Query 024209
Match_columns 271
No_of_seqs 250 out of 1791
Neff 6.5
Searched_HMMs 29240
Date Mon Mar 25 04:16:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024209.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/024209hhsearch_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 6.2E-27 2.1E-31 189.2 9.3 77 106-190 5-85 (124)
2 2lli_A Protein AIR2; RNA surve 99.9 1.5E-24 5E-29 175.2 10.8 78 48-126 4-85 (124)
3 3nyb_B Protein AIR2; polya RNA 99.6 3.6E-17 1.2E-21 123.3 3.0 62 169-264 5-68 (83)
4 2li8_A Protein LIN-28 homolog 99.5 5.9E-15 2E-19 108.9 4.7 66 178-265 2-69 (74)
5 3nyb_B Protein AIR2; polya RNA 99.5 1.3E-14 4.5E-19 109.2 3.3 60 131-190 5-67 (83)
6 2a51_A Nucleocapsid protein; s 99.3 5.8E-13 2E-17 86.3 3.4 38 223-260 1-39 (39)
7 2bl6_A Nucleocapsid protein P1 99.3 1.3E-12 4.5E-17 83.6 2.7 37 223-260 1-37 (37)
8 2ec7_A GAG polyprotein (PR55GA 99.3 2.1E-12 7E-17 87.8 3.5 42 222-263 6-48 (49)
9 1a1t_A Nucleocapsid protein; s 99.2 1.9E-12 6.6E-17 89.8 2.6 44 221-264 11-55 (55)
10 2ihx_A Nucleocapsid (NC) prote 99.2 2.4E-12 8.2E-17 91.3 2.9 43 222-264 4-52 (61)
11 2cqf_A RNA-binding protein LIN 99.2 7.3E-12 2.5E-16 89.4 4.5 44 221-264 6-51 (63)
12 1cl4_A Protein (GAG polyprotei 99.2 4.1E-12 1.4E-16 89.7 2.3 42 223-264 2-52 (60)
13 2li8_A Protein LIN-28 homolog 99.2 1.3E-11 4.3E-16 91.0 4.5 38 152-189 26-66 (74)
14 1a1t_A Nucleocapsid protein; s 99.1 3.7E-11 1.3E-15 83.3 2.9 48 37-84 1-50 (55)
15 2bl6_A Nucleocapsid protein P1 99.1 4.8E-11 1.7E-15 76.2 3.0 36 152-187 2-37 (37)
16 2a51_A Nucleocapsid protein; s 99.0 1.1E-10 3.9E-15 75.3 3.8 36 152-187 2-39 (39)
17 2cqf_A RNA-binding protein LIN 99.0 4E-10 1.4E-14 80.3 5.1 36 153-188 10-48 (63)
18 2ihx_A Nucleocapsid (NC) prote 98.9 4.3E-10 1.5E-14 79.6 3.7 22 169-190 30-51 (61)
19 2ec7_A GAG polyprotein (PR55GA 98.9 1.2E-09 4.2E-14 73.9 4.5 38 47-84 5-44 (49)
20 3ts2_A Protein LIN-28 homolog 98.9 1E-09 3.6E-14 90.9 3.8 43 222-264 97-141 (148)
21 1cl4_A Protein (GAG polyprotei 98.8 1.5E-09 5.1E-14 76.4 3.1 49 133-190 3-51 (60)
22 3ts2_A Protein LIN-28 homolog 98.6 2.5E-08 8.4E-13 82.6 3.5 40 151-190 98-140 (148)
23 1dsq_A Nucleic acid binding pr 98.0 1.6E-06 5.4E-11 50.9 1.8 20 243-262 3-22 (26)
24 1a6b_B Momulv, zinc finger pro 98.0 4E-06 1.4E-10 54.2 2.8 19 222-240 10-28 (40)
25 1nc8_A Nucleocapsid protein; H 97.8 5.4E-06 1.8E-10 49.8 1.5 18 223-240 7-24 (29)
26 1dsq_A Nucleic acid binding pr 97.7 1.1E-05 3.9E-10 47.2 2.0 19 223-241 3-21 (26)
27 1a6b_B Momulv, zinc finger pro 97.7 2.6E-05 8.9E-10 50.4 2.8 24 44-67 6-29 (40)
28 1nc8_A Nucleocapsid protein; H 97.6 2.8E-05 9.6E-10 46.6 1.8 21 47-67 5-25 (29)
29 1u6p_A GAG polyprotein; MLV, A 97.5 3.5E-05 1.2E-09 53.3 2.1 20 221-240 22-41 (56)
30 1u6p_A GAG polyprotein; MLV, A 97.2 0.00021 7.1E-09 49.5 2.6 26 241-266 22-47 (56)
31 2ysa_A Retinoblastoma-binding 96.9 0.0002 6.7E-09 49.4 0.6 18 223-240 8-25 (55)
32 2ysa_A Retinoblastoma-binding 96.2 0.0021 7.1E-08 44.2 2.0 22 241-262 6-27 (55)
33 2yuc_A TNF receptor-associated 66.4 12 0.0004 25.9 5.3 42 222-264 16-72 (76)
