Query 019350
Match_columns 342
No_of_seqs 254 out of 1645
Neff 5.8
Searched_HMMs 29240
Date Mon Mar 25 14:44:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019350.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/019350hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2lli_A Protein AIR2; RNA surve 99.9 6.6E-26 2.3E-30 190.9 12.2 119 180-318 4-123 (124)
2 2lli_A Protein AIR2; RNA surve 99.7 3.9E-18 1.3E-22 143.3 8.3 83 181-267 23-123 (124)
3 3nyb_B Protein AIR2; polya RNA 99.5 1.7E-15 5.8E-20 119.5 3.1 63 248-320 4-66 (83)
4 3nyb_B Protein AIR2; polya RNA 99.4 1.3E-13 4.3E-18 108.8 4.2 60 205-269 7-66 (83)
5 2li8_A Protein LIN-28 homolog 99.1 2.4E-11 8.1E-16 93.7 3.8 65 189-269 2-66 (74)
6 2li8_A Protein LIN-28 homolog 99.1 3.5E-11 1.2E-15 92.8 4.1 60 231-295 2-65 (74)
7 1a1t_A Nucleocapsid protein; s 99.0 3.2E-11 1.1E-15 87.5 1.2 49 164-221 3-51 (55)
8 2a51_A Nucleocapsid protein; s 99.0 1.8E-10 6.2E-15 77.9 3.3 38 181-220 1-38 (39)
9 2a51_A Nucleocapsid protein; s 99.0 3.3E-10 1.1E-14 76.6 4.2 38 224-267 2-39 (39)
10 2bl6_A Nucleocapsid protein P1 98.9 5.9E-10 2E-14 74.5 2.8 35 182-220 2-36 (37)
11 2ec7_A GAG polyprotein (PR55GA 98.9 1.3E-09 4.6E-14 77.2 4.6 40 223-268 7-46 (49)
12 2ec7_A GAG polyprotein (PR55GA 98.9 1E-09 3.5E-14 77.9 3.6 39 181-221 7-45 (49)
13 2bl6_A Nucleocapsid protein P1 98.9 8.3E-10 2.8E-14 73.8 2.8 36 224-267 2-37 (37)
14 2ihx_A Nucleocapsid (NC) prote 98.8 3E-09 1E-13 78.7 4.2 48 249-321 4-51 (61)
15 2cqf_A RNA-binding protein LIN 98.8 4.9E-09 1.7E-13 78.1 5.3 41 223-268 8-48 (63)
16 1cl4_A Protein (GAG polyprotei 98.8 1.9E-09 6.4E-14 79.4 2.9 47 223-269 2-50 (60)
17 1cl4_A Protein (GAG polyprotei 98.8 1.5E-09 5E-14 80.0 1.9 49 181-242 2-50 (60)
18 2ihx_A Nucleocapsid (NC) prote 98.8 3E-09 1E-13 78.7 3.4 46 181-242 5-50 (61)
19 1a1t_A Nucleocapsid protein; s 98.8 3.3E-09 1.1E-13 76.7 3.5 40 223-268 13-52 (55)
20 2cqf_A RNA-binding protein LIN 98.8 6.3E-09 2.1E-13 77.6 4.8 41 181-241 8-48 (63)
21 3ts2_A Protein LIN-28 homolog 98.6 2.5E-08 8.6E-13 86.3 3.7 41 180-221 97-137 (148)
22 3ts2_A Protein LIN-28 homolog 98.5 5.4E-08 1.9E-12 84.2 3.3 41 223-268 98-138 (148)
23 1dsq_A Nucleic acid binding pr 97.8 1.1E-05 3.7E-10 49.7 2.3 22 300-321 2-23 (26)
24 1a6b_B Momulv, zinc finger pro 97.4 7.6E-05 2.6E-09 50.7 3.1 24 298-321 8-31 (40)
25 1dsq_A Nucleic acid binding pr 97.4 3.9E-05 1.3E-09 47.2 1.4 19 181-199 3-21 (26)
26 1nc8_A Nucleocapsid protein; H 97.3 7E-05 2.4E-09 47.2 1.8 20 180-199 6-25 (29)
27 1nc8_A Nucleocapsid protein; H 97.3 7.4E-05 2.5E-09 47.0 1.7 21 300-320 6-26 (29)
28 1a6b_B Momulv, zinc finger pro 97.1 0.00045 1.5E-08 46.8 3.8 22 247-268 8-29 (40)
29 1u6p_A GAG polyprotein; MLV, A 97.1 0.00028 9.5E-09 51.3 2.8 23 299-321 22-44 (56)
30 1u6p_A GAG polyprotein; MLV, A 96.8 0.00051 1.7E-08 49.9 2.1 22 178-199 21-42 (56)
31 2ysa_A Retinoblastoma-binding 96.3 0.0017 5.7E-08 47.0 2.3 23 299-321 6-28 (55)
32 2ysa_A Retinoblastoma-binding 96.1 0.0022 7.4E-08 46.4 2.1 19 181-199 8-26 (55)
33 1u57_A GAG polyprotein, HIV-1; 69.7 1.1 3.6E-05 31.0 0.3 31 142-172 1-46 (48)
34 2hqh_E Restin; beta/BETA struc 59.5 2.6 9E-05 25.6 0.6 19 249-267 3-21 (26)
35 2ysm_A Myeloid/lymphoid or mix 49.7 13 0.00043 29.4 3.4 90 223-338 8-104 (111)
36 2ysm_A Myeloid/lymphoid or mix 48.1 24 0.00083 27.7 4.8 31 251-293 56-86 (111)
37 2fiy_A Protein FDHE homolog; F 46.0 5.7 0.0002 37.7 0.9 57 273-342 205-263 (309)
38 3alr_A Nanos protein; zinc-fin 42.4 9.2 0.00032 30.7 1.4 39 181-221 37-92 (106)
39 3alr_A Nanos protein; zinc-fin 40.7 7.8 0.00027 31.2 0.8 18 250-267 72-92 (106)
40 2pzo_E CAP-Gly domain-containi 31.4 13 0.00045 25.0 0.6 21 247-267 18-38 (42)
41 2yuc_A TNF receptor-associated 30.5 1.3E+02 0.0045 21.3 6.1 16 213-229 7-24 (76)
42 2bl5_A MGC83862 protein, quaki 23.0 4.6 0.00016 34.1 -3.7 85 89-175 21-122 (140)
43 2yql_A PHD finger protein 21A; 20.1 68 0.0023 22.0 2.6 10 277-286 10-19 (56)
No 1
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=99.93 E-value=6.6e-26 Score=190.91 Aligned_cols=119 Identities=28% Similarity=0.555 Sum_probs=97.6
Q ss_pred ccccccccccCcccccccccccCCCCcccccCC-CCccccCCCCccCccccCCCCCCCCCCCCCCCCCccCccccCCCCC
Q 019350 180 WQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSL-EHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDS 258 (342)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~-GH~~~~Cp~~~~C~~C~~~GH~ardCp~~~~~g~~~~~~C~~CG~~ 258 (342)
...||+|++.||++++||.. .||+||+. ||++++||....||+|++.||++++||..+. ...||+|++.
