29% Similarity=0.706 Sum_probs=17.5
Q ss_pred ccccccccCCCCccccccccc
Q 013098 47 GACANCGAMTHDAKSCMERPR 67 (449)
Q Consensus 47 GACeNCGAmtHk~KDClERPR 67 (449)
+.|=|||.++|-.+||..+++
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 469999999999999988754
No 4
>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=88.33 E-value=0.19 Score=36.03 Aligned_cols=25 Identities=36% Similarity=0.676 Sum_probs=21.9
Q ss_pred cccccccccCCCCcccccccccccc
Q 013098 46 KGACANCGAMTHDAKSCMERPRKMG 70 (449)
Q Consensus 46 KGACeNCGAmtHk~KDClERPRK~G 70 (449)
+..|-|||-.+|-++||-.++++-.
T Consensus 10 ~~~C~~Cgk~GH~ardCP~~~~~~r 34 (40)
T 1a6b_B 10 RDQCAYCKEKGHWAKDCPKKPRGPR 34 (40)
T ss_dssp SSSCSSSCCTTCCTTSCSSSCCCTT
T ss_pred CCeeeECCCCCcchhhCcCCcccCC
Confidence 6789999999999999999887543
No 5
>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=87.90 E-value=0.22 Score=37.56 Aligned_cols=27 Identities=26% Similarity=0.549 Sum_probs=23.4
Q ss_pred ccccccccccCCCCccccccccccccc
Q 013098 45 RKGACANCGAMTHDAKSCMERPRKMGA 71 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClERPRK~GA 71 (449)
+.+.|-+||..+|..+||.++..+.|.
T Consensus 29 ~~~~C~~Cg~~GH~ar~C~~~~~~~G~ 55 (60)
T 1cl4_A 29 VPGLCPRCKRGKHWANECKSKTDNQGN 55 (60)
T ss_dssp CCCSCSSCSSCSSCSTTCCCTTSSSSC
T ss_pred CCcceeECCCCCCccCcCCCccccCCC
Confidence 457899999999999999999876664
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=87.53 E-value=0.22 Score=36.40 Aligned_cols=21 Identities=38% Similarity=0.811 Sum_probs=16.6
Q ss_pred ccccccccccCCCCccccccc
Q 013098 45 RKGACANCGAMTHDAKSCMER 65 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClER 65 (449)
+++.|-+||..+|..+||.++
T Consensus 26 ~~~~C~~Cg~~GH~~~~C~~~ 46 (49)
T 2ec7_A 26 RRQGCWKCGKTGHVMAKCPER 46 (49)
T ss_dssp SCCSCSSSCCSSCCGGGCCSS
T ss_pred CCCeeCcCCCcCCccCCCcCC
Confidence 456788888888888888765
No 7
>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=87.24 E-value=0.25 Score=36.66 Aligned_cols=21 Identities=48% Similarity=0.947 Sum_probs=12.7
Q ss_pred ccccccccccCCCCccccccc
Q 013098 45 RKGACANCGAMTHDAKSCMER 65 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClER 65 (449)
|++.|-+||..+|..+||.++
T Consensus 32 ~~~~C~~Cg~~GH~~~~C~~~ 52 (55)
T 1a1t_A 32 RKKGCWKCGKEGHQMKDCTER 52 (55)
T ss_dssp SCCBCTTTCCBSSCGGGCSSS
T ss_pred CCCEeCCCCCcCCccCCCcCc
Confidence 345566666666666666553