34 2hqh_E Restin; beta/BETA struc 62.3 1.9 6.6E-05 24.7 0.3 18 223-240 4-21 (26)
35 2pk2_A Cyclin-T1, protein TAT; 57.8 2.1 7.3E-05 39.4 0.0 7 181-187 268-274 (358)
36 2yuc_A TNF receptor-associated 55.2 24 0.00083 24.2 5.3 23 223-246 45-74 (76)
37 2pzo_E CAP-Gly domain-containi 30.2 13 0.00044 23.7 0.3 19 222-240 20-38 (42)
38 2ysm_A Myeloid/lymphoid or mix 24.7 80 0.0027 23.4 4.1 75 48-143 7-81 (111)
39 3alr_A Nanos protein; zinc-fin 23.5 51 0.0017 25.1 2.6 7 161-167 85-91 (106)
40 3e2u_E CAP-Gly domain-containi 21.7 23 0.00078 22.6 0.3 19 222-240 20-38 (42)
No 1
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=99.94 E-value=6.2e-27 Score=189.19 Aligned_cols=77 Identities=27% Similarity=0.758 Sum_probs=69.3
Q ss_pred CccccCCCCCcCCCCCCCCcccCCCCcccccCCCC-CCCCcCCCCCccccccCCCCcccccCCCC---CCCCccccCCcC
Q 024209 106 GICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKP-GHIAADCTNDKACKNCRKTGHIARDCQNE---PVCNLCNIAGHV 181 (271)
Q Consensus 106 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~Cg~~-GH~a~dC~~~~~C~~Cg~~GH~~~~Cp~~---~~C~~C~~~GH~ 181 (271)
..||+|++.||++++||.+ .|++|++. ||++.+||+...|++|++.||++++||+. +.||+|++.||+
T Consensus 5 ~~C~~C~~~GH~~~~Cp~~--------~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~ 76 (124)
T 2lli_A 5 PKCNNCSQRGHLKKDCPHI--------ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHS 76 (124)
T ss_dssp SCCSSCSSSSCCTTTTTSC--------CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCC
T ss_pred CcccCCCCCCcCcccCcCC--------cCcCCCCcCCccCcccCCcccccccCCCCCccccCcCcccCccCCCCCcCCcc
Confidence 5699999999999999863 79999998 99999999888899999999999999974 689999999999
Q ss_pred CCCCCCCCC
Q 024209 182 ARQCPKGDS 190 (271)
Q Consensus 182 a~~Cp~~~~ 190 (271)
+++||+.+.
T Consensus 77 ~~~Cp~~~~ 85 (124)
T 2lli_A 77 KERCPSIWR 85 (124)
T ss_dssp TTTCCCSTT
T ss_pred hhhCCCccc
Confidence 999998765
No 2
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=99.91 E-value=1.5e-24 Score=175.23 Aligned_cols=78 Identities=31% Similarity=0.856 Sum_probs=68.6
Q ss_pred CcccccCCCCCCCCCCCCCCcccccCCCC-CCccCCCCCcccCcCCCCCCCCCCCCCCC---CccccCCCCCcCCCCCCC
Q 024209 48 GNLCNNCKRPGHFARECPNVAVCNNCGLP-GHIASECTTQARCWNCREPGHMASNCHNE---GICHSCGKTGHRARDCST 123 (271)
Q Consensus 48 ~~~C~nCg~~GH~~~~Cp~~~~C~~Cg~~-GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~~---~~C~~Cg~~GH~~~~Cp~ 123 (271)
++.||+|+++||++++||.. +||+|++. ||++.+||....||+|++.||++++||+. ..|++|++.||++++||.
T Consensus 4 ~~~C~~C~~~GH~~~~Cp~~-~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~~~~Cp~ 82 (124)
T 2lli_A 4 APKCNNCSQRGHLKKDCPHI-ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPS 82 (124)
T ss_dssp SSCCSSCSSSSCCTTTTTSC-CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCCTTTCCC
T ss_pred CCcccCCCCCCcCcccCcCC-cCcCCCCcCCccCcccCCcccccccCCCCCccccCcCcccCccCCCCCcCCcchhhCCC
Confidence 57899999999999999985 89999998 99999999877899999999999999975 578888888888888888
Q ss_pred Ccc
Q 024209 124 HVQ 126 (271)
Q Consensus 124 ~~~ 126 (271)
.|.