T Consensus 4 ~~~C~~C~~~GH~~~~Cp~~-----~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~-----~~~C~~Cg~~ 73 (124)
T 2lli_A 4 APKCNNCSQRGHLKKDCPHI-----ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWK-----KVQCTLCKSK 73 (124)
T ss_dssp SSCCSSCSSSSCCTTTTTSC-----CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCC-----CCSSSSSCSS
T ss_pred CCcccCCCCCCcCcccCcCC-----cCcCCCCcCCccCcccCCcccccccCCCCCccccCcCccc-----CccCCCCCcC
Confidence 46799999999999999985 89999998 9999999998899999999999999998653 4789999999
Q ss_pred CccCCCCCCCCCCCCcCCccccccCCCCcCcccCCCCCCCCCccccccCCCCCCCCCCCC
Q 019350 259 GHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLVSSL 318 (342)
Q Consensus 259 GH~a~dCp~~~~~~~~~~~~C~~Cg~~GH~~c~~~~~~~~~~~~Cy~CG~~GH~~~dC~~ 318 (342)
||++++||..|+.+..... .+.. .+.......+.||+||+.|||++|||.
T Consensus 74 GH~~~~Cp~~~~~y~~~~~-------~~~~---~~~~~~~~~~~Cy~Cg~~GH~a~dCp~ 123 (124)
T 2lli_A 74 KHSKERCPSIWRAYILVDD-------NEKA---KPKVLPFHTIYCYNCGGKGHFGDDCKE 123 (124)
T ss_dssp CCCTTTCCCSTTSCCSSSC-------CCCC---CCSCCCCCCCCTTTTSSSCTTTTTSCC
T ss_pred CcchhhCCCccccccccCc-------cccc---cccccCCCCCCcCCCCCCCcCcccCcC
Confidence 9999999999875433210 0000 011122357899999999999999996
No 2
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=99.73 E-value=3.9e-18 Score=143.33 Aligned_cols=83 Identities=28% Similarity=0.644 Sum_probs=66.3
Q ss_pred ccccccccc-CcccccccccccCCCCcccccCCCCccccCCCC---ccCccccCCCCCCCCCCCCCCC------------
Q 019350 181 QTCYNCGEE-GHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKA---QDCFICKKGGHRAKDCPDKHKS------------ 244 (342)
Q Consensus 181 ~~C~~CG~~-GH~a~~Cp~~~~~~~~C~~CG~~GH~~~~Cp~~---~~C~~C~~~GH~ardCp~~~~~------------ 244 (342)
..||+||+. ||++++||.. ..|++|++.||++++||.. ..||+|++.||++++||..+..
T Consensus 23 ~~C~~Cg~~~gH~~~~C~~~----~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~y~~~~~~~~~~~ 98 (124)
T 2lli_A 23 IICSYCGATDDHYSRHCPKA----IQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKP 98 (124)
T ss_dssp CCCTTTCCTTTCCTTTGGGS----SCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCCTTTCCCSTTSCCSSSCCCCCCC
T ss_pred CcCcCCCCcCCccCcccCCc----ccccccCCCCCccccCcCcccCccCCCCCcCCcchhhCCCccccccccCccccccc
Confidence 479999999 9999999985 5899999999999999974 6899999999999999997652
Q ss_pred --CCccCccccCCCCCCccCCCCCC
Q 019350 245 --GFQNAQVCLKCGDSGHDMFSCRN 267 (342)
Q Consensus 245 --g~~~~~~C~~CG~~GH~a~dCp~ 267 (342)
.+...+.||+|++.||+++|||.
T Consensus 99 ~~~~~~~~~Cy~Cg~~GH~a~dCp~ 123 (124)
T 2lli_A 99 KVLPFHTIYCYNCGGKGHFGDDCKE 123 (124)
T ss_dssp SCCCCCCCCTTTTSSSCTTTTTSCC
T ss_pred cccCCCCCCcCCCCCCCcCcccCcC
Confidence 01124556666666666666653
No 3
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=99.54 E-value=1.7e-15 Score=119.47 Aligned_cols=63 Identities=19% Similarity=0.326 Sum_probs=42.3
Q ss_pred cCccccCCCCCCccCCCCCCCCCCCCcCCccccccCCCCcCcccCCCCCCCCCccccccCCCCCCCCCCCCCc
Q 019350 248 NAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLVSSLNL 320 (342)
Q Consensus 248 ~~~~C~~CG~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GH~~c~~~~~~~~~~~~Cy~CG~~GH~~~dC~~~~ 320 (342)
..+.||+|++.||++++||..| .||+|+..||++.+++. +...++||+||+.|||++|||+++
T Consensus 4 k~~~C~~Cg~~GH~~~~Cp~~~--------rcY~c~~~gh~~~~c~~--p~~~~~CYnCG~~GH~~rdC~~~r 66 (83)
T 3nyb_B 4 KKVQCTLCKSKKHSKERCPSIW--------RAYILVDDNEKAKPKVL--PFHTIYCYNCGGKGHFGDDCKEKR 66 (83)
T ss_dssp ---CCSSSCCSSSCGGGCGGGT--------CCCCBC---------------CCCBCSSSSCBSSCGGGCSSCC
T ss_pred ccCCCCCCCCCCCccccCCCcc--------cccccccCCcccccccC--CCCCCeecccCCCCcCcccCCccc
Confidence 3578999999999999999876 48999999998733321 235689999999999999999876
No 4
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=99.40 E-value=1.3e-13 Score=108.77 Aligned_cols=60 Identities=23% Similarity=0.484 Sum_probs=32.7
Q ss_pred CcccccCCCCccccCCCCccCccccCCCCCCCCCCCCCCCCCccCccccCCCCCCccCCCCCCCC
Q 019350 205 PCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSY 269 (342)
Q Consensus 205 ~C~~CG~~GH~~~~Cp~~~~C~~C~~~GH~ardCp~~~~~g~~~~~~C~~CG~~GH~a~dCp~~~ 269 (342)
.|++|++.||++++||....||+|+..||.+++|+.+. ..+.||+||+.||+++|||..+
T Consensus 7 ~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p~-----~~~~CYnCG~~GH~~rdC~~~r 66 (83)
T 3nyb_B 7 QCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPF-----HTIYCYNCGGKGHFGDDCKEKR 66 (83)
T ss_dssp CCSSSCCSSSCGGGCGGGTCCCCBC------------------CCCBCSSSSCBSSCGGGCSSCC
T ss_pred CCCCCCCCCCccccCCCcccccccccCCcccccccCCC-----CCCeecccCCCCcCcccCCccc
Confidence 45555555555555555446777777777777777643 2578888888888888888754
No 5
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=99.13 E-value=2.4e-11 Score=93.72 Aligned_cols=65 Identities=22% Similarity=0.384 Sum_probs=36.9
Q ss_pred cCcccccccccccCCCCcccccCCCCccccCCCCccCccccCCCCCCCCCCCCCCCCCccCccccCCCCCCccCCCCCCC
Q 019350 189 EGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (342)
Q Consensus 189 ~GH~a~~Cp~~~~~~~~C~~CG~~GH~~~~Cp~~~~C~~C~~~GH~ardCp~~~~~g~~~~~~C~~CG~~GH~a~dCp~~ 268 (342)
.||++++|+.+.... ....=.....||+|++.||++++||.... ...||+|++.||++++||..