No 8
>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=86.63 E-value=0.29 Score=37.62 Aligned_cols=23 Identities=22% Similarity=0.556 Sum_probs=16.6
Q ss_pred ccccccccccCCCCccccccccc
Q 013098 45 RKGACANCGAMTHDAKSCMERPR 67 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClERPR 67 (449)
+...|-|||..+|..+||.++++
T Consensus 28 ~~~~C~~Cg~~GH~ar~Cp~~~~ 50 (63)
T 2cqf_A 28 QPKKCHFCQSISHMVASCPLKAQ 50 (63)
T ss_dssp CSSCCTTTCCSSSCTTTCTGGGC
T ss_pred CCCccCCcCCcCCccCcCCCccc
Confidence 34667788888888888877663
No 9
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=86.30 E-value=0.37 Score=39.40 Aligned_cols=20 Identities=35% Similarity=0.700 Sum_probs=18.0
Q ss_pred cccccccccCCCCccccccc
Q 013098 46 KGACANCGAMTHDAKSCMER 65 (449)
Q Consensus 46 KGACeNCGAmtHk~KDClER 65 (449)
.-.|=|||..+|-.+||-++
T Consensus 46 ~~~CYnCG~~GH~~rdC~~~ 65 (83)
T 3nyb_B 46 TIYCYNCGGKGHFGDDCKEK 65 (83)
T ss_dssp CCBCSSSSCBSSCGGGCSSC
T ss_pred CCeecccCCCCcCcccCCcc
Confidence 35699999999999999986
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=85.59 E-value=0.31 Score=37.49 Aligned_cols=24 Identities=38% Similarity=0.830 Sum_probs=20.2
Q ss_pred ccccccccccCCCCcccccccccc
Q 013098 45 RKGACANCGAMTHDAKSCMERPRK 68 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClERPRK 68 (449)
|...|-|||..+|..++|.+.++.
T Consensus 6 r~~~C~~Cg~~GH~a~~C~~~~~~ 29 (63)
T 2cqf_A 6 SGDRCYNCGGLDHHAKECKLPPQP 29 (63)
T ss_dssp SCCCCSSSCCSSSCTTTCCSCCCS
T ss_pred CCCcccccCCCCcChhhCCCCCCC
Confidence 446799999999999999886554
No 11
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=84.91 E-value=0.35 Score=33.63 Aligned_cols=20 Identities=35% Similarity=0.813 Sum_probs=16.8
Q ss_pred ccccccccccCCCCcccccc
Q 013098 45 RKGACANCGAMTHDAKSCME 64 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClE 64 (449)
|+..|-|||..+|..+||.+
T Consensus 20 ~~~~C~~Cg~~GH~~~~C~~ 39 (39)
T 2a51_A 20 RQEGCWNCGSKEHRFAQCPK 39 (39)
T ss_dssp CCSSCTTTCCSSSCTTTSCC
T ss_pred CCCccccCCCCCCccCcCcC
Confidence 46789999999999999953
No 12
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=82.08 E-value=0.49 Score=38.66 Aligned_cols=24 Identities=21% Similarity=0.486 Sum_probs=17.2
Q ss_pred ccccccccccccCCCCcccccccc
Q 013098 43 KYRKGACANCGAMTHDAKSCMERP 66 (449)
Q Consensus 43 KyRKGACeNCGAmtHk~KDClERP 66 (449)
|++.-.|-|||.++|..++|.+-.
