Query 021122
Match_columns 317
No_of_seqs 250 out of 1655
Neff 5.9
Searched_HMMs 29240
Date Mon Mar 25 13:04:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021122.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/021122hhsearch_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 1.4E-25 4.8E-30 186.7 11.8 117 180-316 4-121 (124)
2 2lli_A Protein AIR2; RNA surve 99.7 2E-18 7E-23 143.4 8.2 59 181-243 23-85 (124)
3 3nyb_B Protein AIR2; polya RNA 99.5 7.4E-15 2.5E-19 114.4 3.1 54 223-289 6-59 (83)
4 3nyb_B Protein AIR2; polya RNA 99.4 1.2E-13 4.1E-18 107.6 4.1 59 206-269 8-66 (83)
5 2li8_A Protein LIN-28 homolog 99.2 1.6E-11 5.4E-16 93.6 5.3 41 223-268 25-65 (74)
6 2li8_A Protein LIN-28 homolog 99.2 2.5E-11 8.6E-16 92.5 4.8 54 231-289 2-59 (74)
7 1a1t_A Nucleocapsid protein; s 99.1 2.7E-11 9.1E-16 86.8 1.9 50 163-221 2-51 (55)
8 2a51_A Nucleocapsid protein; s 99.0 1.6E-10 5.3E-15 77.3 4.2 38 224-267 2-39 (39)
9 2a51_A Nucleocapsid protein; s 99.0 1.2E-10 4.1E-15 77.9 3.4 38 181-220 1-38 (39)
10 2bl6_A Nucleocapsid protein P1 98.9 4.2E-10 1.4E-14 74.4 3.5 36 224-267 2-37 (37)
11 2ec7_A GAG polyprotein (PR55GA 98.9 7.9E-10 2.7E-14 77.5 4.3 40 223-268 7-46 (49)
12 2ec7_A GAG polyprotein (PR55GA 98.9 6.3E-10 2.2E-14 78.0 3.6 39 181-221 7-45 (49)
13 2bl6_A Nucleocapsid protein P1 98.9 8.6E-10 2.9E-14 72.9 2.5 35 182-220 2-36 (37)
14 1cl4_A Protein (GAG polyprotei 98.8 8.7E-10 3E-14 80.2 2.6 47 223-269 2-50 (60)
15 2cqf_A RNA-binding protein LIN 98.8 2.5E-09 8.5E-14 78.8 4.9 41 181-241 8-48 (63)
16 2ihx_A Nucleocapsid (NC) prote 98.8 1.8E-09 6.2E-14 79.0 3.6 45 223-268 5-49 (61)
17 2ihx_A Nucleocapsid (NC) prote 98.8 1.7E-09 5.7E-14 79.2 3.4 46 181-242 5-50 (61)
18 1cl4_A Protein (GAG polyprotei 98.8 9E-10 3.1E-14 80.1 2.0 49 181-242 2-50 (60)
19 1a1t_A Nucleocapsid protein; s 98.8 2.1E-09 7.1E-14 76.9 3.2 40 223-268 13-52 (55)
20 2cqf_A RNA-binding protein LIN 98.8 4.8E-09 1.6E-13 77.3 4.7 43 222-269 7-49 (63)
21 3ts2_A Protein LIN-28 homolog 98.6 1.5E-08 5.1E-13 86.7 3.7 40 180-220 97-136 (148)
22 3ts2_A Protein LIN-28 homolog 98.6 2.5E-08 8.4E-13 85.3 3.1 42 223-269 98-139 (148)
23 1dsq_A Nucleic acid binding pr 97.6 1.9E-05 6.6E-10 48.0 1.5 19 181-199 3-21 (26)
24 1nc8_A Nucleocapsid protein; H 97.5 3.9E-05 1.3E-09 47.7 1.9 20 180-199 6-25 (29)
25 1dsq_A Nucleic acid binding pr 97.5 5.2E-05 1.8E-09 46.0 2.3 19 250-268 3-21 (26)
26 1a6b_B Momulv, zinc finger pro 97.4 4.9E-05 1.7E-09 51.0 2.1 21 179-199 9-29 (40)
27 1a6b_B Momulv, zinc finger pro 97.2 0.00024 8.4E-09 47.6 3.0 23 247-269 8-30 (40)
28 1u6p_A GAG polyprotein; MLV, A 97.1 0.00025 8.5E-09 50.9 3.0 23 177-199 20-42 (56)
29 1nc8_A Nucleocapsid protein; H 97.0 0.00034 1.2E-08 43.4 2.4 20 249-268 6-25 (29)
30 1u6p_A GAG polyprotein; MLV, A 96.8 0.00059 2E-08 48.9 2.8 23 247-269 21-43 (56)
31 2ysa_A Retinoblastoma-binding 96.8 0.00056 1.9E-08 48.9 2.2 20 180-199 7-26 (55)
32 2ysa_A Retinoblastoma-binding 96.5 0.00093 3.2E-08 47.7 1.9 20 249-268 7-26 (55)
33 2ysm_A Myeloid/lymphoid or mix 71.6 5.8 0.0002 31.0 5.1 13 250-262 23-35 (111)
34 2hqh_E Restin; beta/BETA struc 63.5 1.9 6.6E-05 25.9 0.5 16 183-198 6-21 (26)
35 2hqh_E Restin; beta/BETA struc 62.2 2.1 7.1E-05 25.7 0.5 18 250-267 4-21 (26)
36 2ysm_A Myeloid/lymphoid or mix 54.4 36 0.0012 26.3 6.7 32 251-294 56-87 (111)
37 1u57_A GAG polyprotein, HIV-1; 50.7 3.8 0.00013 27.7 0.4 14 159-172 33-46 (48)
38 3v43_A Histone acetyltransfera 44.2 12 0.00042 29.3 2.5 13 249-261 26-38 (112)
39 3alr_A Nanos protein; zinc-fin 38.7 11 0.00037 29.9 1.3 10 181-190 37-46 (106)
40 2yuc_A TNF receptor-associated 38.0 81 0.0028 22.2 6.0 16 213-229 7-24 (76)
41 2pzo_E CAP-Gly domain-containi 34.4 8.7 0.0003 25.5 0.1 19 222-240 20-38 (42)
42 3alr_A Nanos protein; zinc-fin 33.5 14 0.00048 29.3 1.1 18 250-267 72-92 (106)
43 2kwj_A Zinc finger protein DPF 32.3 32 0.0011 27.0 3.1 39 223-268 2-40 (114)
44 2bl5_A MGC83862 protein, quaki 30.7 4 0.00014 34.1 -2.6 75 99-173 29-120 (140)
45 3e2u_E CAP-Gly domain-containi 27.2 14 0.00049 24.5 0.2 19 222-240 20-38 (42)
