Query 037631
Match_columns 388
No_of_seqs 289 out of 1625
Neff 5.2
Searched_HMMs 29240
Date Mon Mar 25 04:09:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037631.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/037631hhsearch_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 99.8 4.1E-21 1.4E-25 164.6 8.2 96 253-370 4-124 (124)
2 3nyb_B Protein AIR2; polya RNA 99.5 1.4E-15 4.8E-20 122.8 2.0 69 281-379 6-74 (83)
3 2lli_A Protein AIR2; RNA surve 99.5 1.4E-14 4.9E-19 123.8 7.0 79 280-372 4-85 (124)
4 2li8_A Protein LIN-28 homolog 99.4 7.3E-14 2.5E-18 110.5 3.2 66 289-372 2-67 (74)
5 3nyb_B Protein AIR2; polya RNA 99.4 1.2E-13 4.2E-18 111.5 3.6 63 253-332 5-67 (83)
6 2jyl_A Capsid protein P24 (Ca) 99.3 8.6E-14 3E-18 117.0 -1.3 83 137-227 15-104 (105)
7 1baj_A GAG polyprotein; capsid 99.3 1.8E-13 6E-18 114.3 0.3 87 141-235 1-94 (101)
8 2li8_A Protein LIN-28 homolog 99.2 2.4E-12 8E-17 101.8 3.1 61 262-331 2-66 (74)
9 3ds4_A HIV-1 capsid protein; H 99.2 1.4E-12 4.8E-17 105.9 1.5 78 142-227 1-85 (86)
10 2a51_A Nucleocapsid protein; s 99.1 6.7E-11 2.3E-15 82.1 3.2 38 313-369 2-39 (39)
11 2ec7_A GAG polyprotein (PR55GA 99.1 8.4E-11 2.9E-15 85.6 3.7 43 311-372 6-48 (49)
12 1qrj_B HTLV-I capsid protein; 99.0 2.1E-11 7.3E-16 112.9 -0.4 85 133-226 104-197 (199)
13 2a51_A Nucleocapsid protein; s 99.0 1.3E-10 4.6E-15 80.6 3.2 37 255-297 2-38 (39)
14 2ihx_A Nucleocapsid (NC) prote 99.0 2E-10 6.8E-15 87.2 3.7 49 311-373 4-52 (61)
15 1a1t_A Nucleocapsid protein; s 99.0 1.8E-10 6.1E-15 85.4 2.4 43 311-372 12-54 (55)
16 2ec7_A GAG polyprotein (PR55GA 99.0 3.8E-10 1.3E-14 82.1 3.9 41 253-299 6-46 (49)
17 2bl6_A Nucleocapsid protein P1 99.0 2.3E-10 8E-15 78.5 2.6 36 313-369 2-37 (37)
18 1cl4_A Protein (GAG polyprotei 98.9 3.3E-10 1.1E-14 85.4 3.2 49 313-372 3-51 (60)
19 2cqf_A RNA-binding protein LIN 98.9 4.8E-10 1.6E-14 85.7 3.8 43 311-371 7-49 (63)
20 1a1t_A Nucleocapsid protein; s 98.9 8.7E-10 3E-14 81.7 3.8 41 253-299 12-52 (55)
21 2bl6_A Nucleocapsid protein P1 98.9 6.2E-10 2.1E-14 76.3 2.7 34 256-297 3-36 (37)
22 2cqf_A RNA-binding protein LIN 98.9 1.1E-09 3.7E-14 83.7 3.5 41 254-299 8-48 (63)
23 2ihx_A Nucleocapsid (NC) prote 98.8 2E-09 7E-14 81.6 4.0 46 253-299 4-49 (61)
24 1cl4_A Protein (GAG polyprotei 98.8 1.5E-09 5.1E-14 81.8 2.6 18 255-272 3-20 (60)
25 3h47_A Ca, capsid protein P24; 98.8 5.5E-10 1.9E-14 105.5 -0.4 84 136-227 140-230 (231)
26 3ts2_A Protein LIN-28 homolog 98.8 2.3E-09 7.8E-14 94.8 3.4 45 311-373 97-141 (148)
27 3gv2_A Ca, fusion protein cons 98.7 2.8E-09 9.5E-14 105.7 0.7 85 136-228 140-231 (342)
28 3ts2_A Protein LIN-28 homolog 98.6 2.3E-08 8E-13 88.4 3.6 42 253-299 97-138 (148)
29 1eia_A EIAV capsid protein P26 98.5 6.9E-09 2.4E-13 96.6 -0.9 76 136-219 123-207 (207)
30 1eoq_A GAG polyprotein capsid 98.5 1.9E-08 6.5E-13 82.6 1.4 56 151-214 7-68 (96)
31 1d1d_A Protein (capsid protein 98.5 2.7E-08 9.1E-13 95.6 0.7 83 134-225 161-256 (262)
32 3g21_A GAG polyprotein, capsid 98.2 2.3E-07 8E-12 73.5 -0.2 54 151-211 11-69 (77)
33 3g1g_A GAG polyprotein, capsid 98.0 1.6E-06 5.5E-11 70.0 1.2 54 151-211 10-68 (87)
34 1dsq_A Nucleic acid binding pr 97.8 7.5E-06 2.6E-10 52.0 2.3 21 352-372 3-23 (26)
35 1nc8_A Nucleocapsid protein; H 97.6 3.4E-05 1.1E-09 50.1 2.3 22 351-372 6-27 (29)
36 1a6b_B Momulv, zinc finger pro 97.5 5.1E-05 1.7E-09 53.1 3.2 24 350-373 9-32 (40)
37 1nc8_A Nucleocapsid protein; H 97.4 7.2E-05 2.4E-09 48.5 2.2 21 253-273 6-26 (29)
38 1dsq_A Nucleic acid binding pr 97.4 4.5E-05 1.5E-09 48.3 1.2 20 312-331 3-22 (26)
39 3tir_A ROUS sarcoma virus caps 97.2 7.9E-05 2.7E-09 70.2 1.5 72 133-211 138-218 (226)
40 1u6p_A GAG polyprotein; MLV, A 97.2 0.00018 6.3E-09 53.8 2.6 24 350-373 22-45 (56)
41 1a6b_B Momulv, zinc finger pro 97.1 0.00016 5.4E-09 50.6 2.0 22 310-331 9-30 (40)
42 1u6p_A GAG polyprotein; MLV, A 96.7 0.0005 1.7E-08 51.4 1.5 22 310-331 22-43 (56)
43 2ysa_A Retinoblastoma-binding 96.6 0.00064 2.2E-08 50.6 1.7 19 351-369 7-25 (55)
44 1exk_A DNAJ protein; extended 96.5 0.0012 4.1E-08 51.2 2.5 46 81-127 30-78 (79)
45 2ysa_A Retinoblastoma-binding 96.4 0.00076 2.6E-08 50.2 1.1 21 311-331 7-27 (55)
46 2ctt_A DNAJ homolog subfamily 95.0 0.013 4.5E-07 47.9 3.0 47 81-128 47-96 (104)
47 1u57_A GAG polyprotein, HIV-1; 94.0 0.013 4.5E-07 42.0 0.7 27 209-235 2-28 (48)
48 1nlt_A Protein YDJ1, mitochond 92.3 0.076 2.6E-06 50.0 3.4 28 101-128 79-111 (248)
49 1exk_A DNAJ protein; extended 89.3 0.2 6.8E-06 38.4 2.6 46 76-127 8-64 (79)
50 2bx9_A Anti-trap, AT, tryptoph 88.1 0.18 6E-06 37.0 1.5 26 79-113 9-34 (53)
51 3lcz_A YCZA, inhibitor of trap 86.4 0.29 9.9E-06 35.9 1.8 27 79-114 9-35 (53)
52 2ctt_A DNAJ homolog subfamily 85.1 0.44 1.5E-05 38.7 2.5 46 76-127 25-81 (104)
53 1nlt_A Protein YDJ1, mitochond 83.0 0.74 2.5E-05 43.2 3.4 35 80-114 55-108 (248)
54 1dl6_A Transcription factor II 66.6 3.3 0.00011 30.5 2.4 22 76-97 8-37 (58)
55 1pft_A TFIIB, PFTFIIBN; N-term 53.7 5.4 0.00019 28.0 1.6 9 79-87 5-13 (50)
56 3k7a_M Transcription initiatio 45.5 11 0.00037 36.7 2.8 26 70-97 14-49 (345)
57 3alr_A Nanos protein; zinc-fin 44.3 10 0.00035 31.4 2.0 19 281-299 72-93 (106)
58 2hqh_E Restin; beta/BETA struc 42.9 7.7 0.00026 24.5 0.8 20 352-371 4-23 (26)
59 2yuc_A TNF receptor-associated 41.3 39 0.0013 24.9 4.8 29 263-299 7-43 (76)
60 2hqh_E Restin; beta/BETA struc 40.7 9.1 0.00031 24.2 0.9 18 254-271 4-21 (26)
61 3lcz_A YCZA, inhibitor of trap 37.4 13 0.00044 27.0 1.4 25 103-127 10-37 (53)
62 3k1f_M Transcription initiatio 36.1 11 0.00038 34.3 1.1 20 78-97 20-49 (197)
63 2zvv_Y Cyclin-dependent kinase 35.5 4.2 0.00014 25.3 -1.2 18 4-21 7-24 (26)
64 3alr_A Nanos protein; zinc-fin 32.8 16 0.00056 30.2 1.5 32 290-331 54-94 (106)
65 2yuc_A TNF receptor-associated 32.1 46 0.0016 24.5 3.9 10 321-330 34-43 (76)
66 1nui_A DNA primase/helicase; z 31.3 19 0.00065 33.0 1.9 16 73-88 8-23 (255)
67 2jr6_A UPF0434 protein NMA0874 29.3 20 0.0007 27.2 1.4 22 77-98 6-34 (68)
68 2hf1_A Tetraacyldisaccharide-1 29.1 20 0.00069 27.2 1.4 24 76-99 5-35 (68)
69 4bbr_M Transcription initiatio 26.7 19 0.00066 35.1 1.1 26 70-97 14-49 (345)
70 2pk7_A Uncharacterized protein 26.5 25 0.00085 26.8 1.5 23 76-98 5-34 (69)
71 2js4_A UPF0434 protein BB2007; 24.6 28 0.00096 26.6 1.4 23 76-98 5-34 (70)
72 2kpi_A Uncharacterized protein 24.3 31 0.0011 25.1 1.6 25 76-100 7-38 (56)
73 2jny_A Uncharacterized BCR; st 21.7 35 0.0012 25.9 1.4 24 76-99 7-37 (67)
No 1
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=99.83 E-value=4.1e-21 Score=164.59 Aligned_cols=96 Identities=32% Similarity=0.706 Sum_probs=64.8
Q ss_pred ccccccccccCccccCCCCCcCCCCcCcccceecccC-CCccccCCCCCCCCCCCCCCCcceeeecCCCccccCCCCCC-
Q 037631 253 RFYCKHCGREGHRKFYCPELKDGLTDRGFKCRLCGER-GHNRRTCPKSRLSYHNGTVSKHHRCQICRQRGHNRRTCPQV- 330 (388)
Q Consensus 253 ~~~Cf~CG~~GH~ar~CP~~~~~~~~~~~~C~~CG~~-GH~ardCp~~~~~~~~G~~~~~~~C~~CGe~GH~ardCP~~- 330 (388)
...||+|++.||++++||. ..||+||+. ||++++||.. ..||+|++.||++++||+.
T Consensus 4 ~~~C~~C~~~GH~~~~Cp~---------~~C~~Cg~~~gH~~~~C~~~------------~~C~~Cg~~GH~~~~C~~~~ 62 (124)
T 2lli_A 4 APKCNNCSQRGHLKKDCPH---------IICSYCGATDDHYSRHCPKA------------IQCSKCDEVGHYRSQCPHKW 62 (124)
T ss_dssp SSCCSSCSSSSCCTTTTTS---------CCCTTTCCTTTCCTTTGGGS------------SCSSSSSCSSSSTTTSCCCC
T ss_pred CCcccCCCCCCcCcccCcC---------CcCcCCCCcCCccCcccCCc------------ccccccCCCCCccccCcCcc
Confidence 4568888888888888887 257777766 6777777653 3566666666666666653
Q ss_pred ---CCCCCCCCCCCcccCCC--------------------CCCCccccccCCCCcCCCCCCCC
Q 037631 331 ---TGEKRHDNNGQKHIPTS--------------------ASKTCTCRFCGEKGHNIRTCPRR 370 (388)
Q Consensus 331 ---~~~~Cg~~Gh~~~~~~~--------------------~~~~~~Cy~CGe~GH~ardCP~~ 370 (388)
.++.|+..||++. +|. ....++||+|++.|||++|||+.
