Query 030616
Match_columns 174
No_of_seqs 191 out of 1599
Neff 7.3
Searched_HMMs 29240
Date Tue Mar 26 02:54:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030616.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/030616hhsearch_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 100.0 3.2E-28 1.1E-32 179.2 12.2 116 8-143 4-123 (124)
2 2lli_A Protein AIR2; RNA surve 100.0 1.3E-28 4.4E-33 181.3 9.1 100 33-164 3-124 (124)
3 3nyb_B Protein AIR2; polya RNA 99.7 8.9E-18 3.1E-22 115.2 3.0 59 73-165 6-66 (83)
4 3nyb_B Protein AIR2; polya RNA 99.5 5.7E-15 1.9E-19 101.2 4.9 61 34-94 5-68 (83)
5 2li8_A Protein LIN-28 homolog 99.5 5.8E-15 2E-19 99.1 4.7 64 81-166 2-67 (74)
6 2li8_A Protein LIN-28 homolog 99.5 4E-14 1.4E-18 95.0 4.1 54 17-70 2-63 (74)
7 2a51_A Nucleocapsid protein; s 99.4 1.6E-13 5.4E-18 81.1 3.8 38 126-163 1-39 (39)
8 2ec7_A GAG polyprotein (PR55GA 99.3 6.5E-13 2.2E-17 82.2 4.0 42 125-166 6-48 (49)
9 2bl6_A Nucleocapsid protein P1 99.3 4.3E-13 1.5E-17 78.3 2.8 36 127-163 2-37 (37)
10 2cqf_A RNA-binding protein LIN 99.3 1.6E-12 5.5E-17 84.5 5.0 44 125-168 7-52 (63)
11 1a1t_A Nucleocapsid protein; s 99.3 6.7E-13 2.3E-17 84.0 2.8 45 122-166 9-54 (55)
12 2ihx_A Nucleocapsid (NC) prote 99.3 9.2E-13 3.1E-17 85.1 3.1 42 125-166 4-51 (61)
13 1cl4_A Protein (GAG polyprotei 99.3 1.4E-12 4.9E-17 83.8 2.7 41 126-166 2-51 (60)
14 2a51_A Nucleocapsid protein; s 99.3 3.9E-12 1.3E-16 75.0 3.9 39 9-52 1-39 (39)
15 2ihx_A Nucleocapsid (NC) prote 99.2 1.3E-11 4.4E-16 79.7 4.3 20 8-27 4-23 (61)
16 2bl6_A Nucleocapsid protein P1 99.2 9.6E-12 3.3E-16 72.4 3.2 35 10-51 2-36 (37)
17 2ec7_A GAG polyprotein (PR55GA 99.2 2.3E-11 7.7E-16 75.2 4.4 40 8-52 6-45 (49)
18 2cqf_A RNA-binding protein LIN 99.1 6.2E-11 2.1E-15 77.0 4.6 40 9-52 8-47 (63)
19 1a1t_A Nucleocapsid protein; s 99.1 6.3E-11 2.2E-15 74.7 3.3 36 35-70 13-50 (55)
20 1cl4_A Protein (GAG polyprotei 99.0 5.7E-11 2E-15 76.2 1.9 18 10-27 3-20 (60)
21 3ts2_A Protein LIN-28 homolog 99.0 3.5E-10 1.2E-14 85.2 3.8 43 125-167 97-141 (148)
22 3ts2_A Protein LIN-28 homolog 98.8 4.3E-09 1.5E-13 79.2 3.8 37 34-70 97-136 (148)
23 1dsq_A Nucleic acid binding pr 98.2 6.7E-07 2.3E-11 47.7 2.0 20 146-165 3-22 (26)
24 1a6b_B Momulv, zinc finger pro 98.2 1.5E-06 5E-11 51.1 3.2 18 126-143 11-28 (40)
25 1dsq_A Nucleic acid binding pr 98.0 3.2E-06 1.1E-10 45.0 2.4 21 8-28 2-22 (26)
26 1nc8_A Nucleocapsid protein; H 97.9 3E-06 1E-10 46.3 1.7 19 126-144 7-25 (29)
27 1nc8_A Nucleocapsid protein; H 97.8 9.5E-06 3.2E-10 44.2 2.1 21 8-28 6-26 (29)
28 1u6p_A GAG polyprotein; MLV, A 97.8 9.9E-06 3.4E-10 51.0 2.3 20 124-143 22-41 (56)
29 1a6b_B Momulv, zinc finger pro 97.8 2.4E-05 8.3E-10 45.9 3.6 22 8-29 10-31 (40)
30 2ysa_A Retinoblastoma-binding 97.4 6.8E-05 2.3E-09 46.9 2.4 18 126-143 8-25 (55)
31 1u6p_A GAG polyprotein; MLV, A 97.4 0.00011 3.8E-09 46.1 3.1 28 144-171 22-49 (56)
32 2ysa_A Retinoblastoma-binding 97.1 0.00021 7.1E-09 44.7 1.9 22 6-27 5-26 (55)
33 2hqh_E Restin; beta/BETA struc 66.0 1.8 6.3E-05 22.4 0.7 18 73-90 4-21 (26)
34 2yuc_A TNF receptor-associated 65.2 22 0.00075 22.1 6.1 33 133-166 32-71 (76)
35 3alr_A Nanos protein; zinc-fin 45.7 13 0.00044 25.7 2.4 19 74-92 73-94 (106)
36 3alr_A Nanos protein; zinc-fin 42.5 12 0.00042 25.8 1.9 43 125-167 36-96 (106)
37 2ysm_A Myeloid/lymphoid or mix 38.2 64 0.0022 21.7 5.2 28 34-65 7-34 (111)