46 1exk_A DNAJ protein; extended 25.8 56 0.0019 23.3 3.3 12 277-288 51-62 (79)
47 1weq_A PHD finger protein 7; s 23.4 1.1E+02 0.0039 23.1 4.6 36 275-311 45-81 (85)
48 2zjr_Z 50S ribosomal protein L 20.9 54 0.0018 23.2 2.2 11 275-285 29-39 (60)
49 2l5u_A Chromodomain-helicase-D 20.8 41 0.0014 23.4 1.6 47 249-310 11-59 (61)
No 1
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=99.93 E-value=1.4e-25 Score=186.71 Aligned_cols=117 Identities=28% Similarity=0.572 Sum_probs=94.6
Q ss_pred ccccccccccCcccccccccccCCCCcccccCC-CCCcccCCCCccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCC
Q 021122 180 WQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSL-EHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDS 258 (317)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~-GH~a~~Cp~~~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~ 258 (317)
...||+|++.||++++||.. .||+||+. ||++++||....||+|++.||++++||..+. ...||+|++.
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 35799999999999999985 89999998 9999999988899999999999999998653 4789999999
Q ss_pred CcCCCCCCCCCCCCCccCccccccCCCCcCcccCCCCCCCCCccccCCCCCCcccCCC
Q 021122 259 GHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLVS 316 (317)
Q Consensus 259 GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~C~~~~~~~~~~~~C~~Cg~~GH~~~d~ 316 (317)
||++++||..|+.|.+... .+-. .+.......+.||+||+.|||+.|+
T Consensus 74 GH~~~~Cp~~~~~y~~~~~-------~~~~---~~~~~~~~~~~Cy~Cg~~GH~a~dC 121 (124)
T 2lli_A 74 KHSKERCPSIWRAYILVDD-------NEKA---KPKVLPFHTIYCYNCGGKGHFGDDC 121 (124)
T ss_dssp CCCTTTCCCSTTSCCSSSC-------CCCC---CCSCCCCCCCCTTTTSSSCTTTTTS
T ss_pred CcchhhCCCccccccccCc-------cccc---cccccCCCCCCcCCCCCCCcCcccC
Confidence 9999999999976543210 0000 0011112468999999999999986
No 2
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=99.75 E-value=2e-18 Score=143.37 Aligned_cols=59 Identities=29% Similarity=0.706 Sum_probs=54.2
Q ss_pred ccccccccc-CcccccccccccCCCCcccccCCCCCcccCCCC---ccccccccCCCCCCCCCCCCC
Q 021122 181 QTCYNCGEE-GHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKA---QDCFICKKGGHRAKDCPDKHK 243 (317)
Q Consensus 181 ~~C~~CG~~-GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~~---~~C~~C~~~GH~ar~Cp~~~~ 243 (317)
..||+||+. ||++++||.. ..|++|++.||++++||.. ..|++|++.||++++||..+.
T Consensus 23 ~~C~~Cg~~~gH~~~~C~~~----~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~~~~Cp~~~~ 85 (124)
T 2lli_A 23 IICSYCGATDDHYSRHCPKA----IQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPSIWR 85 (124)
T ss_dssp CCCTTTCCTTTCCTTTGGGS----SCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCCTTTCCCSTT
T ss_pred CcCcCCCCcCCccCcccCCc----ccccccCCCCCccccCcCcccCccCCCCCcCCcchhhCCCccc
Confidence 479999999 9999999985 5799999999999999974 689999999999999999875
No 3
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=99.49 E-value=7.4e-15 Score=114.45 Aligned_cols=54 Identities=22% Similarity=0.448 Sum_probs=27.2
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCc
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLC 289 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~ 289 (317)
+.|++|++.||++++||+.+ .||+|+..||++++|+.+ ...++||+||+.|||+
T Consensus 6 ~~C~~Cg~~GH~~~~Cp~~~--------rcY~c~~~gh~~~~c~~p-----~~~~~CYnCG~~GH~~ 59 (83)
T 3nyb_B 6 VQCTLCKSKKHSKERCPSIW--------RAYILVDDNEKAKPKVLP-----FHTIYCYNCGGKGHFG 59 (83)
T ss_dssp -CCSSSCCSSSCGGGCGGGT--------CCCCBC------------------CCCBCSSSSCBSSCG
T ss_pred CCCCCCCCCCCccccCCCcc--------cccccccCCcccccccCC-----CCCCeecccCCCCcCc
Confidence 46777777777777777643 367777777777777543 2346677777777776
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=1.2e-13 Score=107.57 Aligned_cols=59 Identities=24% Similarity=0.493 Sum_probs=29.2
Q ss_pred cccccCCCCCcccCCCCccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCC
Q 021122 206 CFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSY 269 (317)
Q Consensus 206 C~~CG~~GH~a~~Cp~~~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~ 269 (317)
|++|++.||++++||....||+|+..||++++|+.+. ..+.||+||+.||+++|||...