T Consensus 2 ~gh~~rdc~~~~~~~-----------~~~~~~r~~~C~~Cg~~GH~a~~C~~~~~-----~~~C~~Cg~~GH~ar~Cp~~ 65 (74)
T 2li8_A 2 SGLVPRGSHMPKGKS-----------MQKRRSKGDRCYNCGGLDHHAKECKLPPQ-----PKKCHFCQSISHMVASCPLK 65 (74)
T ss_dssp ----------CCCCC-----------CCSCCSTTSCCTTTCCSSSCTTTCSSCCC-----CCCCTTTCCTTSCGGGCTTG
T ss_pred CccccCcCCCCCcCc-----------cccccCCCCcccccCCcCcCcccCCCCCC-----CCccCCcCCcCCccCcCcCC
Confidence 589999999862211 00010123578889989999999986432 47899999999999999875
Q ss_pred C
Q 019350 269 Y 269 (342)
Q Consensus 269 ~ 269 (342)
.
T Consensus 66 ~ 66 (74)
T 2li8_A 66 A 66 (74)
T ss_dssp G
T ss_pred c
Confidence 3
No 6
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=99.11 E-value=3.5e-11 Score=92.80 Aligned_cols=60 Identities=15% Similarity=0.370 Sum_probs=37.7
Q ss_pred CCCCCCCCCCCCCCC----CccCccccCCCCCCccCCCCCCCCCCCCcCCccccccCCCCcCcccCCCC
Q 019350 231 GGHRAKDCPDKHKSG----FQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISD 295 (342)
Q Consensus 231 ~GH~ardCp~~~~~g----~~~~~~C~~CG~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GH~~c~~~~~ 295 (342)
.||+++||+.+..+. ......||+||+.||++++||... ....||+|++.||++.+++..
T Consensus 2 ~gh~~rdc~~~~~~~~~~~~~r~~~C~~Cg~~GH~a~~C~~~~-----~~~~C~~Cg~~GH~ar~Cp~~ 65 (74)
T 2li8_A 2 SGLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLPP-----QPKKCHFCQSISHMVASCPLK 65 (74)
T ss_dssp ----------CCCCCCCSCCSTTSCCTTTCCSSSCTTTCSSCC-----CCCCCTTTCCTTSCGGGCTTG
T ss_pred CccccCcCCCCCcCccccccCCCCcccccCCcCcCcccCCCCC-----CCCccCCcCCcCCccCcCcCC
Confidence 588999998765431 234578999999999999999642 347899999999998555443
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=99.05 E-value=3.2e-11 Score=87.45 Aligned_cols=49 Identities=43% Similarity=0.990 Sum_probs=34.3
Q ss_pred HHhhCCCCCCCCCCccccccccccccCcccccccccccCCCCcccccCCCCccccCCC
Q 019350 164 RKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSK 221 (342)
Q Consensus 164 r~~~r~~Ryf~~~~~~~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~~~~Cp~ 221 (342)
+++|++++. ...||+||+.||++++||.+ +...||+||+.||++++||.
T Consensus 3 ~~~f~g~~~-------~~~C~~Cg~~GH~a~~C~~~--~~~~C~~Cg~~GH~~~~C~~ 51 (55)
T 1a1t_A 3 KGNFRNQRK-------TVKCFNCGKEGHIAKNCRAP--RKKGCWKCGKEGHQMKDCTE 51 (55)
T ss_dssp CGGGGGGGG-------TCBCTTTCCBSSCGGGCSSC--SCCBCTTTCCBSSCGGGCSS
T ss_pred ccccCCCCC-------CcceeeeCCCCcChhhcCCC--CCCEeCCCCCcCCccCCCcC
Confidence 455666544 36799999999999999885 33456666666666666654
No 8
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=99.00 E-value=1.8e-10 Score=77.91 Aligned_cols=38 Identities=50% Similarity=1.109 Sum_probs=26.2
Q ss_pred cccccccccCcccccccccccCCCCcccccCCCCccccCC
Q 019350 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCS 220 (342)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~~~~Cp 220 (342)
+.||+||+.||++++||.+ +...||+||+.||++++||
T Consensus 1 i~C~~Cg~~GH~a~~C~~~--~~~~C~~Cg~~GH~~~~C~ 38 (39)
T 2a51_A 1 LTCFNCGKPGHTARMCRQP--RQEGCWNCGSKEHRFAQCP 38 (39)
T ss_dssp CBCTTTCCBSSCTTTCCSC--CCSSCTTTCCSSSCTTTSC
T ss_pred CeeeccCCCCcccccCCCC--CCCccccCCCCCCccCcCc
Confidence 3588888888888888875 3345666666666655555
No 9
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=98.98 E-value=3.3e-10 Score=76.61 Aligned_cols=38 Identities=34% Similarity=0.859 Sum_probs=28.8
Q ss_pred cCccccCCCCCCCCCCCCCCCCCccCccccCCCCCCccCCCCCC
Q 019350 224 DCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRN 267 (342)
Q Consensus 224 ~C~~C~~~GH~ardCp~~~~~g~~~~~~C~~CG~~GH~a~dCp~ 267 (342)
.||+|++.||++++||.+. ...||+||+.||++++||+
T Consensus 2 ~C~~Cg~~GH~a~~C~~~~------~~~C~~Cg~~GH~~~~C~~ 39 (39)
T 2a51_A 2 TCFNCGKPGHTARMCRQPR------QEGCWNCGSKEHRFAQCPK 39 (39)
T ss_dssp BCTTTCCBSSCTTTCCSCC------CSSCTTTCCSSSCTTTSCC
T ss_pred eeeccCCCCcccccCCCCC------CCccccCCCCCCccCcCcC
Confidence 5778888888888887753 3578888888888888873
No 10
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=98.90 E-value=5.9e-10 Score=74.54 Aligned_cols=35 Identities=49% Similarity=1.145 Sum_probs=22.0
Q ss_pred ccccccccCcccccccccccCCCCcccccCCCCccccCC
Q 019350 182 TCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCS 220 (342)
Q Consensus 182 ~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~~~~Cp 220 (342)
.||+||+.||++++||.+ ..||+||+.||++++||
T Consensus 2 ~C~~Cg~~GH~~~~C~~~----~~C~~Cg~~GH~a~~C~ 36 (37)
T 2bl6_A 2 TCYNCGKPGHLSSQCRAP----KVCFKCKQPGHFSKQCR 36 (37)
T ss_dssp CBSSSCCSSCCTTTSSCB----TTCSSCCCTTGGGGTTC
T ss_pred cccccCCCCcchhhCcCc----CeEccCCCcCCccCcCc
Confidence 477777777777777664 35555555555555554
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=98.89 E-value=1.3e-09 Score=77.24 Aligned_cols=40 Identities=40% Similarity=0.896 Sum_probs=28.4
Q ss_pred ccCccccCCCCCCCCCCCCCCCCCccCccccCCCCCCccCCCCCCC
Q 019350 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (342)
Q Consensus 223 ~~C~~C~~~GH~ardCp~~~~~g~~~~~~C~~CG~~GH~a~dCp~~ 268 (342)
..||+|++.||++++||.+. ...||+||+.||++++||..