T Consensus 83 ~~~ 85 (124)
T 2lli_A 83 IWR 85 (124)
T ss_dssp STT
T ss_pred ccc
Confidence 775
No 3
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=99.65 E-value=3.6e-17 Score=123.32 Aligned_cols=62 Identities=29% Similarity=0.581 Sum_probs=38.4
Q ss_pred CCCCCccccCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccCCCCCcCCCCCCC--CcceE
Q 024209 169 EPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGP--LIICR 246 (271)
Q Consensus 169 ~~~C~~C~~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp~~--~~~C~ 246 (271)
.+.||+|++.||++++||+. ..||+|++.+|++++|+.+ .++||
T Consensus 5 ~~~C~~Cg~~GH~~~~Cp~~----------------------------------~rcY~c~~~gh~~~~c~~p~~~~~CY 50 (83)
T 3nyb_B 5 KVQCTLCKSKKHSKERCPSI----------------------------------WRAYILVDDNEKAKPKVLPFHTIYCY 50 (83)
T ss_dssp --CCSSSCCSSSCGGGCGGG----------------------------------TCCCCBC-------------CCCBCS
T ss_pred cCCCCCCCCCCCccccCCCc----------------------------------ccccccccCCcccccccCCCCCCeec
Confidence 46788888888888888763 2488888888888888653 58899
Q ss_pred cCCCCCcCCCCCCCCCcC
Q 024209 247 NCGGRGHMAYECPSGRIA 264 (271)
Q Consensus 247 ~Cg~~GH~~~~Cp~~~~~ 264 (271)
|||+.|||++|||+.+.+
T Consensus 51 nCG~~GH~~rdC~~~r~s 68 (83)
T 3nyb_B 51 NCGGKGHFGDDCKEKRSS 68 (83)
T ss_dssp SSSCBSSCGGGCSSCCSC
T ss_pred ccCCCCcCcccCCccccC
Confidence 999999999999888754
No 4
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=99.52 E-value=5.9e-15 Score=108.88 Aligned_cols=66 Identities=21% Similarity=0.395 Sum_probs=42.2
Q ss_pred CCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccCCCCCcCCCCCC--CCcceEcCCCCCcCC
Q 024209 178 AGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG--PLIICRNCGGRGHMA 255 (271)
Q Consensus 178 ~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp~--~~~~C~~Cg~~GH~~ 255 (271)
.|||++||+++....... + ....+.||+|+++||++++||. ..+.||+|++.||++
T Consensus 2 ~gh~~rdc~~~~~~~~~~--------------------~--~~r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~a 59 (74)
T 2li8_A 2 SGLVPRGSHMPKGKSMQK--------------------R--RSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMV 59 (74)
T ss_dssp ----------CCCCCCCS--------------------C--CSTTSCCTTTCCSSSCTTTCSSCCCCCCCTTTCCTTSCG
T ss_pred CccccCcCCCCCcCcccc--------------------c--cCCCCcccccCCcCcCcccCCCCCCCCccCCcCCcCCcc
Confidence 589999999875321000 0 0135789999999999999997 368999999999999
Q ss_pred CCCCCCCcCC
Q 024209 256 YECPSGRIAD 265 (271)
Q Consensus 256 ~~Cp~~~~~~ 265 (271)
+|||+..+..
T Consensus 60 r~Cp~~~~~~ 69 (74)
T 2li8_A 60 ASCPLKAQQG 69 (74)
T ss_dssp GGCTTGGGTC
T ss_pred CcCcCCcCCC
Confidence 9999876543
No 5
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=99.47 E-value=1.3e-14 Score=109.24 Aligned_cols=60 Identities=18% Similarity=0.250 Sum_probs=39.0
Q ss_pred CcccccCCCCCCCCcCCCCCccccccCCCCcccccCCC---CCCCCccccCCcCCCCCCCCCC
Q 024209 131 LRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQN---EPVCNLCNIAGHVARQCPKGDS 190 (271)
Q Consensus 131 ~~~C~~Cg~~GH~a~dC~~~~~C~~Cg~~GH~~~~Cp~---~~~C~~C~~~GH~a~~Cp~~~~ 190 (271)
.+.|++|++.||++.+||+.+.||+|+..+|++++|+. .+.||+|++.|||++|||+...
T Consensus 5 ~~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~~r~ 67 (83)
T 3nyb_B 5 KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKRS 67 (83)
T ss_dssp --CCSSSCCSSSCGGGCGGGTCCCCBC-------------CCCBCSSSSCBSSCGGGCSSCCS
T ss_pred cCCCCCCCCCCCccccCCCcccccccccCCcccccccCCCCCCeecccCCCCcCcccCCcccc
Confidence 45788888888888888776678888888888888864 4789999999999999998753
No 6
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=99.33 E-value=5.8e-13 Score=86.26 Aligned_cols=38 Identities=37% Similarity=0.862 Sum_probs=35.3
Q ss_pred ccccccCCCCCcCCCCCCC-CcceEcCCCCCcCCCCCCC
Q 024209 223 VICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPS 260 (271)
Q Consensus 223 ~~C~~C~~~gH~~~dCp~~-~~~C~~Cg~~GH~~~~Cp~ 260 (271)
++||+|+++||++++||++ .+.||+|++.||+++|||+
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 4799999999999999975 6899999999999999996
No 7
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=99.27 E-value=1.3e-12 Score=83.59 Aligned_cols=37 Identities=35% Similarity=0.916 Sum_probs=34.3
Q ss_pred ccccccCCCCCcCCCCCCCCcceEcCCCCCcCCCCCCC
Q 024209 223 VICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPS 260 (271)
Q Consensus 223 ~~C~~C~~~gH~~~dCp~~~~~C~~Cg~~GH~~~~Cp~ 260 (271)
+.||+|+++||++++||.+ +.||+|++.||++++||+
T Consensus 1 ~~C~~Cg~~GH~~~~C~~~-~~C~~Cg~~GH~a~~C~~ 37 (37)
T 2bl6_A 1 QTCYNCGKPGHLSSQCRAP-KVCFKCKQPGHFSKQCRS 37 (37)
T ss_dssp CCBSSSCCSSCCTTTSSCB-TTCSSCCCTTGGGGTTCC
T ss_pred CcccccCCCCcchhhCcCc-CeEccCCCcCCccCcCcC
Confidence 4699999999999999965 899999999999999995
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=99.27 E-value=2.1e-12 Score=87.76 Aligned_cols=42 Identities=33% Similarity=0.840 Sum_probs=38.2
Q ss_pred CccccccCCCCCcCCCCCCC-CcceEcCCCCCcCCCCCCCCCc
Q 024209 222 DVICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPSGRI 263 (271)
Q Consensus 222 ~~~C~~C~~~gH~~~dCp~~-~~~C~~Cg~~GH~~~~Cp~~~~ 263 (271)
.+.||+|+++||+++|||.+ .+.||+|++.||+++|||+...