T Consensus 8 C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p~-----~~~~CYnCG~~GH~~rdC~~~r 66 (83)
T 3nyb_B 8 CTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPF-----HTIYCYNCGGKGHFGDDCKEKR 66 (83)
T ss_dssp CSSSCCSSSCGGGCGGGTCCCCBC------------------CCCBCSSSSCBSSCGGGCSSCC
T ss_pred CCCCCCCCCccccCCCcccccccccCCcccccccCCC-----CCCeecccCCCCcCcccCCccc
Confidence 4444444444444443335677777777777776542 2477888888888888888754
No 5
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=99.19 E-value=1.6e-11 Score=93.62 Aligned_cols=41 Identities=27% Similarity=0.563 Sum_probs=29.0
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCC
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~ 268 (317)
..||+|++.||++++||.... ...||+|++.||++++||..
T Consensus 25 ~~C~~Cg~~GH~a~~C~~~~~-----~~~C~~Cg~~GH~ar~Cp~~ 65 (74)
T 2li8_A 25 DRCYNCGGLDHHAKECKLPPQ-----PKKCHFCQSISHMVASCPLK 65 (74)
T ss_dssp SCCTTTCCSSSCTTTCSSCCC-----CCCCTTTCCTTSCGGGCTTG
T ss_pred CcccccCCcCcCcccCCCCCC-----CCccCCcCCcCCccCcCcCC
Confidence 467777777777777775431 35777777777777777764
No 6
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=99.15 E-value=2.5e-11 Score=92.47 Aligned_cols=54 Identities=17% Similarity=0.450 Sum_probs=33.1
Q ss_pred CCCCCCCCCCCCCCC----CCCCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCc
Q 021122 231 GGHRAKDCPDKHKSG----FQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLC 289 (317)
Q Consensus 231 ~GH~ar~Cp~~~~~~----~~~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~ 289 (317)
.||++++|+.+..+. ......||+|++.||++++||... ....||+|++.||++
T Consensus 2 ~gh~~rdc~~~~~~~~~~~~~r~~~C~~Cg~~GH~a~~C~~~~-----~~~~C~~Cg~~GH~a 59 (74)
T 2li8_A 2 SGLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLPP-----QPKKCHFCQSISHMV 59 (74)
T ss_dssp ----------CCCCCCCSCCSTTSCCTTTCCSSSCTTTCSSCC-----CCCCCTTTCCTTSCG
T ss_pred CccccCcCCCCCcCccccccCCCCcccccCCcCcCcccCCCCC-----CCCccCCcCCcCCcc
Confidence 588888888765331 224567999999999999998642 346899999999998
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=99.08 E-value=2.7e-11 Score=86.83 Aligned_cols=50 Identities=42% Similarity=0.959 Sum_probs=34.7
Q ss_pred HhhhcCCCCCCCCCCcCccccccccccCcccccccccccCCCCcccccCCCCCcccCCC
Q 021122 163 LRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSK 221 (317)
Q Consensus 163 ~R~~~r~~r~f~~~~~~~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~ 221 (317)
++++|++++. ...||+||+.||++++||.+ +...||+||+.||++++||.
T Consensus 2 q~~~f~g~~~-------~~~C~~Cg~~GH~a~~C~~~--~~~~C~~Cg~~GH~~~~C~~ 51 (55)
T 1a1t_A 2 QKGNFRNQRK-------TVKCFNCGKEGHIAKNCRAP--RKKGCWKCGKEGHQMKDCTE 51 (55)
T ss_dssp CCGGGGGGGG-------TCBCTTTCCBSSCGGGCSSC--SCCBCTTTCCBSSCGGGCSS
T ss_pred CccccCCCCC-------CcceeeeCCCCcChhhcCCC--CCCEeCCCCCcCCccCCCcC
Confidence 3556666544 26799999999999999885 33456666666666666654
No 8
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=99.04 E-value=1.6e-10 Score=77.33 Aligned_cols=38 Identities=34% Similarity=0.859 Sum_probs=30.2
Q ss_pred cccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCC
Q 021122 224 DCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRN 267 (317)
Q Consensus 224 ~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~ 267 (317)
.||+|++.||++++||.+. ...||+|++.||++++||+
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 5888888888888888753 3678888888888888874
No 9
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=99.03 E-value=1.2e-10 Score=77.86 Aligned_cols=38 Identities=50% Similarity=1.109 Sum_probs=27.3
Q ss_pred cccccccccCcccccccccccCCCCcccccCCCCCcccCC
Q 021122 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCS 220 (317)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp 220 (317)
+.||+||+.||++++||.+ +...|++||+.||++++||
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 3699999999999999875 3345666666666666665
No 10
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=98.94 E-value=4.2e-10 Score=74.36 Aligned_cols=36 Identities=39% Similarity=0.944 Sum_probs=25.3
Q ss_pred cccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCC
Q 021122 224 DCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRN 267 (317)
Q Consensus 224 ~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~ 267 (317)
.||+|++.||++++||.+ ..||+|++.||++++||+
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 477777777777777753 467777777777777763
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=98.92 E-value=7.9e-10 Score=77.50 Aligned_cols=40 Identities=40% Similarity=0.896 Sum_probs=28.5
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCC
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~ 268 (317)
..||+|++.||++++||.+. ...||+|++.||++++||..
