Query 040625
Match_columns 395
No_of_seqs 192 out of 241
Neff 4.5
Searched_HMMs 29240
Date Mon Mar 25 16:24:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040625.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/040625hhsearch_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 85.5 0.35 1.2E-05 31.3 1.7 18 1-19 12-29 (29)
2 1u6p_A GAG polyprotein; MLV, A 61.6 4.4 0.00015 30.3 2.3 20 1-20 29-48 (56)
3 1dsq_A Nucleic acid binding pr 58.0 4.2 0.00014 25.5 1.4 16 1-16 8-23 (26)
4 1q42_A MTR2, mRNA transport re 53.2 4.4 0.00015 37.6 1.3 42 239-282 122-164 (201)
5 3eop_A Thymocyte nuclear prote 47.4 7.7 0.00026 35.3 1.9 19 152-172 86-104 (176)
6 2ar1_A Hypothetical protein; s 46.8 7.9 0.00027 35.1 1.9 18 152-171 93-110 (172)
7 2eve_A Hypothetical protein ps 46.6 8.1 0.00028 34.6 1.9 18 152-171 75-92 (157)
8 1cl4_A Protein (GAG polyprotei 43.1 11 0.00039 27.5 2.0 20 1-20 36-55 (60)
9 2ysa_A Retinoblastoma-binding 37.8 20 0.0007 26.5 2.6 13 1-13 13-25 (55)
10 2ec7_A GAG polyprotein (PR55GA 34.4 15 0.00053 25.9 1.4 14 1-14 33-46 (49)
11 2cqf_A RNA-binding protein LIN 33.9 16 0.00056 27.2 1.6 16 1-16 35-50 (63)
12 1a6b_B Momulv, zinc finger pro 32.8 19 0.00066 25.1 1.7 18 1-18 16-33 (40)
13 2ihx_A Nucleocapsid (NC) prote 29.5 20 0.0007 26.4 1.4 13 1-13 10-22 (61)
14 2e6i_A Tyrosine-protein kinase 24.0 22 0.00075 27.4 0.7 34 263-302 5-39 (64)
15 2cqf_A RNA-binding protein LIN 23.3 37 0.0013 25.2 1.9 16 1-16 13-28 (63)
16 2a51_A Nucleocapsid protein; s 23.0 33 0.0011 22.9 1.4 11 1-11 27-37 (39)
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=85.53 E-value=0.35 Score=31.25 Aligned_cols=18 Identities=44% Similarity=1.042 Sum_probs=16.3
Q ss_pred CCCCCCCcccccccccccc
Q 040625 1 CGAMTHNAKSCMERPRKIG 19 (395)
Q Consensus 1 CGAmTHk~KDClERPRK~G 19 (395)
||-.+|-.++|-. |||+|
T Consensus 12 Cgk~GH~ar~C~~-prkkg 29 (29)
T 1nc8_A 12 CGKEGHSARQCRA-PRRQG 29 (29)
T ss_dssp TSCBSSCGGGCCS-SSSCC
T ss_pred CCccccCHhHCcc-cccCC
Confidence 9999999999987 88876
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=61.59 E-value=4.4 Score=30.31 Aligned_cols=20 Identities=35% Similarity=0.625 Sum_probs=17.6
Q ss_pred CCCCCCCccccccccccccc
Q 040625 1 CGAMTHNAKSCMERPRKIGA 20 (395)
Q Consensus 1 CGAmTHk~KDClERPRK~GA 20 (395)
||-.+|-.+||-.+||+...