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 57899999999999999975 4789999999999999998754
No 9
>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=99.25 E-value=1.9e-12 Score=89.80 Aligned_cols=44 Identities=30% Similarity=0.782 Sum_probs=39.4
Q ss_pred cCccccccCCCCCcCCCCCCC-CcceEcCCCCCcCCCCCCCCCcC
Q 024209 221 HDVICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPSGRIA 264 (271)
Q Consensus 221 ~~~~C~~C~~~gH~~~dCp~~-~~~C~~Cg~~GH~~~~Cp~~~~~ 264 (271)
..+.||+|+++||++++||.+ ...||+|++.||+++|||+..++
T Consensus 11 ~~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~~~~n 55 (55)
T 1a1t_A 11 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 55 (55)
T ss_dssp GTCBCTTTCCBSSCGGGCSSCSCCBCTTTCCBSSCGGGCSSSCCC
T ss_pred CCcceeeeCCCCcChhhcCCCCCCEeCCCCCcCCccCCCcCcCCC
Confidence 458899999999999999975 57899999999999999987653
No 10
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=99.24 E-value=2.4e-12 Score=91.31 Aligned_cols=43 Identities=28% Similarity=0.601 Sum_probs=37.7
Q ss_pred CccccccCCCCCcCCCCCCC------CcceEcCCCCCcCCCCCCCCCcC
Q 024209 222 DVICRSCNQMGHMSRDCVGP------LIICRNCGGRGHMAYECPSGRIA 264 (271)
Q Consensus 222 ~~~C~~C~~~gH~~~dCp~~------~~~C~~Cg~~GH~~~~Cp~~~~~ 264 (271)
.+.||+|+++||+++|||.+ .+.||+|++.||+++|||+.+.+
T Consensus 4 ~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~~~ 52 (61)
T 2ihx_A 4 RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGN 52 (61)
T ss_dssp TTBCSSSCCBTCCGGGCTTTTSSSCCCSBCTTTCCBSSCGGGCCCCC--
T ss_pred CCcccccCCCCeehhhCcCCcCCCCCCCeeCCCCCCCCCcCCCcCCCcC
Confidence 57899999999999999985 37899999999999999988764
No 11
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=99.22 E-value=7.3e-12 Score=89.42 Aligned_cols=44 Identities=25% Similarity=0.578 Sum_probs=38.9
Q ss_pred cCccccccCCCCCcCCCCCCC--CcceEcCCCCCcCCCCCCCCCcC
Q 024209 221 HDVICRSCNQMGHMSRDCVGP--LIICRNCGGRGHMAYECPSGRIA 264 (271)
Q Consensus 221 ~~~~C~~C~~~gH~~~dCp~~--~~~C~~Cg~~GH~~~~Cp~~~~~ 264 (271)
....||+|+++||+++|||.+ .+.||+|+++||+++|||+....
T Consensus 6 r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~~~~ 51 (63)
T 2cqf_A 6 SGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQ 51 (63)
T ss_dssp SCCCCSSSCCSSSCTTTCCSCCCSSCCTTTCCSSSCTTTCTGGGCS
T ss_pred CCCcccccCCCCcChhhCCCCCCCCccCCcCCcCCccCcCCCcccc
Confidence 357899999999999999973 78999999999999999986543
No 12
>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=99.20 E-value=4.1e-12 Score=89.69 Aligned_cols=42 Identities=29% Similarity=0.593 Sum_probs=20.4
Q ss_pred ccccccCCCCCcCCCCCCC---------CcceEcCCCCCcCCCCCCCCCcC
Q 024209 223 VICRSCNQMGHMSRDCVGP---------LIICRNCGGRGHMAYECPSGRIA 264 (271)
Q Consensus 223 ~~C~~C~~~gH~~~dCp~~---------~~~C~~Cg~~GH~~~~Cp~~~~~ 264 (271)
..||+|+++||+++|||+. .+.||+|++.|||++|||+....
T Consensus 2 ~~Cf~Cg~~GH~a~~C~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~~~ 52 (60)
T 1cl4_A 2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKTDN 52 (60)
T ss_dssp ---------------------------CCCSCSSCSSCSSCSTTCCCTTSS
T ss_pred CccccCCCCCcCHhhCcCCCCCccccCCCcceeECCCCCCccCcCCCcccc
Confidence 4699999999999999974 58899999999999999988643
No 13
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=99.19 E-value=1.3e-11 Score=90.98 Aligned_cols=38 Identities=29% Similarity=0.797 Sum_probs=25.9
Q ss_pred cccccCCCCcccccCC---CCCCCCccccCCcCCCCCCCCC
Q 024209 152 ACKNCRKTGHIARDCQ---NEPVCNLCNIAGHVARQCPKGD 189 (271)
Q Consensus 152 ~C~~Cg~~GH~~~~Cp---~~~~C~~C~~~GH~a~~Cp~~~ 189 (271)
.||+|++.||++++|+ ....||+|+++||++++||+..