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 25678888888888888754
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=98.91 E-value=6.3e-10 Score=77.99 Aligned_cols=39 Identities=41% Similarity=1.069 Sum_probs=27.8
Q ss_pred cccccccccCcccccccccccCCCCcccccCCCCCcccCCC
Q 021122 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSK 221 (317)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~ 221 (317)
..||+||+.||++++||.+ +...||+||+.||++++||.
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 6799999999999999885 23456666666666666653
No 13
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=98.86 E-value=8.6e-10 Score=72.85 Aligned_cols=35 Identities=49% Similarity=1.145 Sum_probs=24.0
Q ss_pred ccccccccCcccccccccccCCCCcccccCCCCCcccCC
Q 021122 182 TCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCS 220 (317)
Q Consensus 182 ~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp 220 (317)
.||+||+.||++++||.+ ..|++||+.||++++||
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 478888888888888764 35666666666666665
No 14
>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=98.85 E-value=8.7e-10 Score=80.22 Aligned_cols=47 Identities=28% Similarity=0.630 Sum_probs=18.3
Q ss_pred ccccccccCCCCCCCCCCCCCCC--CCCCcccCCCCCCCcCCCCCCCCC
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSG--FQNAQVCLKCGDSGHDMFSCRNSY 269 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~--~~~~~~C~~Cg~~GH~a~dCp~~~ 269 (317)
..||+|++.||++++||...... ......||+|++.||++++||...
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 35888888888888888754211 012468999999999999999764
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=98.84 E-value=2.5e-09 Score=78.82 Aligned_cols=41 Identities=34% Similarity=0.849 Sum_probs=28.2
Q ss_pred cccccccccCcccccccccccCCCCcccccCCCCCcccCCCCccccccccCCCCCCCCCCC
Q 021122 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDK 241 (317)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~~~~C~~C~~~GH~ar~Cp~~ 241 (317)
..||+|++.||++++||.+ .. ...||+|++.||++++||..
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 5688888888888888874 11 24566666666666666654
No 16
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=98.83 E-value=1.8e-09 Score=78.97 Aligned_cols=45 Identities=36% Similarity=0.839 Sum_probs=28.1
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCC
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~ 268 (317)
..||+|++.||++++||.....+ .....||+|++.||++++||..
T Consensus 5 ~~C~~Cg~~GH~a~~C~~~~~~~-~~~~~C~~Cg~~GH~ar~C~~~ 49 (61)
T 2ihx_A 5 GLCYTCGSPGHYQAQCPKKRKSG-NSRERCQLCNGMGHNAKQCRKR 49 (61)
T ss_dssp TBCSSSCCBTCCGGGCTTTTSSS-CCCSBCTTTCCBSSCGGGCCCC
T ss_pred CcccccCCCCeehhhCcCCcCCC-CCCCeeCCCCCCCCCcCCCcCC
Confidence 45666666677777776653211 1235677777777777777754
No 17
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=98.83 E-value=1.7e-09 Score=79.18 Aligned_cols=46 Identities=33% Similarity=0.821 Sum_probs=33.6
Q ss_pred cccccccccCcccccccccccCCCCcccccCCCCCcccCCCCccccccccCCCCCCCCCCCC
Q 021122 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKH 242 (317)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~~~~C~~C~~~GH~ar~Cp~~~ 242 (317)
..||+|++.||++++||.+.... .....||+|++.||++++||...
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 57999999999999999862211 11356777888888888887754
No 18
>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=98.83 E-value=9e-10 Score=80.15 Aligned_cols=49 Identities=33% Similarity=0.783 Sum_probs=17.2
Q ss_pred cccccccccCcccccccccccCCCCcccccCCCCCcccCCCCccccccccCCCCCCCCCCCC
Q 021122 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKH 242 (317)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~~~~C~~C~~~GH~ar~Cp~~~ 242 (317)
..||+|++.||++++||....... .......||+|++.||++++||+..
T Consensus 2 ~~Cf~Cg~~GH~a~~C~~~~~~~~-------------~~~~~~~C~~Cg~~GH~ar~C~~~~ 50 (60)
T 1cl4_A 2 GSCFKCGKKGHFAKNCHEHAHNNA-------------EPKVPGLCPRCKRGKHWANECKSKT 50 (60)
T ss_dssp ----------------------------------------CCCSCSSCSSCSSCSTTCCCTT
T ss_pred CccccCCCCCcCHhhCcCCCCCcc-------------ccCCCcceeECCCCCCccCcCCCcc
Confidence 469999999999999998621110 0112357888888888888888765
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=98.80 E-value=2.1e-09 Score=76.88 Aligned_cols=40 Identities=43% Similarity=0.944 Sum_probs=26.4
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCC
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~ 268 (317)
..||+|++.||++++||.+. ...||+|++.||++++||..
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 45666666666666666542 25677777777777777753
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=98.78 E-value=4.8e-09 Score=77.26 Aligned_cols=43 Identities=26% Similarity=0.518 Sum_probs=36.5
Q ss_pred CccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCC
Q 021122 222 AQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSY 269 (317)
Q Consensus 222 ~~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~ 269 (317)
...||+|++.||++++||.+. ....||+|++.||++++||...