T Consensus 63 ~~~~C~~Cg~~GH~~~-~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~~ 124 (124)
T 2lli_A 63 KKVQCTLCKSKKHSKE-RCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 124 (124)
T ss_dssp CCCSSSSSCSSCCCTT-TCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCCC
T ss_pred cCccCCCCCcCCcchh-hCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcCC
Confidence 2455555555541 111 12357899999999999999974
No 2
>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=1.4e-15 Score=122.85 Aligned_cols=69 Identities=25% Similarity=0.522 Sum_probs=43.9
Q ss_pred ccceecccCCCccccCCCCCCCCCCCCCCCcceeeecCCCccccCCCCCCCCCCCCCCCCCcccCCCCCCCccccccCCC
Q 037631 281 FKCRLCGERGHNRRTCPKSRLSYHNGTVSKHHRCQICRQRGHNRRTCPQVTGEKRHDNNGQKHIPTSASKTCTCRFCGEK 360 (388)
Q Consensus 281 ~~C~~CG~~GH~ardCp~~~~~~~~G~~~~~~~C~~CGe~GH~ardCP~~~~~~Cg~~Gh~~~~~~~~~~~~~Cy~CGe~ 360 (388)
+.|++|++.||++++||+. ..||+|++.||++++|+.+. ..+.||+||+.
T Consensus 6 ~~C~~Cg~~GH~~~~Cp~~------------~rcY~c~~~gh~~~~c~~p~------------------~~~~CYnCG~~ 55 (83)
T 3nyb_B 6 VQCTLCKSKKHSKERCPSI------------WRAYILVDDNEKAKPKVLPF------------------HTIYCYNCGGK 55 (83)
T ss_dssp -CCSSSCCSSSCGGGCGGG------------TCCCCBC-------------------------------CCCBCSSSSCB
T ss_pred CCCCCCCCCCCccccCCCc------------ccccccccCCcccccccCCC------------------CCCeecccCCC
Confidence 6788888888888888874 36888888888888887542 24679999999
Q ss_pred CcCCCCCCCCCCCCcchHH
Q 037631 361 GHNIRTCPRRNLEQLKSEE 379 (388)
Q Consensus 361 GH~ardCP~~~~s~~~s~~ 379 (388)
|||++|||+++.+.++..+
T Consensus 56 GH~~rdC~~~r~s~~p~~~ 74 (83)
T 3nyb_B 56 GHFGDDCKEKRSSRVPNED 74 (83)
T ss_dssp SSCGGGCSSCCSCSSCCSS
T ss_pred CcCcccCCccccCcCCCCC
Confidence 9999999998877776543
No 3
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=99.51 E-value=1.4e-14 Score=123.84 Aligned_cols=79 Identities=28% Similarity=0.642 Sum_probs=68.3
Q ss_pred cccceecccCCCccccCCCCCCCCCCCCCCCcceeeecCCC-ccccCCCCCC-CCCCCCCCCCCcccCCCCC-CCccccc
Q 037631 280 GFKCRLCGERGHNRRTCPKSRLSYHNGTVSKHHRCQICRQR-GHNRRTCPQV-TGEKRHDNNGQKHIPTSAS-KTCTCRF 356 (388)
Q Consensus 280 ~~~C~~CG~~GH~ardCp~~~~~~~~G~~~~~~~C~~CGe~-GH~ardCP~~-~~~~Cg~~Gh~~~~~~~~~-~~~~Cy~ 356 (388)
...||+|++.||++++||.. .||+|++. ||++++||.. .+++|+..||++. +|... ....||+
T Consensus 4 ~~~C~~C~~~GH~~~~Cp~~-------------~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~-~C~~~~~~~~C~~ 69 (124)
T 2lli_A 4 APKCNNCSQRGHLKKDCPHI-------------ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRS-QCPHKWKKVQCTL 69 (124)
T ss_dssp SSCCSSCSSSSCCTTTTTSC-------------CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTT-TSCCCCCCCSSSS
T ss_pred CCcccCCCCCCcCcccCcCC-------------cCcCCCCcCCccCcccCCcccccccCCCCCccc-cCcCcccCccCCC
Confidence 36899999999999999983 79999999 9999999985 6899999999973 45432 3478999
Q ss_pred cCCCCcCCCCCCCCCC
Q 037631 357 CGEKGHNIRTCPRRNL 372 (388)
Q Consensus 357 CGe~GH~ardCP~~~~ 372 (388)
|++.||+++|||+...
T Consensus 70 Cg~~GH~~~~Cp~~~~ 85 (124)
T 2lli_A 70 CKSKKHSKERCPSIWR 85 (124)
T ss_dssp SCSSCCCTTTCCCSTT
T ss_pred CCcCCcchhhCCCccc
Confidence 9999999999998765
No 4
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=99.40 E-value=7.3e-14 Score=110.49 Aligned_cols=66 Identities=23% Similarity=0.447 Sum_probs=37.3
Q ss_pred CCCccccCCCCCCCCCCCCCCCcceeeecCCCccccCCCCCCCCCCCCCCCCCcccCCCCCCCccccccCCCCcCCCCCC
Q 037631 289 RGHNRRTCPKSRLSYHNGTVSKHHRCQICRQRGHNRRTCPQVTGEKRHDNNGQKHIPTSASKTCTCRFCGEKGHNIRTCP 368 (388)
Q Consensus 289 ~GH~ardCp~~~~~~~~G~~~~~~~C~~CGe~GH~ardCP~~~~~~Cg~~Gh~~~~~~~~~~~~~Cy~CGe~GH~ardCP 368 (388)
.||+++||+++.......+......||+|++.||++++||... ....||+|++.||++++||
T Consensus 2 ~gh~~rdc~~~~~~~~~~~~~r~~~C~~Cg~~GH~a~~C~~~~------------------~~~~C~~Cg~~GH~ar~Cp 63 (74)
T 2li8_A 2 SGLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLPP------------------QPKKCHFCQSISHMVASCP 63 (74)
T ss_dssp ----------CCCCCCCSCCSTTSCCTTTCCSSSCTTTCSSCC------------------CCCCCTTTCCTTSCGGGCT
T ss_pred CccccCcCCCCCcCccccccCCCCcccccCCcCcCcccCCCCC------------------CCCccCCcCCcCCccCcCc
Confidence 4666666665543221112233567888888888888888643 1357888888888888888
Q ss_pred CCCC
Q 037631 369 RRNL 372 (388)
Q Consensus 369 ~~~~ 372 (388)
+...
T Consensus 64 ~~~~ 67 (74)
T 2li8_A 64 LKAQ 67 (74)
T ss_dssp TGGG
T ss_pred CCcC
Confidence 7653
No 5
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=99.39 E-value=1.2e-13 Score=111.50 Aligned_cols=63 Identities=17% Similarity=0.416 Sum_probs=43.3
Q ss_pred ccccccccccCccccCCCCCcCCCCcCcccceecccCCCccccCCCCCCCCCCCCCCCcceeeecCCCccccCCCCCCCC
Q 037631 253 RFYCKHCGREGHRKFYCPELKDGLTDRGFKCRLCGERGHNRRTCPKSRLSYHNGTVSKHHRCQICRQRGHNRRTCPQVTG 332 (388)
Q Consensus 253 ~~~Cf~CG~~GH~ar~CP~~~~~~~~~~~~C~~CG~~GH~ardCp~~~~~~~~G~~~~~~~C~~CGe~GH~ardCP~~~~ 332 (388)
.+.|++|++.||++++||+. ..||+|+..||++++|+.+.. ...||+||+.||+++|||+.+.
T Consensus 5 ~~~C~~Cg~~GH~~~~Cp~~--------~rcY~c~~~gh~~~~c~~p~~---------~~~CYnCG~~GH~~rdC~~~r~ 67 (83)
T 3nyb_B 5 KVQCTLCKSKKHSKERCPSI--------WRAYILVDDNEKAKPKVLPFH---------TIYCYNCGGKGHFGDDCKEKRS 67 (83)
T ss_dssp --CCSSSCCSSSCGGGCGGG--------TCCCCBC-------------C---------CCBCSSSSCBSSCGGGCSSCCS
T ss_pred cCCCCCCCCCCCccccCCCc--------ccccccccCCcccccccCCCC---------CCeecccCCCCcCcccCCcccc
Confidence 46899999999999999984 379999999999999987532 5799999999999999999764
No 6
>2jyl_A Capsid protein P24 (Ca); HIV-1, carboxy-terminal, dimerization domain, CTD, 3D- NMR, capsid protein (Ca), double mutant; NMR {Human immunodeficiency virus 1} PDB: 2k1c_A* 2l6e_A*
Probab=99.32 E-value=8.6e-14 Score=116.97 Aligned_cols=83 Identities=13% Similarity=0.119 Sum_probs=70.0
Q ss_pred hhcccCCccccccc--ccchhhhhhccccccccccCCCChhHH-----HHHHHHHHHhhhccchhHHHHHHhcCCchhHH
Q 037631 137 NAHSVSPLKVKEDD--EVDNLEIKVGVKKKSKRVYHSPPPEVG-----LKISRSLKSLNAKTGLFTKRMKIIHRDPKLHA 209 (388)
Q Consensus 137 ~~~~~spl~ike~~--~~~~~~~~~~~~~k~kR~y~~l~ae~~-----~~~t~~Lk~~na~~~~~s~~~Kal~~~p~l~a 209 (388)
.|+||||+.|.+++ |+++|++|++ |||+++++|++ .||+++|.++||||++ +.+|++++...++ +
T Consensus 15 ~~~~~sp~si~~IkQGpKEPf~dyVd------R~~k~l~ae~~~~~vK~~mt~tL~~qNANpdC-k~ilk~lg~~~tl-e 86 (105)
T 2jyl_A 15 VPRGSHMTSILDIRQGPKEPFRDYVD------RFYKTLRAEQASQEVKNAATETLLVQNANPDC-KTILKALGPGATL-E 86 (105)
T ss_dssp -------CCGGGCCCCSSSCHHHHHH------HHHHHHHHHCCCTTTTTSCHHHHHHHTSCHHH-HHHHHHHCTTCCH-H
T ss_pred eeeeecCcchhhhhcCCCCcHHHHHH------HHHHHHHHhhcchhhHHHhhhhhhHhhcCcch-hhHHHccCCCCCH-H
Confidence 58999999999999 8999999999 99999999886 5999999999999999 7899999999999 8
Q ss_pred HHHHHHHhcCChhHHHHH
Q 037631 210 QRVAAIKKAKGTAAARKH 227 (388)
Q Consensus 210 ~rvaA~q~~kG~~~~rr~ 227 (388)
+|+.||++++|+.++.+.
T Consensus 87 e~~~acqgvGgp~~Kar~ 104 (105)
T 2jyl_A 87 EMMTACQGVGGPGHKARV 104 (105)
T ss_dssp HHHHHHHHSCCCCSSSCC
T ss_pred HHHHHccccCCccccccC
Confidence 899999999999877653
No 7
>1baj_A GAG polyprotein; capsid, HIV-1 assembly protein, viral protein; 2.60A {Human immunodeficiency virus 1} SCOP: a.28.3.1
Probab=99.31 E-value=1.8e-13 Score=114.29 Aligned_cols=87 Identities=16% Similarity=0.202 Sum_probs=59.5
Q ss_pred cCCccccccc--ccchhhhhhccccccccccCCCChhHH-----HHHHHHHHHhhhccchhHHHHHHhcCCchhHHHHHH
Q 037631 141 VSPLKVKEDD--EVDNLEIKVGVKKKSKRVYHSPPPEVG-----LKISRSLKSLNAKTGLFTKRMKIIHRDPKLHAQRVA 213 (388)
Q Consensus 141 ~spl~ike~~--~~~~~~~~~~~~~k~kR~y~~l~ae~~-----~~~t~~Lk~~na~~~~~s~~~Kal~~~p~l~a~rva 213 (388)
|||++|.+++ |+++|++|++ |||+++++|++ .||+++|.++||||++ +.+||+++...++ ++|+.
T Consensus 1 ~sp~s~~~ikQGpkepf~d~v~------R~~k~l~~e~~~~~vK~~~~~tL~~qnanp~C-k~~lk~l~~~~~l-~e~~~ 72 (101)
T 1baj_A 1 MSPTSILDIRQGPKEPFRDYVD------RFYKTLRAEQASQEVKNWMTETLLVQNANPDC-KTILKALGPGATL-EEMMT 72 (101)
T ss_dssp ---CGGGGCCCCSSCCHHHHHH------HHHHHHHHTTCCHHHHHHHHHTHHHHTSCHHH-HHHHHHHCSSCCH-HHHHH
T ss_pred CCCcchhhhhcCCCCcHHHHHH------HHHHHHHHhhccHHHHHHHhhhHHHHhhchhh-hHHHHccCCCCCH-HHHHH
Confidence 6899999999 9999999999 99988888775 5999999999999999 7899999999999 88999
Q ss_pred HHHhcCChhHHHHHHHHHHHhh
Q 037631 214 AIKKAKGTAAARKHASETLKAF 235 (388)
Q Consensus 214 A~q~~kG~~~~rr~~seam~~~ 235 (388)
||++++|+.++.+.++++|..+
T Consensus 73 ac~~vg~p~~ka~~laea~~q~ 94 (101)
T 1baj_A 73 ACQGVGGPGHKARVLAEAMSQV 94 (101)
T ss_dssp HC--------------------
T ss_pred hccccCCcchhhHHHHHHHHHh
Confidence 9999999999999999998764
No 8
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=99.24 E-value=2.4e-12 Score=101.82 Aligned_cols=61 Identities=21% Similarity=0.447 Sum_probs=41.1
Q ss_pred cCccccCCCCCcCCC----CcCcccceecccCCCccccCCCCCCCCCCCCCCCcceeeecCCCccccCCCCCCC
Q 037631 262 EGHRKFYCPELKDGL----TDRGFKCRLCGERGHNRRTCPKSRLSYHNGTVSKHHRCQICRQRGHNRRTCPQVT 331 (388)
Q Consensus 262 ~GH~ar~CP~~~~~~----~~~~~~C~~CG~~GH~ardCp~~~~~~~~G~~~~~~~C~~CGe~GH~ardCP~~~ 331 (388)
.||++|+|+.+.... ..+...||+||+.||++++|+.... ...||+|++.||++++||+..
