Query psy4218
Match_columns 520
No_of_seqs 169 out of 222
Neff 4.2
Searched_HMMs 29240
Date Fri Aug 16 19:51:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4218.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/4218hhsearch_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 94.4 0.017 5.8E-07 39.1 2.0 24 115-139 6-29 (29)
2 1u6p_A GAG polyprotein; MLV, A 89.6 0.17 5.7E-06 39.6 2.3 25 115-139 23-47 (56)
3 1dsq_A Nucleic acid binding pr 89.0 0.15 5.2E-06 33.6 1.5 21 116-136 3-23 (26)
4 1a6b_B Momulv, zinc finger pro 82.9 0.5 1.7E-05 34.6 1.7 25 114-138 9-33 (40)
5 1cl4_A Protein (GAG polyprotei 81.9 0.56 1.9E-05 36.0 1.8 26 114-139 29-54 (60)
6 2ec7_A GAG polyprotein (PR55GA 81.6 0.57 2E-05 34.9 1.6 21 114-134 26-46 (49)
7 1a1t_A Nucleocapsid protein; s 81.3 0.64 2.2E-05 35.1 1.8 19 115-133 33-51 (55)
8 2cqf_A RNA-binding protein LIN 79.3 0.79 2.7E-05 35.9 1.8 21 115-135 29-49 (63)
9 3nyb_B Protein AIR2; polya RNA 78.5 0.97 3.3E-05 37.6 2.2 19 116-134 47-65 (83)
10 2a51_A Nucleocapsid protein; s 77.5 0.89 3.1E-05 32.2 1.5 19 114-132 20-38 (39)
11 2cqf_A RNA-binding protein LIN 77.4 0.89 3E-05 35.6 1.6 24 114-137 6-29 (63)
12 2ihx_A Nucleocapsid (NC) prote 74.1 1.2 4.2E-05 34.5 1.6 22 116-137 31-52 (61)
13 3ts2_A Protein LIN-28 homolog 72.2 1.4 4.8E-05 40.0 1.7 23 116-138 98-120 (148)
14 2li8_A Protein LIN-28 homolog 71.2 1.8 6.1E-05 35.2 2.0 23 113-135 22-44 (74)
15 3nyb_B Protein AIR2; polya RNA 69.7 1.5 5.3E-05 36.4 1.3 23 112-134 2-24 (83)
16 2ec7_A GAG polyprotein (PR55GA 66.7 2 6.9E-05 31.9 1.3 21 114-134 5-25 (49)
17 2li8_A Protein LIN-28 homolog 63.8 2.6 8.9E-05 34.2 1.5 22 114-135 45-66 (74)
18 2ihx_A Nucleocapsid (NC) prote 63.2 2.9 0.0001 32.3 1.6 21 115-135 4-24 (61)
19 2ysa_A Retinoblastoma-binding 62.9 3.3 0.00011 32.1 1.9 19 115-133 7-25 (55)
20 3ts2_A Protein LIN-28 homolog 58.4 3.9 0.00013 37.0 1.9 23 115-137 119-141 (148)
21 2bl6_A Nucleocapsid protein P1 55.8 4 0.00014 28.4 1.1 17 117-133 2-18 (37)
22 1a1t_A Nucleocapsid protein; s 55.4 4.3 0.00015 30.5 1.3 20 114-133 11-30 (55)
23 2qdq_A Talin-1; dimerisation d 55.2 5.5 0.00019 30.7 1.9 14 30-43 16-29 (50)
24 2a51_A Nucleocapsid protein; s 54.3 4.3 0.00015 28.6 1.1 17 117-133 2-18 (39)
25 2hqh_E Restin; beta/BETA struc 50.9 4.3 0.00015 27.4 0.6 17 117-133 5-21 (26)
26 1cl4_A Protein (GAG polyprotei 50.8 3.3 0.00011 31.7 0.0 20 116-135 2-21 (60)
27 2bl6_A Nucleocapsid protein P1 50.0 5 0.00017 27.9 0.9 17 116-132 20-36 (37)
28 3eop_A Thymocyte nuclear prote 43.3 9.6 0.00033 36.0 1.9 43 260-312 86-128 (176)
29 2lli_A Protein AIR2; RNA surve 42.1 9.7 0.00033 32.8 1.7 22 115-136 64-85 (124)