T Consensus 7 ~~C~~Cg~~GH~a~~C~~~~------~~~C~~Cg~~GH~~~~C~~~ 46 (49)
T 2ec7_A 7 IRCWNCGKEGHSARQCRAPR------RQGCWKCGKTGHVMAKCPER 46 (49)
T ss_dssp CBCTTTCCBTCCTTTCCCSS------CCSCSSSCCSSCCGGGCCSS
T ss_pred CeeeecCCCCcChhhCcCCC------CCeeCcCCCcCCccCCCcCC
Confidence 46777777777777777643 25688888888888888764
No 12
>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=98.88 E-value=1e-09 Score=77.86 Aligned_cols=39 Identities=41% Similarity=1.069 Sum_probs=26.8
Q ss_pred cccccccccCcccccccccccCCCCcccccCCCCccccCCC
Q 019350 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSK 221 (342)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~~~~Cp~ 221 (342)
..||+||+.||++++||.+ +...||+||+.||++++||.
T Consensus 7 ~~C~~Cg~~GH~a~~C~~~--~~~~C~~Cg~~GH~~~~C~~ 45 (49)
T 2ec7_A 7 IRCWNCGKEGHSARQCRAP--RRQGCWKCGKTGHVMAKCPE 45 (49)
T ss_dssp CBCTTTCCBTCCTTTCCCS--SCCSCSSSCCSSCCGGGCCS
T ss_pred CeeeecCCCCcChhhCcCC--CCCeeCcCCCcCCccCCCcC
Confidence 6788888888888888875 23456666666666555553
No 13
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=98.87 E-value=8.3e-10 Score=73.79 Aligned_cols=36 Identities=39% Similarity=0.944 Sum_probs=25.0
Q ss_pred cCccccCCCCCCCCCCCCCCCCCccCccccCCCCCCccCCCCCC
Q 019350 224 DCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRN 267 (342)
Q Consensus 224 ~C~~C~~~GH~ardCp~~~~~g~~~~~~C~~CG~~GH~a~dCp~ 267 (342)
.||+|++.||++++||.+ ..||+|++.||++++||+
T Consensus 2 ~C~~Cg~~GH~~~~C~~~--------~~C~~Cg~~GH~a~~C~~ 37 (37)
T 2bl6_A 2 TCYNCGKPGHLSSQCRAP--------KVCFKCKQPGHFSKQCRS 37 (37)
T ss_dssp CBSSSCCSSCCTTTSSCB--------TTCSSCCCTTGGGGTTCC
T ss_pred cccccCCCCcchhhCcCc--------CeEccCCCcCCccCcCcC
Confidence 467777777777777652 467777777777777763
No 14
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=98.80 E-value=3e-09 Score=78.72 Aligned_cols=48 Identities=23% Similarity=0.518 Sum_probs=35.4
Q ss_pred CccccCCCCCCccCCCCCCCCCCCCcCCccccccCCCCcCcccCCCCCCCCCccccccCCCCCCCCCCCCCcc
Q 019350 249 AQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLVSSLNLS 321 (342)
Q Consensus 249 ~~~C~~CG~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GH~~c~~~~~~~~~~~~Cy~CG~~GH~~~dC~~~~~ 321 (342)
...||+|++.||++++||..... + ...+.||+||+.||++++||..+.
T Consensus 4 ~~~C~~Cg~~GH~a~~C~~~~~~--------------~-----------~~~~~C~~Cg~~GH~ar~C~~~~~ 51 (61)
T 2ihx_A 4 RGLCYTCGSPGHYQAQCPKKRKS--------------G-----------NSRERCQLCNGMGHNAKQCRKRDG 51 (61)
T ss_dssp TTBCSSSCCBTCCGGGCTTTTSS--------------S-----------CCCSBCTTTCCBSSCGGGCCCCC-
T ss_pred CCcccccCCCCeehhhCcCCcCC--------------C-----------CCCCeeCCCCCCCCCcCCCcCCCc
Confidence 46788888888888888864210 0 124689999999999999988664
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=98.80 E-value=4.9e-09 Score=78.15 Aligned_cols=41 Identities=27% Similarity=0.563 Sum_probs=28.9
Q ss_pred ccCccccCCCCCCCCCCCCCCCCCccCccccCCCCCCccCCCCCCC
Q 019350 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (342)
Q Consensus 223 ~~C~~C~~~GH~ardCp~~~~~g~~~~~~C~~CG~~GH~a~dCp~~ 268 (342)
..||+|++.||++++||.+.. ...||+|++.||++++||..
T Consensus 8 ~~C~~Cg~~GH~a~~C~~~~~-----~~~C~~Cg~~GH~ar~Cp~~ 48 (63)
T 2cqf_A 8 DRCYNCGGLDHHAKECKLPPQ-----PKKCHFCQSISHMVASCPLK 48 (63)
T ss_dssp CCCSSSCCSSSCTTTCCSCCC-----SSCCTTTCCSSSCTTTCTGG
T ss_pred CcccccCCCCcChhhCCCCCC-----CCccCCcCCcCCccCcCCCc
Confidence 457777777777777776432 36788888888888888764
No 16
>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=98.80 E-value=1.9e-09 Score=79.38 Aligned_cols=47 Identities=28% Similarity=0.630 Sum_probs=18.3
Q ss_pred ccCccccCCCCCCCCCCCCCCCC--CccCccccCCCCCCccCCCCCCCC
Q 019350 223 QDCFICKKGGHRAKDCPDKHKSG--FQNAQVCLKCGDSGHDMFSCRNSY 269 (342)
Q Consensus 223 ~~C~~C~~~GH~ardCp~~~~~g--~~~~~~C~~CG~~GH~a~dCp~~~ 269 (342)
..||+|++.||++++||...... ......||+|++.||++++||...