T Consensus 26 ~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~~ 66 (74)
T 2li8_A 26 RCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKA 66 (74)
T ss_dssp CCTTTCCSSSCTTTCSSCCCCCCCTTTCCTTSCGGGCTTGG
T ss_pred cccccCCcCcCcccCCCCCCCCccCCcCCcCCccCcCcCCc
Confidence 4555555555555555 2567888888999999998764
No 14
>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=99.09 E-value=3.7e-11 Score=83.27 Aligned_cols=48 Identities=31% Similarity=0.713 Sum_probs=33.7
Q ss_pred cchhccccCCCCcccccCCCCCCCCCCCCCC--cccccCCCCCCccCCCC
Q 024209 37 LRRETRRSFSQGNLCNNCKRPGHFARECPNV--AVCNNCGLPGHIASECT 84 (271)
Q Consensus 37 ~~r~~~~~~~~~~~C~nCg~~GH~~~~Cp~~--~~C~~Cg~~GH~~~~Cp 84 (271)
||+.+++....++.||+|+++||++++||.. ..|++|++.||++.+||
T Consensus 1 ~q~~~f~g~~~~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~ 50 (55)
T 1a1t_A 1 MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50 (55)
T ss_dssp CCCGGGGGGGGTCBCTTTCCBSSCGGGCSSCSCCBCTTTCCBSSCGGGCS
T ss_pred CCccccCCCCCCcceeeeCCCCcChhhcCCCCCCEeCCCCCcCCccCCCc
Confidence 5677777777788999999999999999864 34444444444444444
No 15
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=99.08 E-value=4.8e-11 Score=76.23 Aligned_cols=36 Identities=39% Similarity=0.987 Sum_probs=24.5
Q ss_pred cccccCCCCcccccCCCCCCCCccccCCcCCCCCCC
Q 024209 152 ACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPK 187 (271)
Q Consensus 152 ~C~~Cg~~GH~~~~Cp~~~~C~~C~~~GH~a~~Cp~ 187 (271)
.||+|++.||++++||....||+|+++||++++||+
T Consensus 2 ~C~~Cg~~GH~~~~C~~~~~C~~Cg~~GH~a~~C~~ 37 (37)
T 2bl6_A 2 TCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37 (37)
T ss_dssp CBSSSCCSSCCTTTSSCBTTCSSCCCTTGGGGTTCC
T ss_pred cccccCCCCcchhhCcCcCeEccCCCcCCccCcCcC
Confidence 466666666666666666677777777777777764
No 16
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=99.05 E-value=1.1e-10 Score=75.32 Aligned_cols=36 Identities=44% Similarity=0.870 Sum_probs=25.7
Q ss_pred cccccCCCCcccccCCC--CCCCCccccCCcCCCCCCC
Q 024209 152 ACKNCRKTGHIARDCQN--EPVCNLCNIAGHVARQCPK 187 (271)
Q Consensus 152 ~C~~Cg~~GH~~~~Cp~--~~~C~~C~~~GH~a~~Cp~ 187 (271)
.||+|++.||++++||+ ...||+|+++||++++||+
T Consensus 2 ~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~ 39 (39)
T 2a51_A 2 TCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK 39 (39)
T ss_dssp BCTTTCCBSSCTTTCCSCCCSSCTTTCCSSSCTTTSCC
T ss_pred eeeccCCCCcccccCCCCCCCccccCCCCCCccCcCcC
Confidence 46666666666666664 3678888888888888874
No 17
>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=98.99 E-value=4e-10 Score=80.33 Aligned_cols=36 Identities=31% Similarity=0.815 Sum_probs=17.8
Q ss_pred ccccCCCCcccccCCC---CCCCCccccCCcCCCCCCCC
Q 024209 153 CKNCRKTGHIARDCQN---EPVCNLCNIAGHVARQCPKG 188 (271)
Q Consensus 153 C~~Cg~~GH~~~~Cp~---~~~C~~C~~~GH~a~~Cp~~ 188 (271)
||+|++.||++++||. .+.||+|+++||++++||+.
T Consensus 10 C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~ 48 (63)
T 2cqf_A 10 CYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLK 48 (63)
T ss_dssp CSSSCCSSSCTTTCCSCCCSSCCTTTCCSSSCTTTCTGG
T ss_pred ccccCCCCcChhhCCCCCCCCccCCcCCcCCccCcCCCc
Confidence 4444444444444442 34555555555555555553
No 18
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=98.94 E-value=4.3e-10 Score=79.62 Aligned_cols=22 Identities=50% Similarity=0.913 Sum_probs=18.7
Q ss_pred CCCCCccccCCcCCCCCCCCCC
Q 024209 169 EPVCNLCNIAGHVARQCPKGDS 190 (271)
Q Consensus 169 ~~~C~~C~~~GH~a~~Cp~~~~ 190 (271)
..+||+|+++||++++||+...
T Consensus 30 ~~~C~~Cg~~GH~ar~C~~~~~ 51 (61)
T 2ihx_A 30 RERCQLCNGMGHNAKQCRKRDG 51 (61)
T ss_dssp CSBCTTTCCBSSCGGGCCCCC-
T ss_pred CCeeCCCCCCCCCcCCCcCCCc
Confidence 3679999999999999998754
No 19
>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=98.90 E-value=1.2e-09 Score=73.95 Aligned_cols=38 Identities=37% Similarity=0.831 Sum_probs=22.9
Q ss_pred CCcccccCCCCCCCCCCCCCC--cccccCCCCCCccCCCC
Q 024209 47 QGNLCNNCKRPGHFARECPNV--AVCNNCGLPGHIASECT 84 (271)
Q Consensus 47 ~~~~C~nCg~~GH~~~~Cp~~--~~C~~Cg~~GH~~~~Cp 84 (271)
.++.||+|+++||++++||.. ..||+|++.||++.+||
T Consensus 5 r~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~ 44 (49)
T 2ec7_A 5 KVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCP 44 (49)
T ss_dssp CCCBCTTTCCBTCCTTTCCCSSCCSCSSSCCSSCCGGGCC
T ss_pred CcCeeeecCCCCcChhhCcCCCCCeeCcCCCcCCccCCCc
Confidence 357788888888888888764 23444444444444443
No 20
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*
Probab=98.86 E-value=1e-09 Score=90.88 Aligned_cols=43 Identities=26% Similarity=0.593 Sum_probs=38.0
Q ss_pred CccccccCCCCCcCCCCCCC--CcceEcCCCCCcCCCCCCCCCcC
Q 024209 222 DVICRSCNQMGHMSRDCVGP--LIICRNCGGRGHMAYECPSGRIA 264 (271)
Q Consensus 222 ~~~C~~C~~~gH~~~dCp~~--~~~C~~Cg~~GH~~~~Cp~~~~~ 264 (271)
.+.||+|++.||++++||.+ ...||+|++.||+++|||+..+.