T Consensus 7 ~~~C~~Cg~~GH~a~~C~~~~-----~~~~C~~Cg~~GH~ar~Cp~~~ 49 (63)
T 2cqf_A 7 GDRCYNCGGLDHHAKECKLPP-----QPKKCHFCQSISHMVASCPLKA 49 (63)
T ss_dssp CCCCSSSCCSSSCTTTCCSCC-----CSSCCTTTCCSSSCTTTCTGGG
T ss_pred CCcccccCCCCcChhhCCCCC-----CCCccCCcCCcCCccCcCCCcc
Confidence 357999999999999999753 2478999999999999999754
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=98.63 E-value=1.5e-08 Score=86.67 Aligned_cols=40 Identities=38% Similarity=0.844 Sum_probs=27.3
Q ss_pred ccccccccccCcccccccccccCCCCcccccCCCCCcccCC
Q 021122 180 WQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCS 220 (317)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp 220 (317)
...||+||+.||++++||.+ .....|++||+.||++++||
T Consensus 97 ~~~C~~Cg~~GH~a~~C~~~-~~~~~C~~Cg~~GH~~r~Cp 136 (148)
T 3ts2_A 97 GDRCYNCGGLDHHAKECKLP-PQPKKCHFCQSINHMVASCP 136 (148)
T ss_dssp SCCCTTTCCSSCCGGGCCSC-CCCCCCTTTCCSSCCGGGCT
T ss_pred CCcccEeCCccchhhhCCCC-CCCCcccccCCcCCEeccCc
Confidence 47799999999999999985 22334555555555555554
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=98.55 E-value=2.5e-08 Score=85.29 Aligned_cols=42 Identities=26% Similarity=0.532 Sum_probs=30.5
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCC
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSY 269 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~ 269 (317)
..||+|++.||++++||.+.. ...||+|++.||++++||+..
T Consensus 98 ~~C~~Cg~~GH~a~~C~~~~~-----~~~C~~Cg~~GH~~r~Cp~~~ 139 (148)
T 3ts2_A 98 DRCYNCGGLDHHAKECKLPPQ-----PKKCHFCQSINHMVASCPLKA 139 (148)
T ss_dssp CCCTTTCCSSCCGGGCCSCCC-----CCCCTTTCCSSCCGGGCTTTT
T ss_pred CcccEeCCccchhhhCCCCCC-----CCcccccCCcCCEeccCcCCC
Confidence 467777777777777776432 357888888888888888653
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=97.60 E-value=1.9e-05 Score=47.98 Aligned_cols=19 Identities=32% Similarity=1.153 Sum_probs=17.2
Q ss_pred cccccccccCccccccccc
Q 021122 181 QTCYNCGEEGHMAVNCRSA 199 (317)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~ 199 (317)
..||+||+.||++++||.+
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 5799999999999999986
No 24
>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=97.48 E-value=3.9e-05 Score=47.74 Aligned_cols=20 Identities=50% Similarity=1.124 Sum_probs=18.0
Q ss_pred ccccccccccCccccccccc
Q 021122 180 WQTCYNCGEEGHMAVNCRSA 199 (317)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~ 199 (317)
.+.||+||++||++++|+.+
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 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=97.48 E-value=5.2e-05 Score=46.03 Aligned_cols=19 Identities=37% Similarity=0.997 Sum_probs=15.1
Q ss_pred cccCCCCCCCcCCCCCCCC
Q 021122 250 QVCLKCGDSGHDMFSCRNS 268 (317)
Q Consensus 250 ~~C~~Cg~~GH~a~dCp~~ 268 (317)
..||+||+.||++++||..
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 5688888888888888764
No 26
>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=4.9e-05 Score=50.99 Aligned_cols=21 Identities=33% Similarity=0.751 Sum_probs=18.8
Q ss_pred CccccccccccCccccccccc
Q 021122 179 GWQTCYNCGEEGHMAVNCRSA 199 (317)
Q Consensus 179 ~~~~C~~CG~~GH~a~~Cp~~ 199 (317)
....||+||+.|||+++||.+
T Consensus 9 ~~~~C~~Cgk~GH~ardCP~~ 29 (40)
T 1a6b_B 9 DRDQCAYCKEKGHWAKDCPKK 29 (40)
T ss_dssp CSSSCSSSCCTTCCTTSCSSS
T ss_pred CCCeeeECCCCCcchhhCcCC
Confidence 457899999999999999986
No 27
>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=97.16 E-value=0.00024 Score=47.56 Aligned_cols=23 Identities=22% Similarity=0.481 Sum_probs=18.8
Q ss_pred CCCcccCCCCCCCcCCCCCCCCC
Q 021122 247 QNAQVCLKCGDSGHDMFSCRNSY 269 (317)
Q Consensus 247 ~~~~~C~~Cg~~GH~a~dCp~~~ 269 (317)
.....||+|++.|||+++||...
T Consensus 8 ~~~~~C~~Cgk~GH~ardCP~~~ 30 (40)
T 1a6b_B 8 LDRDQCAYCKEKGHWAKDCPKKP 30 (40)
T ss_dssp CCSSSCSSSCCTTCCTTSCSSSC
T ss_pred CCCCeeeECCCCCcchhhCcCCc
Confidence 34578999999999999999754
No 28
>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=97.13 E-value=0.00025 Score=50.93 Aligned_cols=23 Identities=30% Similarity=0.667 Sum_probs=19.9
Q ss_pred CcCccccccccccCccccccccc
Q 021122 177 DRGWQTCYNCGEEGHMAVNCRSA 199 (317)
Q Consensus 177 ~~~~~~C~~CG~~GH~a~~Cp~~ 199 (317)
......||+||+.|||+++||..