T Consensus 2 ~~Cf~Cg~~GH~a~~C~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~ 50 (60)
T 1cl4_A 2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKT 50 (60)
T ss_dssp ---------------------------CCCSCSSCSSCSSCSTTCCCTT
T ss_pred CccccCCCCCcCHhhCcCCCCCccccCCCcceeECCCCCCccCcCCCcc
Confidence 35778888888888887753211 012478999999999999999764
No 17
>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=98.78 E-value=1.5e-09 Score=79.96 Aligned_cols=49 Identities=33% Similarity=0.774 Sum_probs=16.9
Q ss_pred cccccccccCcccccccccccCCCCcccccCCCCccccCCCCccCccccCCCCCCCCCCCCC
Q 019350 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKH 242 (342)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~~~~Cp~~~~C~~C~~~GH~ardCp~~~ 242 (342)
..||+|++.||++++||....... . ......||+|++.||++++||...
T Consensus 2 ~~Cf~Cg~~GH~a~~C~~~~~~~~------------~-~~~~~~C~~Cg~~GH~ar~C~~~~ 50 (60)
T 1cl4_A 2 GSCFKCGKKGHFAKNCHEHAHNNA------------E-PKVPGLCPRCKRGKHWANECKSKT 50 (60)
T ss_dssp ----------------------------------------CCCSCSSCSSCSSCSTTCCCTT
T ss_pred CccccCCCCCcCHhhCcCCCCCcc------------c-cCCCcceeECCCCCCccCcCCCcc
Confidence 469999999999999998622110 0 112357888888888888888764
No 18
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=98.78 E-value=3e-09 Score=78.75 Aligned_cols=46 Identities=33% Similarity=0.821 Sum_probs=32.9
Q ss_pred cccccccccCcccccccccccCCCCcccccCCCCccccCCCCccCccccCCCCCCCCCCCCC
Q 019350 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKH 242 (342)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~~~~Cp~~~~C~~C~~~GH~ardCp~~~ 242 (342)
..||+|++.||++++||.+.... .....||+|++.||++++||...
T Consensus 5 ~~C~~Cg~~GH~a~~C~~~~~~~----------------~~~~~C~~Cg~~GH~ar~C~~~~ 50 (61)
T 2ihx_A 5 GLCYTCGSPGHYQAQCPKKRKSG----------------NSRERCQLCNGMGHNAKQCRKRD 50 (61)
T ss_dssp TBCSSSCCBTCCGGGCTTTTSSS----------------CCCSBCTTTCCBSSCGGGCCCCC
T ss_pred CcccccCCCCeehhhCcCCcCCC----------------CCCCeeCCCCCCCCCcCCCcCCC
Confidence 67999999999999999862211 11356777777777777777754
No 19
>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=98.77 E-value=3.3e-09 Score=76.74 Aligned_cols=40 Identities=43% Similarity=0.944 Sum_probs=24.7
Q ss_pred ccCccccCCCCCCCCCCCCCCCCCccCccccCCCCCCccCCCCCCC
Q 019350 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (342)
Q Consensus 223 ~~C~~C~~~GH~ardCp~~~~~g~~~~~~C~~CG~~GH~a~dCp~~ 268 (342)
..||+|++.||++++||.+. ...||+||+.||++++||..
T Consensus 13 ~~C~~Cg~~GH~a~~C~~~~------~~~C~~Cg~~GH~~~~C~~~ 52 (55)
T 1a1t_A 13 VKCFNCGKEGHIAKNCRAPR------KKGCWKCGKEGHQMKDCTER 52 (55)
T ss_dssp CBCTTTCCBSSCGGGCSSCS------CCBCTTTCCBSSCGGGCSSS
T ss_pred cceeeeCCCCcChhhcCCCC------CCEeCCCCCcCCccCCCcCc
Confidence 35666666666666665542 25677777777777777653
No 20
>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=98.76 E-value=6.3e-09 Score=77.57 Aligned_cols=41 Identities=34% Similarity=0.849 Sum_probs=26.9
Q ss_pred cccccccccCcccccccccccCCCCcccccCCCCccccCCCCccCccccCCCCCCCCCCCC
Q 019350 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDK 241 (342)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~~~~Cp~~~~C~~C~~~GH~ardCp~~ 241 (342)
..||+|++.||++++||.+ .. ...||+|++.||++++||..
T Consensus 8 ~~C~~Cg~~GH~a~~C~~~-~~-------------------~~~C~~Cg~~GH~ar~Cp~~ 48 (63)
T 2cqf_A 8 DRCYNCGGLDHHAKECKLP-PQ-------------------PKKCHFCQSISHMVASCPLK 48 (63)
T ss_dssp CCCSSSCCSSSCTTTCCSC-CC-------------------SSCCTTTCCSSSCTTTCTGG
T ss_pred CcccccCCCCcChhhCCCC-CC-------------------CCccCCcCCcCCccCcCCCc
Confidence 5688888888888888764 11 24566666666666666654
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=98.57 E-value=2.5e-08 Score=86.29 Aligned_cols=41 Identities=37% Similarity=0.806 Sum_probs=27.6
Q ss_pred ccccccccccCcccccccccccCCCCcccccCCCCccccCCC
Q 019350 180 WQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSK 221 (342)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~~~~Cp~ 221 (342)
...||+||+.||++++||.+ .....||+||+.||++++||.
T Consensus 97 ~~~C~~Cg~~GH~a~~C~~~-~~~~~C~~Cg~~GH~~r~Cp~ 137 (148)
T 3ts2_A 97 GDRCYNCGGLDHHAKECKLP-PQPKKCHFCQSINHMVASCPL 137 (148)
T ss_dssp SCCCTTTCCSSCCGGGCCSC-CCCCCCTTTCCSSCCGGGCTT
T ss_pred CCcccEeCCccchhhhCCCC-CCCCcccccCCcCCEeccCcC
Confidence 47799999999999999985 223345555555555555543
No 22
>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=98.48 E-value=5.4e-08 Score=84.17 Aligned_cols=41 Identities=27% Similarity=0.563 Sum_probs=29.4
Q ss_pred ccCccccCCCCCCCCCCCCCCCCCccCccccCCCCCCccCCCCCCC
Q 019350 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (342)
Q Consensus 223 ~~C~~C~~~GH~ardCp~~~~~g~~~~~~C~~CG~~GH~a~dCp~~ 268 (342)
..||+|++.||++++||.+.. ...||+|++.||++++||+.