38 2pzo_E CAP-Gly domain-containi 37.2 10 0.00035 21.8 0.7 19 72-90 20-38 (42)
39 3e2u_E CAP-Gly domain-containi 25.6 23 0.00077 20.4 0.8 18 73-90 21-38 (42)
No 1
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=99.95 E-value=3.2e-28 Score=179.18 Aligned_cols=116 Identities=24% Similarity=0.635 Sum_probs=90.0
Q ss_pred CCCCccCCCCCcCcCCCCCCccCCCCcccccccCCC-CCCCccccCcccccccccCCccccCCCCC---ccccccccCCC
Q 030616 8 EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKP-GHIAADCTNDKACKNCRKTGHIARDCQNE---PVCNLCNIAGH 83 (174)
Q Consensus 8 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~C~~~-GH~~~~C~~~~~C~~Cg~~GH~~~~Cp~~---~~C~~C~~~GH 83 (174)
...||+|+++||++++||.. +||+|+++ ||++.+||..+.|++|++.||++++||+. ..|++|++.||
T Consensus 4 ~~~C~~C~~~GH~~~~Cp~~--------~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH 75 (124)
T 2lli_A 4 APKCNNCSQRGHLKKDCPHI--------ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKH 75 (124)
T ss_dssp SSCCSSCSSSSCCTTTTTSC--------CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCC
T ss_pred CCcccCCCCCCcCcccCcCC--------cCcCCCCcCCccCcccCCcccccccCCCCCccccCcCcccCccCCCCCcCCc
Confidence 46899999999999999984 89999999 99999999988999999999999999975 68999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccccCCCCCCCCCCCCC
Q 030616 84 VARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG 143 (174)
Q Consensus 84 ~~~~Cp~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~dCp~ 143 (174)
++++||+.|..+........+ .....+...++||+|+++|||++|||+
T Consensus 76 ~~~~Cp~~~~~y~~~~~~~~~------------~~~~~~~~~~~Cy~Cg~~GH~a~dCp~ 123 (124)
T 2lli_A 76 SKERCPSIWRAYILVDDNEKA------------KPKVLPFHTIYCYNCGGKGHFGDDCKE 123 (124)
T ss_dssp CTTTCCCSTTSCCSSSCCCCC------------CCSCCCCCCCCTTTTSSSCTTTTTSCC
T ss_pred chhhCCCccccccccCccccc------------cccccCCCCCCcCCCCCCCcCcccCcC
Confidence 999999998754432210000 000011234567777777777776663
No 2
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=99.95 E-value=1.3e-28 Score=181.32 Aligned_cols=100 Identities=35% Similarity=0.819 Sum_probs=91.2
Q ss_pred CcccccccCCCCCCCccccCcccccccccC-CccccCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 030616 33 DLRLCNNCYKPGHIAADCTNDKACKNCRKT-GHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGG 111 (174)
Q Consensus 33 ~~~~C~~C~~~GH~~~~C~~~~~C~~Cg~~-GH~~~~Cp~~~~C~~C~~~GH~~~~Cp~~~~~~~~~g~~~~~~~~~~~~ 111 (174)
..+.||+|++.||++.+||. .+||+|++. ||++++||+...|++|++.||++++||..+.
T Consensus 3 ~~~~C~~C~~~GH~~~~Cp~-~~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~------------------ 63 (124)
T 2lli_A 3 AAPKCNNCSQRGHLKKDCPH-IICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWK------------------ 63 (124)
T ss_dssp CSSCCSSCSSSSCCTTTTTS-CCCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCC------------------
T ss_pred CCCcccCCCCCCcCcccCcC-CcCcCCCCcCCccCcccCCcccccccCCCCCccccCcCccc------------------
Confidence 35789999999999999999 799999998 9999999988899999999999999998642
Q ss_pred CCCCCCCcccCccccccccCCCCCCCCCCCCCC---------------------CcceeccCCCCcCCCCCCCC
Q 030616 112 DGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGP---------------------LIICRNCGGRGHMAYECPSG 164 (174)
Q Consensus 112 ~~~~~~~~~~~~~~~~C~~Cg~~GH~~~dCp~~---------------------~~~C~~Cg~~GH~a~~C~~~ 164 (174)
.+.||+|+++||+++|||.. .++||+|++.||||+|||+.