T Consensus 2 ~gh~~rdc~~~~~~~~~~~~~r~~~C~~Cg~~GH~a~~C~~~~~---------~~~C~~Cg~~GH~ar~Cp~~~ 66 (74)
T 2li8_A 2 SGLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLPPQ---------PKKCHFCQSISHMVASCPLKA 66 (74)
T ss_dssp ----------CCCCCCCSCCSTTSCCTTTCCSSSCTTTCSSCCC---------CCCCTTTCCTTSCGGGCTTGG
T ss_pred CccccCcCCCCCcCccccccCCCCcccccCCcCcCcccCCCCCC---------CCccCCcCCcCCccCcCcCCc
Confidence 599999999875432 1245789999999999999997531 468999999999999999865
No 9
>3ds4_A HIV-1 capsid protein; HIV, mutant, polyprotein, complex(viral protein/peptide), mainly alpha; 1.12A {Human immunodeficiency virus 1} PDB: 3dph_A 1a43_A 2xt1_A 2buo_A 3lry_A 2kod_A 3ds1_A 3dtj_A 3ds0_A 3ds5_A 3ds2_A 3ds3_A 2jo0_A 2jyg_A 2xxm_A 2xv6_A 2ont_A 1aum_A 1a8o_A 4arg_B ...
Probab=99.23 E-value=1.4e-12 Score=105.89 Aligned_cols=78 Identities=15% Similarity=0.162 Sum_probs=64.8
Q ss_pred CCccccccc--ccchhhhhhccccccccccCCCChhHH-----HHHHHHHHHhhhccchhHHHHHHhcCCchhHHHHHHH
Q 037631 142 SPLKVKEDD--EVDNLEIKVGVKKKSKRVYHSPPPEVG-----LKISRSLKSLNAKTGLFTKRMKIIHRDPKLHAQRVAA 214 (388)
Q Consensus 142 spl~ike~~--~~~~~~~~~~~~~k~kR~y~~l~ae~~-----~~~t~~Lk~~na~~~~~s~~~Kal~~~p~l~a~rvaA 214 (388)
||+++.+++ |+++|+++++ |||+++++|++ .||+++|.++|||+++ +.+|++++.+.++ ++|+.|
T Consensus 1 ~p~s~~~i~QGpkEpf~dfv~------rl~k~l~~e~~~~~vK~~m~~tL~~qNAnp~C-k~il~~l~~~~~l-ee~~~a 72 (86)
T 3ds4_A 1 SPTSILDIRQGPKEPFRDYVD------RFYKTLRAEQASQEVKNWMTETLLVQNANPDC-KTILKALGPGATS-EEMMTA 72 (86)
T ss_dssp --CCGGGCCCCTTSCHHHHHH------HHHHHHHHC-CCHHHHHHHHHHHHHHTSCHHH-HHHHHHHCTTCCH-HHHHHH
T ss_pred CcchhhccccCCCCcHHHHHH------HHHHHHHHhccchhHHHHHHHhHHHHhccHHH-HHHHHccCCCCCH-HHHHHH
Confidence 689999998 9999999999 99999887764 5999999999999999 7899999999999 999999
Q ss_pred HHhcCChhHHHHH
Q 037631 215 IKKAKGTAAARKH 227 (388)
Q Consensus 215 ~q~~kG~~~~rr~ 227 (388)
|++++|+.++.++
T Consensus 73 C~~vG~p~~K~~~ 85 (86)
T 3ds4_A 73 CQGVGGPGHKARV 85 (86)
T ss_dssp HTTSSCC------
T ss_pred ccccCCccccccc
Confidence 9999999998764
No 10
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=99.06 E-value=6.7e-11 Score=82.13 Aligned_cols=38 Identities=37% Similarity=0.849 Sum_probs=30.3
Q ss_pred eeeecCCCccccCCCCCCCCCCCCCCCCCcccCCCCCCCccccccCCCCcCCCCCCC
Q 037631 313 RCQICRQRGHNRRTCPQVTGEKRHDNNGQKHIPTSASKTCTCRFCGEKGHNIRTCPR 369 (388)
Q Consensus 313 ~C~~CGe~GH~ardCP~~~~~~Cg~~Gh~~~~~~~~~~~~~Cy~CGe~GH~ardCP~ 369 (388)
.||+|++.||++++||.+. ...||+|++.||++++||+
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 5888888888888888652 2568888888888888885
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=99.05 E-value=8.4e-11 Score=85.58 Aligned_cols=43 Identities=35% Similarity=0.801 Sum_probs=32.3
Q ss_pred cceeeecCCCccccCCCCCCCCCCCCCCCCCcccCCCCCCCccccccCCCCcCCCCCCCCCC
Q 037631 311 HHRCQICRQRGHNRRTCPQVTGEKRHDNNGQKHIPTSASKTCTCRFCGEKGHNIRTCPRRNL 372 (388)
Q Consensus 311 ~~~C~~CGe~GH~ardCP~~~~~~Cg~~Gh~~~~~~~~~~~~~Cy~CGe~GH~ardCP~~~~ 372 (388)
...||+|++.||++++||.+. ...||+||+.||++++||+...
T Consensus 6 ~~~C~~Cg~~GH~a~~C~~~~-------------------~~~C~~Cg~~GH~~~~C~~~~~ 48 (49)
T 2ec7_A 6 VIRCWNCGKEGHSARQCRAPR-------------------RQGCWKCGKTGHVMAKCPERQA 48 (49)
T ss_dssp CCBCTTTCCBTCCTTTCCCSS-------------------CCSCSSSCCSSCCGGGCCSSCC
T ss_pred cCeeeecCCCCcChhhCcCCC-------------------CCeeCcCCCcCCccCCCcCCCC
Confidence 457888888888888888653 2468888888888888887653
No 12
>1qrj_B HTLV-I capsid protein; retrovirus, two-domain protein, alpha helical protein, heteronuclear spectroscopy; NMR {Human t-cell lymphotrophic virus TYPE1} SCOP: a.28.3.1 a.73.1.1
Probab=99.03 E-value=2.1e-11 Score=112.86 Aligned_cols=85 Identities=15% Similarity=0.019 Sum_probs=76.0
Q ss_pred Ccchh-hcccCCccccccc--ccchhhhhhccccccccccCCCChhHH-----HHHHHHHHHhhhccchhHHHHHHhc-C
Q 037631 133 QPWEN-AHSVSPLKVKEDD--EVDNLEIKVGVKKKSKRVYHSPPPEVG-----LKISRSLKSLNAKTGLFTKRMKIIH-R 203 (388)
Q Consensus 133 ~~~~~-~~~~spl~ike~~--~~~~~~~~~~~~~k~kR~y~~l~ae~~-----~~~t~~Lk~~na~~~~~s~~~Kal~-~ 203 (388)
..|.+ +++++|+++.+++ |+++|++|++ |||+.+++|++ .||+++|.++||||++ +.+||+++ .
T Consensus 104 ~a~~ki~~~~~~~s~~~IkQGpkEPf~dfVd------R~~k~l~ae~~~~~vK~~~~~tL~~qNANpdC-k~ilk~l~~~ 176 (199)
T 1qrj_B 104 AAFAALPGSAKDPSWASILQGLEEPYHAFVE------RLNIALDNGLPEGTPKDPILRSLAYSNANKEC-QKLLQARGHT 176 (199)
T ss_dssp HHHHTSSSSCCCCSGGGCCBCTTSCHHHHHH------HHHHHHHTTCCTTSCCHHHHHHHHTTTBCHHH-HHHHHHTTCS
T ss_pred HHHHHHhcccCCCCcchhhcCCCCcHHHHHH------HHHHHHHhhcCchhhhhHHHHHHHHHhcCchh-HHHHHhcCCC
Confidence 45655 8999999999999 9999999999 99999888886 5999999999999999 88999998 8
Q ss_pred CchhHHHHHHHHHhcCChhHHHH
Q 037631 204 DPKLHAQRVAAIKKAKGTAAARK 226 (388)
Q Consensus 204 ~p~l~a~rvaA~q~~kG~~~~rr 226 (388)
..++ ++|+.||++++ |.++.+
T Consensus 177 ~~tl-ee~~~aCq~vg-p~~ka~ 197 (199)
T 1qrj_B 177 NSPL-GDMLRACQTWT-PKDKTK 197 (199)
T ss_dssp SSCH-HHHHHHHTTCC-CCCCCC
T ss_pred CCCH-HHHHHHhccCC-CccccC
Confidence 8999 89999999976 777654
No 13
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=99.01 E-value=1.3e-10 Score=80.60 Aligned_cols=37 Identities=32% Similarity=0.844 Sum_probs=22.0
Q ss_pred ccccccccCccccCCCCCcCCCCcCcccceecccCCCccccCC
Q 037631 255 YCKHCGREGHRKFYCPELKDGLTDRGFKCRLCGERGHNRRTCP 297 (388)
Q Consensus 255 ~Cf~CG~~GH~ar~CP~~~~~~~~~~~~C~~CG~~GH~ardCp 297 (388)
.||+||++||++++||.++. ..||+||+.||++++||
T Consensus 2 ~C~~Cg~~GH~a~~C~~~~~------~~C~~Cg~~GH~~~~C~ 38 (39)
T 2a51_A 2 TCFNCGKPGHTARMCRQPRQ------EGCWNCGSKEHRFAQCP 38 (39)
T ss_dssp BCTTTCCBSSCTTTCCSCCC------SSCTTTCCSSSCTTTSC
T ss_pred eeeccCCCCcccccCCCCCC------CccccCCCCCCccCcCc
Confidence 46666666666666665422 45666666666666665
No 14
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=98.99 E-value=2e-10 Score=87.18 Aligned_cols=49 Identities=27% Similarity=0.695 Sum_probs=35.6
Q ss_pred cceeeecCCCccccCCCCCCCCCCCCCCCCCcccCCCCCCCccccccCCCCcCCCCCCCCCCC
Q 037631 311 HHRCQICRQRGHNRRTCPQVTGEKRHDNNGQKHIPTSASKTCTCRFCGEKGHNIRTCPRRNLE 373 (388)
Q Consensus 311 ~~~C~~CGe~GH~ardCP~~~~~~Cg~~Gh~~~~~~~~~~~~~Cy~CGe~GH~ardCP~~~~s 373 (388)
...||+|++.||++++||...... .....||+|++.||+++|||+...+
T Consensus 4 ~~~C~~Cg~~GH~a~~C~~~~~~~--------------~~~~~C~~Cg~~GH~ar~C~~~~~~ 52 (61)
T 2ihx_A 4 RGLCYTCGSPGHYQAQCPKKRKSG--------------NSRERCQLCNGMGHNAKQCRKRDGN 52 (61)
T ss_dssp TTBCSSSCCBTCCGGGCTTTTSSS--------------CCCSBCTTTCCBSSCGGGCCCCC--
T ss_pred CCcccccCCCCeehhhCcCCcCCC--------------CCCCeeCCCCCCCCCcCCCcCCCcC
Confidence 467888888888888888764210 1236799999999999999988764
No 15
>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=98.96 E-value=1.8e-10 Score=85.44 Aligned_cols=43 Identities=28% Similarity=0.757 Sum_probs=31.9
Q ss_pred cceeeecCCCccccCCCCCCCCCCCCCCCCCcccCCCCCCCccccccCCCCcCCCCCCCCCC
Q 037631 311 HHRCQICRQRGHNRRTCPQVTGEKRHDNNGQKHIPTSASKTCTCRFCGEKGHNIRTCPRRNL 372 (388)
Q Consensus 311 ~~~C~~CGe~GH~ardCP~~~~~~Cg~~Gh~~~~~~~~~~~~~Cy~CGe~GH~ardCP~~~~ 372 (388)
...||+|++.||++++||.+. ...||+|++.||+++|||+.+.
T Consensus 12 ~~~C~~Cg~~GH~a~~C~~~~-------------------~~~C~~Cg~~GH~~~~C~~~~~ 54 (55)
T 1a1t_A 12 TVKCFNCGKEGHIAKNCRAPR-------------------KKGCWKCGKEGHQMKDCTERQA 54 (55)
T ss_dssp TCBCTTTCCBSSCGGGCSSCS-------------------CCBCTTTCCBSSCGGGCSSSCC
T ss_pred CcceeeeCCCCcChhhcCCCC-------------------CCEeCCCCCcCCccCCCcCcCC
Confidence 457888888888888887642 2468888888888888887653
No 16
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1
Probab=98.95 E-value=3.8e-10 Score=82.08 Aligned_cols=41 Identities=34% Similarity=0.814 Sum_probs=24.4
Q ss_pred ccccccccccCccccCCCCCcCCCCcCcccceecccCCCccccCCCC
Q 037631 253 RFYCKHCGREGHRKFYCPELKDGLTDRGFKCRLCGERGHNRRTCPKS 299 (388)
Q Consensus 253 ~~~Cf~CG~~GH~ar~CP~~~~~~~~~~~~C~~CG~~GH~ardCp~~ 299 (388)
...||+||+.||++++||.+.. ..||+||+.||++++||+.
