Query 012460
Match_columns 463
No_of_seqs 170 out of 998
Neff 2.6
Searched_HMMs 29240
Date Mon Mar 25 09:52:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012460.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/012460hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1baj_A GAG polyprotein; capsid 99.8 4.1E-21 1.4E-25 160.6 -1.4 67 302-389 25-92 (101)
2 3ds4_A HIV-1 capsid protein; H 99.7 8.7E-20 3E-24 149.2 -0.9 61 303-384 25-86 (86)
3 2jyl_A Capsid protein P24 (Ca) 99.7 3.9E-19 1.3E-23 150.7 -5.3 62 302-384 43-105 (105)
4 1qrj_B HTLV-I capsid protein; 99.6 8.3E-17 2.8E-21 148.8 -2.7 70 284-384 127-199 (199)
5 1eoq_A GAG polyprotein capsid 99.4 4.9E-15 1.7E-19 125.1 -0.9 52 303-360 20-76 (96)
6 3h47_A Ca, capsid protein P24; 99.4 6.6E-15 2.3E-19 139.1 -2.7 60 304-384 171-231 (231)
7 1a1t_A Nucleocapsid protein; s 99.4 3.1E-14 1.1E-18 105.8 1.1 41 421-462 11-51 (55)
8 2a51_A Nucleocapsid protein; s 99.4 2.8E-13 9.5E-18 95.3 3.3 39 423-462 1-39 (39)
9 1eia_A EIAV capsid protein P26 99.4 4.2E-14 1.4E-18 131.7 -1.4 51 304-360 156-207 (207)
10 2ec7_A GAG polyprotein (PR55GA 99.3 9.1E-13 3.1E-17 96.8 3.6 41 421-462 5-45 (49)
11 3gv2_A Ca, fusion protein cons 99.3 1.4E-13 4.8E-18 136.2 -1.4 54 304-368 171-225 (342)
12 2cqf_A RNA-binding protein LIN 99.2 3.7E-12 1.2E-16 98.0 3.5 42 421-462 6-47 (63)
13 2bl6_A Nucleocapsid protein P1 99.2 3.3E-12 1.1E-16 88.9 2.9 36 424-462 2-37 (37)
14 3ts2_A Protein LIN-28 homolog 99.2 6.9E-12 2.4E-16 110.2 4.1 42 421-462 96-137 (148)
15 2li8_A Protein LIN-28 homolog 99.2 6.7E-12 2.3E-16 100.1 3.5 42 421-462 23-64 (74)
16 2ihx_A Nucleocapsid (NC) prote 99.2 9.4E-12 3.2E-16 94.8 3.3 42 421-462 3-48 (61)
17 1cl4_A Protein (GAG polyprotei 99.2 6.3E-12 2.2E-16 94.8 2.0 40 423-462 2-48 (60)
18 1d1d_A Protein (capsid protein 99.1 6E-12 2.1E-16 120.8 -2.9 52 303-360 195-251 (262)
19 3g21_A GAG polyprotein, capsid 99.0 3.3E-11 1.1E-15 98.5 -1.0 38 303-344 24-61 (77)
20 1u57_A GAG polyprotein, HIV-1; 98.8 8.2E-10 2.8E-14 81.5 2.4 42 351-413 3-45 (48)
21 3g1g_A GAG polyprotein, capsid 98.8 1.5E-10 5.3E-15 96.4 -2.1 38 303-344 23-60 (87)
22 3nyb_B Protein AIR2; polya RNA 98.8 1.8E-09 6.2E-14 87.9 2.3 39 424-462 26-64 (83)
23 2lli_A Protein AIR2; RNA surve 98.7 8.7E-09 3E-13 86.5 5.0 41 422-462 42-82 (124)
24 2lli_A Protein AIR2; RNA surve 98.7 6.7E-09 2.3E-13 87.2 3.4 42 422-463 64-124 (124)
25 3nyb_B Protein AIR2; polya RNA 98.4 9.4E-08 3.2E-12 77.9 1.7 38 421-461 4-41 (83)