T Consensus 64 -------------~~~C~~Cg~~GH~~~~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~~ 124 (124)
T 2lli_A 64 -------------KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 124 (124)
T ss_dssp -------------CCSSSSSCSSCCCTTTCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCCC
T ss_pred -------------CccCCCCCcCCcchhhCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcCC
Confidence 25799999999999999973 47999999999999999974
No 3
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=99.68 E-value=8.9e-18 Score=115.21 Aligned_cols=59 Identities=31% Similarity=0.593 Sum_probs=32.9
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccccCCCCCCCCCCCCCC--Ccceec
Q 030616 73 PVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGP--LIICRN 150 (174)
Q Consensus 73 ~~C~~C~~~GH~~~~Cp~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~dCp~~--~~~C~~ 150 (174)
+.|++|++.||++++||+.| .||+|++.||++++|+.+ .+.||+
T Consensus 6 ~~C~~Cg~~GH~~~~Cp~~~----------------------------------rcY~c~~~gh~~~~c~~p~~~~~CYn 51 (83)
T 3nyb_B 6 VQCTLCKSKKHSKERCPSIW----------------------------------RAYILVDDNEKAKPKVLPFHTIYCYN 51 (83)
T ss_dssp -CCSSSCCSSSCGGGCGGGT----------------------------------CCCCBC-------------CCCBCSS
T ss_pred CCCCCCCCCCCccccCCCcc----------------------------------cccccccCCcccccccCCCCCCeecc
Confidence 46677777777777776654 277777777777777543 577888
Q ss_pred cCCCCcCCCCCCCCC
Q 030616 151 CGGRGHMAYECPSGR 165 (174)
Q Consensus 151 Cg~~GH~a~~C~~~~ 165 (174)
||+.|||++|||+++
T Consensus 52 CG~~GH~~rdC~~~r 66 (83)
T 3nyb_B 52 CGGKGHFGDDCKEKR 66 (83)
T ss_dssp SSCBSSCGGGCSSCC
T ss_pred cCCCCcCcccCCccc
Confidence 888888888887766
No 4
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=99.53 E-value=5.7e-15 Score=101.20 Aligned_cols=61 Identities=18% Similarity=0.234 Sum_probs=39.1
Q ss_pred cccccccCCCCCCCccccCcccccccccCCccccCCCC---CccccccccCCCCCCCCCCCCCC
Q 030616 34 LRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQN---EPVCNLCNIAGHVARQCPKGDSL 94 (174)
Q Consensus 34 ~~~C~~C~~~GH~~~~C~~~~~C~~Cg~~GH~~~~Cp~---~~~C~~C~~~GH~~~~Cp~~~~~ 94 (174)
.+.|++|++.||++++||+...||+|++.||++++|+. .+.||+|++.||++++||+...+
T Consensus 5 ~~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~~r~s 68 (83)
T 3nyb_B 5 KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKRSS 68 (83)
T ss_dssp --CCSSSCCSSSCGGGCGGGTCCCCBC-------------CCCBCSSSSCBSSCGGGCSSCCSC
T ss_pred cCCCCCCCCCCCccccCCCcccccccccCCcccccccCCCCCCeecccCCCCcCcccCCccccC
Confidence 46788888888888888875578888888888888864 36899999999999999887654
No 5
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=99.53 E-value=5.8e-15 Score=99.11 Aligned_cols=64 Identities=20% Similarity=0.373 Sum_probs=41.1
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccccCCCCCCCCCCCCC--CCcceeccCCCCcCC
Q 030616 81 AGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG--PLIICRNCGGRGHMA 158 (174)
Q Consensus 81 ~GH~~~~Cp~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~dCp~--~~~~C~~Cg~~GH~a 158 (174)
.||+++||++........ .....+.||+|+++||+++||+. ..+.||+|++.||++
T Consensus 2 ~gh~~rdc~~~~~~~~~~----------------------~~~r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~a 59 (74)
T 2li8_A 2 SGLVPRGSHMPKGKSMQK----------------------RRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMV 59 (74)
T ss_dssp ----------CCCCCCCS----------------------CCSTTSCCTTTCCSSSCTTTCSSCCCCCCCTTTCCTTSCG
T ss_pred CccccCcCCCCCcCcccc----------------------ccCCCCcccccCCcCcCcccCCCCCCCCccCCcCCcCCcc
Confidence 588999998875431100 01234689999999999999997 368999999999999
Q ss_pred CCCCCCCC
Q 030616 159 YECPSGRI 166 (174)
Q Consensus 159 ~~C~~~~~ 166 (174)
++||+...
T Consensus 60 r~Cp~~~~ 67 (74)
T 2li8_A 60 ASCPLKAQ 67 (74)
T ss_dssp GGCTTGGG
T ss_pred CcCcCCcC
Confidence 99998754
No 6
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=99.45 E-value=4e-14 Score=94.99 Aligned_cols=54 Identities=24% Similarity=0.484 Sum_probs=23.7
Q ss_pred CCcCcCCCCCCccCC-----CCcccccccCCCCCCCccccC---cccccccccCCccccCCC
Q 030616 17 TGHRARDCSTHVQSG-----GDLRLCNNCYKPGHIAADCTN---DKACKNCRKTGHIARDCQ 70 (174)
Q Consensus 17 ~GH~~~~Cp~~~~~~-----~~~~~C~~C~~~GH~~~~C~~---~~~C~~Cg~~GH~~~~Cp 70 (174)
.||+++||+.++... .....||+|+++||++.+|+. .+.||+|++.||++++||
T Consensus 2 ~gh~~rdc~~~~~~~~~~~~~r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp 63 (74)
T 2li8_A 2 SGLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCP 63 (74)
T ss_dssp ----------CCCCCCCSCCSTTSCCTTTCCSSSCTTTCSSCCCCCCCTTTCCTTSCGGGCT
T ss_pred CccccCcCCCCCcCccccccCCCCcccccCCcCcCcccCCCCCCCCccCCcCCcCCccCcCc
Confidence 699999999875431 244567777777777777764 233444444444444444
No 7
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=99.40 E-value=1.6e-13 Score=81.05 Aligned_cols=38 Identities=37% Similarity=0.862 Sum_probs=35.1
Q ss_pred cccccCCCCCCCCCCCCCC-CcceeccCCCCcCCCCCCC
Q 030616 126 VICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPS 163 (174)
Q Consensus 126 ~~C~~Cg~~GH~~~dCp~~-~~~C~~Cg~~GH~a~~C~~ 163 (174)
++||+|+++||+++|||.+ .+.||+|++.||++++||+
T Consensus 1 i~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~ 39 (39)
T 2a51_A 1 LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK 39 (39)
T ss_dssp CBCTTTCCBSSCTTTCCSCCCSSCTTTCCSSSCTTTSCC
T ss_pred CeeeccCCCCcccccCCCCCCCccccCCCCCCccCcCcC
Confidence 4699999999999999985 6899999999999999985
No 8
>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=99.34 E-value=6.5e-13 Score=82.21 Aligned_cols=42 Identities=33% Similarity=0.840 Sum_probs=37.7
Q ss_pred ccccccCCCCCCCCCCCCCC-CcceeccCCCCcCCCCCCCCCC
Q 030616 125 DVICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPSGRI 166 (174)
Q Consensus 125 ~~~C~~Cg~~GH~~~dCp~~-~~~C~~Cg~~GH~a~~C~~~~~ 166 (174)
.+.||+|+++||+++|||.+ .+.||+|++.||++++||+...