T Consensus 29 Cge~GH~ardCp~~~~~~~~ 48 (56)
T 1u6p_A 29 CKEKGHWAKDCPKKPRGPRG 48 (56)
T ss_dssp SCCBSSCGGGCTTCCCSSCS
T ss_pred CCCCCcccccCcCCccccCC
Confidence 99999999999998886554
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=57.99 E-value=4.2 Score=25.51 Aligned_cols=16 Identities=31% Similarity=0.769 Sum_probs=13.1
Q ss_pred CCCCCCCccccccccc
Q 040625 1 CGAMTHNAKSCMERPR 16 (395)
Q Consensus 1 CGAmTHk~KDClERPR 16 (395)
||..+|-.+||...++
T Consensus 8 CG~~GH~ardC~~~~~ 23 (26)
T 1dsq_A 8 CGKTGHIKRDCKEEXX 23 (26)
T ss_dssp TCCBSSCTTTTTCC--
T ss_pred CCCCCcccccCCCccc
Confidence 9999999999988543
No 4
>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=53.22 E-value=4.4 Score=37.62 Aligned_cols=42 Identities=29% Similarity=0.595 Sum_probs=17.7
Q ss_pred ccchheeeccccccccCcccccccccchhh-hccCCCceeeeccc
Q 040625 239 QSERQVEYDRAGRIIQGVESFLPRSKYEED-VYINNHTSVWGSWW 282 (395)
Q Consensus 239 qtE~yvEY~~~G~~ikg~~k~~~kSkY~ED-v~~nnHTsVWGSy~ 282 (395)
+.---|-|+.+|+--=|+.-.+..- .+= +-.+++..||||||
T Consensus 122 ~asGkVrFDesgr~~fgQsf~Lta~--~~~~~~~~~~Rp~wg~~f 164 (201)
T 1q42_A 122 HFSAKVRFDQSGRNRLGESADLFQE--NNSIVSKTNQRPIWGSWF 164 (201)
T ss_dssp EEEEEEEEBCSSCCTTSCCC-----------------CCCBCCCE
T ss_pred EEeEEEEECCCCcCcCCCcEEEecc--cCCcCCCCCCCccccccc
Confidence 3334477777774333322111100 000 22568899999999
No 5
>3eop_A Thymocyte nuclear protein 1; unknown function, nucleus, phosphoprotein; 2.30A {Homo sapiens} SCOP: b.122.1.0
Probab=47.40 E-value=7.7 Score=35.34 Aligned_cols=19 Identities=26% Similarity=0.728 Sum_probs=14.7
Q ss_pred cCCCCCCccCCCCcccccCCC
Q 040625 152 NLDVNSAYYDPKTRSMREDPL 172 (395)
Q Consensus 152 NLD~nSA~YDPKTRsMRdnp~ 172 (395)
-.||+|.||||||-. +||-
T Consensus 86 ~fDp~s~YyDpkS~~--~~pr 104 (176)
T 3eop_A 86 QFEKNNPHYDPSSKE--DNPK 104 (176)
T ss_dssp GTCTTSTTCCTTCCT--TSCS
T ss_pred ccCCCCCCCCccCcC--CCCC
Confidence 379999999999754 5654
No 6
>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=46.78 E-value=7.9 Score=35.12 Aligned_cols=18 Identities=44% Similarity=0.768 Sum_probs=14.6
Q ss_pred cCCCCCCccCCCCcccccCC
Q 040625 152 NLDVNSAYYDPKTRSMREDP 171 (395)
Q Consensus 152 NLD~nSA~YDPKTRsMRdnp 171 (395)
..||+|.||||||.. ++|
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 479999999999874 565
No 7
>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=46.56 E-value=8.1 Score=34.59 Aligned_cols=18 Identities=39% Similarity=0.540 Sum_probs=14.6
Q ss_pred cCCCCCCccCCCCcccccCC
Q 040625 152 NLDVNSAYYDPKTRSMREDP 171 (395)
Q Consensus 152 NLD~nSA~YDPKTRsMRdnp 171 (395)
..||+|.||||||-. ++|
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 579999999999763 555
No 8
>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=43.14 E-value=11 Score=27.47 Aligned_cols=20 Identities=25% Similarity=0.504 Sum_probs=15.5
Q ss_pred CCCCCCCccccccccccccc
Q 040625 1 CGAMTHNAKSCMERPRKIGA 20 (395)
Q Consensus 1 CGAmTHk~KDClERPRK~GA 20 (395)
||..+|..+||.++....|.
T Consensus 36 Cg~~GH~ar~C~~~~~~~G~ 55 (60)
T 1cl4_A 36 CKRGKHWANECKSKTDNQGN 55 (60)
T ss_dssp CSSCSSCSTTCCCTTSSSSC
T ss_pred CCCCCCccCcCCCccccCCC
Confidence 88888999999887665553
No 9
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=37.75 E-value=20 Score=26.54 Aligned_cols=13 Identities=38% Similarity=0.797 Sum_probs=11.9
Q ss_pred CCCCCCCcccccc
Q 040625 1 CGAMTHNAKSCME 13 (395)
Q Consensus 1 CGAmTHk~KDClE 13 (395)
||..+|-.++|-.