T Consensus 6 ~~~C~~Cg~~GH~a~~C~~~~~------~~C~~Cg~~GH~~~~C~~~ 46 (49)
T 2ec7_A 6 VIRCWNCGKEGHSARQCRAPRR------QGCWKCGKTGHVMAKCPER 46 (49)
T ss_dssp CCBCTTTCCBTCCTTTCCCSSC------CSCSSSCCSSCCGGGCCSS
T ss_pred cCeeeecCCCCcChhhCcCCCC------CeeCcCCCcCCccCCCcCC
Confidence 3456666666666666665432 4566666666666666653
No 17
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=98.95 E-value=2.3e-10 Score=78.49 Aligned_cols=36 Identities=28% Similarity=0.650 Sum_probs=26.4
Q ss_pred eeeecCCCccccCCCCCCCCCCCCCCCCCcccCCCCCCCccccccCCCCcCCCCCCC
Q 037631 313 RCQICRQRGHNRRTCPQVTGEKRHDNNGQKHIPTSASKTCTCRFCGEKGHNIRTCPR 369 (388)
Q Consensus 313 ~C~~CGe~GH~ardCP~~~~~~Cg~~Gh~~~~~~~~~~~~~Cy~CGe~GH~ardCP~ 369 (388)
.||+|++.||++++||.+ ..||+|++.||++++||+
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 357888888888888774
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=98.94 E-value=3.3e-10 Score=85.41 Aligned_cols=49 Identities=18% Similarity=0.461 Sum_probs=18.4
Q ss_pred eeeecCCCccccCCCCCCCCCCCCCCCCCcccCCCCCCCccccccCCCCcCCCCCCCCCC
Q 037631 313 RCQICRQRGHNRRTCPQVTGEKRHDNNGQKHIPTSASKTCTCRFCGEKGHNIRTCPRRNL 372 (388)
Q Consensus 313 ~C~~CGe~GH~ardCP~~~~~~Cg~~Gh~~~~~~~~~~~~~Cy~CGe~GH~ardCP~~~~ 372 (388)
.||+|++.||++++||...... . .......||+|++.||+++|||+...
T Consensus 3 ~Cf~Cg~~GH~a~~C~~~~~~~------~-----~~~~~~~C~~Cg~~GH~ar~C~~~~~ 51 (60)
T 1cl4_A 3 SCFKCGKKGHFAKNCHEHAHNN------A-----EPKVPGLCPRCKRGKHWANECKSKTD 51 (60)
T ss_dssp -------------------------------------CCCSCSSCSSCSSCSTTCCCTTS
T ss_pred ccccCCCCCcCHhhCcCCCCCc------c-----ccCCCcceeECCCCCCccCcCCCccc
Confidence 5778888888888887654210 0 00124679999999999999988764
No 19
>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=98.93 E-value=4.8e-10 Score=85.69 Aligned_cols=43 Identities=26% Similarity=0.690 Sum_probs=28.1
Q ss_pred cceeeecCCCccccCCCCCCCCCCCCCCCCCcccCCCCCCCccccccCCCCcCCCCCCCCC
Q 037631 311 HHRCQICRQRGHNRRTCPQVTGEKRHDNNGQKHIPTSASKTCTCRFCGEKGHNIRTCPRRN 371 (388)
Q Consensus 311 ~~~C~~CGe~GH~ardCP~~~~~~Cg~~Gh~~~~~~~~~~~~~Cy~CGe~GH~ardCP~~~ 371 (388)
...||+|++.||++++||... ....||+|++.||+++|||+..
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 356777777777777776542 1245777777777777777654
No 20
>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=98.89 E-value=8.7e-10 Score=81.67 Aligned_cols=41 Identities=32% Similarity=0.798 Sum_probs=30.7
Q ss_pred ccccccccccCccccCCCCCcCCCCcCcccceecccCCCccccCCCC
Q 037631 253 RFYCKHCGREGHRKFYCPELKDGLTDRGFKCRLCGERGHNRRTCPKS 299 (388)
Q Consensus 253 ~~~Cf~CG~~GH~ar~CP~~~~~~~~~~~~C~~CG~~GH~ardCp~~ 299 (388)
...||+||+.||++++||.+.. ..||+||+.||++++||..
T Consensus 12 ~~~C~~Cg~~GH~a~~C~~~~~------~~C~~Cg~~GH~~~~C~~~ 52 (55)
T 1a1t_A 12 TVKCFNCGKEGHIAKNCRAPRK------KGCWKCGKEGHQMKDCTER 52 (55)
T ss_dssp TCBCTTTCCBSSCGGGCSSCSC------CBCTTTCCBSSCGGGCSSS
T ss_pred CcceeeeCCCCcChhhcCCCCC------CEeCCCCCcCCccCCCcCc
Confidence 4578888888888888877532 5678888888888887764
No 21
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=98.89 E-value=6.2e-10 Score=76.34 Aligned_cols=34 Identities=32% Similarity=0.786 Sum_probs=17.5
Q ss_pred cccccccCccccCCCCCcCCCCcCcccceecccCCCccccCC
Q 037631 256 CKHCGREGHRKFYCPELKDGLTDRGFKCRLCGERGHNRRTCP 297 (388)
Q Consensus 256 Cf~CG~~GH~ar~CP~~~~~~~~~~~~C~~CG~~GH~ardCp 297 (388)
||+||+.||++++||.+ ..||+||+.||++++||
T Consensus 3 C~~Cg~~GH~~~~C~~~--------~~C~~Cg~~GH~a~~C~ 36 (37)
T 2bl6_A 3 CYNCGKPGHLSSQCRAP--------KVCFKCKQPGHFSKQCR 36 (37)
T ss_dssp BSSSCCSSCCTTTSSCB--------TTCSSCCCTTGGGGTTC
T ss_pred ccccCCCCcchhhCcCc--------CeEccCCCcCCccCcCc
Confidence 55555555555555542 24555555555555554
No 22
>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=98.86 E-value=1.1e-09 Score=83.74 Aligned_cols=41 Identities=27% Similarity=0.536 Sum_probs=20.5
Q ss_pred cccccccccCccccCCCCCcCCCCcCcccceecccCCCccccCCCC
Q 037631 254 FYCKHCGREGHRKFYCPELKDGLTDRGFKCRLCGERGHNRRTCPKS 299 (388)
Q Consensus 254 ~~Cf~CG~~GH~ar~CP~~~~~~~~~~~~C~~CG~~GH~ardCp~~ 299 (388)
..||+|+++||++++||.+.. ...||+|++.||++++||..
T Consensus 8 ~~C~~Cg~~GH~a~~C~~~~~-----~~~C~~Cg~~GH~ar~Cp~~ 48 (63)
T 2cqf_A 8 DRCYNCGGLDHHAKECKLPPQ-----PKKCHFCQSISHMVASCPLK 48 (63)
T ss_dssp CCCSSSCCSSSCTTTCCSCCC-----SSCCTTTCCSSSCTTTCTGG
T ss_pred CcccccCCCCcChhhCCCCCC-----CCccCCcCCcCCccCcCCCc
Confidence 345555555555555554321 13455555555555555543
No 23
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=98.83 E-value=2e-09 Score=81.57 Aligned_cols=46 Identities=35% Similarity=0.797 Sum_probs=23.7
Q ss_pred ccccccccccCccccCCCCCcCCCCcCcccceecccCCCccccCCCC
Q 037631 253 RFYCKHCGREGHRKFYCPELKDGLTDRGFKCRLCGERGHNRRTCPKS 299 (388)
Q Consensus 253 ~~~Cf~CG~~GH~ar~CP~~~~~~~~~~~~C~~CG~~GH~ardCp~~ 299 (388)
...||+|+++||++++||...... .....||+||+.||++++||+.
T Consensus 4 ~~~C~~Cg~~GH~a~~C~~~~~~~-~~~~~C~~Cg~~GH~ar~C~~~ 49 (61)
T 2ihx_A 4 RGLCYTCGSPGHYQAQCPKKRKSG-NSRERCQLCNGMGHNAKQCRKR 49 (61)
T ss_dssp TTBCSSSCCBTCCGGGCTTTTSSS-CCCSBCTTTCCBSSCGGGCCCC
T ss_pred CCcccccCCCCeehhhCcCCcCCC-CCCCeeCCCCCCCCCcCCCcCC
Confidence 345666666666666666643210 0123455555555555555544
No 24
>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=98.81 E-value=1.5e-09 Score=81.79 Aligned_cols=18 Identities=39% Similarity=0.838 Sum_probs=0.0
Q ss_pred ccccccccCccccCCCCC
Q 037631 255 YCKHCGREGHRKFYCPEL 272 (388)
Q Consensus 255 ~Cf~CG~~GH~ar~CP~~ 272 (388)
.||+|+++||++++||..
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 466666666666666654
No 25
>3h47_A Ca, capsid protein P24; hexamer, engineered disulfide bonds, viral protein; 1.90A {Human immunodeficiency virus type 1} PDB: 3h4e_A 2lf4_A 3mge_A 3p05_A 3p0a_A 3dik_A 3nte_A 1e6j_P
Probab=98.79 E-value=5.5e-10 Score=105.48 Aligned_cols=84 Identities=15% Similarity=0.161 Sum_probs=61.5
Q ss_pred hhhcccCCccccccc--ccchhhhhhccccccccccCCCChhHH-----HHHHHHHHHhhhccchhHHHHHHhcCCchhH
Q 037631 136 ENAHSVSPLKVKEDD--EVDNLEIKVGVKKKSKRVYHSPPPEVG-----LKISRSLKSLNAKTGLFTKRMKIIHRDPKLH 208 (388)
Q Consensus 136 ~~~~~~spl~ike~~--~~~~~~~~~~~~~k~kR~y~~l~ae~~-----~~~t~~Lk~~na~~~~~s~~~Kal~~~p~l~ 208 (388)
+-+++|+|+++.+++ |+++|+++++ |||+++++|++ .||+++|..+|||+++ +.+|++|+.+.++
T Consensus 140 kivk~~~P~s~~~IkQGpkEPf~DfV~------Rl~kal~~e~~~~~vK~~m~~tL~~qNANp~C-k~ilk~l~~~a~L- 211 (231)
T 3h47_A 140 KIVRMYSPTSILDIRQGPKEPFRDYVD------RFYKTLRAEQASQEVKNAATETLLVQNANPDC-KTILKALGPGATL- 211 (231)
T ss_dssp HHHHHHCCSCGGGCCCCTTCCHHHHHH------HHHHHHHHC------------CHHHHTSCHHH-HHHHHHHCTTCCH-
T ss_pred HHhhcccccchhhhccCCCCcHHHHHH------HHHHHHHhhcccchhhhHhHHhHHhhccCHHH-HHHHhccCCCCCH-
Confidence 447899999999888 9999999999 99999988775 4999999999999999 7899999999999
Q ss_pred HHHHHHHHhcCChhHHHHH
Q 037631 209 AQRVAAIKKAKGTAAARKH 227 (388)
Q Consensus 209 a~rvaA~q~~kG~~~~rr~ 227 (388)
++++.||++++|+.++.+.
T Consensus 212 ee~i~aCq~VG~p~hKar~ 230 (231)
T 3h47_A 212 EEMMTACQGVGGPGHKARV 230 (231)
T ss_dssp HHHHHHTC-----------
T ss_pred HHHHHHccccCChhhhccc
Confidence 9999999999999988764
No 26
>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=98.78 E-value=2.3e-09 Score=94.84 Aligned_cols=45 Identities=24% Similarity=0.642 Sum_probs=36.4
Q ss_pred cceeeecCCCccccCCCCCCCCCCCCCCCCCcccCCCCCCCccccccCCCCcCCCCCCCCCCC
Q 037631 311 HHRCQICRQRGHNRRTCPQVTGEKRHDNNGQKHIPTSASKTCTCRFCGEKGHNIRTCPRRNLE 373 (388)
Q Consensus 311 ~~~C~~CGe~GH~ardCP~~~~~~Cg~~Gh~~~~~~~~~~~~~Cy~CGe~GH~ardCP~~~~s 373 (388)
...||+|++.||++++||.... ...||+|++.||++++||+....