26 1nc8_A Nucleocapsid protein; H 98.1 9.2E-07 3.1E-11 59.2 2.5 23 421-443 5-27 (29)
27 3tir_A ROUS sarcoma virus caps 98.1 3.8E-07 1.3E-11 86.3 -1.1 37 304-344 174-210 (226)
28 2li8_A Protein LIN-28 homolog 98.0 2.1E-06 7.3E-11 68.4 2.0 32 431-462 2-42 (74)
29 1dsq_A Nucleic acid binding pr 97.8 6.2E-06 2.1E-10 54.1 1.7 21 423-443 3-23 (26)
30 1a6b_B Momulv, zinc finger pro 97.6 2.8E-05 9.4E-10 56.4 2.5 23 421-443 9-31 (40)
31 1dsq_A Nucleic acid binding pr 97.5 3.2E-05 1.1E-09 50.7 1.6 18 445-462 3-20 (26)
32 1u6p_A GAG polyprotein; MLV, A 97.3 0.00013 4.4E-09 56.1 3.4 24 420-443 21-44 (56)
33 2cqf_A RNA-binding protein LIN 97.3 0.00015 5E-09 55.7 3.3 32 421-453 28-59 (63)
34 1nc8_A Nucleocapsid protein; H 97.2 0.00011 3.9E-09 49.0 1.7 21 442-462 4-24 (29)
35 2ysa_A Retinoblastoma-binding 97.1 0.00016 5.4E-09 55.5 1.5 21 421-441 6-26 (55)
36 1a6b_B Momulv, zinc finger pro 97.0 0.00031 1.1E-08 50.9 2.3 18 445-462 11-28 (40)
37 2a51_A Nucleocapsid protein; s 96.7 0.00085 2.9E-08 46.9 2.8 25 416-440 15-39 (39)
38 1u6p_A GAG polyprotein; MLV, A 96.7 0.00061 2.1E-08 52.4 2.0 18 445-462 24-41 (56)
39 2ec7_A GAG polyprotein (PR55GA 96.6 0.0015 5.2E-08 47.7 3.3 27 416-442 21-47 (49)
40 2bl6_A Nucleocapsid protein P1 96.5 0.0015 5E-08 45.2 2.8 19 422-440 19-37 (37)
41 2ysa_A Retinoblastoma-binding 96.4 0.0012 4.3E-08 50.5 2.2 18 445-462 8-25 (55)
42 1a1t_A Nucleocapsid protein; s 96.4 0.0015 5E-08 48.3 2.6 26 417-442 28-53 (55)
43 2ihx_A Nucleocapsid (NC) prote 96.1 0.002 6.7E-08 48.9 1.9 22 422-443 30-51 (61)
44 1cl4_A Protein (GAG polyprotei 96.1 0.0024 8.2E-08 47.9 2.4 21 422-442 30-50 (60)
45 3ts2_A Protein LIN-28 homolog 94.6 0.012 4.2E-07 51.6 2.0 18 445-462 98-115 (148)
46 3alr_A Nanos protein; zinc-fin 45.1 6.7 0.00023 33.9 1.1 30 432-462 54-92 (106)
47 2yuc_A TNF receptor-associated 21.6 83 0.0028 23.3 3.5 40 421-463 15-69 (76)
48 2hqh_E Restin; beta/BETA struc 20.9 27 0.00092 23.7 0.6 18 423-440 4-21 (26)
No 1
>1baj_A GAG polyprotein; capsid, HIV-1 assembly protein, viral protein; 2.60A {Human immunodeficiency virus 1} SCOP: a.28.3.1
Probab=99.79 E-value=4.1e-21 Score=160.63 Aligned_cols=67 Identities=21% Similarity=0.240 Sum_probs=45.1
Q ss_pred cccccccchHHHHHHHHHHhhhhccCCCCcccccccccccccCCCCCCcc-ccccccccCCccccCcchhhhHHhhhhhh
Q 012460 302 VSGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS-DMRLGRRVEDTVSVGPIVGERQQKKRRKK 380 (463)
Q Consensus 302 ~q~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgpe~~~tLe-mMTaCqGVgGgv~~gPs~~Em~QKkkthK 380 (463)