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 47899999999999999973 48999999999999999987665
No 21
>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=1.5e-09 Score=76.40 Aligned_cols=49 Identities=24% Similarity=0.557 Sum_probs=19.5
Q ss_pred ccccCCCCCCCCcCCCCCccccccCCCCcccccCCCCCCCCccccCCcCCCCCCCCCC
Q 024209 133 LCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDS 190 (271)
Q Consensus 133 ~C~~Cg~~GH~a~dC~~~~~C~~Cg~~GH~~~~Cp~~~~C~~C~~~GH~a~~Cp~~~~ 190 (271)
.||+|++.||++++||.... +- .......+||+|++.||+|++||+...
T Consensus 3 ~Cf~Cg~~GH~a~~C~~~~~-------~~--~~~~~~~~C~~Cg~~GH~ar~C~~~~~ 51 (60)
T 1cl4_A 3 SCFKCGKKGHFAKNCHEHAH-------NN--AEPKVPGLCPRCKRGKHWANECKSKTD 51 (60)
T ss_dssp -----------------------------------CCCSCSSCSSCSSCSTTCCCTTS
T ss_pred ccccCCCCCcCHhhCcCCCC-------Cc--cccCCCcceeECCCCCCccCcCCCccc
Confidence 46666666666666654310 00 000124689999999999999998753
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=98.57 E-value=2.5e-08 Score=82.57 Aligned_cols=40 Identities=28% Similarity=0.733 Sum_probs=31.9
Q ss_pred ccccccCCCCcccccCCC---CCCCCccccCCcCCCCCCCCCC
Q 024209 151 KACKNCRKTGHIARDCQN---EPVCNLCNIAGHVARQCPKGDS 190 (271)
Q Consensus 151 ~~C~~Cg~~GH~~~~Cp~---~~~C~~C~~~GH~a~~Cp~~~~ 190 (271)
..||+|++.||++++||+ ...||+|++.||++++||+...
T Consensus 98 ~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp~~~~ 140 (148)
T 3ts2_A 98 DRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQ 140 (148)
T ss_dssp CCCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCTTTTC
T ss_pred CcccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCcCCCC
Confidence 357777777777777775 5789999999999999998654
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=98.04 E-value=1.6e-06 Score=50.90 Aligned_cols=20 Identities=30% Similarity=0.868 Sum_probs=12.0
Q ss_pred cceEcCCCCCcCCCCCCCCC
Q 024209 243 IICRNCGGRGHMAYECPSGR 262 (271)
Q Consensus 243 ~~C~~Cg~~GH~~~~Cp~~~ 262 (271)
+.||+||+.|||++|||++.
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 45666666666666666554
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=97.96 E-value=4e-06 Score=54.21 Aligned_cols=19 Identities=32% Similarity=0.793 Sum_probs=9.9
Q ss_pred CccccccCCCCCcCCCCCC
Q 024209 222 DVICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 222 ~~~C~~C~~~gH~~~dCp~ 240 (271)
..+||+|++.||||+|||.
T Consensus 10 ~~~C~~Cgk~GH~ardCP~ 28 (40)
T 1a6b_B 10 RDQCAYCKEKGHWAKDCPK 28 (40)
T ss_dssp SSSCSSSCCTTCCTTSCSS
T ss_pred CCeeeECCCCCcchhhCcC
Confidence 3455555555555555554
No 25
>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=97.82 E-value=5.4e-06 Score=49.80 Aligned_cols=18 Identities=33% Similarity=0.940 Sum_probs=9.0
Q ss_pred ccccccCCCCCcCCCCCC
Q 024209 223 VICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 223 ~~C~~C~~~gH~~~dCp~ 240 (271)
++||+|+++||+++||+.
T Consensus 7 ~~C~nCgk~GH~ar~C~~ 24 (29)
T 1nc8_A 7 IRCWNCGKEGHSARQCRA 24 (29)
T ss_dssp CBCTTTSCBSSCGGGCCS
T ss_pred CEEEECCccccCHhHCcc
Confidence 445555555555555543
No 26
>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=97.74 E-value=1.1e-05 Score=47.18 Aligned_cols=19 Identities=42% Similarity=1.011 Sum_probs=17.6
Q ss_pred ccccccCCCCCcCCCCCCC
Q 024209 223 VICRSCNQMGHMSRDCVGP 241 (271)
Q Consensus 223 ~~C~~C~~~gH~~~dCp~~ 241 (271)
.+||+|+++||+++|||.+
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 6899999999999999965
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=97.65 E-value=2.6e-05 Score=50.38 Aligned_cols=24 Identities=38% Similarity=0.895 Sum_probs=19.9
Q ss_pred cCCCCcccccCCCCCCCCCCCCCC
Q 024209 44 SFSQGNLCNNCKRPGHFARECPNV 67 (271)
Q Consensus 44 ~~~~~~~C~nCg~~GH~~~~Cp~~ 67 (271)
.......||+|++.|||+.+||..