T Consensus 98 ~~C~~Cg~~GH~a~~C~~~~~-----~~~C~~Cg~~GH~~r~Cp~~ 138 (148)
T 3ts2_A 98 DRCYNCGGLDHHAKECKLPPQ-----PKKCHFCQSINHMVASCPLK 138 (148)
T ss_dssp CCCTTTCCSSCCGGGCCSCCC-----CCCCTTTCCSSCCGGGCTTT
T ss_pred CcccEeCCccchhhhCCCCCC-----CCcccccCCcCCEeccCcCC
Confidence 457777777777777776432 35788888888888888864
No 23
>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=97.77 E-value=1.1e-05 Score=49.71 Aligned_cols=22 Identities=27% Similarity=0.566 Sum_probs=17.9
Q ss_pred CccccccCCCCCCCCCCCCCcc
Q 019350 300 EVSCFRCGQLGHTGLVSSLNLS 321 (342)
Q Consensus 300 ~~~Cy~CG~~GH~~~dC~~~~~ 321 (342)
...||+||+.||++++||....
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 4679999999999999997643
No 24
>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=97.45 E-value=7.6e-05 Score=50.68 Aligned_cols=24 Identities=17% Similarity=0.199 Sum_probs=20.4
Q ss_pred CCCccccccCCCCCCCCCCCCCcc
Q 019350 298 PGEVSCFRCGQLGHTGLVSSLNLS 321 (342)
Q Consensus 298 ~~~~~Cy~CG~~GH~~~dC~~~~~ 321 (342)
.....||+||+.|||+++||.+..
T Consensus 8 ~~~~~C~~Cgk~GH~ardCP~~~~ 31 (40)
T 1a6b_B 8 LDRDQCAYCKEKGHWAKDCPKKPR 31 (40)
T ss_dssp CCSSSCSSSCCTTCCTTSCSSSCC
T ss_pred CCCCeeeECCCCCcchhhCcCCcc
Confidence 356899999999999999998653
No 25
>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=97.44 E-value=3.9e-05 Score=47.17 Aligned_cols=19 Identities=32% Similarity=1.153 Sum_probs=16.8
Q ss_pred cccccccccCccccccccc
Q 019350 181 QTCYNCGEEGHMAVNCRSA 199 (342)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~ 199 (342)
..||+||+.||++++||.+
T Consensus 3 ~~Cf~CG~~GH~ardC~~~ 21 (26)
T 1dsq_A 3 PVCFSCGKTGHIKRDCKEE 21 (26)
T ss_dssp CBCTTTCCBSSCTTTTTCC
T ss_pred CeeEeCCCCCcccccCCCc
Confidence 5699999999999999986
No 26
>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=97.35 E-value=7e-05 Score=47.15 Aligned_cols=20 Identities=50% Similarity=1.124 Sum_probs=17.8
Q ss_pred ccccccccccCccccccccc
Q 019350 180 WQTCYNCGEEGHMAVNCRSA 199 (342)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~ 199 (342)
.+.||+||++||++++||.+
T Consensus 6 ~~~C~nCgk~GH~ar~C~~p 25 (29)
T 1nc8_A 6 VIRCWNCGKEGHSARQCRAP 25 (29)
T ss_dssp CCBCTTTSCBSSCGGGCCSS
T ss_pred CCEEEECCccccCHhHCccc
Confidence 36799999999999999986
No 27
>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=97.32 E-value=7.4e-05 Score=47.03 Aligned_cols=21 Identities=24% Similarity=0.631 Sum_probs=17.8
Q ss_pred CccccccCCCCCCCCCCCCCc
Q 019350 300 EVSCFRCGQLGHTGLVSSLNL 320 (342)
Q Consensus 300 ~~~Cy~CG~~GH~~~dC~~~~ 320 (342)
.+.|||||+.||++++|+..+
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 478999999999999998643
No 28
>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=97.10 E-value=0.00045 Score=46.84 Aligned_cols=22 Identities=23% Similarity=0.549 Sum_probs=15.2
Q ss_pred ccCccccCCCCCCccCCCCCCC
Q 019350 247 QNAQVCLKCGDSGHDMFSCRNS 268 (342)
Q Consensus 247 ~~~~~C~~CG~~GH~a~dCp~~ 268 (342)
.....||+||+.|||+++||..
T Consensus 8 ~~~~~C~~Cgk~GH~ardCP~~ 29 (40)
T 1a6b_B 8 LDRDQCAYCKEKGHWAKDCPKK 29 (40)
T ss_dssp CCSSSCSSSCCTTCCTTSCSSS
T ss_pred CCCCeeeECCCCCcchhhCcCC
Confidence 3456677777777777777764
No 29
>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=97.08 E-value=0.00028 Score=51.31 Aligned_cols=23 Identities=17% Similarity=0.241 Sum_probs=19.7
Q ss_pred CCccccccCCCCCCCCCCCCCcc
Q 019350 299 GEVSCFRCGQLGHTGLVSSLNLS 321 (342)
Q Consensus 299 ~~~~Cy~CG~~GH~~~dC~~~~~ 321 (342)
....||+||+.|||+++||.+..
T Consensus 22 ~~~~C~~Cge~GH~ardCp~~~~ 44 (56)
T 1u6p_A 22 DRDQCAYCKEKGHWAKDCPKKPR 44 (56)
T ss_dssp CTTBCSSSCCBSSCGGGCTTCCC
T ss_pred CCCcceeCCCCCcccccCcCCcc
Confidence 46789999999999999988654
No 30
>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=96.78 E-value=0.00051 Score=49.91 Aligned_cols=22 Identities=32% Similarity=0.684 Sum_probs=19.0
Q ss_pred ccccccccccccCccccccccc
Q 019350 178 RGWQTCYNCGEEGHMAVNCRSA 199 (342)
Q Consensus 178 ~~~~~C~~CG~~GH~a~~Cp~~ 199 (342)
.....||+||+.|||+++||..
T Consensus 21 ~~~~~C~~Cge~GH~ardCp~~ 42 (56)
T 1u6p_A 21 LDRDQCAYCKEKGHWAKDCPKK 42 (56)
T ss_dssp CCTTBCSSSCCBSSCGGGCTTC
T ss_pred CCCCcceeCCCCCcccccCcCC
Confidence 4457899999999999999986
No 31
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=96.32 E-value=0.0017 Score=46.99 Aligned_cols=23 Identities=35% Similarity=0.602 Sum_probs=18.0
Q ss_pred CCccccccCCCCCCCCCCCCCcc
Q 019350 299 GEVSCFRCGQLGHTGLVSSLNLS 321 (342)
Q Consensus 299 ~~~~Cy~CG~~GH~~~dC~~~~~ 321 (342)
....||+||+.|||+.+||.+..