+.+|++||++++||+|||+||++||||||||+| |++||+ +++|+ ||++|||||| |+ ||
T Consensus 25 ~k~l~~e~~~~~vK~~~~~tL~~qnanp~Ck~~----lk~l~~--~~~l~e~~~ac~~vg~-----p~----------~k 83 (101)
T 1baj_A 25 YKTLRAEQASQEVKNWMTETLLVQNANPDCKTI----LKALGP--GATLEEMMTACQGVGG-----PG----------HK 83 (101)
T ss_dssp HHHHHHTTCCHHHHHHHHHTHHHHTSCHHHHHH----HHHHCS--SCCHHHHHHHC------------------------
T ss_pred HHHHHHhhccHHHHHHHhhhHHHHhhchhhhHH----HHccCC--CCCHHHHHHhccccCC-----cc----------hh
Confidence 345899999999999999999999999999999 999987 56778 9999999995 88 99
Q ss_pred hhhhhhhhc
Q 012460 381 TRVIEAKDK 389 (463)
Q Consensus 381 aRVLAEams 389 (463)
++|+|++|+
T Consensus 84 a~~laea~~ 92 (101)
T 1baj_A 84 ARVLAEAMS 92 (101)
T ss_dssp ---------
T ss_pred hHHHHHHHH
Confidence 999999874
No 2
>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=99.74 E-value=8.7e-20 Score=149.21 Aligned_cols=61 Identities=21% Similarity=0.254 Sum_probs=49.4
Q ss_pred ccccccchHHHHHHHHHHhhhhccCCCCcccccccccccccCCCCCCcc-ccccccccCCccccCcchhhhHHhhhhhhh
Q 012460 303 SGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS-DMRLGRRVEDTVSVGPIVGERQQKKRRKKT 381 (463)
Q Consensus 303 q~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgpe~~~tLe-mMTaCqGVgGgv~~gPs~~Em~QKkkthKa 381 (463)
..|++||++++||+|||+||++||||||||+| |++|++ +++|+ ||++|||||| |+ ||+
T Consensus 25 k~l~~e~~~~~vK~~m~~tL~~qNAnp~Ck~i----l~~l~~--~~~lee~~~aC~~vG~-----p~----------~K~ 83 (86)
T 3ds4_A 25 KTLRAEQASQEVKNWMTETLLVQNANPDCKTI----LKALGP--GATSEEMMTACQGVGG-----PG----------HKA 83 (86)
T ss_dssp HHHHHC-CCHHHHHHHHHHHHHHTSCHHHHHH----HHHHCT--TCCHHHHHHHHTTSSC-----C--------------
T ss_pred HHHHHhccchhHHHHHHHhHHHHhccHHHHHH----HHccCC--CCCHHHHHHHccccCC-----cc----------ccc
Confidence 46789999999999999999999999999999 999987 67788 9999999996 98 899
Q ss_pred hhh
Q 012460 382 RVI 384 (463)
Q Consensus 382 RVL 384 (463)
||+
T Consensus 84 ~~~ 86 (86)
T 3ds4_A 84 RVL 86 (86)
T ss_dssp ---
T ss_pred ccC
Confidence 875
No 3
>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=99.68 E-value=3.9e-19 Score=150.70 Aligned_cols=62 Identities=24% Similarity=0.301 Sum_probs=56.2
Q ss_pred cccccccchHHHHHHHHHHhhhhccCCCCcccccccccccccCCCCCCcc-ccccccccCCccccCcchhhhHHhhhhhh
Q 012460 302 VSGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS-DMRLGRRVEDTVSVGPIVGERQQKKRRKK 380 (463)
Q Consensus 302 ~q~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgpe~~~tLe-mMTaCqGVgGgv~~gPs~~Em~QKkkthK 380 (463)
+.+|++||++|+||+|||+||++||||||||+| |++||+ +++|+ ||++|||||| |+ ||