T Consensus 6 ~~~~~~~C~~Cgk~GH~ardCP~~ 29 (40)
T 1a6b_B 6 SQLDRDQCAYCKEKGHWAKDCPKK 29 (40)
T ss_dssp CSCCSSSCSSSCCTTCCTTSCSSS
T ss_pred CCCCCCeeeECCCCCcchhhCcCC
Confidence 345578999999999999999875
No 28
>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=97.55 E-value=2.8e-05 Score=46.59 Aligned_cols=21 Identities=38% Similarity=0.708 Sum_probs=17.8
Q ss_pred CCcccccCCCCCCCCCCCCCC
Q 024209 47 QGNLCNNCKRPGHFARECPNV 67 (271)
Q Consensus 47 ~~~~C~nCg~~GH~~~~Cp~~ 67 (271)
.++.||||+++||++++|+.+
T Consensus 5 ~~~~C~nCgk~GH~ar~C~~p 25 (29)
T 1nc8_A 5 KVIRCWNCGKEGHSARQCRAP 25 (29)
T ss_dssp CCCBCTTTSCBSSCGGGCCSS
T ss_pred CCCEEEECCccccCHhHCccc
Confidence 367899999999999999764
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=97.51 E-value=3.5e-05 Score=53.35 Aligned_cols=20 Identities=30% Similarity=0.760 Sum_probs=13.9
Q ss_pred cCccccccCCCCCcCCCCCC
Q 024209 221 HDVICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 221 ~~~~C~~C~~~gH~~~dCp~ 240 (271)
...+||+|++.|||++|||.
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 34667777777777777775
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=97.15 E-value=0.00021 Score=49.46 Aligned_cols=26 Identities=31% Similarity=0.604 Sum_probs=22.2
Q ss_pred CCcceEcCCCCCcCCCCCCCCCcCCC
Q 024209 241 PLIICRNCGGRGHMAYECPSGRIADR 266 (271)
Q Consensus 241 ~~~~C~~Cg~~GH~~~~Cp~~~~~~~ 266 (271)
....||+|++.|||++|||+....++
T Consensus 22 ~~~~C~~Cge~GH~ardCp~~~~~~~ 47 (56)
T 1u6p_A 22 DRDQCAYCKEKGHWAKDCPKKPRGPR 47 (56)
T ss_dssp CTTBCSSSCCBSSCGGGCTTCCCSSC
T ss_pred CCCcceeCCCCCcccccCcCCccccC
Confidence 57899999999999999998765443
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=96.89 E-value=0.0002 Score=49.38 Aligned_cols=18 Identities=28% Similarity=0.768 Sum_probs=13.0
Q ss_pred ccccccCCCCCcCCCCCC
Q 024209 223 VICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 223 ~~C~~C~~~gH~~~dCp~ 240 (271)
..||+|+++|||++|||.
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 467777777777777773
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=96.17 E-value=0.0021 Score=44.21 Aligned_cols=22 Identities=32% Similarity=0.754 Sum_probs=19.0
Q ss_pred CCcceEcCCCCCcCCCCCCCCC
Q 024209 241 PLIICRNCGGRGHMAYECPSGR 262 (271)
Q Consensus 241 ~~~~C~~Cg~~GH~~~~Cp~~~ 262 (271)
....||+||+.|||+++||+..
T Consensus 6 ~~~~C~kCGk~GH~~k~Cp~~~ 27 (55)
T 2ysa_A 6 SGYTCFRCGKPGHYIKNCPTNG 27 (55)
T ss_dssp SSCCCTTTCCTTSCGGGCSGGG
T ss_pred CCCccccCCCcCcccccCCCCC
Confidence 4678999999999999999544
No 33
>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=66.45 E-value=12 Score=25.90 Aligned_cols=42 Identities=26% Similarity=0.570 Sum_probs=32.3
Q ss_pred Cccc-cccCC-------CCCcCCCCCCCCcceEcCCCCC-------cCCCCCCCCCcC
Q 024209 222 DVIC-RSCNQ-------MGHMSRDCVGPLIICRNCGGRG-------HMAYECPSGRIA 264 (271)
Q Consensus 222 ~~~C-~~C~~-------~gH~~~dCp~~~~~C~~Cg~~G-------H~~~~Cp~~~~~ 264 (271)
.+.| ..|+. .-|...+||...+.|-.|+..- |. .+||..-+.
T Consensus 16 ~v~C~~~C~~~v~r~~l~~H~~~~C~~r~v~C~~C~~~~~~~~l~~H~-~~Cp~~~v~ 72 (76)
T 2yuc_A 16 VIPCPNRCPMKLSRRDLPAHLQHDCPKRRLKCEFCGCDFSGEAYESHE-GMCPQESSG 72 (76)
T ss_dssp CCBCTTCCSCBCCSSSSTTTTTTSCTTSCCCCSSSCCCCCHHHHHHTT-TSCTTSSCC
T ss_pred ccCCCccccHHhhHhHHHhhCHhhCCCcceECCCCCCccCHHHHHHHH-hHCCCCccC
Confidence 3566 56653 4699999999999999998877 88 689876543
No 34
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=62.30 E-value=1.9 Score=24.74 Aligned_cols=18 Identities=28% Similarity=0.827 Sum_probs=15.2
Q ss_pred ccccccCCCCCcCCCCCC
Q 024209 223 VICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 223 ~~C~~C~~~gH~~~dCp~ 240 (271)
..|-+|...||+..||+.