T Consensus 6 ~~~~C~kCGk~GH~~k~Cp~~~~ 28 (55)
T 2ysa_A 6 SGYTCFRCGKPGHYIKNCPTNGD 28 (55)
T ss_dssp SSCCCTTTCCTTSCGGGCSGGGC
T ss_pred CCCccccCCCcCcccccCCCCCC
Confidence 45679999999999999986543
No 32
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=96.15 E-value=0.0022 Score=46.39 Aligned_cols=19 Identities=42% Similarity=1.086 Sum_probs=13.6
Q ss_pred cccccccccCccccccccc
Q 019350 181 QTCYNCGEEGHMAVNCRSA 199 (342)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~ 199 (342)
..||+||+.||++++||..
T Consensus 8 ~~C~kCGk~GH~~k~Cp~~ 26 (55)
T 2ysa_A 8 YTCFRCGKPGHYIKNCPTN 26 (55)
T ss_dssp CCCTTTCCTTSCGGGCSGG
T ss_pred CccccCCCcCcccccCCCC
Confidence 4577777777777777743
No 33
>1u57_A GAG polyprotein, HIV-1; particle assembly, viral protein; NMR {Human immunodeficiency virus 1}
Probab=69.69 E-value=1.1 Score=30.98 Aligned_cols=31 Identities=23% Similarity=0.232 Sum_probs=20.1
Q ss_pred hhhhhccccccc--------------cccc-hhHHHHHHhhCCCCC
Q 019350 142 VETADNGDEGVT--------------TVEI-SDNIVLRKLLRGPRY 172 (342)
Q Consensus 142 le~~~~A~e~v~--------------~v~~-~~n~~~r~~~r~~Ry 172 (342)
||+|++|+++|. +++. +.+++++++|+++|.
T Consensus 1 leem~~acqgvggp~hKarvlAEAMsq~~~~~~immqr~nf~g~rk 46 (48)
T 1u57_A 1 LEEMMTACQGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRK 46 (48)
T ss_dssp CCTHHHHBTTTSBCTTHHHHHHHHHHHHHHHHHHHHHTTTTTTCSS
T ss_pred CchhhhhccCCCCCcchhhHHHHHHHHhccccchhhhcccccCCCC
Confidence 356677776665 2221 346789999998875
No 34
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=59.50 E-value=2.6 Score=25.62 Aligned_cols=19 Identities=26% Similarity=0.510 Sum_probs=15.0
Q ss_pred CccccCCCCCCccCCCCCC
Q 019350 249 AQVCLKCGDSGHDMFSCRN 267 (342)
Q Consensus 249 ~~~C~~CG~~GH~a~dCp~ 267 (342)
...|..|...||+..+|+.
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 3678888888888888865
No 35
>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}
Probab=49.73 E-value=13 Score=29.40 Aligned_cols=90 Identities=20% Similarity=0.409 Sum_probs=48.0
Q ss_pred ccCccccCCCCCCCCCCCCCCCCCccCccccCCCCCCccCCCCCCCCCC----CCc---CCccccccCCCCcCcccCCCC
Q 019350 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSL----DDL---KEVQCYICRCFGHLCCVNISD 295 (342)
Q Consensus 223 ~~C~~C~~~GH~ardCp~~~~~g~~~~~~C~~CG~~GH~a~dCp~~~~~----~~~---~~~~C~~Cg~~GH~~c~~~~~ 295 (342)
..|..|+..|.+ ...+.|..|++..|.. |-.+... +.. .=..|..|++.++-
T Consensus 8 ~~C~~C~~~g~~------------~~ll~C~~C~~~~H~~--Cl~~~~~~~~~~~W~C~~C~~C~~C~~~~~~------- 66 (111)
T 2ysm_A 8 ANCAVCDSPGDL------------LDQFFCTTCGQHYHGM--CLDIAVTPLKRAGWQCPECKVCQNCKQSGED------- 66 (111)
T ss_dssp SCBTTTCCCCCT------------TTSEECSSSCCEECTT--TTTCCCCTTTSTTCCCTTTCCCTTTCCCSCC-------
T ss_pred CCCcCCCCCCCC------------cCCeECCCCCCCcChH--HhCCccccccccCccCCcCCcccccCccCCC-------
Confidence 467778776643 1237788888888865 5332211 111 11246666666542
Q ss_pred CCCCCccccccCCCCCCCCCCCCCccccccceeeEEeeccccc
Q 019350 296 AVPGEVSCFRCGQLGHTGLVSSLNLSIEILVIIYWEMRGCFNL 338 (342)
Q Consensus 296 ~~~~~~~Cy~CG~~GH~~~dC~~~~~~~~~~~~~~~~~~~~~~ 338 (342)
...+.|-.|...-|+.=--| ++..++...|-=..|..|
T Consensus 67 --~~ll~Cd~C~~~yH~~Cl~p---pl~~~P~g~W~C~~C~~c 104 (111)
T 2ysm_A 67 --SKMLVCDTCDKGYHTFCLQP---VMKSVPTNGWKCKNCRIC 104 (111)
T ss_dssp --TTEEECSSSCCEEEGGGSSS---CCSSCCSSCCCCHHHHCC
T ss_pred --CCeeECCCCCcHHhHHhcCC---ccccCCCCCcCCcCCcCc
Confidence 13577888888878763222 222223367743334333
No 36
>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}
Probab=48.11 E-value=24 Score=27.71 Aligned_cols=31 Identities=35% Similarity=0.659 Sum_probs=21.7
Q ss_pred cccCCCCCCccCCCCCCCCCCCCcCCccccccCCCCcCcccCC
Q 019350 251 VCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNI 293 (342)
Q Consensus 251 ~C~~CG~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GH~~c~~~ 293 (342)
.|..|+..++. ..-+.|..|...=|+.|-.|
T Consensus 56 ~C~~C~~~~~~------------~~ll~Cd~C~~~yH~~Cl~p 86 (111)
T 2ysm_A 56 VCQNCKQSGED------------SKMLVCDTCDKGYHTFCLQP 86 (111)
T ss_dssp CCTTTCCCSCC------------TTEEECSSSCCEEEGGGSSS
T ss_pred cccccCccCCC------------CCeeECCCCCcHHhHHhcCC
Confidence 57777776542 13578888998889987654
No 37
>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1
Probab=45.98 E-value=5.7 Score=37.70 Aligned_cols=57 Identities=19% Similarity=0.403 Sum_probs=31.1
Q ss_pred CcCCccccccCCCCcCcccCCCCCCCCCccccccCCCCCCCCCCCCC--ccccccceeeEEeecccccccCC
Q 019350 273 DLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLVSSLN--LSIEILVIIYWEMRGCFNLHAYC 342 (342)
Q Consensus 273 ~~~~~~C~~Cg~~GH~~c~~~~~~~~~~~~Cy~CG~~GH~~~dC~~~--~~~~~~~~~~~~~~~~~~~~~~~ 342 (342)
+.+...|..|+..=|+ ....|-+||..+++..-=-.. +++ ....+.-..|..||.|+
T Consensus 205 G~R~l~Cs~C~t~W~~----------~R~~C~~Cg~~~~l~y~~~e~~~~~~---~~~~~r~e~C~~C~~Yl 263 (309)
T 2fiy_A 205 GLRYLSCSLCACEWHY----------VRIKCSHCEESKHLAYLSLEHDGQPA---EKAVLRAETCPSCQGYL 263 (309)
T ss_dssp CEEEEEETTTCCEEEC----------CTTSCSSSCCCSCCEEECCCC-CCCS---TTCSEEEEEETTTTEEE
T ss_pred CcEEEEeCCCCCEEee----------cCcCCcCCCCCCCeeEEEecCccccC---CCcceEEEEcccccchH
Confidence 3346677777776666 246778888776543211000 000 11334456788888773
No 38
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=42.44 E-value=9.2 Score=30.75 Aligned_cols=39 Identities=33% Similarity=0.720 Sum_probs=21.8
Q ss_pred cccccccccC--------ccccc------ccccccCCCCcccccCCC---CccccCCC
Q 019350 181 QTCYNCGEEG--------HMAVN------CRSAVKRKKPCFVCGSLE---HGVRQCSK 221 (342)
Q Consensus 181 ~~C~~CG~~G--------H~a~~------Cp~~~~~~~~C~~CG~~G---H~~~~Cp~ 221 (342)
..|..|..-| |.-++ ||.. +...|-.||..| |..+-||.