T Consensus 6 ~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~~~~ 48 (49)
T 2ec7_A 6 VIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPERQA 48 (49)
T ss_dssp CCBCTTTCCBTCCTTTCCCSSCCSCSSSCCSSCCGGGCCSSCC
T ss_pred cCeeeecCCCCcChhhCcCCCCCeeCcCCCcCCccCCCcCCCC
Confidence 46899999999999999985 4789999999999999998653
No 9
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=99.34 E-value=4.3e-13 Score=78.25 Aligned_cols=36 Identities=36% Similarity=0.955 Sum_probs=33.7
Q ss_pred ccccCCCCCCCCCCCCCCCcceeccCCCCcCCCCCCC
Q 030616 127 ICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPS 163 (174)
Q Consensus 127 ~C~~Cg~~GH~~~dCp~~~~~C~~Cg~~GH~a~~C~~ 163 (174)
.||+|+++||++++||.+ +.||+|++.||++++||+
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 699999999999999974 799999999999999985
No 10
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=99.32 E-value=1.6e-12 Score=84.50 Aligned_cols=44 Identities=23% Similarity=0.521 Sum_probs=38.7
Q ss_pred ccccccCCCCCCCCCCCCC--CCcceeccCCCCcCCCCCCCCCCCC
Q 030616 125 DVICRSCNQMGHMSRDCVG--PLIICRNCGGRGHMAYECPSGRIAD 168 (174)
Q Consensus 125 ~~~C~~Cg~~GH~~~dCp~--~~~~C~~Cg~~GH~a~~C~~~~~~~ 168 (174)
.+.||+|+++||+++|||. ..+.||+|++.||++++||+.....
T Consensus 7 ~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~~~~~ 52 (63)
T 2cqf_A 7 GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQG 52 (63)
T ss_dssp CCCCSSSCCSSSCTTTCCSCCCSSCCTTTCCSSSCTTTCTGGGCSC
T ss_pred CCcccccCCCCcChhhCCCCCCCCccCCcCCcCCccCcCCCccccC
Confidence 3679999999999999997 3789999999999999999875433
No 11
>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=99.31 E-value=6.7e-13 Score=83.95 Aligned_cols=45 Identities=29% Similarity=0.747 Sum_probs=39.5
Q ss_pred CccccccccCCCCCCCCCCCCCC-CcceeccCCCCcCCCCCCCCCC
Q 030616 122 GYHDVICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPSGRI 166 (174)
Q Consensus 122 ~~~~~~C~~Cg~~GH~~~dCp~~-~~~C~~Cg~~GH~a~~C~~~~~ 166 (174)
....+.||+|++.||++++||.+ ...||+|++.||++++||+.+.
T Consensus 9 ~~~~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~~~~ 54 (55)
T 1a1t_A 9 QRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54 (55)
T ss_dssp GGGTCBCTTTCCBSSCGGGCSSCSCCBCTTTCCBSSCGGGCSSSCC
T ss_pred CCCCcceeeeCCCCcChhhcCCCCCCEeCCCCCcCCccCCCcCcCC
Confidence 34557899999999999999985 5789999999999999998764
No 12
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=99.30 E-value=9.2e-13 Score=85.12 Aligned_cols=42 Identities=29% Similarity=0.618 Sum_probs=37.2
Q ss_pred ccccccCCCCCCCCCCCCCC------CcceeccCCCCcCCCCCCCCCC
Q 030616 125 DVICRSCNQMGHMSRDCVGP------LIICRNCGGRGHMAYECPSGRI 166 (174)
Q Consensus 125 ~~~C~~Cg~~GH~~~dCp~~------~~~C~~Cg~~GH~a~~C~~~~~ 166 (174)
.++||+|+++||+++|||.+ .+.||+|++.||++++||+.+.
T Consensus 4 ~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~~ 51 (61)
T 2ihx_A 4 RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDG 51 (61)
T ss_dssp TTBCSSSCCBTCCGGGCTTTTSSSCCCSBCTTTCCBSSCGGGCCCCC-
T ss_pred CCcccccCCCCeehhhCcCCcCCCCCCCeeCCCCCCCCCcCCCcCCCc
Confidence 46899999999999999985 3679999999999999998765
No 13
>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=99.27 E-value=1.4e-12 Score=83.82 Aligned_cols=41 Identities=29% Similarity=0.609 Sum_probs=19.9
Q ss_pred cccccCCCCCCCCCCCCCC---------CcceeccCCCCcCCCCCCCCCC
Q 030616 126 VICRSCNQMGHMSRDCVGP---------LIICRNCGGRGHMAYECPSGRI 166 (174)
Q Consensus 126 ~~C~~Cg~~GH~~~dCp~~---------~~~C~~Cg~~GH~a~~C~~~~~ 166 (174)
..||+|+++||+++|||.. .+.||+|++.||+++|||+...