30 2eve_A Hypothetical protein ps 42.0 11 0.00036 35.2 1.9 18 260-279 75-92 (157)
31 2ar1_A Hypothetical protein; s 41.5 11 0.00037 35.6 1.9 18 260-279 93-110 (172)
32 2lli_A Protein AIR2; RNA surve 31.2 18 0.00061 31.1 1.6 20 114-133 104-123 (124)
33 3pmk_N Phosphoprotein; chapero 23.7 24 0.00083 28.4 0.9 46 32-85 21-66 (68)
34 1kil_E Complexin I snare-compl 20.9 1.5E+02 0.0051 22.6 4.7 18 342-359 31-48 (49)
35 3fac_A Putative uncharacterize 20.3 32 0.0011 29.1 1.1 15 114-128 66-80 (118)
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=94.44 E-value=0.017 Score=39.09 Aligned_cols=24 Identities=33% Similarity=0.646 Sum_probs=20.1
Q ss_pred cccccccccCCCCccccccCccccc
Q psy4218 115 KGACENCGAMTHKKKDCLERPRKVL 139 (520)
Q Consensus 115 KGACeNCGAmtHkkKDClERPRK~G 139 (520)
...|-|||..+|-.+||-. |||+|
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 3569999999999999975 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=89.55 E-value=0.17 Score=39.60 Aligned_cols=25 Identities=32% Similarity=0.679 Sum_probs=22.3
Q ss_pred cccccccccCCCCccccccCccccc
Q psy4218 115 KGACENCGAMTHKKKDCLERPRKVL 139 (520)
Q Consensus 115 KGACeNCGAmtHkkKDClERPRK~G 139 (520)
+..|-|||..+|-.+||-.++|+..
T Consensus 23 ~~~C~~Cge~GH~ardCp~~~~~~~ 47 (56)
T 1u6p_A 23 RDQCAYCKEKGHWAKDCPKKPRGPR 47 (56)
T ss_dssp TTBCSSSCCBSSCGGGCTTCCCSSC
T ss_pred CCcceeCCCCCcccccCcCCccccC
Confidence 5779999999999999999988654
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=89.01 E-value=0.15 Score=33.62 Aligned_cols=21 Identities=38% Similarity=0.820 Sum_probs=17.3
Q ss_pred ccccccccCCCCccccccCcc
Q psy4218 116 GACENCGAMTHKKKDCLERPR 136 (520)
Q Consensus 116 GACeNCGAmtHkkKDClERPR 136 (520)
+.|=|||..+|-.+||..+.+
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 469999999999999988643
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=82.93 E-value=0.5 Score=34.56 Aligned_cols=25 Identities=32% Similarity=0.704 Sum_probs=21.6
Q ss_pred ccccccccccCCCCccccccCcccc
Q psy4218 114 RKGACENCGAMTHKKKDCLERPRKV 138 (520)
Q Consensus 114 RKGACeNCGAmtHkkKDClERPRK~ 138 (520)
.+..|-|||-.+|-++||-.++++-
T Consensus 9 ~~~~C~~Cgk~GH~ardCP~~~~~~ 33 (40)
T 1a6b_B 9 DRDQCAYCKEKGHWAKDCPKKPRGP 33 (40)
T ss_dssp CSSSCSSSCCTTCCTTSCSSSCCCT
T ss_pred CCCeeeECCCCCcchhhCcCCcccC
Confidence 3578999999999999999987654
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=81.95 E-value=0.56 Score=36.03 Aligned_cols=26 Identities=19% Similarity=0.426 Sum_probs=22.3
Q ss_pred ccccccccccCCCCccccccCccccc
Q psy4218 114 RKGACENCGAMTHKKKDCLERPRKVL 139 (520)
Q Consensus 114 RKGACeNCGAmtHkkKDClERPRK~G 139 (520)
+.+.|-+||...|..+||-++....|
T Consensus 29 ~~~~C~~Cg~~GH~ar~C~~~~~~~G 54 (60)