T Consensus 20 ~~~~~~C~~Cge~GH~ardCp~~ 42 (56)
T 1u6p_A 20 QLDRDQCAYCKEKGHWAKDCPKK 42 (56)
T ss_dssp TCCTTBCSSSCCBSSCGGGCTTC
T ss_pred CCCCCcceeCCCCCcccccCcCC
Confidence 34567899999999999999986
No 29
>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=97.01 E-value=0.00034 Score=43.38 Aligned_cols=20 Identities=35% Similarity=0.871 Sum_probs=13.5
Q ss_pred CcccCCCCCCCcCCCCCCCC
Q 021122 249 AQVCLKCGDSGHDMFSCRNS 268 (317)
Q Consensus 249 ~~~C~~Cg~~GH~a~dCp~~ 268 (317)
...||+||+.||++++|+.+
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 35677777777777777654
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=96.84 E-value=0.00059 Score=48.94 Aligned_cols=23 Identities=22% Similarity=0.481 Sum_probs=16.1
Q ss_pred CCCcccCCCCCCCcCCCCCCCCC
Q 021122 247 QNAQVCLKCGDSGHDMFSCRNSY 269 (317)
Q Consensus 247 ~~~~~C~~Cg~~GH~a~dCp~~~ 269 (317)
.....||+||+.|||+++||...
T Consensus 21 ~~~~~C~~Cge~GH~ardCp~~~ 43 (56)
T 1u6p_A 21 LDRDQCAYCKEKGHWAKDCPKKP 43 (56)
T ss_dssp CCTTBCSSSCCBSSCGGGCTTCC
T ss_pred CCCCcceeCCCCCcccccCcCCc
Confidence 33566888888888888887643
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=96.77 E-value=0.00056 Score=48.89 Aligned_cols=20 Identities=40% Similarity=0.966 Sum_probs=16.6
Q ss_pred ccccccccccCccccccccc
Q 021122 180 WQTCYNCGEEGHMAVNCRSA 199 (317)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~ 199 (317)
...||+||+.|||+++||..
T Consensus 7 ~~~C~kCGk~GH~~k~Cp~~ 26 (55)
T 2ysa_A 7 GYTCFRCGKPGHYIKNCPTN 26 (55)
T ss_dssp SCCCTTTCCTTSCGGGCSGG
T ss_pred CCccccCCCcCcccccCCCC
Confidence 35699999999999999854
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=96.52 E-value=0.00093 Score=47.75 Aligned_cols=20 Identities=30% Similarity=0.931 Sum_probs=17.9
Q ss_pred CcccCCCCCCCcCCCCCCCC
Q 021122 249 AQVCLKCGDSGHDMFSCRNS 268 (317)
Q Consensus 249 ~~~C~~Cg~~GH~a~dCp~~ 268 (317)
...||+||+.||++++||..
T Consensus 7 ~~~C~kCGk~GH~~k~Cp~~ 26 (55)
T 2ysa_A 7 GYTCFRCGKPGHYIKNCPTN 26 (55)
T ss_dssp SCCCTTTCCTTSCGGGCSGG
T ss_pred CCccccCCCcCcccccCCCC
Confidence 57899999999999999953
No 33
>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=71.65 E-value=5.8 Score=31.05 Aligned_cols=13 Identities=38% Similarity=0.846 Sum_probs=7.4
Q ss_pred cccCCCCCCCcCC
Q 021122 250 QVCLKCGDSGHDM 262 (317)
Q Consensus 250 ~~C~~Cg~~GH~a 262 (317)
..|..|++..|..
T Consensus 23 l~C~~C~~~~H~~ 35 (111)
T 2ysm_A 23 FFCTTCGQHYHGM 35 (111)
T ss_dssp EECSSSCCEECTT
T ss_pred eECCCCCCCcChH
Confidence 4566666655553
No 34
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=63.51 E-value=1.9 Score=25.86 Aligned_cols=16 Identities=44% Similarity=0.852 Sum_probs=13.8
Q ss_pred cccccccCcccccccc
Q 021122 183 CYNCGEEGHMAVNCRS 198 (317)
Q Consensus 183 C~~CG~~GH~a~~Cp~ 198 (317)
|-.|..+||+..+|+.
T Consensus 6 Ce~CE~FGH~t~~C~d 21 (26)
T 2hqh_E 6 CEICEMFGHWATNCND 21 (26)
T ss_dssp ETTTTEESSCGGGCCT
T ss_pred chHHHHhCcccccCCc
Confidence 8889999999999865
No 35
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=62.16 E-value=2.1 Score=25.73 Aligned_cols=18 Identities=28% Similarity=0.549 Sum_probs=12.7
Q ss_pred cccCCCCCCCcCCCCCCC
Q 021122 250 QVCLKCGDSGHDMFSCRN 267 (317)
Q Consensus 250 ~~C~~Cg~~GH~a~dCp~ 267 (317)
..|-.|...||+..+|+.
T Consensus 4 pYCe~CE~FGH~t~~C~d 21 (26)
T 2hqh_E 4 PYCEICEMFGHWATNCND 21 (26)
T ss_dssp CEETTTTEESSCGGGCCT
T ss_pred ccchHHHHhCcccccCCc
Confidence 467777777777777754
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=54.37 E-value=36 Score=26.33 Aligned_cols=32 Identities=34% Similarity=0.629 Sum_probs=23.0
Q ss_pred ccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCcccCCC
Q 021122 251 VCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNIS 294 (317)
Q Consensus 251 ~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~C~~~~ 294 (317)
.|..|++.++. ...+.|..|...=|+.|-.|+
T Consensus 56 ~C~~C~~~~~~------------~~ll~Cd~C~~~yH~~Cl~pp 87 (111)
T 2ysm_A 56 VCQNCKQSGED------------SKMLVCDTCDKGYHTFCLQPV 87 (111)
T ss_dssp CCTTTCCCSCC------------TTEEECSSSCCEEEGGGSSSC
T ss_pred cccccCccCCC------------CCeeECCCCCcHHhHHhcCCc
Confidence 57777776541 245789999999999986653
No 37
>1u57_A GAG polyprotein, HIV-1; particle assembly, viral protein; NMR {Human immunodeficiency virus 1}
Probab=50.65 E-value=3.8 Score=27.70 Aligned_cols=14 Identities=21% Similarity=0.235 Sum_probs=11.0
Q ss_pred hhHHHhhhcCCCCC
Q 021122 159 DNIVLRKLLRGPRY 172 (317)
Q Consensus 159 ~n~~~R~~~r~~r~ 172 (317)
.++++|++|+++|.