T Consensus 97 ~~~C~~Cg~~GH~a~~C~~~~~------------------~~~C~~Cg~~GH~~r~Cp~~~~~ 141 (148)
T 3ts2_A 97 GDRCYNCGGLDHHAKECKLPPQ------------------PKKCHFCQSINHMVASCPLKAQQ 141 (148)
T ss_dssp SCCCTTTCCSSCCGGGCCSCCC------------------CCCCTTTCCSSCCGGGCTTTTC-
T ss_pred CCcccEeCCccchhhhCCCCCC------------------CCcccccCCcCCEeccCcCCCCC
Confidence 4679999999999999987532 35799999999999999987654
No 27
>3gv2_A Ca, fusion protein consisting of capsid protein P24, carbon dioxide-concentrating mechanism...; hexameric retroviral capsid; 7.00A {Human immunodeficiency virus type 1}
Probab=98.67 E-value=2.8e-09 Score=105.70 Aligned_cols=85 Identities=18% Similarity=0.164 Sum_probs=67.2
Q ss_pred hhhcccCCccccccc--ccchhhhhhccccccccccCCCChhHH-----HHHHHHHHHhhhccchhHHHHHHhcCCchhH
Q 037631 136 ENAHSVSPLKVKEDD--EVDNLEIKVGVKKKSKRVYHSPPPEVG-----LKISRSLKSLNAKTGLFTKRMKIIHRDPKLH 208 (388)
Q Consensus 136 ~~~~~~spl~ike~~--~~~~~~~~~~~~~k~kR~y~~l~ae~~-----~~~t~~Lk~~na~~~~~s~~~Kal~~~p~l~ 208 (388)
+-+|+|+|+++.+++ |+++|+++++ |||+++++|++ .||+++|..+|||+++ +.+|++++.+.+|
T Consensus 140 ki~~m~~P~s~~~IkQGPkEPf~DfVd------Rl~kal~~e~~~~~vK~~mt~tL~~qNANp~C-k~ilk~lg~~a~L- 211 (342)
T 3gv2_A 140 KIVRMYSPTSILDIRQGPKEPFRDYVD------RFYKTLRAEQASQEVKNAATETLLVQNANPDC-KTILKALGPGATL- 211 (342)
T ss_dssp HHHTTTCSSCGGGCCCCTTCCHHHHHH------HHHHHHHHTTCCHHHHHHHHHTHHHHTSCHHH-HHHHHHHCTTCCH-
T ss_pred hccccccccchhhhccCCCCcHHHHHH------HHHHHHHhhccccchhhhhhhhhhhhccCHHH-HHHHhccCCCCCH-
Confidence 447899999999988 9999999999 99998887774 5999999999999999 8899999999999
Q ss_pred HHHHHHHHhcCChhHHHHHH
Q 037631 209 AQRVAAIKKAKGTAAARKHA 228 (388)
Q Consensus 209 a~rvaA~q~~kG~~~~rr~~ 228 (388)
++|+.||++++|+.++.-.+
T Consensus 212 ee~~~aCq~VG~p~hK~m~~ 231 (342)
T 3gv2_A 212 EEMMTACQGVGGTRPELMSA 231 (342)
T ss_dssp HHHHHHTC------------
T ss_pred HHHHHHccccCCchhhhhhc
Confidence 89999999999998876443
No 28
>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=2.3e-08 Score=88.35 Aligned_cols=42 Identities=26% Similarity=0.516 Sum_probs=23.4
Q ss_pred ccccccccccCccccCCCCCcCCCCcCcccceecccCCCccccCCCC
Q 037631 253 RFYCKHCGREGHRKFYCPELKDGLTDRGFKCRLCGERGHNRRTCPKS 299 (388)
Q Consensus 253 ~~~Cf~CG~~GH~ar~CP~~~~~~~~~~~~C~~CG~~GH~ardCp~~ 299 (388)
...||+||+.||++++||.+.. ...||+||+.||++++||+.
T Consensus 97 ~~~C~~Cg~~GH~a~~C~~~~~-----~~~C~~Cg~~GH~~r~Cp~~ 138 (148)
T 3ts2_A 97 GDRCYNCGGLDHHAKECKLPPQ-----PKKCHFCQSINHMVASCPLK 138 (148)
T ss_dssp SCCCTTTCCSSCCGGGCCSCCC-----CCCCTTTCCSSCCGGGCTTT
T ss_pred CCcccEeCCccchhhhCCCCCC-----CCcccccCCcCCEeccCcCC
Confidence 3456666666666666655322 14566666666666666553
No 29
>1eia_A EIAV capsid protein P26; viral capsid, HIV, lentivirus, viral protein; 2.70A {Equine infectious anemia virus} SCOP: a.28.3.1 a.73.1.1 PDB: 2eia_A
Probab=98.54 E-value=6.9e-09 Score=96.58 Aligned_cols=76 Identities=13% Similarity=0.119 Sum_probs=67.7
Q ss_pred hh-hc-ccCCccccccc--ccchhhhhhccccccccccCCCChhHH-----HHHHHHHHHhhhccchhHHHHHHhcCCch
Q 037631 136 EN-AH-SVSPLKVKEDD--EVDNLEIKVGVKKKSKRVYHSPPPEVG-----LKISRSLKSLNAKTGLFTKRMKIIHRDPK 206 (388)
Q Consensus 136 ~~-~~-~~spl~ike~~--~~~~~~~~~~~~~k~kR~y~~l~ae~~-----~~~t~~Lk~~na~~~~~s~~~Kal~~~p~ 206 (388)
.+ |+ +++|+++.+++ |+++|++|++ |||++++++++ .||+++|.++||||++ +.+||+++...+
T Consensus 123 ~k~v~~~~sp~s~~~IkQGpKEPf~dfVd------R~~k~l~~e~~~~~vK~~mt~tL~~qNANpdC-k~ilk~lg~~~t 195 (207)
T 1eia_A 123 SEGIKVMIGKPKAQNIRQGAKEPYPEFVD------RLLSQIKSEGHPQEISKFLTDTLTIQNANEEC-RNAMRHLRPEDT 195 (207)
T ss_dssp HHHHHHHHTSCCGGGCCCCTTCCHHHHHH------HHHHHHHTTCCCTTHHHHHHHHHHHHTSCHHH-HHHTTTCCTTSC
T ss_pred HHHHHHhcccccccccccCCCCcHHHHHH------HHHHHHHhhccchhhhHHhhhhHHHHhcCHHH-HHHHHhhCCCCC
Confidence 44 67 69999999999 8999999999 89988777764 6999999999999999 789999999998
Q ss_pred hHHHHHHHHHhcC
Q 037631 207 LHAQRVAAIKKAK 219 (388)
Q Consensus 207 l~a~rvaA~q~~k 219 (388)
+ ++|+.||++++
T Consensus 196 L-ee~~~aCqgvG 207 (207)
T 1eia_A 196 L-EEKMYACRDIG 207 (207)
T ss_dssp H-HHHHHHTTTCC
T ss_pred H-HHHHHHhccCC
Confidence 8 88999998864
No 30
>1eoq_A GAG polyprotein capsid protein P27; virus/viral protein; NMR {Rous sarcoma virus - prague C} SCOP: a.28.3.1
Probab=98.52 E-value=1.9e-08 Score=82.60 Aligned_cols=56 Identities=2% Similarity=-0.078 Sum_probs=49.3
Q ss_pred ccchhhhhhccccccccccCCCChhHH-----HHHHHHHHHhhhccchhHHHHHHh-cCCchhHHHHHHH
Q 037631 151 EVDNLEIKVGVKKKSKRVYHSPPPEVG-----LKISRSLKSLNAKTGLFTKRMKII-HRDPKLHAQRVAA 214 (388)
Q Consensus 151 ~~~~~~~~~~~~~k~kR~y~~l~ae~~-----~~~t~~Lk~~na~~~~~s~~~Kal-~~~p~l~a~rvaA 214 (388)
|+|+|++|+| |||+++++|++ .||+++|++|||||++ +.+||++ +...++ ++|+.=
T Consensus 7 PkEPFrDyVd------Rf~kalraeqa~~~vK~wmt~tLlvQNANPdC-k~iLkal~g~~~tl-~em~~y 68 (96)
T 1eoq_A 7 PSESFVDFAN------RLIKAVEGSDLPPSARAPVIIDCFRQKSQPDI-QQLIRTAPSTLTTP-GEIIKY 68 (96)
T ss_dssp TTCCHHHHHH------HHHHHHHTTTCCHHHHHHHHHHHHHHHSCHHH-HHHHHHCCSCCCSH-HHHHHH
T ss_pred CCCcHHHHHH------HHHHHHHHhhccHhHhhhhHHHHHHHhcCHHH-HHHHHccCCCCCCH-HHHHHH
Confidence 8999999999 99999999875 5999999999999999 8999999 777887 566443
No 31
>1d1d_A Protein (capsid protein); two independent domains helical bundles, virus/viral protein; NMR {Rous sarcoma virus} SCOP: a.28.3.1 a.73.1.1
Probab=98.45 E-value=2.7e-08 Score=95.55 Aligned_cols=83 Identities=4% Similarity=-0.021 Sum_probs=68.0
Q ss_pred cchhh--cccCCccccccc--ccchhhhhhccccccccccCCCChhHH-----HHHHHHHHHhhhccchhHHHHHH----
Q 037631 134 PWENA--HSVSPLKVKEDD--EVDNLEIKVGVKKKSKRVYHSPPPEVG-----LKISRSLKSLNAKTGLFTKRMKI---- 200 (388)
Q Consensus 134 ~~~~~--~~~spl~ike~~--~~~~~~~~~~~~~k~kR~y~~l~ae~~-----~~~t~~Lk~~na~~~~~s~~~Ka---- 200 (388)
-|..+ ++++|+++.+++ |+|+|++||| |||++|++|++ .||..+++++|||+++ +.+|++
T Consensus 161 aw~~l~~~~~s~~si~~IkQGPkEpf~dfVd------Rl~kalrae~~~~~~~~~~~~~~l~qnAnpdc-k~~lraal~p 233 (262)
T 1d1d_A 161 AFREVARLAEPAGPWADITQGPSESFVDFAN------RLIKAVEGSDLPPSARAPVIIDCFRQKSQPDI-QQLIRAAPST 233 (262)
T ss_dssp HHHHHHHCCCCCCTTTSCCCCSSSCHHHHHH------HHHHHHHTSSCCTTTTTHHHHHHHTTSSCHHH-HHHHHTSCTT
T ss_pred HHHHhccccCCCCCHhHhhhcCCCcHHHHHH------HHHHHHHhhccCcccchhhHHHHHHHhcCHHH-HHHHHHhhhc
Confidence 57664 689999999999 9999999999 99999988643 4885444889999999 889999
Q ss_pred hcCCchhHHHHHHHHHhcCChhHHH
Q 037631 201 IHRDPKLHAQRVAAIKKAKGTAAAR 225 (388)
Q Consensus 201 l~~~p~l~a~rvaA~q~~kG~~~~r 225 (388)
++...+| ++|+.||++++ +..+.
T Consensus 234 l~~~~tL-ee~m~aCq~VG-p~~~q 256 (262)
T 1d1d_A 234 LTTPGEI-IKYVLDRQKIA-PLTDQ 256 (262)
T ss_dssp CCSTTHH-HHHHHHHHCCC-C----
T ss_pred CCCCCCH-HHHHHHHcccC-hHHHH
Confidence 8888889 99999999886 55443
No 32
>3g21_A GAG polyprotein, capsid protein; alpha-helical bundle, virion, viral protein, retrovirus; 0.90A {Rous sarcoma virus} PDB: 3g1i_A 3g28_A 3g29_A 3g26_A 3g0v_A
Probab=98.16 E-value=2.3e-07 Score=73.45 Aligned_cols=54 Identities=2% Similarity=-0.060 Sum_probs=48.2
Q ss_pred ccchhhhhhccccccccccCCCChhH-----HHHHHHHHHHhhhccchhHHHHHHhcCCchhHHHH
Q 037631 151 EVDNLEIKVGVKKKSKRVYHSPPPEV-----GLKISRSLKSLNAKTGLFTKRMKIIHRDPKLHAQR 211 (388)
Q Consensus 151 ~~~~~~~~~~~~~k~kR~y~~l~ae~-----~~~~t~~Lk~~na~~~~~s~~~Kal~~~p~l~a~r 211 (388)
|.|+|.++++ |||+++++|+ .+||+++|+++|||+++ +.+|++++.+..+.+|+
T Consensus 11 PkEPF~dfVd------Rl~kal~~e~~~~~vk~~m~~tLl~QNANpdC-k~ilk~l~~~~~~~~e~ 69 (77)
T 3g21_A 11 PSESFVDFAN------RLIKAVEGSDLPPSARAPVIIDCFRQKSQPDI-QQLIRTAPSTLTTPGEI 69 (77)
T ss_dssp TTCCHHHHHH------HHHHHHHTSSSCHHHHHHHHHHHHHHHSCHHH-HHHHTTSCTTCCSHHHH
T ss_pred CCccHHHHHH------HHHHHHHHhhChHHHHHHHHHHHHHHhcCHHH-HHHHHhCCCCCCCHHHH
Confidence 8899999999 9999877664 47999999999999999 89999999988886665
No 33
>3g1g_A GAG polyprotein, capsid protein; alpha-helical bundle, virion, viral protein, retrovirus; 2.01A {Rous sarcoma virus}
Probab=97.97 E-value=1.6e-06 Score=70.04 Aligned_cols=54 Identities=2% Similarity=-0.041 Sum_probs=47.8
Q ss_pred ccchhhhhhccccccccccCCCChh-----HHHHHHHHHHHhhhccchhHHHHHHhcCCchhHHHH
Q 037631 151 EVDNLEIKVGVKKKSKRVYHSPPPE-----VGLKISRSLKSLNAKTGLFTKRMKIIHRDPKLHAQR 211 (388)
Q Consensus 151 ~~~~~~~~~~~~~k~kR~y~~l~ae-----~~~~~t~~Lk~~na~~~~~s~~~Kal~~~p~l~a~r 211 (388)
|.|+|.++++ |||+++++| +.+||+++|+++|||+++ +.+|++++.+..+.+|+
T Consensus 10 PkEPF~dfVd------Rl~kal~~eq~~~~vK~~m~~tLlvQNANpdC-k~Il~~~~~~~~~~~e~ 68 (87)
T 3g1g_A 10 PSESFVDFAN------RLIKAVEGSDLPPSARAPVIIDCFRQKSQPDI-QQLIRTAPSTLTTPGEI 68 (87)
T ss_dssp TTCCHHHHHH------HHHHHHHHSSSCGGGHHHHHHHHHHHHSCHHH-HHHHHTSCTTCCSHHHH
T ss_pred CCCcHHHHHH------HHHHHHHHhhchHHHHHHHHHHHHHHhcCHHH-HHHHHhCCCCCCChHHH
Confidence 8899999999 999987664 467999999999999999 89999999988886555
No 34
>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=97.83 E-value=7.5e-06 Score=51.99 Aligned_cols=21 Identities=33% Similarity=0.717 Sum_probs=16.3
Q ss_pred ccccccCCCCcCCCCCCCCCC
Q 037631 352 CTCRFCGEKGHNIRTCPRRNL 372 (388)
Q Consensus 352 ~~Cy~CGe~GH~ardCP~~~~ 372 (388)
..||+||+.||+++|||++..