T 1cl4_A 29 VPGLCPRCKRGKHWANECKSKTDNQG 54 (60)
T ss_dssp CCCSCSSCSSCSSCSTTCCCTTSSSS
T ss_pred CCcceeECCCCCCccCcCCCccccCC
Confidence 45789999999999999999876655
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=81.58 E-value=0.57 Score=34.87 Aligned_cols=21 Identities=38% Similarity=0.816 Sum_probs=16.3
Q ss_pred ccccccccccCCCCccccccC
Q psy4218 114 RKGACENCGAMTHKKKDCLER 134 (520)
Q Consensus 114 RKGACeNCGAmtHkkKDClER 134 (520)
+.+.|-+||..+|..+||-++
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 346788888888888888765
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=81.30 E-value=0.64 Score=35.11 Aligned_cols=19 Identities=47% Similarity=0.929 Sum_probs=10.9
Q ss_pred cccccccccCCCCcccccc
Q psy4218 115 KGACENCGAMTHKKKDCLE 133 (520)
Q Consensus 115 KGACeNCGAmtHkkKDClE 133 (520)
++.|-+||..+|..+||-+
T Consensus 33 ~~~C~~Cg~~GH~~~~C~~ 51 (55)
T 1a1t_A 33 KKGCWKCGKEGHQMKDCTE 51 (55)
T ss_dssp CCBCTTTCCBSSCGGGCSS
T ss_pred CCEeCCCCCcCCccCCCcC
Confidence 3456666666666666654
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=79.35 E-value=0.79 Score=35.90 Aligned_cols=21 Identities=19% Similarity=0.551 Sum_probs=13.5
Q ss_pred cccccccccCCCCccccccCc
Q psy4218 115 KGACENCGAMTHKKKDCLERP 135 (520)
Q Consensus 115 KGACeNCGAmtHkkKDClERP 135 (520)
...|-|||...|..+||-+++
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 355666666666666666654
No 9
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=78.53 E-value=0.97 Score=37.60 Aligned_cols=19 Identities=42% Similarity=0.781 Sum_probs=17.5
Q ss_pred ccccccccCCCCccccccC
Q psy4218 116 GACENCGAMTHKKKDCLER 134 (520)
Q Consensus 116 GACeNCGAmtHkkKDClER 134 (520)
-.|=|||..+|-.+||-++
T Consensus 47 ~~CYnCG~~GH~~rdC~~~ 65 (83)
T 3nyb_B 47 IYCYNCGGKGHFGDDCKEK 65 (83)
T ss_dssp CBCSSSSCBSSCGGGCSSC
T ss_pred CeecccCCCCcCcccCCcc
Confidence 4699999999999999986
No 10
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=77.50 E-value=0.89 Score=32.19 Aligned_cols=19 Identities=37% Similarity=0.872 Sum_probs=16.2
Q ss_pred ccccccccccCCCCccccc
Q psy4218 114 RKGACENCGAMTHKKKDCL 132 (520)
Q Consensus 114 RKGACeNCGAmtHkkKDCl 132 (520)
|+..|-|||..+|..+||-
T Consensus 20 ~~~~C~~Cg~~GH~~~~C~ 38 (39)
T 2a51_A 20 RQEGCWNCGSKEHRFAQCP 38 (39)
T ss_dssp CCSSCTTTCCSSSCTTTSC
T ss_pred CCCccccCCCCCCccCcCc
Confidence 4578999999999999995
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=77.35 E-value=0.89 Score=35.61 Aligned_cols=24 Identities=33% Similarity=0.812 Sum_probs=20.0
Q ss_pred ccccccccccCCCCccccccCccc
Q psy4218 114 RKGACENCGAMTHKKKDCLERPRK 137 (520)
Q Consensus 114 RKGACeNCGAmtHkkKDClERPRK 137 (520)
|...|-|||...|..+||...++.