T Consensus 2 ~~k~~~C~~Cg~~GH~~~~Cp~~~ 25 (83)
T 3nyb_B 2 SWKKVQCTLCKSKKHSKERCPSIW 25 (83)
T ss_dssp -----CCSSSCCSSSCGGGCGGGT
T ss_pred CcccCCCCCCCCCCCccccCCCcc
Confidence 677788999999999999998743
No 13
>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=82.06 E-value=0.51 Score=42.08 Aligned_cols=23 Identities=39% Similarity=0.865 Sum_probs=18.8
Q ss_pred ccccccccCCCCccccccccccc
Q 013098 47 GACANCGAMTHDAKSCMERPRKM 69 (449)
Q Consensus 47 GACeNCGAmtHk~KDClERPRK~ 69 (449)
..|-|||..+|..++|-..|+.+
T Consensus 98 ~~C~~Cg~~GH~a~~C~~~~~~~ 120 (148)
T 3ts2_A 98 DRCYNCGGLDHHAKECKLPPQPK 120 (148)
T ss_dssp CCCTTTCCSSCCGGGCCSCCCCC
T ss_pred CcccEeCCccchhhhCCCCCCCC
Confidence 36999999999999998877644
No 14
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=81.64 E-value=0.56 Score=35.67 Aligned_cols=22 Identities=36% Similarity=0.777 Sum_probs=17.1
Q ss_pred ccccccccCCCCcccccccccc
Q 013098 47 GACANCGAMTHDAKSCMERPRK 68 (449)
Q Consensus 47 GACeNCGAmtHk~KDClERPRK 68 (449)
+.|-|||.+.|..+||.++..-
T Consensus 31 ~~C~~Cg~~GH~ar~C~~~~~~ 52 (61)
T 2ihx_A 31 ERCQLCNGMGHNAKQCRKRDGN 52 (61)
T ss_dssp SBCTTTCCBSSCGGGCCCCC--
T ss_pred CeeCCCCCCCCCcCCCcCCCcC
Confidence 5699999999999999877643
No 15
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=81.18 E-value=0.69 Score=36.88 Aligned_cols=23 Identities=39% Similarity=0.868 Sum_probs=14.4
Q ss_pred cccccccccccCCCCcccccccc
Q 013098 44 YRKGACANCGAMTHDAKSCMERP 66 (449)
Q Consensus 44 yRKGACeNCGAmtHk~KDClERP 66 (449)
.|...|-|||..+|..++|...+
T Consensus 22 ~r~~~C~~Cg~~GH~a~~C~~~~ 44 (74)
T 2li8_A 22 SKGDRCYNCGGLDHHAKECKLPP 44 (74)
T ss_dssp STTSCCTTTCCSSSCTTTCSSCC
T ss_pred CCCCcccccCCcCcCcccCCCCC
Confidence 34456777777777777776543
No 16
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=78.20 E-value=0.92 Score=31.45 Aligned_cols=17 Identities=41% Similarity=0.960 Sum_probs=15.7
Q ss_pred cccccccCCCCcccccc
Q 013098 48 ACANCGAMTHDAKSCME 64 (449)
Q Consensus 48 ACeNCGAmtHk~KDClE 64 (449)
.|-|||..+|..++|..
T Consensus 2 ~C~~Cg~~GH~a~~C~~ 18 (39)
T 2a51_A 2 TCFNCGKPGHTARMCRQ 18 (39)
T ss_dssp BCTTTCCBSSCTTTCCS
T ss_pred eeeccCCCCcccccCCC
Confidence 48999999999999986
No 17
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=77.89 E-value=1.5 Score=33.38 Aligned_cols=20 Identities=30% Similarity=0.575 Sum_probs=17.1
Q ss_pred ccccccccccCCCCcccccc
Q 013098 45 RKGACANCGAMTHDAKSCME 64 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClE 64 (449)
++..|=.||..+|-.++|-.
T Consensus 6 ~~~~C~kCGk~GH~~k~Cp~ 25 (55)
T 2ysa_A 6 SGYTCFRCGKPGHYIKNCPT 25 (55)
T ss_dssp SSCCCTTTCCTTSCGGGCSG
T ss_pred CCCccccCCCcCcccccCCC
Confidence 34579999999999999964
No 18
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=76.14 E-value=1 Score=35.93 Aligned_cols=23 Identities=22% Similarity=0.556 Sum_probs=20.1
Q ss_pred ccccccccccCCCCccccccccc
Q 013098 45 RKGACANCGAMTHDAKSCMERPR 67 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClERPR 67 (449)
+...|-+||..+|..+||.+++.
T Consensus 45 ~~~~C~~Cg~~GH~ar~Cp~~~~ 67 (74)
T 2li8_A 45 QPKKCHFCQSISHMVASCPLKAQ 67 (74)
T ss_dssp CCCCCTTTCCTTSCGGGCTTGGG
T ss_pred CCCccCCcCCcCCccCcCcCCcC
Confidence 45789999999999999988763
No 19
>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=75.89 E-value=0.96 Score=32.96 Aligned_cols=21 Identities=33% Similarity=0.681 Sum_probs=18.2
Q ss_pred ccccccccccCCCCccccccc
Q 013098 45 RKGACANCGAMTHDAKSCMER 65 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClER 65 (449)
|...|-|||..+|..++|...