T Consensus 2 ~~Cf~Cg~~GH~a~~C~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~~ 51 (60)
T 1cl4_A 2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKTD 51 (60)
T ss_dssp ---------------------------CCCSCSSCSSCSSCSTTCCCTTS
T ss_pred CccccCCCCCcCHhhCcCCCCCccccCCCcceeECCCCCCccCcCCCccc
Confidence 3699999999999999984 5789999999999999998764
No 14
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=99.26 E-value=3.9e-12 Score=74.99 Aligned_cols=39 Identities=38% Similarity=0.707 Sum_probs=30.7
Q ss_pred CCCccCCCCCcCcCCCCCCccCCCCcccccccCCCCCCCccccC
Q 030616 9 GICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTN 52 (174)
Q Consensus 9 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~C~~~GH~~~~C~~ 52 (174)
+.||+|++.||++++||.+. ...||+|++.||++++||+
T Consensus 1 i~C~~Cg~~GH~a~~C~~~~-----~~~C~~Cg~~GH~~~~C~~ 39 (39)
T 2a51_A 1 LTCFNCGKPGHTARMCRQPR-----QEGCWNCGSKEHRFAQCPK 39 (39)
T ss_dssp CBCTTTCCBSSCTTTCCSCC-----CSSCTTTCCSSSCTTTSCC
T ss_pred CeeeccCCCCcccccCCCCC-----CCccccCCCCCCccCcCcC
Confidence 36889999999999998752 3678888888888888874
No 15
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=99.20 E-value=1.3e-11 Score=79.67 Aligned_cols=20 Identities=35% Similarity=1.039 Sum_probs=12.3
Q ss_pred CCCCccCCCCCcCcCCCCCC
Q 030616 8 EGICHSCGKTGHRARDCSTH 27 (174)
Q Consensus 8 ~~~C~~Cg~~GH~~~~Cp~~ 27 (174)
...||+|+++||++++||..
T Consensus 4 ~~~C~~Cg~~GH~a~~C~~~ 23 (61)
T 2ihx_A 4 RGLCYTCGSPGHYQAQCPKK 23 (61)
T ss_dssp TTBCSSSCCBTCCGGGCTTT
T ss_pred CCcccccCCCCeehhhCcCC
Confidence 34566666666666666654
No 16
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=99.19 E-value=9.6e-12 Score=72.44 Aligned_cols=35 Identities=37% Similarity=1.072 Sum_probs=18.2
Q ss_pred CCccCCCCCcCcCCCCCCccCCCCcccccccCCCCCCCcccc
Q 030616 10 ICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCT 51 (174)
Q Consensus 10 ~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~C~~~GH~~~~C~ 51 (174)
.||+|++.||++++||.+ ..||+|++.||++++||
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 355555555555555543 34555555555555554
No 17
>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=99.17 E-value=2.3e-11 Score=75.18 Aligned_cols=40 Identities=40% Similarity=0.816 Sum_probs=26.8
Q ss_pred CCCCccCCCCCcCcCCCCCCccCCCCcccccccCCCCCCCccccC
Q 030616 8 EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTN 52 (174)
Q Consensus 8 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~C~~~GH~~~~C~~ 52 (174)
...||+|++.||++++||.+. ...||+|++.||++++||+
T Consensus 6 ~~~C~~Cg~~GH~a~~C~~~~-----~~~C~~Cg~~GH~~~~C~~ 45 (49)
T 2ec7_A 6 VIRCWNCGKEGHSARQCRAPR-----RQGCWKCGKTGHVMAKCPE 45 (49)
T ss_dssp CCBCTTTCCBTCCTTTCCCSS-----CCSCSSSCCSSCCGGGCCS
T ss_pred cCeeeecCCCCcChhhCcCCC-----CCeeCcCCCcCCccCCCcC
Confidence 356777777777777777652 2467777777777766665
No 18
>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=99.11 E-value=6.2e-11 Score=76.95 Aligned_cols=40 Identities=28% Similarity=0.684 Sum_probs=19.9
Q ss_pred CCCccCCCCCcCcCCCCCCccCCCCcccccccCCCCCCCccccC
Q 030616 9 GICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTN 52 (174)
Q Consensus 9 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~C~~~GH~~~~C~~ 52 (174)
..||+|+++||++++||.+. ..+.||+|+++||++++||+
T Consensus 8 ~~C~~Cg~~GH~a~~C~~~~----~~~~C~~Cg~~GH~ar~Cp~ 47 (63)
T 2cqf_A 8 DRCYNCGGLDHHAKECKLPP----QPKKCHFCQSISHMVASCPL 47 (63)
T ss_dssp CCCSSSCCSSSCTTTCCSCC----CSSCCTTTCCSSSCTTTCTG
T ss_pred CcccccCCCCcChhhCCCCC----CCCccCCcCCcCCccCcCCC
Confidence 45555555555555555431 12344555544454444444
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=99.07 E-value=6.3e-11 Score=74.75 Aligned_cols=36 Identities=47% Similarity=0.966 Sum_probs=17.9
Q ss_pred ccccccCCCCCCCccccCc--ccccccccCCccccCCC
Q 030616 35 RLCNNCYKPGHIAADCTND--KACKNCRKTGHIARDCQ 70 (174)
Q Consensus 35 ~~C~~C~~~GH~~~~C~~~--~~C~~Cg~~GH~~~~Cp 70 (174)
+.||+|++.||++.+|+.. ..||+|++.||++++||
T Consensus 13 ~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~ 50 (55)
T 1a1t_A 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50 (55)
T ss_dssp CBCTTTCCBSSCGGGCSSCSCCBCTTTCCBSSCGGGCS
T ss_pred cceeeeCCCCcChhhcCCCCCCEeCCCCCcCCccCCCc
Confidence 3455555555555555442 34555555555555554
No 20
>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=99.04 E-value=5.7e-11 Score=76.25 Aligned_cols=18 Identities=50% Similarity=1.202 Sum_probs=0.0
Q ss_pred CCccCCCCCcCcCCCCCC
Q 030616 10 ICHSCGKTGHRARDCSTH 27 (174)
Q Consensus 10 ~C~~Cg~~GH~~~~Cp~~ 27 (174)
.||+|+++||++++||..