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 346799999999999999886553
No 12
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=74.13 E-value=1.2 Score=34.45 Aligned_cols=22 Identities=32% Similarity=0.746 Sum_probs=17.1
Q ss_pred ccccccccCCCCccccccCccc
Q psy4218 116 GACENCGAMTHKKKDCLERPRK 137 (520)
Q Consensus 116 GACeNCGAmtHkkKDClERPRK 137 (520)
+.|-|||.+.|..+||.++..-
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 5699999999999999886543
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=72.18 E-value=1.4 Score=40.00 Aligned_cols=23 Identities=35% Similarity=0.842 Sum_probs=17.9
Q ss_pred ccccccccCCCCccccccCcccc
Q psy4218 116 GACENCGAMTHKKKDCLERPRKV 138 (520)
Q Consensus 116 GACeNCGAmtHkkKDClERPRK~ 138 (520)
..|-|||..+|..++|-..|+.+
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 35888888888888888766643
No 14
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=71.25 E-value=1.8 Score=35.18 Aligned_cols=23 Identities=35% Similarity=0.836 Sum_probs=15.4
Q ss_pred cccccccccccCCCCccccccCc
Q psy4218 113 FRKGACENCGAMTHKKKDCLERP 135 (520)
Q Consensus 113 yRKGACeNCGAmtHkkKDClERP 135 (520)
.|...|-|||..+|..++|...+
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 15
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=69.70 E-value=1.5 Score=36.38 Aligned_cols=23 Identities=26% Similarity=0.608 Sum_probs=16.7
Q ss_pred ccccccccccccCCCCccccccC
Q psy4218 112 KFRKGACENCGAMTHKKKDCLER 134 (520)
Q Consensus 112 KyRKGACeNCGAmtHkkKDClER 134 (520)
|++.-.|-|||..+|..++|-+-
T Consensus 2 ~~k~~~C~~Cg~~GH~~~~Cp~~ 24 (83)
T 3nyb_B 2 SWKKVQCTLCKSKKHSKERCPSI 24 (83)
T ss_dssp -----CCSSSCCSSSCGGGCGGG
T ss_pred CcccCCCCCCCCCCCccccCCCc
Confidence 56677899999999999999774
No 16
>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=66.69 E-value=2 Score=31.87 Aligned_cols=21 Identities=29% Similarity=0.623 Sum_probs=18.1
Q ss_pred ccccccccccCCCCccccccC
Q psy4218 114 RKGACENCGAMTHKKKDCLER 134 (520)
Q Consensus 114 RKGACeNCGAmtHkkKDClER 134 (520)
|...|-|||..+|..++|-..
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 346799999999999999773
No 17
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=63.84 E-value=2.6 Score=34.21 Aligned_cols=22 Identities=18% Similarity=0.549 Sum_probs=19.2
Q ss_pred ccccccccccCCCCccccccCc
Q psy4218 114 RKGACENCGAMTHKKKDCLERP 135 (520)
Q Consensus 114 RKGACeNCGAmtHkkKDClERP 135 (520)
+...|-+||..+|..+||-+++
T Consensus 45 ~~~~C~~Cg~~GH~ar~Cp~~~ 66 (74)
T 2li8_A 45 QPKKCHFCQSISHMVASCPLKA 66 (74)
T ss_dssp CCCCCTTTCCTTSCGGGCTTGG
T ss_pred CCCccCCcCCcCCccCcCcCCc
Confidence 3568999999999999998865
No 18
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=63.16 E-value=2.9 Score=32.31 Aligned_cols=21 Identities=29% Similarity=0.812 Sum_probs=18.1
Q ss_pred cccccccccCCCCccccccCc
Q psy4218 115 KGACENCGAMTHKKKDCLERP 135 (520)
Q Consensus 115 KGACeNCGAmtHkkKDClERP 135 (520)
...|-|||...|..+||-...
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 357999999999999997753
No 19
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=62.85 E-value=3.3 Score=32.12 Aligned_cols=19 Identities=32% Similarity=0.595 Sum_probs=16.6
Q ss_pred cccccccccCCCCcccccc
Q psy4218 115 KGACENCGAMTHKKKDCLE 133 (520)
Q Consensus 115 KGACeNCGAmtHkkKDClE 133 (520)
+..|=.||..+|-.++|-.
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 4569999999999999964
No 20
>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=58.44 E-value=3.9 Score=37.02 Aligned_cols=23 Identities=17% Similarity=0.533 Sum_probs=20.2
Q ss_pred cccccccccCCCCccccccCccc
Q psy4218 115 KGACENCGAMTHKKKDCLERPRK 137 (520)
Q Consensus 115 KGACeNCGAmtHkkKDClERPRK 137 (520)
...|-+||..+|..+||-++|..
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 36799999999999999999876
No 21
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=55.83 E-value=4 Score=28.44 Aligned_cols=17 Identities=35% Similarity=0.817 Sum_probs=15.0
Q ss_pred cccccccCCCCcccccc
Q psy4218 117 ACENCGAMTHKKKDCLE 133 (520)
Q Consensus 117 ACeNCGAmtHkkKDClE 133 (520)
.|-|||..+|..++|-.