T Consensus 5 r~~~C~~Cg~~GH~a~~C~~~ 25 (49)
T 2ec7_A 5 KVIRCWNCGKEGHSARQCRAP 25 (49)
T ss_dssp CCCBCTTTCCBTCCTTTCCCS
T ss_pred CcCeeeecCCCCcChhhCcCC
Confidence 457899999999999999773
No 20
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=75.16 E-value=1.2 Score=33.85 Aligned_cols=21 Identities=29% Similarity=0.770 Sum_probs=18.3
Q ss_pred cccccccccCCCCcccccccc
Q 013098 46 KGACANCGAMTHDAKSCMERP 66 (449)
Q Consensus 46 KGACeNCGAmtHk~KDClERP 66 (449)
...|-|||...|..++|...+
T Consensus 4 ~~~C~~Cg~~GH~a~~C~~~~ 24 (61)
T 2ihx_A 4 RGLCYTCGSPGHYQAQCPKKR 24 (61)
T ss_dssp TTBCSSSCCBTCCGGGCTTTT
T ss_pred CCcccccCCCCeehhhCcCCc
Confidence 467999999999999997754
No 21
>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=71.14 E-value=1.7 Score=38.63 Aligned_cols=24 Identities=21% Similarity=0.470 Sum_probs=20.5
Q ss_pred cccccccccCCCCccccccccccc
Q 013098 46 KGACANCGAMTHDAKSCMERPRKM 69 (449)
Q Consensus 46 KGACeNCGAmtHk~KDClERPRK~ 69 (449)
...|-+||..+|..+||.++|..-
T Consensus 119 ~~~C~~Cg~~GH~~r~Cp~~~~~~ 142 (148)
T 3ts2_A 119 PKKCHFCQSINHMVASCPLKAQQG 142 (148)
T ss_dssp CCCCTTTCCSSCCGGGCTTTTC--
T ss_pred CCcccccCCcCCEeccCcCCCCCC
Confidence 468999999999999999998763
No 22
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=66.72 E-value=2 Score=29.32 Aligned_cols=17 Identities=35% Similarity=0.806 Sum_probs=15.0
Q ss_pred cccccccCCCCcccccc
Q 013098 48 ACANCGAMTHDAKSCME 64 (449)
Q Consensus 48 ACeNCGAmtHk~KDClE 64 (449)
.|-|||..+|..++|..
T Consensus 2 ~C~~Cg~~GH~~~~C~~ 18 (37)
T 2bl6_A 2 TCYNCGKPGHLSSQCRA 18 (37)
T ss_dssp CBSSSCCSSCCTTTSSC
T ss_pred cccccCCCCcchhhCcC
Confidence 48899999999999965
No 23
>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=66.33 E-value=2.2 Score=31.45 Aligned_cols=20 Identities=40% Similarity=0.753 Sum_probs=17.7
Q ss_pred ccccccccccCCCCcccccc
Q 013098 45 RKGACANCGAMTHDAKSCME 64 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClE 64 (449)
|...|-|||..+|..++|..
T Consensus 11 ~~~~C~~Cg~~GH~a~~C~~ 30 (55)
T 1a1t_A 11 KTVKCFNCGKEGHIAKNCRA 30 (55)
T ss_dssp GTCBCTTTCCBSSCGGGCSS
T ss_pred CCcceeeeCCCCcChhhcCC
Confidence 34679999999999999976
No 24
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=64.89 E-value=2.2 Score=29.18 Aligned_cols=17 Identities=29% Similarity=0.618 Sum_probs=15.8
Q ss_pred ccccccccCCCCccccc
Q 013098 47 GACANCGAMTHDAKSCM 63 (449)
Q Consensus 47 GACeNCGAmtHk~KDCl 63 (449)
+.|-+||..+|..+||.