T Consensus 3 ~Cf~Cg~~GH~a~~C~~~ 20 (60)
T 1cl4_A 3 SCFKCGKKGHFAKNCHEH 20 (60)
T ss_dssp ------------------
T ss_pred ccccCCCCCcCHhhCcCC
Confidence 477777777777777765
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=98.96 E-value=3.5e-10 Score=85.18 Aligned_cols=43 Identities=26% Similarity=0.593 Sum_probs=37.9
Q ss_pred ccccccCCCCCCCCCCCCCC--CcceeccCCCCcCCCCCCCCCCC
Q 030616 125 DVICRSCNQMGHMSRDCVGP--LIICRNCGGRGHMAYECPSGRIA 167 (174)
Q Consensus 125 ~~~C~~Cg~~GH~~~dCp~~--~~~C~~Cg~~GH~a~~C~~~~~~ 167 (174)
.+.||+|++.||++++||.+ ...||+|++.||++++||+..+.
T Consensus 97 ~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp~~~~~ 141 (148)
T 3ts2_A 97 GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQQ 141 (148)
T ss_dssp SCCCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCTTTTC-
T ss_pred CCcccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCcCCCCC
Confidence 46799999999999999973 47899999999999999988654
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=98.76 E-value=4.3e-09 Score=79.17 Aligned_cols=37 Identities=30% Similarity=0.650 Sum_probs=21.5
Q ss_pred cccccccCCCCCCCccccC---cccccccccCCccccCCC
Q 030616 34 LRLCNNCYKPGHIAADCTN---DKACKNCRKTGHIARDCQ 70 (174)
Q Consensus 34 ~~~C~~C~~~GH~~~~C~~---~~~C~~Cg~~GH~~~~Cp 70 (174)
...||+|++.||++++||. ...||+|++.||++++||
T Consensus 97 ~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp 136 (148)
T 3ts2_A 97 GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCP 136 (148)
T ss_dssp SCCCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCT
T ss_pred CCcccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCc
Confidence 4567777777777777776 233444444444444444
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=98.18 E-value=6.7e-07 Score=47.73 Aligned_cols=20 Identities=30% Similarity=0.868 Sum_probs=10.2
Q ss_pred cceeccCCCCcCCCCCCCCC
Q 030616 146 IICRNCGGRGHMAYECPSGR 165 (174)
Q Consensus 146 ~~C~~Cg~~GH~a~~C~~~~ 165 (174)
+.||+|++.||+|++||++.
T Consensus 3 ~~Cf~CG~~GH~ardC~~~~ 22 (26)
T 1dsq_A 3 PVCFSCGKTGHIKRDCKEEX 22 (26)
T ss_dssp CBCTTTCCBSSCTTTTTCC-
T ss_pred CeeEeCCCCCcccccCCCcc
Confidence 34555555555555555443
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=98.15 E-value=1.5e-06 Score=51.13 Aligned_cols=18 Identities=33% Similarity=0.842 Sum_probs=9.1
Q ss_pred cccccCCCCCCCCCCCCC
Q 030616 126 VICRSCNQMGHMSRDCVG 143 (174)
Q Consensus 126 ~~C~~Cg~~GH~~~dCp~ 143 (174)
.+||+|++.|||++|||.
T Consensus 11 ~~C~~Cgk~GH~ardCP~ 28 (40)
T 1a6b_B 11 DQCAYCKEKGHWAKDCPK 28 (40)
T ss_dssp SSCSSSCCTTCCTTSCSS
T ss_pred CeeeECCCCCcchhhCcC
Confidence 445555555555555554
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=98.00 E-value=3.2e-06 Score=45.05 Aligned_cols=21 Identities=52% Similarity=1.101 Sum_probs=16.5
Q ss_pred CCCCccCCCCCcCcCCCCCCc
Q 030616 8 EGICHSCGKTGHRARDCSTHV 28 (174)
Q Consensus 8 ~~~C~~Cg~~GH~~~~Cp~~~ 28 (174)
...||+|++.||++++||.+.