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 22
>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=55.39 E-value=4.3 Score=30.48 Aligned_cols=20 Identities=35% Similarity=0.722 Sum_probs=17.6
Q ss_pred ccccccccccCCCCcccccc
Q psy4218 114 RKGACENCGAMTHKKKDCLE 133 (520)
Q Consensus 114 RKGACeNCGAmtHkkKDClE 133 (520)
|...|-|||..+|..++|-.
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 23
>2qdq_A Talin-1; dimerisation domain, C-terminal actin binding site, ABS3, latch domain, structural protein; 2.20A {Mus musculus}
Probab=55.20 E-value=5.5 Score=30.66 Aligned_cols=14 Identities=71% Similarity=0.847 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHh
Q psy4218 30 EDWRKAKELEEARK 43 (520)
Q Consensus 30 e~~rk~keLeeaRK 43 (520)
+=+|+.||||+||+
T Consensus 16 ~iLr~ErELEeAr~ 29 (50)
T 2qdq_A 16 EMLRKERELEEARK 29 (50)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 45799999999997
No 24
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=54.34 E-value=4.3 Score=28.59 Aligned_cols=17 Identities=35% Similarity=0.835 Sum_probs=15.7
Q ss_pred cccccccCCCCcccccc
Q psy4218 117 ACENCGAMTHKKKDCLE 133 (520)
Q Consensus 117 ACeNCGAmtHkkKDClE 133 (520)
.|-|||..+|..++|-.
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 25
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=50.89 E-value=4.3 Score=27.38 Aligned_cols=17 Identities=29% Similarity=0.710 Sum_probs=15.5
Q ss_pred cccccccCCCCcccccc
Q psy4218 117 ACENCGAMTHKKKDCLE 133 (520)
Q Consensus 117 ACeNCGAmtHkkKDClE 133 (520)
.|++|..-+|.+.||-+
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 26
>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=50.79 E-value=3.3 Score=31.69 Aligned_cols=20 Identities=40% Similarity=0.884 Sum_probs=0.0
Q ss_pred ccccccccCCCCccccccCc
Q psy4218 116 GACENCGAMTHKKKDCLERP 135 (520)
Q Consensus 116 GACeNCGAmtHkkKDClERP 135 (520)
+.|-|||...|..+||-..+
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 46999999999999997753
No 27
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=50.05 E-value=5 Score=27.93 Aligned_cols=17 Identities=29% Similarity=0.595 Sum_probs=15.6
Q ss_pred ccccccccCCCCccccc
Q psy4218 116 GACENCGAMTHKKKDCL 132 (520)
Q Consensus 116 GACeNCGAmtHkkKDCl 132 (520)
+.|-+||..+|..+||-
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 57999999999999995
No 28
>3eop_A Thymocyte nuclear protein 1; unknown function, nucleus, phosphoprotein; 2.30A {Homo sapiens} SCOP: b.122.1.0
Probab=43.28 E-value=9.6 Score=36.04 Aligned_cols=43 Identities=26% Similarity=0.455 Sum_probs=26.1
Q ss_pred ccCCCCCccCCCcccccCCCCCCCCCCCCCCccCCCccccccchHHHHHHHHH
Q psy4218 260 NLDPNSAYYDPKTRSMRDNPYETVANPEDVDYAGENFVRFSGDTRKHATAQLF 312 (520)
Q Consensus 260 NLd~nSA~YDPKTRsMRdnP~~~~~~~~~~~faGdnF~R~SGda~e~~~lQ~F 312 (520)
-.||+|.||||||-. +||-=...+ =-|+|.-.-...+..|...