T Consensus 43 ~k~l~ae~~~~~vK~~mt~tL~~qNANpdCk~i----lk~lg~--~~tlee~~~acqgvGg-----p~----------~K 101 (105)
T 2jyl_A 43 YKTLRAEQASQEVKNAATETLLVQNANPDCKTI----LKALGP--GATLEEMMTACQGVGG-----PG----------HK 101 (105)
T ss_dssp HHHHHHHCCCTTTTTSCHHHHHHHTSCHHHHHH----HHHHCT--TCCHHHHHHHHHHSCC-----CC----------SS
T ss_pred HHHHHHhhcchhhHHHhhhhhhHhhcCcchhhH----HHccCC--CCCHHHHHHHccccCC-----cc----------cc
Confidence 345899999999999999999999999999999 999987 66778 9999999996 88 88
Q ss_pred hhhh
Q 012460 381 TRVI 384 (463)
Q Consensus 381 aRVL 384 (463)
+||+
T Consensus 102 ar~l 105 (105)
T 2jyl_A 102 ARVL 105 (105)
T ss_dssp SCCC
T ss_pred ccCC
Confidence 8875
No 4
>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=99.57 E-value=8.3e-17 Score=148.80 Aligned_cols=70 Identities=14% Similarity=0.202 Sum_probs=60.0
Q ss_pred cce-EEeeeecccCCcccccccccccchHHHHHHHHHHhhhhccCCCCccccccccccccc-CCCCCCcc-ccccccccC
Q 012460 284 NSF-EVIDLCLSSTDDDKSVSGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLR-LEDDKPLS-DMRLGRRVE 360 (463)
Q Consensus 284 ns~-~~~~l~~Ss~dd~e~~q~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLg-pe~~~tLe-mMTaCqGVg 360 (463)
+.| .|+++.|. +||+||++++||+|||+||++||||||||+| |++|| + +++|+ ||++|||||
T Consensus 127 EPf~dfVdR~~k---------~l~ae~~~~~vK~~~~~tL~~qNANpdCk~i----lk~l~~~--~~tlee~~~aCq~vg 191 (199)
T 1qrj_B 127 EPYHAFVERLNI---------ALDNGLPEGTPKDPILRSLAYSNANKECQKL----LQARGHT--NSPLGDMLRACQTWT 191 (199)
T ss_dssp SCHHHHHHHHHH---------HHHTTCCTTSCCHHHHHHHHTTTBCHHHHHH----HHHTTCS--SSCHHHHHHHHTTCC
T ss_pred CcHHHHHHHHHH---------HHHhhcCchhhhhHHHHHHHHHhcCchhHHH----HHhcCCC--CCCHHHHHHHhccCC
Confidence 344 45666554 4899999999999999999999999999999 99998 7 66778 999999987
Q ss_pred CccccCcchhhhHHhhhhhhhhhh
Q 012460 361 DTVSVGPIVGERQQKKRRKKTRVI 384 (463)
Q Consensus 361 Ggv~~gPs~~Em~QKkkthKaRVL 384 (463)
|+ ||+||+
T Consensus 192 ------p~----------~ka~~l 199 (199)
T 1qrj_B 192 ------PK----------DKTKVL 199 (199)
T ss_dssp ------CC----------CCCCCC
T ss_pred ------Cc----------cccCCC
Confidence 88 888875
No 5
>1eoq_A GAG polyprotein capsid protein P27; virus/viral protein; NMR {Rous sarcoma virus - prague C} SCOP: a.28.3.1
Probab=99.45 E-value=4.9e-15 Score=125.07 Aligned_cols=52 Identities=4% Similarity=-0.047 Sum_probs=46.3
Q ss_pred ccccccchHHHHHHHHHHhhhhccCCCCcccccccccccc-cCCCCCCcc-ccc---cccccC
Q 012460 303 SGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSL-RLEDDKPLS-DMR---LGRRVE 360 (463)