T Consensus 2 ~~~Cf~CG~~GH~ardC~~~~ 22 (26)
T 1dsq_A 2 GPVCFSCGKTGHIKRDCKEEX 22 (26)
T ss_dssp CCBCTTTCCBSSCTTTTTCC-
T ss_pred CCeeEeCCCCCcccccCCCcc
Confidence 467888888888888888764
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=97.95 E-value=3e-06 Score=46.29 Aligned_cols=19 Identities=37% Similarity=1.024 Sum_probs=12.1
Q ss_pred cccccCCCCCCCCCCCCCC
Q 030616 126 VICRSCNQMGHMSRDCVGP 144 (174)
Q Consensus 126 ~~C~~Cg~~GH~~~dCp~~ 144 (174)
++||+|+++||+++||+.+
T Consensus 7 ~~C~nCgk~GH~ar~C~~p 25 (29)
T 1nc8_A 7 IRCWNCGKEGHSARQCRAP 25 (29)
T ss_dssp CBCTTTSCBSSCGGGCCSS
T ss_pred CEEEECCccccCHhHCccc
Confidence 5566666666666666653
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=97.80 E-value=9.5e-06 Score=44.24 Aligned_cols=21 Identities=43% Similarity=0.844 Sum_probs=16.6
Q ss_pred CCCCccCCCCCcCcCCCCCCc
Q 030616 8 EGICHSCGKTGHRARDCSTHV 28 (174)
Q Consensus 8 ~~~C~~Cg~~GH~~~~Cp~~~ 28 (174)
++.||+|+++||++++|+.+.
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 467888888888888888763
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=97.79 E-value=9.9e-06 Score=51.00 Aligned_cols=20 Identities=30% Similarity=0.760 Sum_probs=12.7
Q ss_pred cccccccCCCCCCCCCCCCC
Q 030616 124 HDVICRSCNQMGHMSRDCVG 143 (174)
Q Consensus 124 ~~~~C~~Cg~~GH~~~dCp~ 143 (174)
...+||+|++.|||++|||.
T Consensus 22 ~~~~C~~Cge~GH~ardCp~ 41 (56)
T 1u6p_A 22 DRDQCAYCKEKGHWAKDCPK 41 (56)
T ss_dssp CTTBCSSSCCBSSCGGGCTT
T ss_pred CCCcceeCCCCCcccccCcC
Confidence 34566666666666666665
No 29
>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=97.76 E-value=2.4e-05 Score=45.86 Aligned_cols=22 Identities=32% Similarity=0.791 Sum_probs=15.1
Q ss_pred CCCCccCCCCCcCcCCCCCCcc
Q 030616 8 EGICHSCGKTGHRARDCSTHVQ 29 (174)
Q Consensus 8 ~~~C~~Cg~~GH~~~~Cp~~~~ 29 (174)
...||+|++.||++++||....
T Consensus 10 ~~~C~~Cgk~GH~ardCP~~~~ 31 (40)
T 1a6b_B 10 RDQCAYCKEKGHWAKDCPKKPR 31 (40)
T ss_dssp SSSCSSSCCTTCCTTSCSSSCC
T ss_pred CCeeeECCCCCcchhhCcCCcc
Confidence 3567777777777777777643
No 30
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=97.43 E-value=6.8e-05 Score=46.93 Aligned_cols=18 Identities=28% Similarity=0.768 Sum_probs=14.5
Q ss_pred cccccCCCCCCCCCCCCC
Q 030616 126 VICRSCNQMGHMSRDCVG 143 (174)
Q Consensus 126 ~~C~~Cg~~GH~~~dCp~ 143 (174)
..||+|+++||+++|||.
T Consensus 8 ~~C~kCGk~GH~~k~Cp~ 25 (55)
T 2ysa_A 8 YTCFRCGKPGHYIKNCPT 25 (55)
T ss_dssp CCCTTTCCTTSCGGGCSG
T ss_pred CccccCCCcCcccccCCC
Confidence 468888888888888884
No 31
>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=97.39 E-value=0.00011 Score=46.14 Aligned_cols=28 Identities=32% Similarity=0.603 Sum_probs=23.5
Q ss_pred CCcceeccCCCCcCCCCCCCCCCCCCCC
Q 030616 144 PLIICRNCGGRGHMAYECPSGRIADRGY 171 (174)
Q Consensus 144 ~~~~C~~Cg~~GH~a~~C~~~~~~~~~~ 171 (174)
....||+|++.|||++|||+...-++.+
T Consensus 22 ~~~~C~~Cge~GH~ardCp~~~~~~~~~ 49 (56)
T 1u6p_A 22 DRDQCAYCKEKGHWAKDCPKKPRGPRGP 49 (56)
T ss_dssp CTTBCSSSCCBSSCGGGCTTCCCSSCSC
T ss_pred CCCcceeCCCCCcccccCcCCccccCCC
Confidence 4688999999999999999987655543
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=97.08 E-value=0.00021 Score=44.71 Aligned_cols=22 Identities=36% Similarity=0.884 Sum_probs=14.8
Q ss_pred CCCCCCccCCCCCcCcCCCCCC
Q 030616 6 HNEGICHSCGKTGHRARDCSTH 27 (174)
Q Consensus 6 ~~~~~C~~Cg~~GH~~~~Cp~~ 27 (174)
|...+||+|+++||++++||..
T Consensus 5 p~~~~C~kCGk~GH~~k~Cp~~ 26 (55)
T 2ysa_A 5 SSGYTCFRCGKPGHYIKNCPTN 26 (55)
T ss_dssp SSSCCCTTTCCTTSCGGGCSGG
T ss_pred CCCCccccCCCcCcccccCCCC
Confidence 3455677777777777777744
No 33
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=65.99 E-value=1.8 Score=22.40 Aligned_cols=18 Identities=39% Similarity=1.078 Sum_probs=11.0
Q ss_pred ccccccccCCCCCCCCCC
Q 030616 73 PVCNLCNIAGHVARQCPK 90 (174)
Q Consensus 73 ~~C~~C~~~GH~~~~Cp~ 90 (174)
+.|-.|...||...+|+.