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 578899999999999974
No 35
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C
Probab=57.84 E-value=2.1 Score=39.40 Aligned_cols=7 Identities=14% Similarity=-0.111 Sum_probs=0.0
Q ss_pred CCCCCCC
Q 024209 181 VARQCPK 187 (271)
Q Consensus 181 ~a~~Cp~ 187 (271)
...++..
T Consensus 268 ~~~~~~~ 274 (358)
T 2pk2_A 268 KADDRGT 274 (358)
T ss_dssp -------
T ss_pred cccCccc
Confidence 3344444
No 36
>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=55.16 E-value=24 Score=24.18 Aligned_cols=23 Identities=17% Similarity=0.098 Sum_probs=14.1
Q ss_pred ccccccCCCC-------CcCCCCCCCCcceE
Q 024209 223 VICRSCNQMG-------HMSRDCVGPLIICR 246 (271)
Q Consensus 223 ~~C~~C~~~g-------H~~~dCp~~~~~C~ 246 (271)
+.|..|+..- |. .+||...+.|-
T Consensus 45 v~C~~C~~~~~~~~l~~H~-~~Cp~~~v~C~ 74 (76)
T 2yuc_A 45 LKCEFCGCDFSGEAYESHE-GMCPQESSGPS 74 (76)
T ss_dssp CCCSSSCCCCCHHHHHHTT-TSCTTSSCCCS
T ss_pred eECCCCCCccCHHHHHHHH-hHCCCCccCCC
Confidence 5666666554 66 56776666553
No 37
>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=30.15 E-value=13 Score=23.67 Aligned_cols=19 Identities=26% Similarity=0.779 Sum_probs=16.5
Q ss_pred CccccccCCCCCcCCCCCC
Q 024209 222 DVICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 222 ~~~C~~C~~~gH~~~dCp~ 240 (271)
..+|-+|.-.||+..+|+.
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 4789999999999999974
No 38
>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=24.71 E-value=80 Score=23.40 Aligned_cols=75 Identities=25% Similarity=0.618 Sum_probs=39.9
Q ss_pred CcccccCCCCCCCCCCCCCCcccccCCCCCCccCCCCCcccCcCCCCCCCCCCCCCCCCccccCCCCCcCCCCCCCCccc
Q 024209 48 GNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQS 127 (271)
Q Consensus 48 ~~~C~nCg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~~~~~ 127 (271)
..+|..|++.|.+. ....|..|.+..|.. |-...+ . ..--....|++=..|..|++.+..
T Consensus 7 ~~~C~~C~~~g~~~----~ll~C~~C~~~~H~~--Cl~~~~--~--~~~~~~W~C~~C~~C~~C~~~~~~---------- 66 (111)
T 2ysm_A 7 GANCAVCDSPGDLL----DQFFCTTCGQHYHGM--CLDIAV--T--PLKRAGWQCPECKVCQNCKQSGED---------- 66 (111)
T ss_dssp CSCBTTTCCCCCTT----TSEECSSSCCEECTT--TTTCCC--C--TTTSTTCCCTTTCCCTTTCCCSCC----------
T ss_pred CCCCcCCCCCCCCc----CCeECCCCCCCcChH--HhCCcc--c--cccccCccCCcCCcccccCccCCC----------
Confidence 46788888888653 235777787777764 432110 0 000012345554456777766431
Q ss_pred CCCCcccccCCCCCCC
Q 024209 128 GGDLRLCNNCYKPGHI 143 (271)
Q Consensus 128 ~~~~~~C~~Cg~~GH~ 143 (271)
...+.|..|...=|+
T Consensus 67 -~~ll~Cd~C~~~yH~ 81 (111)
T 2ysm_A 67 -SKMLVCDTCDKGYHT 81 (111)
T ss_dssp -TTEEECSSSCCEEEG
T ss_pred -CCeeECCCCCcHHhH
Confidence 123456666655554
No 39
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=23.47 E-value=51 Score=25.07 Aligned_cols=7 Identities=43% Similarity=0.785 Sum_probs=2.5
Q ss_pred cccccCC
Q 024209 161 HIARDCQ 167 (271)
Q Consensus 161 H~~~~Cp 167 (271)
|+.+-||
T Consensus 85 HT~kYCP 91 (106)
T 3alr_A 85 HTKRFCP 91 (106)
T ss_dssp CCGGGCT
T ss_pred cceecCC
Confidence 3333333
No 40
>3e2u_E CAP-Gly domain-containing linker protein 1; structural protein microtubule binding, dynactin, cytoskelet associated protein, P150glued; 2.60A {Homo sapiens}
Probab=21.74 E-value=23 Score=22.57 Aligned_cols=19 Identities=26% Similarity=0.779 Sum_probs=17.0
Q ss_pred CccccccCCCCCcCCCCCC
Q 024209 222 DVICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 222 ~~~C~~C~~~gH~~~dCp~ 240 (271)
..+|-+|.-.||+..+|+.
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 4689999999999999985
Done!