T Consensus 3 ~~Cf~CG~~GH~ardC~~~~~ 23 (26)
T 1dsq_A 3 PVCFSCGKTGHIKRDCKEEXX 23 (26)
T ss_dssp CBCTTTCCBSSCTTTTTCC--
T ss_pred CeeEeCCCCCcccccCCCccc
Confidence 568999999999999988754
No 35
>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=97.56 E-value=3.4e-05 Score=50.08 Aligned_cols=22 Identities=32% Similarity=0.767 Sum_probs=18.1
Q ss_pred CccccccCCCCcCCCCCCCCCC
Q 037631 351 TCTCRFCGEKGHNIRTCPRRNL 372 (388)
Q Consensus 351 ~~~Cy~CGe~GH~ardCP~~~~ 372 (388)
...||+||+.||++++||.+.+
T Consensus 6 ~~~C~nCgk~GH~ar~C~~prk 27 (29)
T 1nc8_A 6 VIRCWNCGKEGHSARQCRAPRR 27 (29)
T ss_dssp CCBCTTTSCBSSCGGGCCSSSS
T ss_pred CCEEEECCccccCHhHCccccc
Confidence 4679999999999999987754
No 36
>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=97.54 E-value=5.1e-05 Score=53.11 Aligned_cols=24 Identities=33% Similarity=0.858 Sum_probs=19.6
Q ss_pred CCccccccCCCCcCCCCCCCCCCC
Q 037631 350 KTCTCRFCGEKGHNIRTCPRRNLE 373 (388)
Q Consensus 350 ~~~~Cy~CGe~GH~ardCP~~~~s 373 (388)
....||+||+.||+++|||.....
T Consensus 9 ~~~~C~~Cgk~GH~ardCP~~~~~ 32 (40)
T 1a6b_B 9 DRDQCAYCKEKGHWAKDCPKKPRG 32 (40)
T ss_dssp CSSSCSSSCCTTCCTTSCSSSCCC
T ss_pred CCCeeeECCCCCcchhhCcCCccc
Confidence 356799999999999999987753
No 37
>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=97.38 E-value=7.2e-05 Score=48.50 Aligned_cols=21 Identities=33% Similarity=0.776 Sum_probs=15.7
Q ss_pred ccccccccccCccccCCCCCc
Q 037631 253 RFYCKHCGREGHRKFYCPELK 273 (388)
Q Consensus 253 ~~~Cf~CG~~GH~ar~CP~~~ 273 (388)
...||+||++||++++|+.++
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 456888888888888887654
No 38
>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=97.38 E-value=4.5e-05 Score=48.33 Aligned_cols=20 Identities=30% Similarity=0.669 Sum_probs=14.8
Q ss_pred ceeeecCCCccccCCCCCCC
Q 037631 312 HRCQICRQRGHNRRTCPQVT 331 (388)
Q Consensus 312 ~~C~~CGe~GH~ardCP~~~ 331 (388)
..||+||+.||++++||+..
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 46888888888888888754
No 39
>3tir_A ROUS sarcoma virus capsid protein P27; viral capsid protein, viral protein; 4.10A {Rous sarcoma virus} PDB: 2x8q_A
Probab=97.23 E-value=7.9e-05 Score=70.15 Aligned_cols=72 Identities=6% Similarity=0.007 Sum_probs=55.8
Q ss_pred Ccchh-hcccCCccc-cccc--ccchhhhhhccccccccccCCCCh-----hHHHHHHHHHHHhhhccchhHHHHHHhcC
Q 037631 133 QPWEN-AHSVSPLKV-KEDD--EVDNLEIKVGVKKKSKRVYHSPPP-----EVGLKISRSLKSLNAKTGLFTKRMKIIHR 203 (388)
Q Consensus 133 ~~~~~-~~~~spl~i-ke~~--~~~~~~~~~~~~~k~kR~y~~l~a-----e~~~~~t~~Lk~~na~~~~~s~~~Kal~~ 203 (388)
..|.+ +++++|... .++. |.|+|.++++ |++.+++. ++.+||+++|..+|||+++ +.+|++++.
T Consensus 138 ~aw~~l~~~~~~~~~~~~I~QGp~Epf~dfv~------rl~~a~~~~~~~~~~~~~~~~~l~~qNAN~~c-k~il~~~~~ 210 (226)
T 3tir_A 138 QAFREVARLAEPAGPWADIMQGPSESFVDFAN------RLIKAVEGSDLPPSARAPVIIDCFRQKSQPDI-QQLIRTAPS 210 (226)
T ss_dssp HHHHHHHHHC----CGGGCCCCTTCCHHHHHH------HHHHHHHTSSSCHHHHHHHHHHHHHHHSCHHH-HHHHHTSCT
T ss_pred HHHHhccccCCCCcchhHhhcCCCCcHHHHHH------HHHHHHHHHcCcHHHHHHHHHHHHHHhCCHHH-HHHHHhCCC
Confidence 37877 467787753 4555 9999999999 88876554 5567999999999999999 899999999
Q ss_pred CchhHHHH
Q 037631 204 DPKLHAQR 211 (388)
Q Consensus 204 ~p~l~a~r 211 (388)
+..+.+|+
T Consensus 211 ~~~~~~e~ 218 (226)
T 3tir_A 211 TLTTPGEI 218 (226)
T ss_dssp TCCSHHHH
T ss_pred CCCChHHH
Confidence 88886665
No 40
>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=97.16 E-value=0.00018 Score=53.77 Aligned_cols=24 Identities=33% Similarity=0.858 Sum_probs=19.6
Q ss_pred CCccccccCCCCcCCCCCCCCCCC
Q 037631 350 KTCTCRFCGEKGHNIRTCPRRNLE 373 (388)
Q Consensus 350 ~~~~Cy~CGe~GH~ardCP~~~~s 373 (388)
....||+||+.|||++|||.....
T Consensus 22 ~~~~C~~Cge~GH~ardCp~~~~~ 45 (56)
T 1u6p_A 22 DRDQCAYCKEKGHWAKDCPKKPRG 45 (56)
T ss_dssp CTTBCSSSCCBSSCGGGCTTCCCS
T ss_pred CCCcceeCCCCCcccccCcCCccc
Confidence 356799999999999999987753
No 41
>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=97.15 E-value=0.00016 Score=50.61 Aligned_cols=22 Identities=27% Similarity=0.943 Sum_probs=18.0
Q ss_pred CcceeeecCCCccccCCCCCCC
Q 037631 310 KHHRCQICRQRGHNRRTCPQVT 331 (388)
Q Consensus 310 ~~~~C~~CGe~GH~ardCP~~~ 331 (388)
....||+|++.||++++||...
T Consensus 9 ~~~~C~~Cgk~GH~ardCP~~~ 30 (40)
T 1a6b_B 9 DRDQCAYCKEKGHWAKDCPKKP 30 (40)
T ss_dssp CSSSCSSSCCTTCCTTSCSSSC
T ss_pred CCCeeeECCCCCcchhhCcCCc
Confidence 3568999999999999998865
No 42
>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=96.69 E-value=0.0005 Score=51.40 Aligned_cols=22 Identities=27% Similarity=0.943 Sum_probs=18.1
Q ss_pred CcceeeecCCCccccCCCCCCC
Q 037631 310 KHHRCQICRQRGHNRRTCPQVT 331 (388)
Q Consensus 310 ~~~~C~~CGe~GH~ardCP~~~ 331 (388)
....||+||+.||++++||...
T Consensus 22 ~~~~C~~Cge~GH~ardCp~~~ 43 (56)
T 1u6p_A 22 DRDQCAYCKEKGHWAKDCPKKP 43 (56)
T ss_dssp CTTBCSSSCCBSSCGGGCTTCC
T ss_pred CCCcceeCCCCCcccccCcCCc
Confidence 4568999999999999998765
No 43
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=96.62 E-value=0.00064 Score=50.63 Aligned_cols=19 Identities=47% Similarity=1.086 Sum_probs=14.2
Q ss_pred CccccccCCCCcCCCCCCC
Q 037631 351 TCTCRFCGEKGHNIRTCPR 369 (388)
Q Consensus 351 ~~~Cy~CGe~GH~ardCP~ 369 (388)
.+.||+||+.||++++||.
T Consensus 7 ~~~C~kCGk~GH~~k~Cp~ 25 (55)
T 2ysa_A 7 GYTCFRCGKPGHYIKNCPT 25 (55)
T ss_dssp SCCCTTTCCTTSCGGGCSG
T ss_pred CCccccCCCcCcccccCCC
Confidence 4568888888888888873
No 44
>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} SCOP: g.54.1.1
Probab=96.47 E-value=0.0012 Score=51.20 Aligned_cols=46 Identities=28% Similarity=0.831 Sum_probs=29.4
Q ss_pred cCCCCCCCccccccccCCCccccCCCcccCccce---eeecccCceeecc
Q 037631 81 PCPSCRGRGYTPCVECGIERTRSDCSLCNGKGIM---TCRQCSGDCVIWE 127 (388)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~---~~~~~~~~~~~~~ 127 (388)
.||.|+|.|+..-.+ |.-.....|+.|+|.|.. .|..|.|.-++.|
T Consensus 30 ~C~~C~G~G~~~~~~-g~~~~~~~C~~C~G~G~~~~~~C~~C~G~G~~~~ 78 (79)
T 1exk_A 30 TCPTCHGSGQVQMRQ-GFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRVER 78 (79)
T ss_dssp ECTTTTTSSEEEEEE-TTEEEEEECTTTTTSSEECSSBCGGGTTSSEEEC
T ss_pred CCCCCcCeEEEEEEc-CCCEEeeECcCCCCccEECCCcCCCCCCeEEEee
Confidence 455555555544333 322333578888888887 7888888877755
No 45
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=96.44 E-value=0.00076 Score=50.23 Aligned_cols=21 Identities=29% Similarity=0.661 Sum_probs=16.4
Q ss_pred cceeeecCCCccccCCCCCCC
Q 037631 311 HHRCQICRQRGHNRRTCPQVT 331 (388)
Q Consensus 311 ~~~C~~CGe~GH~ardCP~~~ 331 (388)
.+.||+||+.||++++||...