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 456666666666666644
No 34
>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=65.15 E-value=22 Score=22.06 Aligned_cols=33 Identities=27% Similarity=0.515 Sum_probs=26.1
Q ss_pred CCCCCCCCCCCCCcceeccCCCC-------cCCCCCCCCCC
Q 030616 133 QMGHMSRDCVGPLIICRNCGGRG-------HMAYECPSGRI 166 (174)
Q Consensus 133 ~~GH~~~dCp~~~~~C~~Cg~~G-------H~a~~C~~~~~ 166 (174)
...|+..+||...+.|-.|+..- |. ..||....
T Consensus 32 l~~H~~~~C~~r~v~C~~C~~~~~~~~l~~H~-~~Cp~~~v 71 (76)
T 2yuc_A 32 LPAHLQHDCPKRRLKCEFCGCDFSGEAYESHE-GMCPQESS 71 (76)
T ss_dssp STTTTTTSCTTSCCCCSSSCCCCCHHHHHHTT-TSCTTSSC
T ss_pred HHhhCHhhCCCcceECCCCCCccCHHHHHHHH-hHCCCCcc
Confidence 35688889999889999998876 77 67887654
No 35
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=45.71 E-value=13 Score=25.69 Aligned_cols=19 Identities=47% Similarity=1.017 Sum_probs=9.4
Q ss_pred cccccccCC---CCCCCCCCCC
Q 030616 74 VCNLCNIAG---HVARQCPKGD 92 (174)
Q Consensus 74 ~C~~C~~~G---H~~~~Cp~~~ 92 (174)
+|-+|+..| |..+-||...
T Consensus 73 ~CpiCGATGd~AHT~kYCP~~~ 94 (106)
T 3alr_A 73 KCPLCGATGAKAHTKRFCPMVD 94 (106)
T ss_dssp CCTTTCCCGGGCCCGGGCTTCG
T ss_pred cCCCCCCcCCcccceecCCCCC
Confidence 444454444 5555555444
No 36
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=42.50 E-value=12 Score=25.82 Aligned_cols=43 Identities=26% Similarity=0.557 Sum_probs=30.6
Q ss_pred ccccccCCCC--------CCCCCC------CCC-CCcceeccCCCC---cCCCCCCCCCCC
Q 030616 125 DVICRSCNQM--------GHMSRD------CVG-PLIICRNCGGRG---HMAYECPSGRIA 167 (174)
Q Consensus 125 ~~~C~~Cg~~--------GH~~~d------Cp~-~~~~C~~Cg~~G---H~a~~C~~~~~~ 167 (174)
...|..|... .|..+| ||. ...+|-.|+..| |..+-||.....
T Consensus 36 ~~~C~FCrnNGE~~~vy~SH~LKd~~G~V~CPvLR~Y~CpiCGATGd~AHT~kYCP~~~~~ 96 (106)
T 3alr_A 36 RKFCSFCKHNGETEAVYTSHYLKNRDGDVMCPYLRQYKCPLCGATGAKAHTKRFCPMVDKN 96 (106)
T ss_dssp --CCHHHHHTTCCHHHHTSBCSBCTTSCBCCTTGGGCCCTTTCCCGGGCCCGGGCTTCGGG
T ss_pred CCEeECCCCCCcccCccccceeECCCCCCcCCCcccccCCCCCCcCCcccceecCCCCCCc
Confidence 3456666544 388888 886 357899999888 888899987643
No 37
>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=38.17 E-value=64 Score=21.65 Aligned_cols=28 Identities=25% Similarity=0.502 Sum_probs=14.5
Q ss_pred cccccccCCCCCCCccccCcccccccccCCcc
Q 030616 34 LRLCNNCYKPGHIAADCTNDKACKNCRKTGHI 65 (174)
Q Consensus 34 ~~~C~~C~~~GH~~~~C~~~~~C~~Cg~~GH~ 65 (174)
..+|..|++.|.+.. . +.|..|.+.-|.
T Consensus 7 ~~~C~~C~~~g~~~~---l-l~C~~C~~~~H~ 34 (111)
T 2ysm_A 7 GANCAVCDSPGDLLD---Q-FFCTTCGQHYHG 34 (111)
T ss_dssp CSCBTTTCCCCCTTT---S-EECSSSCCEECT
T ss_pred CCCCcCCCCCCCCcC---C-eECCCCCCCcCh
Confidence 456677766664421 1 345555555554
No 38
>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=37.15 E-value=10 Score=21.80 Aligned_cols=19 Identities=37% Similarity=1.029 Sum_probs=11.2
Q ss_pred CccccccccCCCCCCCCCC
Q 030616 72 EPVCNLCNIAGHVARQCPK 90 (174)
Q Consensus 72 ~~~C~~C~~~GH~~~~Cp~ 90 (174)
++.|-+|...||...+|..
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 3566666666666666643
No 39
>3e2u_E CAP-Gly domain-containing linker protein 1; structural protein microtubule binding, dynactin, cytoskelet associated protein, P150glued; 2.60A {Homo sapiens}
Probab=25.56 E-value=23 Score=20.37 Aligned_cols=18 Identities=39% Similarity=1.078 Sum_probs=10.2
Q ss_pred ccccccccCCCCCCCCCC
Q 030616 73 PVCNLCNIAGHVARQCPK 90 (174)
Q Consensus 73 ~~C~~C~~~GH~~~~Cp~ 90 (174)
+.|-.|-..||...+|..
T Consensus 21 pYCe~CEVFGH~t~eC~d 38 (42)
T 3e2u_E 21 PYCEICEMFGHWATNCND 38 (42)
T ss_dssp CEETTTTEESSCGGGCCT
T ss_pred cccccceecccccccCCc
Confidence 455556566665555544
Done!