Q Consensus 303 q~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaL-gpe~~~tLe-mMT---aCqGVg 360 (463)
.+||+||++|+||+|||+||++||||||||+| |++| |+ ++|++ |+. .|+-+|
T Consensus 20 kalraeqa~~~vK~wmt~tLlvQNANPdCk~i----Lkal~g~--~~tl~em~~yi~~~~d~g 76 (96)
T 1eoq_A 20 KAVEGSDLPPSARAPVIIDCFRQKSQPDIQQL----IRTAPST--LTTPGEIIKYVLDRQKTA 76 (96)
T ss_dssp HHHHTTTCCHHHHHHHHHHHHHHHSCHHHHHH----HHHCCSC--CCSHHHHHHHHHHHSCCC
T ss_pred HHHHHhhccHhHhhhhHHHHHHHhcCHHHHHH----HHccCCC--CCCHHHHHHHHHHHHhhC
Confidence 46899999999999999999999999999999 9999 55 78877 444 788888
No 6
>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=99.41 E-value=6.6e-15 Score=139.11 Aligned_cols=60 Identities=25% Similarity=0.317 Sum_probs=33.2
Q ss_pred cccccchHHHHHHHHHHhhhhccCCCCcccccccccccccCCCCCCcc-ccccccccCCccccCcchhhhHHhhhhhhhh
Q 012460 304 GVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS-DMRLGRRVEDTVSVGPIVGERQQKKRRKKTR 382 (463)
Q Consensus 304 ~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgpe~~~tLe-mMTaCqGVgGgv~~gPs~~Em~QKkkthKaR 382 (463)
.|++++++++||+||++||++||||||||+| |++|++ +++|+ ||++|||||| |+ ||+|
T Consensus 171 al~~e~~~~~vK~~m~~tL~~qNANp~Ck~i----lk~l~~--~a~Lee~i~aCq~VG~-----p~----------hKar 229 (231)
T 3h47_A 171 TLRAEQASQEVKNAATETLLVQNANPDCKTI----LKALGP--GATLEEMMTACQGVGG-----PG----------HKAR 229 (231)
T ss_dssp HHHHC------------CHHHHTSCHHHHHH----HHHHCT--TCCHHHHHHHTC-------------------------
T ss_pred HHHhhcccchhhhHhHHhHHhhccCHHHHHH----HhccCC--CCCHHHHHHHccccCC-----hh----------hhcc
Confidence 5789999999999999999999999999999 999987 67788 9999999996 88 8988
Q ss_pred hh
Q 012460 383 VI 384 (463)
Q Consensus 383 VL 384 (463)
|+
T Consensus 230 ~~ 231 (231)
T 3h47_A 230 VL 231 (231)
T ss_dssp --
T ss_pred cC
Confidence 74
No 7
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A
Probab=99.41 E-value=3.1e-14 Score=105.82 Aligned_cols=41 Identities=39% Similarity=0.948 Sum_probs=37.6
Q ss_pred CcccccccCCCCcccccccCCCCCCCceecCCCcccccCCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
+...||+||+.||++++||.++. ..||+||+.||++++||+
T Consensus 11 ~~~~C~~Cg~~GH~a~~C~~~~~-~~C~~Cg~~GH~~~~C~~ 51 (55)
T 1a1t_A 11 KTVKCFNCGKEGHIAKNCRAPRK-KGCWKCGKEGHQMKDCTE 51 (55)
T ss_dssp GTCBCTTTCCBSSCGGGCSSCSC-CBCTTTCCBSSCGGGCSS
T ss_pred CCcceeeeCCCCcChhhcCCCCC-CEeCCCCCcCCccCCCcC
Confidence 56899999999999999999864 679999999999999996
No 8
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=99.36 E-value=2.8e-13 Score=95.29 Aligned_cols=39 Identities=46% Similarity=1.011 Sum_probs=36.0