T Consensus 20 ~~C~~Cg~~GH~a~~C~ 36 (37)
T 2bl6_A 20 KVCFKCKQPGHFSKQCR 36 (37)
T ss_dssp TTCSSCCCTTGGGGTTC
T ss_pred CeEccCCCcCCccCcCc
Confidence 67999999999999995
No 25
>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=62.34 E-value=1.6 Score=32.77 Aligned_cols=20 Identities=45% Similarity=0.926 Sum_probs=0.0
Q ss_pred ccccccccCCCCcccccccc
Q 013098 47 GACANCGAMTHDAKSCMERP 66 (449)
Q Consensus 47 GACeNCGAmtHk~KDClERP 66 (449)
+.|-|||..+|..++|-..+
T Consensus 2 ~~Cf~Cg~~GH~a~~C~~~~ 21 (60)
T 1cl4_A 2 GSCFKCGKKGHFAKNCHEHA 21 (60)
T ss_dssp --------------------
T ss_pred CccccCCCCCcCHhhCcCCC
Confidence 46999999999999998754
No 26
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=58.06 E-value=4 Score=34.61 Aligned_cols=23 Identities=26% Similarity=0.514 Sum_probs=18.6
Q ss_pred ccccccccccCCCCccccccccc
Q 013098 45 RKGACANCGAMTHDAKSCMERPR 67 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClERPR 67 (449)
+...|-+||.++|..+||.+..|
T Consensus 63 ~~~~C~~Cg~~GH~~~~Cp~~~~ 85 (124)
T 2lli_A 63 KKVQCTLCKSKKHSKERCPSIWR 85 (124)
T ss_dssp CCCSSSSSCSSCCCTTTCCCSTT
T ss_pred cCccCCCCCcCCcchhhCCCccc
Confidence 45679999999999999987655
No 27
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=56.70 E-value=3.1 Score=27.42 Aligned_cols=17 Identities=29% Similarity=0.651 Sum_probs=15.4
Q ss_pred cccccccCCCCcccccc
Q 013098 48 ACANCGAMTHDAKSCME 64 (449)
Q Consensus 48 ACeNCGAmtHk~KDClE 64 (449)
.|++|..-+|.+-+|-+
T Consensus 5 YCe~CE~FGH~t~~C~d 21 (26)
T 2hqh_E 5 YCEICEMFGHWATNCND 21 (26)
T ss_dssp EETTTTEESSCGGGCCT
T ss_pred cchHHHHhCcccccCCc
Confidence 59999999999999954
No 28
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=44.44 E-value=8.2 Score=32.63 Aligned_cols=20 Identities=35% Similarity=0.665 Sum_probs=17.8
Q ss_pred ccccccccccCCCCcccccc
Q 013098 45 RKGACANCGAMTHDAKSCME 64 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClE 64 (449)
....|-|||.++|-.+||.+
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 35789999999999999975
No 29
>3fac_A Putative uncharacterized protein; complete proteome, structural genomics, PSI-2, protein structure initiative; 2.50A {Rhodobacter sphaeroides 2}
Probab=43.81 E-value=7.2 Score=32.58 Aligned_cols=53 Identities=17% Similarity=0.339 Sum_probs=18.4
Q ss_pred ccccccccccCCCCccccccccccccccccCCcCCCCcceeccccccccccCccCC
Q 013098 45 RKGACANCGAMTHDAKSCMERPRKMGAKWTNINIAPDEKIETFELDYDGKRDRWNG 100 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClERPRK~GAk~t~~dI~~De~iq~~~ldyDaKRDRWnG 100 (449)