T Consensus 13 CGk~GH~~k~Cp~ 25 (55)
T 2ysa_A 13 CGKPGHYIKNCPT 25 (55)
T ss_dssp TCCTTSCGGGCSG
T ss_pred CCCcCcccccCCC
Confidence 9999999999964
No 10
>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=34.42 E-value=15 Score=25.92 Aligned_cols=14 Identities=43% Similarity=0.861 Sum_probs=11.0
Q ss_pred CCCCCCCccccccc
Q 040625 1 CGAMTHNAKSCMER 14 (395)
Q Consensus 1 CGAmTHk~KDClER 14 (395)
||..+|..+||.++
T Consensus 33 Cg~~GH~~~~C~~~ 46 (49)
T 2ec7_A 33 CGKTGHVMAKCPER 46 (49)
T ss_dssp SCCSSCCGGGCCSS
T ss_pred CCCcCCccCCCcCC
Confidence 78888888888764
No 11
>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=33.94 E-value=16 Score=27.18 Aligned_cols=16 Identities=25% Similarity=0.669 Sum_probs=12.0
Q ss_pred CCCCCCCccccccccc
Q 040625 1 CGAMTHNAKSCMERPR 16 (395)
Q Consensus 1 CGAmTHk~KDClERPR 16 (395)
||..+|..+||.++++
T Consensus 35 Cg~~GH~ar~Cp~~~~ 50 (63)
T 2cqf_A 35 CQSISHMVASCPLKAQ 50 (63)
T ss_dssp TCCSSSCTTTCTGGGC
T ss_pred cCCcCCccCcCCCccc
Confidence 7788888888877653
No 12
>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=32.83 E-value=19 Score=25.05 Aligned_cols=18 Identities=39% Similarity=0.704 Sum_probs=15.7
Q ss_pred CCCCCCCccccccccccc
Q 040625 1 CGAMTHNAKSCMERPRKI 18 (395)
Q Consensus 1 CGAmTHk~KDClERPRK~ 18 (395)
||-.+|-++||-.++++-
T Consensus 16 Cgk~GH~ardCP~~~~~~ 33 (40)
T 1a6b_B 16 CKEKGHWAKDCPKKPRGP 33 (40)
T ss_dssp SCCTTCCTTSCSSSCCCT
T ss_pred CCCCCcchhhCcCCcccC
Confidence 999999999999977643
No 13
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=29.49 E-value=20 Score=26.36 Aligned_cols=13 Identities=31% Similarity=0.774 Sum_probs=6.8
Q ss_pred CCCCCCCcccccc
Q 040625 1 CGAMTHNAKSCME 13 (395)
Q Consensus 1 CGAmTHk~KDClE 13 (395)
||...|..++|..
T Consensus 10 Cg~~GH~a~~C~~ 22 (61)
T 2ihx_A 10 CGSPGHYQAQCPK 22 (61)
T ss_dssp SCCBTCCGGGCTT
T ss_pred cCCCCeehhhCcC
Confidence 4555555555544
No 14
>2e6i_A Tyrosine-protein kinase ITK/TSK; BTK, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=24.03 E-value=22 Score=27.36 Aligned_cols=34 Identities=26% Similarity=0.547 Sum_probs=21.4
Q ss_pred ccchhhhccCCCceeeeccccCCcccccccccccccc-ccc
Q 040625 263 SKYEEDVYINNHTSVWGSWWKDHQWGYKCCKQTIKNN-LMK 302 (395)
Q Consensus 263 SkY~EDv~~nnHTsVWGSy~~~~~WGY~CC~s~~kns-yCt 302 (395)
|++-.+.+.--|..+| .+|+| -||+++.|+. =|+
T Consensus 5 s~~N~~ll~~yHPg~~----~~GkW--~CC~q~~k~a~GC~ 39 (64)
T 2e6i_A 5 SSGNNSLVPKYHPNFW----MDGKW--RCCSQLEKLATGCA 39 (64)
T ss_dssp CCCCCSSCCEECSSCB----CSSSB--SSSCCSCTTCCCCE
T ss_pred cccChhhhhhcCCCce----eCCeE--CCCCCCCccCCCCc
Confidence 3344444444455554 56665 6999999997 465
No 15
>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=23.28 E-value=37 Score=25.17 Aligned_cols=16 Identities=44% Similarity=1.039 Sum_probs=13.8
Q ss_pred CCCCCCCccccccccc
Q 040625 1 CGAMTHNAKSCMERPR 16 (395)
Q Consensus 1 CGAmTHk~KDClERPR 16 (395)
||..+|..++|...++
T Consensus 13 Cg~~GH~a~~C~~~~~ 28 (63)
T 2cqf_A 13 CGGLDHHAKECKLPPQ 28 (63)
T ss_dssp SCCSSSCTTTCCSCCC
T ss_pred cCCCCcChhhCCCCCC
Confidence 8999999999987543
No 16
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=23.04 E-value=33 Score=22.93 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=6.6
Q ss_pred CCCCCCCcccc
Q 040625 1 CGAMTHNAKSC 11 (395)
Q Consensus 1 CGAmTHk~KDC 11 (395)
||..+|..+||
T Consensus 27 Cg~~GH~~~~C 37 (39)
T 2a51_A 27 CGSKEHRFAQC 37 (39)
T ss_dssp TCCSSSCTTTS
T ss_pred CCCCCCccCcC
Confidence 55566666665
Done!