T Consensus 7 ~~~C~kCGk~GH~~k~Cp~~~ 27 (55)
T 2ysa_A 7 GYTCFRCGKPGHYIKNCPTNG 27 (55)
T ss_dssp SCCCTTTCCTTSCGGGCSGGG
T ss_pred CCccccCCCcCcccccCCCCC
Confidence 567888888888888888543
No 46
>2ctt_A DNAJ homolog subfamily A member 3; ZING finger, beta-hairpin, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=94.97 E-value=0.013 Score=47.91 Aligned_cols=47 Identities=30% Similarity=0.639 Sum_probs=30.0
Q ss_pred cCCCCCCCccccccccCCCccccCCCcccCccce---eeecccCceeeccc
Q 037631 81 PCPSCRGRGYTPCVECGIERTRSDCSLCNGKGIM---TCRQCSGDCVIWEE 128 (388)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~---~~~~~~~~~~~~~~ 128 (388)
.||.|+|.|+..-.+ |.-.....|+.|+|.|.. .|..|.|.-++-++
T Consensus 47 ~C~~C~G~G~~~~~~-G~~~~~~~C~~C~G~G~~i~~~C~~C~G~G~v~~~ 96 (104)
T 2ctt_A 47 HCHYCGGSGMETINT-GPFVMRSTCRRCGGRGSIIISPCVVCRGAGQAKQK 96 (104)
T ss_dssp ECSSSSSSCEEEEEE-TTEEEEEECSSSSSSSEECSSCCSSSSSCSEECCC
T ss_pred cCCCCCCCEEEEEEe-CCEEEEEECCcCCCcceECCCcCCCCCCeeEEEEE
Confidence 455566555544333 322334578888888876 58888888777543
No 47
>1u57_A GAG polyprotein, HIV-1; particle assembly, viral protein; NMR {Human immunodeficiency virus 1}
Probab=94.00 E-value=0.013 Score=42.02 Aligned_cols=27 Identities=11% Similarity=0.198 Sum_probs=24.9
Q ss_pred HHHHHHHHhcCChhHHHHHHHHHHHhh
Q 037631 209 AQRVAAIKKAKGTAAARKHASETLKAF 235 (388)
Q Consensus 209 a~rvaA~q~~kG~~~~rr~~seam~~~ 235 (388)
++|++||++++||.++.|+++|+|..+
T Consensus 2 eem~~acqgvggp~hKarvlAEAMsq~ 28 (48)
T 1u57_A 2 EEMMTACQGVGGPGHKARVLAEAMSQV 28 (48)
T ss_dssp CTHHHHBTTTSBCTTHHHHHHHHHHHH
T ss_pred chhhhhccCCCCCcchhhHHHHHHHHh
Confidence 568999999999999999999999875
No 48
>1nlt_A Protein YDJ1, mitochondrial protein import protein MAS5; beta-strands, chaperone, heat shock, mitochondrion; 2.70A {Saccharomyces cerevisiae} SCOP: b.4.1.1 b.4.1.1 g.54.1.1
Probab=92.34 E-value=0.076 Score=49.98 Aligned_cols=28 Identities=32% Similarity=0.835 Sum_probs=21.9
Q ss_pred cccCCCcccCcc-----ceeeecccCceeeccc
Q 037631 101 TRSDCSLCNGKG-----IMTCRQCSGDCVIWEE 128 (388)
Q Consensus 101 ~~~~~~~~~~~g-----~~~~~~~~~~~~~~~~ 128 (388)
....|+.|+|.| --.|..|.|.-++-++
T Consensus 79 ~~~~C~~C~G~G~~i~~~~~C~~C~G~g~~~~~ 111 (248)
T 1nlt_A 79 FQTECDVCHGTGDIIDPKDRCKSCNGKKVENER 111 (248)
T ss_dssp EECSCTTCSSSSSCCCTTSBCSSSTTSCEEEEE
T ss_pred EEEcCCCCCCcCEEeccCCCCcccCCCceEeee
Confidence 456799999999 4559999998887654
No 49
>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} SCOP: g.54.1.1
Probab=89.31 E-value=0.2 Score=38.43 Aligned_cols=46 Identities=28% Similarity=0.710 Sum_probs=32.1
Q ss_pred eeccccCCCCCCCccccccccCCCccccCCCcccCccce-----------eeecccCceeecc
Q 037631 76 YIRELPCPSCRGRGYTPCVECGIERTRSDCSLCNGKGIM-----------TCRQCSGDCVIWE 127 (388)
Q Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~-----------~~~~~~~~~~~~~ 127 (388)
|-+.-.|+.|.|.|+.+ ......|+.|+|.|.. +|..|.|.-.|++
T Consensus 8 ~~~~~~C~~C~G~G~~~------~~~~~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~~ 64 (79)
T 1exk_A 8 IPTLEECDVCHGSGAKP------GTQPQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLIK 64 (79)
T ss_dssp CCCEEECGGGTTTSBCS------SSCCEECTTTTTSSEEEEEETTEEEEEECTTTTTSSEECS
T ss_pred cccceECCCCcccccCC------CccCCCCCCCcCeEEEEEEcCCCEEeeECcCCCCccEECC
Confidence 44667788888888776 2223468888888843 6888888777764
No 50
>2bx9_A Anti-trap, AT, tryptophan RNA-binding attenuator protein-inhibit protein; transcription regulation; 2.80A {Bacillus subtilis} PDB: 2ko8_A* 2zp8_E* 2zp9_C*
Probab=88.10 E-value=0.18 Score=37.01 Aligned_cols=26 Identities=38% Similarity=1.030 Sum_probs=21.5
Q ss_pred cccCCCCCCCccccccccCCCccccCCCcccCccc
Q 037631 79 ELPCPSCRGRGYTPCVECGIERTRSDCSLCNGKGI 113 (388)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ 113 (388)
+-+||.|.|.|..+ ...|+.|+|.|.
T Consensus 9 ~~~C~~C~GsG~~~---------~~~C~~C~G~G~ 34 (53)
T 2bx9_A 9 EVACPKCERAGEIE---------GTPCPACSGKGV 34 (53)
T ss_dssp EEECTTTTTSSEET---------TEECTTTTTSSE
T ss_pred cccCCCCcceeccC---------CCCCccCCCCcc
Confidence 45799999999985 246999999997
No 51
>3lcz_A YCZA, inhibitor of trap, regulated by T-box (Trp) seque; anti-trap, tryptophan RNA-binding attenuation PROT transcription attenuation; 2.06A {Bacillus licheniformis} PDB: 3ld0_A
Probab=86.42 E-value=0.29 Score=35.86 Aligned_cols=27 Identities=41% Similarity=1.032 Sum_probs=20.9
Q ss_pred cccCCCCCCCccccccccCCCccccCCCcccCccce
Q 037631 79 ELPCPSCRGRGYTPCVECGIERTRSDCSLCNGKGIM 114 (388)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 114 (388)
+-+||.|.|.|-.. ..-|+.|+|+|..
T Consensus 9 ~~~C~~C~GsG~~i---------~~~C~~C~G~G~v 35 (53)
T 3lcz_A 9 ETTCPNCNGSGREE---------PEPCPKCLGKGVI 35 (53)
T ss_dssp EEECTTTTTSCEET---------TEECTTTTTSSEE
T ss_pred eccCcCCcccccCC---------CCcCCCCCCcEEE
Confidence 45899999999764 1458888899873
No 52
>2ctt_A DNAJ homolog subfamily A member 3; ZING finger, beta-hairpin, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=85.13 E-value=0.44 Score=38.67 Aligned_cols=46 Identities=33% Similarity=0.744 Sum_probs=30.8
Q ss_pred eeccccCCCCCCCccccccccCCCccccCCCcccCccc-----------eeeecccCceeecc
Q 037631 76 YIRELPCPSCRGRGYTPCVECGIERTRSDCSLCNGKGI-----------MTCRQCSGDCVIWE 127 (388)
Q Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~-----------~~~~~~~~~~~~~~ 127 (388)
|-+.-.|+.|.|.|..+ ......|+.|+|.|. .+|..|.|.-.|++
T Consensus 25 ~~~~~~C~~C~G~G~~~------g~~~~~C~~C~G~G~~~~~~G~~~~~~~C~~C~G~G~~i~ 81 (104)
T 2ctt_A 25 VNIMDTCERCNGKGNEP------GTKVQHCHYCGGSGMETINTGPFVMRSTCRRCGGRGSIII 81 (104)
T ss_dssp SSCCEECSSSSSSSSCT------TCCCEECSSSSSSCEEEEEETTEEEEEECSSSSSSSEECS
T ss_pred eeeeeECCCCcCCccCC------CCCCccCCCCCCCEEEEEEeCCEEEEEECCcCCCcceECC
Confidence 44566788888888775 222345777777772 57888888777764
No 53
>1nlt_A Protein YDJ1, mitochondrial protein import protein MAS5; beta-strands, chaperone, heat shock, mitochondrion; 2.70A {Saccharomyces cerevisiae} SCOP: b.4.1.1 b.4.1.1 g.54.1.1
Probab=83.04 E-value=0.74 Score=43.17 Aligned_cols=35 Identities=34% Similarity=0.811 Sum_probs=25.5
Q ss_pred ccCCCCCCCccc---------------cccccCCCcc----ccCCCcccCccce
Q 037631 80 LPCPSCRGRGYT---------------PCVECGIERT----RSDCSLCNGKGIM 114 (388)
Q Consensus 80 ~~~~~~~~~~~~---------------~~~~~~~~~~----~~~~~~~~~~g~~ 114 (388)
-.||.|+|.|+. .|..|+..-. ...|+.|+|+|..
T Consensus 55 ~~C~~C~G~G~~~~~~~~g~~~~~~~~~C~~C~G~G~~i~~~~~C~~C~G~g~~ 108 (248)
T 1nlt_A 55 KKCTSCNGQGIKFVTRQMGPMIQRFQTECDVCHGTGDIIDPKDRCKSCNGKKVE 108 (248)
T ss_dssp CCCTTSSSSSCEEEEEESSSEEEEEECSCTTCSSSSSCCCTTSBCSSSTTSCEE
T ss_pred ccCCCCCCCcEEEEEEecCceEEEEEEcCCCCCCcCEEeccCCCCcccCCCceE
Confidence 568888888753 5777876543 5579999999874
No 54
>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A
Probab=66.63 E-value=3.3 Score=30.55 Aligned_cols=22 Identities=32% Similarity=0.777 Sum_probs=13.3
Q ss_pred eeccccCCCCCC--------CccccccccC
Q 037631 76 YIRELPCPSCRG--------RGYTPCVECG 97 (388)
Q Consensus 76 ~~~~~~~~~~~~--------~~~~~~~~~~ 97 (388)
.+..+.||.|.+ +|-+.|.+||
T Consensus 8 ll~~~~Cp~C~~~~lv~D~~~ge~vC~~CG 37 (58)
T 1dl6_A 8 ALPRVTCPNHPDAILVEDYRAGDMICPECG 37 (58)
T ss_dssp CCSCCSBTTBSSSCCEECSSSCCEECTTTC
T ss_pred ccccccCcCCCCCceeEeCCCCeEEeCCCC
Confidence 345567888865 3455555555
No 55
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Probab=53.74 E-value=5.4 Score=27.97 Aligned_cols=9 Identities=33% Similarity=1.121 Sum_probs=6.2
Q ss_pred cccCCCCCC
Q 037631 79 ELPCPSCRG 87 (388)
Q Consensus 79 ~~~~~~~~~ 87 (388)
.|.||.|.+
T Consensus 5 ~~~CP~C~~ 13 (50)
T 1pft_A 5 QKVCPACES 13 (50)
T ss_dssp CCSCTTTSC
T ss_pred cEeCcCCCC
Confidence 467887765
No 56
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}
Probab=45.46 E-value=11 Score=36.73 Aligned_cols=26 Identities=42% Similarity=0.902 Sum_probs=15.7
Q ss_pred ccCCCceeccccCCCCCC----------CccccccccC
Q 037631 70 FGPNGQYIRELPCPSCRG----------RGYTPCVECG 97 (388)
Q Consensus 70 ~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~ 97 (388)
|+||-. ..+.||.|.+ +|-+-|.+||
T Consensus 14 ~~~~~~--~~~~Cp~Cg~~~~~iv~D~~~G~~vC~~CG 49 (345)
T 3k7a_M 14 RGPNLN--IVLTCPECKVYPPKIVERFSEGDVVCALCG 49 (345)
T ss_dssp ---CCC--CCCCCSTTCCSCCCCCCCSSSCSCCCSSSC
T ss_pred cCcccc--CCCcCcCCCCCCCceEEECCCCCEecCCCC
Confidence 788764 2556998866 4666777777
No 57
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=44.28 E-value=10 Score=31.45 Aligned_cols=19 Identities=53% Similarity=1.328 Sum_probs=10.5
Q ss_pred ccceecccCC---CccccCCCC
Q 037631 281 FKCRLCGERG---HNRRTCPKS 299 (388)
Q Consensus 281 ~~C~~CG~~G---H~ardCp~~ 299 (388)
.+|-.||..| |..+.||..
T Consensus 72 Y~CpiCGATGd~AHT~kYCP~~ 93 (106)
T 3alr_A 72 YKCPLCGATGAKAHTKRFCPMV 93 (106)
T ss_dssp CCCTTTCCCGGGCCCGGGCTTC
T ss_pred ccCCCCCCcCCcccceecCCCC
Confidence 4566665555 555555543
No 58
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=42.88 E-value=7.7 Score=24.51 Aligned_cols=20 Identities=25% Similarity=0.546 Sum_probs=14.3
Q ss_pred ccccccCCCCcCCCCCCCCC
Q 037631 352 CTCRFCGEKGHNIRTCPRRN 371 (388)
Q Consensus 352 ~~Cy~CGe~GH~ardCP~~~ 371 (388)
.+|-+|...||...+|+...
T Consensus 4 pYCe~CE~FGH~t~~C~d~e 23 (26)
T 2hqh_E 4 PYCEICEMFGHWATNCNDDE 23 (26)
T ss_dssp CEETTTTEESSCGGGCCTTC
T ss_pred ccchHHHHhCcccccCCccc
Confidence 46777888888888886543
No 59
>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=41.27 E-value=39 Score=24.89 Aligned_cols=29 Identities=31% Similarity=0.614 Sum_probs=14.8
Q ss_pred CccccCCCCCcCCCCcCcccc-eeccc-------CCCccccCCCC
Q 037631 263 GHRKFYCPELKDGLTDRGFKC-RLCGE-------RGHNRRTCPKS 299 (388)
Q Consensus 263 GH~ar~CP~~~~~~~~~~~~C-~~CG~-------~GH~ardCp~~ 299 (388)
.|. ..|+-.. +.| ..|+. ..|...+||..