+.+.|.+||+..+-... ..|-.++-...--|=.....+..+.+ ||+..+.|.+
T Consensus 66 ~r~FC~~CGs~l~~~~~--~~~~~~~V~~g~ld~~~~~~l~~~~~-~dG~~~~~~~ 118 (118)
T 3fac_A 66 KHWFCRTCGIYTHHQRR--SNPEEYGVNVAILEGVNPRDLGEVPW-TDGVNHPSDR 118 (118)
T ss_dssp EEEEETTTCCEEEEECS--SCTTEEEEEGGGBTTCCGGGGCSCCC-C---------
T ss_pred eeEECCCCCccccCccC--CCCCEEEEEecccCCCChHHcccccc-cCCCCCCCCC
Confidence 45789999997754321 12322221111111011112222333 7999999964
No 30
>3eop_A Thymocyte nuclear protein 1; unknown function, nucleus, phosphoprotein; 2.30A {Homo sapiens} SCOP: b.122.1.0
Probab=41.26 E-value=11 Score=34.97 Aligned_cols=43 Identities=26% Similarity=0.485 Sum_probs=26.2
Q ss_pred cCCCCCCcccCCCcccccCCCCCCCCCCCccCCC-CceecccchHHHHHHHHHH
Q 013098 204 NLDVNSAHYDPKTRSMREDPLPDADPNDKFYGVN-NQYRNSGQALEFKELNIHA 256 (449)
Q Consensus 204 NLd~nSa~YDPKSRsMRe~p~~~~d~~~~~f~Gd-NFvR~SGea~e~~~lQ~FA 256 (449)
-.||+|.||||||-. +|| ..|.=| -|++.-.-...+..|...+
T Consensus 86 ~fDp~s~YyDpkS~~--~~p--------rW~~VdV~~v~~~~~~vtL~eLK~~~ 129 (176)
T 3eop_A 86 QFEKNNPHYDPSSKE--DNP--------KWSMVDVQFVRMMKRFIPLAELKSYH 129 (176)
T ss_dssp GTCTTSTTCCTTCCT--TSC--------SCEEEEEEEEEEEEEEEEHHHHHHHH
T ss_pred ccCCCCCCCCccCcC--CCC--------CEEEEEEEEeeecCCcccHHHHhcCc
Confidence 379999999999833 444 233333 3565555555666665553
No 31
>2ar1_A Hypothetical protein; structural genomics, PSI, protein structure initiative, STRU genomics of pathogenic protozoa consortium, SGPP, unknown F; 1.60A {Leishmania major} SCOP: b.122.1.8
Probab=39.92 E-value=11 Score=34.69 Aligned_cols=18 Identities=39% Similarity=0.584 Sum_probs=14.3
Q ss_pred cCCCCCCcccCCCcccccCC
Q 013098 204 NLDVNSAHYDPKTRSMREDP 223 (449)
Q Consensus 204 NLd~nSa~YDPKSRsMRe~p 223 (449)
..||+|.||||||.- ++|
T Consensus 93 ~fdp~s~YyDpks~~--~~p 110 (172)
T 2ar1_A 93 ALDKTSEYFDPKATK--EKN 110 (172)
T ss_dssp GGCTTSTTCCTTCCS--SCC
T ss_pred cccccCcccCcccCC--CCC
Confidence 469999999999863 555
No 32
>2eve_A Hypothetical protein pspto5229; alpha-beta protein, structural genomics, PSI, protein struct initiative; HET: MPO; 1.60A {Pseudomonas syringae PV} SCOP: b.122.1.8 PDB: 2g2x_A
Probab=39.69 E-value=12 Score=34.17 Aligned_cols=18 Identities=33% Similarity=0.355 Sum_probs=14.2
Q ss_pred cCCCCCCcccCCCcccccCC
Q 013098 204 NLDVNSAHYDPKTRSMREDP 223 (449)
Q Consensus 204 NLd~nSa~YDPKSRsMRe~p 223 (449)
..||+|.||||||-. ++|
T Consensus 75 ~fdp~s~YyDpks~~--~~p 92 (157)
T 2eve_A 75 ALDPDSHYHDAKATT--EKN 92 (157)
T ss_dssp GGCTTSTTCCTTCCS--SCC
T ss_pred cccccCcCcCcccCC--CCC
Confidence 579999999999853 544
No 33