T Consensus 33 ~immqr~nf~g~rk 46 (48)
T 1u57_A 33 TIMMQRGNFRNQRK 46 (48)
T ss_dssp HHHHHTTTTTTCSS
T ss_pred chhhhcccccCCCC
Confidence 45788999998865
No 38
>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A
Probab=44.16 E-value=12 Score=29.34 Aligned_cols=13 Identities=46% Similarity=1.053 Sum_probs=7.4
Q ss_pred CcccCCCCCCCcC
Q 021122 249 AQVCLKCGDSGHD 261 (317)
Q Consensus 249 ~~~C~~Cg~~GH~ 261 (317)
-+.|..|+...|.
T Consensus 26 Ll~C~~C~~~~H~ 38 (112)
T 3v43_A 26 LISCADCGNSGHP 38 (112)
T ss_dssp CEECTTTCCEECH
T ss_pred ceEhhhcCCCCCC
Confidence 3456666666664
No 39
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=38.71 E-value=11 Score=29.95 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=4.5
Q ss_pred cccccccccC
Q 021122 181 QTCYNCGEEG 190 (317)
Q Consensus 181 ~~C~~CG~~G 190 (317)
..|-.|..-|
T Consensus 37 ~~C~FCrnNG 46 (106)
T 3alr_A 37 KFCSFCKHNG 46 (106)
T ss_dssp -CCHHHHHTT
T ss_pred CEeECCCCCC
Confidence 3455555433
No 40
>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=38.00 E-value=81 Score=22.17 Aligned_cols=16 Identities=31% Similarity=0.540 Sum_probs=7.6
Q ss_pred CCCcccCCC-Cccc-cccc
Q 021122 213 EHGVRQCSK-AQDC-FICK 229 (317)
Q Consensus 213 GH~a~~Cp~-~~~C-~~C~ 229 (317)
.|. ..|+. .+.| ..|+
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 55653 2345 4453
No 41
>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=34.43 E-value=8.7 Score=25.54 Aligned_cols=19 Identities=42% Similarity=0.791 Sum_probs=13.3
Q ss_pred CccccccccCCCCCCCCCC
Q 021122 222 AQDCFICKKGGHRAKDCPD 240 (317)
Q Consensus 222 ~~~C~~C~~~GH~ar~Cp~ 240 (317)
...|-+|...||++.+|+.
T Consensus 20 RpYCd~CEvFGH~t~~Cnd 38 (42)
T 2pzo_E 20 RPYCEICEMFGHWATNCND 38 (42)
T ss_dssp -CEETTTTEESSCGGGCCT
T ss_pred CcccccccccCcccccCCc
Confidence 4577777777777777764
No 42
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=33.48 E-value=14 Score=29.32 Aligned_cols=18 Identities=33% Similarity=0.678 Sum_probs=8.6
Q ss_pred cccCCCCCCC---cCCCCCCC
Q 021122 250 QVCLKCGDSG---HDMFSCRN 267 (317)
Q Consensus 250 ~~C~~Cg~~G---H~a~dCp~ 267 (317)
..|-.||..| |..+=||.
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 4455555444 44444543
No 43
>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*
Probab=32.32 E-value=32 Score=27.03 Aligned_cols=39 Identities=28% Similarity=0.600 Sum_probs=21.6
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCC
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~ 268 (317)
..|..|...+.. +...+....-+.|..|+...|.. |-..
T Consensus 2 ~~C~~C~~~~~~-----n~k~g~~~~Li~C~~C~~~~H~~--Cl~~ 40 (114)
T 2kwj_A 2 SYCDFCLGGSNM-----NKKSGRPEELVSCADCGRSGHPT--CLQF 40 (114)
T ss_dssp CCCSSSCCBTTB-----CTTTCCCCCCEECSSSCCEECTT--TTTC
T ss_pred CcCccCCCCccc-----cccCCCCCCCeEeCCCCCccchh--hCCC
Confidence 356667554431 11222223456788888888875 7543
No 44
>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1
Probab=30.72 E-value=4 Score=34.06 Aligned_cols=75 Identities=12% Similarity=0.081 Sum_probs=46.5
Q ss_pred chhhhhccchhhHHHHHHhhhhhhhhhh----------cccccceEEeechhh---hhhhccCccccc----cccchhhH
Q 021122 99 DVIIEDVKSSDKKRIRVRKKKKKEADKI----------EIEDQSVIVRKEEQK---VETADNGDEGVT----TVEISDNI 161 (317)
Q Consensus 99 ~~~~~~~k~~~~~~~~~kk~~k~~~~k~----------~i~~q~v~via~ee~---lee~~~A~e~v~----~~~~~~n~ 161 (317)
+..-.+..++.|+.|||+++.|+.+... .-++.+|.|.+...+ ..++..|.+.|. .++..++.