T Consensus 7 ~H~-~~C~~~~-------v~C~~~C~~~v~r~~l~~H~~~~C~~r 43 (76)
T 2yuc_A 7 GHL-NTCSFNV-------IPCPNRCPMKLSRRDLPAHLQHDCPKR 43 (76)
T ss_dssp CCC-CCCCCSC-------CBCTTCCSCBCCSSSSTTTTTTSCTTS
T ss_pred HHH-HHCCCcc-------cCCCccccHHhhHhHHHhhCHhhCCCc
Confidence 455 5666532 456 55653 23555555553
No 60
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=40.65 E-value=9.1 Score=24.16 Aligned_cols=18 Identities=33% Similarity=0.739 Sum_probs=11.2
Q ss_pred cccccccccCccccCCCC
Q 037631 254 FYCKHCGREGHRKFYCPE 271 (388)
Q Consensus 254 ~~Cf~CG~~GH~ar~CP~ 271 (388)
..|-.|...||...+|..
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 456666666666666643
No 61
>3lcz_A YCZA, inhibitor of trap, regulated by T-box (Trp) seque; anti-trap, tryptophan RNA-binding attenuation PROT transcription attenuation; 2.06A {Bacillus licheniformis} PDB: 3ld0_A
Probab=37.43 E-value=13 Score=26.95 Aligned_cols=25 Identities=40% Similarity=0.905 Sum_probs=17.0
Q ss_pred cCCCcccCccc---eeeecccCceeecc
Q 037631 103 SDCSLCNGKGI---MTCRQCSGDCVIWE 127 (388)
Q Consensus 103 ~~~~~~~~~g~---~~~~~~~~~~~~~~ 127 (388)
..|+.|.|.|. -.|..|.|.-++-+
T Consensus 10 ~~C~~C~GsG~~i~~~C~~C~G~G~v~~ 37 (53)
T 3lcz_A 10 TTCPNCNGSGREEPEPCPKCLGKGVILT 37 (53)
T ss_dssp EECTTTTTSCEETTEECTTTTTSSEEEC
T ss_pred ccCcCCcccccCCCCcCCCCCCcEEEEE
Confidence 35777777776 56777777766644
No 62
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae}
Probab=36.06 E-value=11 Score=34.26 Aligned_cols=20 Identities=40% Similarity=0.987 Sum_probs=16.5
Q ss_pred ccccCCCCCC----------CccccccccC
Q 037631 78 RELPCPSCRG----------RGYTPCVECG 97 (388)
Q Consensus 78 ~~~~~~~~~~----------~~~~~~~~~~ 97 (388)
..+-||.|.+ +|-+.|.+||
T Consensus 20 ~~~~CPECGs~~t~IV~D~erGE~VCsdCG 49 (197)
T 3k1f_M 20 IVLTCPECKVYPPKIVERFSEGDVVCALCG 49 (197)
T ss_dssp CCCCCTTTCCSSCCEEEEGGGTEEEETTTC
T ss_pred cCeECcCCCCcCCeEEEeCCCCEEEEcCCC
Confidence 4567999998 7888888888
No 63
>2zvv_Y Cyclin-dependent kinase inhibitor 1; protein-peptide complex, DNA replication, DNA-binding, nucleus, DNA binding protein; 2.00A {Arabidopsis thaliana} PDB: 1axc_B 2zvw_I
Probab=35.48 E-value=4.2 Score=25.34 Aligned_cols=18 Identities=44% Similarity=0.704 Sum_probs=14.3
Q ss_pred ceEEEEEecCCccccccc
Q 037631 4 KRFLVLYHSKRRVSFSPC 21 (388)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~ 21 (388)
|-.-=|||++++++|.|+
T Consensus 7 Ts~TDFYhsKRRlvf~~r 24 (26)
T 2zvv_Y 7 TSMTDFYHSKRRLIFSXX 24 (26)
T ss_pred cchhHHHhhhceEEEEec
Confidence 334457999999999987
No 64
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=32.78 E-value=16 Score=30.25 Aligned_cols=32 Identities=38% Similarity=0.950 Sum_probs=23.7
Q ss_pred CCcccc------CCCCCCCCCCCCCCCcceeeecCCCc---cccCCCCCCC
Q 037631 290 GHNRRT------CPKSRLSYHNGTVSKHHRCQICRQRG---HNRRTCPQVT 331 (388)
Q Consensus 290 GH~ard------Cp~~~~~~~~G~~~~~~~C~~CGe~G---H~ardCP~~~ 331 (388)
.|..++ ||..+ .+.|-.||..| |..+-||...
T Consensus 54 SH~LKd~~G~V~CPvLR----------~Y~CpiCGATGd~AHT~kYCP~~~ 94 (106)
T 3alr_A 54 SHYLKNRDGDVMCPYLR----------QYKCPLCGATGAKAHTKRFCPMVD 94 (106)
T ss_dssp SBCSBCTTSCBCCTTGG----------GCCCTTTCCCGGGCCCGGGCTTCG
T ss_pred cceeECCCCCCcCCCcc----------cccCCCCCCcCCcccceecCCCCC
Confidence 466666 88765 57888888888 7777788654
No 65
>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=32.13 E-value=46 Score=24.49 Aligned_cols=10 Identities=30% Similarity=0.806 Sum_probs=6.2
Q ss_pred ccccCCCCCC
Q 037631 321 GHNRRTCPQV 330 (388)
Q Consensus 321 GH~ardCP~~ 330 (388)
-|...+||..
T Consensus 34 ~H~~~~C~~r 43 (76)
T 2yuc_A 34 AHLQHDCPKR 43 (76)
T ss_dssp TTTTTSCTTS
T ss_pred hhCHhhCCCc
Confidence 5666666665
No 66
>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2
Probab=31.30 E-value=19 Score=32.99 Aligned_cols=16 Identities=19% Similarity=0.841 Sum_probs=12.5
Q ss_pred CCceeccccCCCCCCC
Q 037631 73 NGQYIRELPCPSCRGR 88 (388)
Q Consensus 73 ~~~~~~~~~~~~~~~~ 88 (388)
.|.|.+..+||.|.|.
T Consensus 8 ~~~~~~~~~CP~Cg~~ 23 (255)
T 1nui_A 8 DSVFLYHIPCDNCGSS 23 (255)
T ss_dssp --CEEEEECCSSSCCS
T ss_pred ccceecCCcCCCCCCC
Confidence 4789999999999874
No 67
>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}
Probab=29.32 E-value=20 Score=27.22 Aligned_cols=22 Identities=23% Similarity=0.389 Sum_probs=14.2
Q ss_pred eccccCCCCCCC-------ccccccccCC
Q 037631 77 IRELPCPSCRGR-------GYTPCVECGI 98 (388)
Q Consensus 77 ~~~~~~~~~~~~-------~~~~~~~~~~ 98 (388)
..-|-||.|.|. |...|..||.
T Consensus 6 L~iL~CP~ck~~L~~~~~~~~LiC~~cg~ 34 (68)
T 2jr6_A 6 LDILVCPVTKGRLEYHQDKQELWSRQAKL 34 (68)
T ss_dssp SCCCBCSSSCCBCEEETTTTEEEETTTTE
T ss_pred hhheECCCCCCcCeEeCCCCEEEcCCCCc
Confidence 456889999984 4555555553
No 68
>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1
Probab=29.06 E-value=20 Score=27.24 Aligned_cols=24 Identities=25% Similarity=0.636 Sum_probs=15.6
Q ss_pred eeccccCCCCCCC-------ccccccccCCC
Q 037631 76 YIRELPCPSCRGR-------GYTPCVECGIE 99 (388)
Q Consensus 76 ~~~~~~~~~~~~~-------~~~~~~~~~~~ 99 (388)
...-|-||.|.|. |...|..||..
T Consensus 5 LL~iL~CP~ck~~L~~~~~~~~LiC~~cg~~ 35 (68)
T 2hf1_A 5 FLEILVCPLCKGPLVFDKSKDELICKGDRLA 35 (68)
T ss_dssp CEEECBCTTTCCBCEEETTTTEEEETTTTEE
T ss_pred HhhheECCCCCCcCeEeCCCCEEEcCCCCcE
Confidence 3456889999884 55556555543
No 69
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M
Probab=26.71 E-value=19 Score=35.12 Aligned_cols=26 Identities=42% Similarity=0.902 Sum_probs=14.1
Q ss_pred ccCCCceeccccCCCCCC----------CccccccccC
Q 037631 70 FGPNGQYIRELPCPSCRG----------RGYTPCVECG 97 (388)
Q Consensus 70 ~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~ 97 (388)
|+||=. -.+-||.|.+ +|-+.|.+||
T Consensus 14 ~~~~l~--~~~~Cp~C~~~~~~lv~D~~~G~~vC~~CG 49 (345)
T 4bbr_M 14 RGPNLN--IVLTCPECKVYPPKIVERFSEGDVVCALCG 49 (345)
T ss_dssp ----------CCCSSCCCSSCCEEEEGGGTEEEETTTC
T ss_pred cCcccc--cCCcCCCCCCCCCceeEECCCCcEEeCCCC
Confidence 355432 2457999986 5777788887
No 70
>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1
Probab=26.52 E-value=25 Score=26.79 Aligned_cols=23 Identities=26% Similarity=0.596 Sum_probs=14.5
Q ss_pred eeccccCCCCCCC-------ccccccccCC
Q 037631 76 YIRELPCPSCRGR-------GYTPCVECGI 98 (388)
Q Consensus 76 ~~~~~~~~~~~~~-------~~~~~~~~~~ 98 (388)
...-|-||.|.|. |...|..||.
T Consensus 5 LLeiL~CP~ck~~L~~~~~~~~LiC~~cg~ 34 (69)
T 2pk7_A 5 LLDILACPICKGPLKLSADKTELISKGAGL 34 (69)
T ss_dssp GGGTCCCTTTCCCCEECTTSSEEEETTTTE
T ss_pred HHhheeCCCCCCcCeEeCCCCEEEcCCCCc
Confidence 3456889999874 4455555553
No 71
>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}
Probab=24.61 E-value=28 Score=26.59 Aligned_cols=23 Identities=30% Similarity=0.699 Sum_probs=14.7
Q ss_pred eeccccCCCCCCC-------ccccccccCC
Q 037631 76 YIRELPCPSCRGR-------GYTPCVECGI 98 (388)
Q Consensus 76 ~~~~~~~~~~~~~-------~~~~~~~~~~ 98 (388)
...-|-||.|.|. |...|..||.
T Consensus 5 LL~iL~CP~ck~~L~~~~~~~~LiC~~cg~ 34 (70)
T 2js4_A 5 LLDILVCPVCKGRLEFQRAQAELVCNADRL 34 (70)
T ss_dssp CCCCCBCTTTCCBEEEETTTTEEEETTTTE
T ss_pred HhhheECCCCCCcCEEeCCCCEEEcCCCCc
Confidence 3456889999883 4555555553
No 72
>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}
Probab=24.27 E-value=31 Score=25.12 Aligned_cols=25 Identities=28% Similarity=0.852 Sum_probs=17.7
Q ss_pred eeccccCCCCCCC-----cccccc--ccCCCc
Q 037631 76 YIRELPCPSCRGR-----GYTPCV--ECGIER 100 (388)
Q Consensus 76 ~~~~~~~~~~~~~-----~~~~~~--~~~~~~ 100 (388)
...-|.||.|.|. |...|. .||..-
T Consensus 7 lL~iL~CP~c~~~L~~~~~~L~C~~~~c~~~Y 38 (56)
T 2kpi_A 7 LLEILACPACHAPLEERDAELICTGQDCGLAY 38 (56)
T ss_dssp CTTSCCCSSSCSCEEEETTEEEECSSSCCCEE
T ss_pred HHhheeCCCCCCcceecCCEEEcCCcCCCcEE
Confidence 3456889999997 666777 676443
No 73
>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1
Probab=21.72 E-value=35 Score=25.89 Aligned_cols=24 Identities=17% Similarity=0.357 Sum_probs=15.1
Q ss_pred eeccccCCCCCC-------CccccccccCCC
Q 037631 76 YIRELPCPSCRG-------RGYTPCVECGIE 99 (388)
Q Consensus 76 ~~~~~~~~~~~~-------~~~~~~~~~~~~ 99 (388)
...-|-||.|.| .|...|..||..
T Consensus 7 LLeiL~CP~ck~~L~~~~~~g~LvC~~c~~~ 37 (67)
T 2jny_A 7 LLEVLACPKDKGPLRYLESEQLLVNERLNLA 37 (67)
T ss_dssp GTCCCBCTTTCCBCEEETTTTEEEETTTTEE
T ss_pred HHHHhCCCCCCCcCeEeCCCCEEEcCCCCcc
Confidence 345688999998 345555555533
Done!