T Consensus 37 ~~C~FCrnNGE~~~vy~SH~LKd~~G~V~CPvL--R~Y~CpiCGATGd~AHT~kYCP~ 92 (106)
T 3alr_A 37 KFCSFCKHNGETEAVYTSHYLKNRDGDVMCPYL--RQYKCPLCGATGAKAHTKRFCPM 92 (106)
T ss_dssp -CCHHHHHTTCCHHHHTSBCSBCTTSCBCCTTG--GGCCCTTTCCCGGGCCCGGGCTT
T ss_pred CEeECCCCCCcccCccccceeECCCCCCcCCCc--ccccCCCCCCcCCcccceecCCC
Confidence 4566666443 66665 6654 335566666655 55555554
No 39
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=40.70 E-value=7.8 Score=31.16 Aligned_cols=18 Identities=33% Similarity=0.678 Sum_probs=11.3
Q ss_pred ccccCCCCCC---ccCCCCCC
Q 019350 250 QVCLKCGDSG---HDMFSCRN 267 (342)
Q Consensus 250 ~~C~~CG~~G---H~a~dCp~ 267 (342)
..|-.||..| |..+-||.
T Consensus 72 Y~CpiCGATGd~AHT~kYCP~ 92 (106)
T 3alr_A 72 YKCPLCGATGAKAHTKRFCPM 92 (106)
T ss_dssp CCCTTTCCCGGGCCCGGGCTT
T ss_pred ccCCCCCCcCCcccceecCCC
Confidence 5666666666 66666664
No 40
>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=31.42 E-value=13 Score=24.98 Aligned_cols=21 Identities=24% Similarity=0.502 Sum_probs=15.4
Q ss_pred ccCccccCCCCCCccCCCCCC
Q 019350 247 QNAQVCLKCGDSGHDMFSCRN 267 (342)
Q Consensus 247 ~~~~~C~~CG~~GH~a~dCp~ 267 (342)
.....|..|...||+..+|+.
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 345789999999999998865
No 41
>2yuc_A TNF receptor-associated factor 4; ZF-TRAF, cysteine-rich domain associated with ring and TRAF domains protein 1, malignant 62; NMR {Homo sapiens}
Probab=30.54 E-value=1.3e+02 Score=21.29 Aligned_cols=16 Identities=31% Similarity=0.540 Sum_probs=7.5
Q ss_pred CCccccCCC-CccC-cccc
Q 019350 213 EHGVRQCSK-AQDC-FICK 229 (342)
Q Consensus 213 GH~~~~Cp~-~~~C-~~C~ 229 (342)
.|. ..|+- .+.| ..|+
T Consensus 7 ~H~-~~C~~~~v~C~~~C~ 24 (76)
T 2yuc_A 7 GHL-NTCSFNVIPCPNRCP 24 (76)
T ss_dssp CCC-CCCCCSCCBCTTCCS
T ss_pred HHH-HHCCCcccCCCcccc
Confidence 455 55553 2345 4453
No 42
>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1
Probab=23.00 E-value=4.6 Score=34.14 Aligned_cols=85 Identities=15% Similarity=0.187 Sum_probs=51.1
Q ss_pred ecCCCCCCCcchhhhhccchhhHHHHHHhhhhhhhhhh----------hcccchhhhhhhhhh---hhhhhccccccc--
Q 019350 89 VVPGPSGTTDDVIIEDVKSSDKKRIRVRKKKKKEADKI----------EIEDQSVIVRKEEQK---VETADNGDEGVT-- 153 (342)
Q Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~kk~~k~~~~~~----------~~e~q~v~~ia~ee~---le~~~~A~e~v~-- 153 (342)
.--||...+.... ...++.|+.||||+|.|+.+... .-|+..|.|.+.... ..++..|.+.+.
T Consensus 21 ~IiGPrG~t~K~i--e~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~~~~~~l~~A~~~I~~l 98 (140)
T 2bl5_A 21 RILGPRGLTAKQL--EAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKL 98 (140)
T ss_dssp HHTTTTHHHHHHH--HHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHHHHH
T ss_pred EEECCCcchHHHH--HHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchhhHHHHHHHHHHHHHHH
Confidence 3445554433333 34478999999999988654211 134456645542221 135666665555
Q ss_pred --cccchhHHHHHHhhCCCCCCCC
Q 019350 154 --TVEISDNIVLRKLLRGPRYFDP 175 (342)
Q Consensus 154 --~v~~~~n~~~r~~~r~~Ryf~~ 175 (342)
.++...+.+.+.+++....+++
T Consensus 99 L~p~~e~~de~K~~QL~eLA~lNG 122 (140)
T 2bl5_A 99 LVPAAEGEDSLKKMKLMELAILNG 122 (140)
T ss_dssp SSCCSSSSSHHHHHHHTGGGSSST
T ss_pred CCCCCcchhHHHHHHHHHHHHhcC
Confidence 3445678889999998887765
No 43
>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=20.06 E-value=68 Score=22.02 Aligned_cols=10 Identities=40% Similarity=0.813 Sum_probs=4.7
Q ss_pred ccccccCCCC
Q 019350 277 VQCYICRCFG 286 (342)
Q Consensus 277 ~~C~~Cg~~G 286 (342)
..|..|+..|
T Consensus 10 ~~C~vC~~~g 19 (56)
T 2yql_A 10 DFCSVCRKSG 19 (56)
T ss_dssp CSCSSSCCSS
T ss_pred CCCccCCCCC
Confidence 3455555444
Done!