>1kil_E Complexin I snare-complex binding region; helix bound to four helix bundle, membrane protein; 2.30A {Rattus norvegicus} SCOP: h.1.15.1
Probab=24.38 E-value=1.1e+02 Score=22.70 Aligned_cols=18 Identities=22% Similarity=0.412 Sum_probs=15.1
Q ss_pred hHHHHHHHHHHHHHHHhc
Q 013098 285 IKDKLKSRTKETIMEKYG 302 (449)
Q Consensus 285 kke~~k~~~k~~ileKYG 302 (449)
+-+......++.|-+|||
T Consensus 31 kmE~eRE~mRq~IRdKY~ 48 (49)
T 1kil_E 31 KMEAEREVMRQGIRDKYG 48 (49)
T ss_dssp HHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHhcC
Confidence 556777888999999998
No 34
>2e6i_A Tyrosine-protein kinase ITK/TSK; BTK, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=24.16 E-value=23 Score=27.69 Aligned_cols=31 Identities=26% Similarity=0.674 Sum_probs=20.2
Q ss_pred ccchhhhccCCCcccccccccCCcccccccccccccc
Q 013098 342 SKYEEDVYINNHTCVWGSWWKDHQWGYKCCKQVIRNS 378 (449)
Q Consensus 342 SkY~EDv~~~nHTsVwGSy~~~~~WGy~CC~s~~k~s 378 (449)
|++..+.+..-|..+| .+|+| .||+++.|+.
T Consensus 5 s~~N~~ll~~yHPg~~----~~GkW--~CC~q~~k~a 35 (64)
T 2e6i_A 5 SSGNNSLVPKYHPNFW----MDGKW--RCCSQLEKLA 35 (64)
T ss_dssp CCCCCSSCCEECSSCB----CSSSB--SSSCCSCTTC
T ss_pred cccChhhhhhcCCCce----eCCeE--CCCCCCCccC
Confidence 4444555555566555 56665 7999999875
No 35
>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=22.82 E-value=25 Score=25.50 Aligned_cols=18 Identities=28% Similarity=0.586 Sum_probs=15.8
Q ss_pred ccccccccCCCCcccccc
Q 013098 47 GACANCGAMTHDAKSCME 64 (449)
Q Consensus 47 GACeNCGAmtHk~KDClE 64 (449)
-.|++|..-+|-+.+|-+
T Consensus 21 pYCd~CEvFGH~t~~Cnd 38 (42)
T 2pzo_E 21 PYCEICEMFGHWATNCND 38 (42)
T ss_dssp CEETTTTEESSCGGGCCT
T ss_pred cccccccccCcccccCCc
Confidence 359999999999999954
No 36
>1q42_A MTR2, mRNA transport regulator MTR2; NTF2-fold, nuclear export, translation; 1.75A {Candida albicans} SCOP: d.17.4.2 PDB: 1q40_A
Probab=22.16 E-value=21 Score=33.72 Aligned_cols=43 Identities=26% Similarity=0.543 Sum_probs=17.9
Q ss_pred ccchhhhhcccccccccCccccccCccchh-hhccCCCcccccccc
Q 013098 317 GQSEREIEYDRAGRIIKGQETALPRSKYEE-DVYINNHTCVWGSWW 361 (449)
Q Consensus 317 ~qtE~yvEY~~~G~vikg~~~~~~kSkY~E-Dv~~~nHTsVwGSy~ 361 (449)
-+.---|.|+..|+---|+.-.+..- .+ -+=.+++..||||||
T Consensus 121 I~asGkVrFDesgr~~fgQsf~Lta~--~~~~~~~~~~Rp~wg~~f 164 (201)
T 1q42_A 121 VHFSAKVRFDQSGRNRLGESADLFQE--NNSIVSKTNQRPIWGSWF 164 (201)
T ss_dssp EEEEEEEEEBCSSCCTTSCCC-----------------CCCBCCCE
T ss_pred EEEeEEEEECCCCcCcCCCcEEEecc--cCCcCCCCCCCccccccc
Confidence 34444567777774333322111100 00 023567899999999
Done!