T Consensus 29 t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~~~~~~l~~A~~~I~~lL~p~~e~~de 108 (140)
T 2bl5_A 29 TAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDS 108 (140)
T ss_dssp HHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHHHHHSSCCSSSSSH
T ss_pred hHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchhhHHHHHHHHHHHHHHHCCCCCcchhH
Confidence 4444566689999999999887654211 123347877775321 125555655554 44556778
Q ss_pred HHhhhcCCCCCC
Q 021122 162 VLRKLLRGPRYF 173 (317)
Q Consensus 162 ~~R~~~r~~r~f 173 (317)
+.+.+++.....
T Consensus 109 ~K~~QL~eLA~l 120 (140)
T 2bl5_A 109 LKKMKLMELAIL 120 (140)
T ss_dssp HHHHHHTGGGSS
T ss_pred HHHHHHHHHHHh
Confidence 888888876544
No 45
>3e2u_E CAP-Gly domain-containing linker protein 1; structural protein microtubule binding, dynactin, cytoskelet associated protein, P150glued; 2.60A {Homo sapiens}
Probab=27.20 E-value=14 Score=24.53 Aligned_cols=19 Identities=42% Similarity=0.791 Sum_probs=13.7
Q ss_pred CccccccccCCCCCCCCCC
Q 021122 222 AQDCFICKKGGHRAKDCPD 240 (317)
Q Consensus 222 ~~~C~~C~~~GH~ar~Cp~ 240 (317)
...|-+|...||+..+|+.
T Consensus 20 RpYCe~CEVFGH~t~eC~d 38 (42)
T 3e2u_E 20 RPYCEICEMFGHWATNCND 38 (42)
T ss_dssp CCEETTTTEESSCGGGCCT
T ss_pred CcccccceecccccccCCc
Confidence 4567777777777777765
No 46
>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} SCOP: g.54.1.1
Probab=25.76 E-value=56 Score=23.35 Aligned_cols=12 Identities=33% Similarity=0.634 Sum_probs=6.8
Q ss_pred ccccccCCCCcC
Q 021122 277 VQCYICRCFGHL 288 (317)
Q Consensus 277 ~~C~~Cg~~GHl 288 (317)
..|..|+..|.+
T Consensus 51 ~~C~~C~G~G~~ 62 (79)
T 1exk_A 51 QTCPHCQGRGTL 62 (79)
T ss_dssp EECTTTTTSSEE
T ss_pred eECcCCCCccEE
Confidence 356666666654
No 47
>1weq_A PHD finger protein 7; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2
Probab=23.40 E-value=1.1e+02 Score=23.11 Aligned_cols=36 Identities=19% Similarity=0.469 Sum_probs=24.6
Q ss_pred cCccccccCCCC-cCcccCCCCCCCCCccccCCCCCCc
Q 021122 275 KEVQCYICRCFG-HLCCVNISDAVPGEVSCFRCGQLGH 311 (317)
Q Consensus 275 ~~~~C~~Cg~~G-Hl~C~~~~~~~~~~~~C~~Cg~~GH 311 (317)
..+.|..||..| |+.|...+. -+..-.|..|-..+-
T Consensus 45 ~L~lC~~Cgs~gtH~~Cs~l~~-~~~~weC~~C~~v~~ 81 (85)
T 1weq_A 45 RLILCATCGSHGTHRDCSSLRP-NSKKWECNECLPASG 81 (85)
T ss_dssp BCEECSSSCCCEECSGGGTCCT-TCSCCCCTTTSCCSS
T ss_pred EEEeCcccCCchhHHHHhCCcC-CCCCEECCcCccccC
Confidence 467899999998 988875432 234567777765543
No 48
>2zjr_Z 50S ribosomal protein L32; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: g.41.8.5 PDB: 1j5a_M* 1jzy_M* 1jzz_M* 1k01_M* 1nkw_Z 1ond_Z* 1sm1_Z* 1yl3_5 2b66_5 2b9n_5 2b9p_5 2zjp_Y* 2zjq_Z 1jzx_M 3cf5_Y* 3dll_Y* 3pio_Z* 3pip_Z* 1nwy_Z* 1nwx_Z* ...
Probab=20.90 E-value=54 Score=23.20 Aligned_cols=11 Identities=18% Similarity=0.395 Sum_probs=6.8
Q ss_pred cCccccccCCC
Q 021122 275 KEVQCYICRCF 285 (317)
Q Consensus 275 ~~~~C~~Cg~~ 285 (317)
..+.|.+||+.
T Consensus 29 ~l~~c~~cG~~ 39 (60)
T 2zjr_Z 29 NLTECPQCHGK 39 (60)
T ss_dssp CCEECTTTCCE
T ss_pred CceECCCCCCE
Confidence 34567777665
No 49
>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}
Probab=20.84 E-value=41 Score=23.42 Aligned_cols=47 Identities=28% Similarity=0.631 Sum_probs=30.1
Q ss_pred CcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCcccCCC--CCCCCCccccCCCCCC
Q 021122 249 AQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNIS--DAVPGEVSCFRCGQLG 310 (317)
Q Consensus 249 ~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~C~~~~--~~~~~~~~C~~Cg~~G 310 (317)
...|..|+..|. .+.|-.|...=|+.|-.++ ......-+|..|-..|
T Consensus 11 ~~~C~vC~~~g~---------------ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~g 59 (61)
T 2l5u_A 11 QDYCEVCQQGGE---------------IILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKEG 59 (61)
T ss_dssp CSSCTTTSCCSS---------------EEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGGS
T ss_pred CCCCccCCCCCc---------------EEECCCCChhhhhhccCCCCCCCCCCceECccccccc
Confidence 467888877532 3567778776688876553 2223567888887654
Done!