T Consensus 86 ~fDp~s~YyDpkS~~--~~prW~~Vd--------V~~v~~~~~~vtL~eLK~~ 128 (176)
T 3eop_A 86 QFEKNNPHYDPSSKE--DNPKWSMVD--------VQFVRMMKRFIPLAELKSY 128 (176)
T ss_dssp GTCTTSTTCCTTCCT--TSCSCEEEE--------EEEEEEEEEEEEHHHHHHH
T ss_pred ccCCCCCCCCccCcC--CCCCEEEEE--------EEEeeecCCcccHHHHhcC
Confidence 379999999999865 666422111 1455554445555555554
No 29
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=42.13 E-value=9.7 Score=32.81 Aligned_cols=22 Identities=32% Similarity=0.534 Sum_probs=18.0
Q ss_pred cccccccccCCCCccccccCcc
Q psy4218 115 KGACENCGAMTHKKKDCLERPR 136 (520)
Q Consensus 115 KGACeNCGAmtHkkKDClERPR 136 (520)
...|-+||.++|..+||-+..|
T Consensus 64 ~~~C~~Cg~~GH~~~~Cp~~~~ 85 (124)
T 2lli_A 64 KVQCTLCKSKKHSKERCPSIWR 85 (124)
T ss_dssp CCSSSSSCSSCCCTTTCCCSTT
T ss_pred CccCCCCCcCCcchhhCCCccc
Confidence 4679999999999999987654
No 30
>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=42.01 E-value=11 Score=35.15 Aligned_cols=18 Identities=39% Similarity=0.702 Sum_probs=15.1
Q ss_pred ccCCCCCccCCCcccccCCC
Q psy4218 260 NLDPNSAYYDPKTRSMRDNP 279 (520)
Q Consensus 260 NLd~nSA~YDPKTRsMRdnP 279 (520)
..|++|.||||||.. ++|
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 579999999999874 666
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=41.50 E-value=11 Score=35.55 Aligned_cols=18 Identities=39% Similarity=0.778 Sum_probs=15.1
Q ss_pred ccCCCCCccCCCcccccCCC
Q psy4218 260 NLDPNSAYYDPKTRSMRDNP 279 (520)
Q Consensus 260 NLd~nSA~YDPKTRsMRdnP 279 (520)
..|++|.||||||.. ++|
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 469999999999884 666
No 32
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=31.25 E-value=18 Score=31.12 Aligned_cols=20 Identities=40% Similarity=0.708 Sum_probs=17.7
Q ss_pred ccccccccccCCCCcccccc
Q psy4218 114 RKGACENCGAMTHKKKDCLE 133 (520)
Q Consensus 114 RKGACeNCGAmtHkkKDClE 133 (520)
....|-|||.++|-.+||-+
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 35789999999999999965
No 33
>3pmk_N Phosphoprotein; chaperone, viral protein; 3.03A {Recombinant vesicular stomatitis indiarvsv-g}
Probab=23.73 E-value=24 Score=28.41 Aligned_cols=46 Identities=22% Similarity=0.354 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHhcCCCCCcccccCCCCCCCcccccccCCcccCCCCCCcccccC
Q psy4218 32 WRKAKELEEARKAGTAPAAVDEHGRDINPHIPQYISSAPWYFGSKGPTLQHQRI 85 (520)
Q Consensus 32 ~rk~keLeeaRKaG~aPa~~De~GkeiNPHIPqYIs~aPWY~~~~~p~LkHQR~ 85 (520)
....-|||+-|.--+.--..-++|-+| .+.|=||....++|.|+.-
T Consensus 21 vqeidelEs~REeKtn~eLFqeeg~e~--------k~~PSYYq~~ed~~~~~~~ 66 (68)
T 3pmk_N 21 VGEIDEIEAQRAEKSNYELFQEDGVEE--------HTKPSYFQAADDSLEHHHH 66 (68)
T ss_dssp HHHHHHHHHHTCCCC---------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCccc--------ccCchHHHhHHHHHHhhcc
Confidence 444568999998877776666788765 5789999999999999864
No 34
>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=20.93 E-value=1.5e+02 Score=22.62 Aligned_cols=18 Identities=33% Similarity=0.528 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHhC
Q psy4218 342 KKEEFKKEVSSSVIDKYG 359 (520)
Q Consensus 342 kke~~k~~~k~~ileKYG 359 (520)
+-+...+..++.|-+|||
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 334556688999999998
No 35
>3fac_A Putative uncharacterized protein; complete proteome, structural genomics, PSI-2, protein structure initiative; 2.50A {Rhodobacter sphaeroides 2}
Probab=20.29 E-value=32 Score=29.13 Aligned_cols=15 Identities=33% Similarity=0.824 Sum_probs=11.3
Q ss_pred ccccccccccCCCCc
Q psy4218 114 RKGACENCGAMTHKK 128 (520)
Q Consensus 114 RKGACeNCGAmtHkk 128 (520)
+.+.|.+||+..+-.
T Consensus 66 ~r~FC~~CGs~l~~~ 80 (118)
T 3fac_A 66 KHWFCRTCGIYTHHQ 80 (118)
T ss_dssp EEEEETTTCCEEEEE
T ss_pred eeEECCCCCccccCc
Confidence 357899999977543
Done!