Q ss_pred ccccccCCCCcccccccCCCCCCCceecCCCcccccCCCC
Q 012460 423 ETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 423 IKCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
+.|||||+.||++++||.++. ..||+||+.||++++||+
T Consensus 1 i~C~~Cg~~GH~a~~C~~~~~-~~C~~Cg~~GH~~~~C~~ 39 (39)
T 2a51_A 1 LTCFNCGKPGHTARMCRQPRQ-EGCWNCGSKEHRFAQCPK 39 (39)
T ss_dssp CBCTTTCCBSSCTTTCCSCCC-SSCTTTCCSSSCTTTSCC
T ss_pred CeeeccCCCCcccccCCCCCC-CccccCCCCCCccCcCcC
Confidence 479999999999999999854 689999999999999996
No 9
>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=99.35 E-value=4.2e-14 Score=131.70 Aligned_cols=51 Identities=24% Similarity=0.341 Sum_probs=47.7
Q ss_pred cccccchHHHHHHHHHHhhhhccCCCCcccccccccccccCCCCCCcc-ccccccccC
Q 012460 304 GVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS-DMRLGRRVE 360 (463)
Q Consensus 304 ~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgpe~~~tLe-mMTaCqGVg 360 (463)
.|++||++++||+|||+||++||||||||+| |++|++ +.+|+ ||++|||||
T Consensus 156 ~l~~e~~~~~vK~~mt~tL~~qNANpdCk~i----lk~lg~--~~tLee~~~aCqgvG 207 (207)
T 1eia_A 156 QIKSEGHPQEISKFLTDTLTIQNANEECRNA----MRHLRP--EDTLEEKMYACRDIG 207 (207)
T ss_dssp HHHTTCCCTTHHHHHHHHHHHHTSCHHHHHH----TTTCCT--TSCHHHHHHHTTTCC
T ss_pred HHHhhccchhhhHHhhhhHHHHhcCHHHHHH----HHhhCC--CCCHHHHHHHhccCC
Confidence 4799999999999999999999999999999 999987 66778 999999997
No 10
>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=99.30 E-value=9.1e-13 Score=96.81 Aligned_cols=41 Identities=34% Similarity=0.852 Sum_probs=37.5
Q ss_pred CcccccccCCCCcccccccCCCCCCCceecCCCcccccCCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
+.+.||+||+.||++++||.++. ..||+||+.||++++||+
T Consensus 5 r~~~C~~Cg~~GH~a~~C~~~~~-~~C~~Cg~~GH~~~~C~~ 45 (49)
T 2ec7_A 5 KVIRCWNCGKEGHSARQCRAPRR-QGCWKCGKTGHVMAKCPE 45 (49)
T ss_dssp CCCBCTTTCCBTCCTTTCCCSSC-CSCSSSCCSSCCGGGCCS
T ss_pred CcCeeeecCCCCcChhhCcCCCC-CeeCcCCCcCCccCCCcC
Confidence 46799999999999999999864 679999999999999996
No 11
>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=99.30 E-value=1.4e-13 Score=136.20 Aligned_cols=54 Identities=20% Similarity=0.224 Sum_probs=45.4
Q ss_pred cccccchHHHHHHHHHHhhhhccCCCCcccccccccccccCCCCCCcc-ccccccccCCccccCcc
Q 012460 304 GVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS-DMRLGRRVEDTVSVGPI 368 (463)
Q Consensus 304 ~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgpe~~~tLe-mMTaCqGVgGgv~~gPs 368 (463)
.|++++++++||+|||+||++||||||||+| |++|++ +++|| ||++|||||| |+
T Consensus 171 al~~e~~~~~vK~~mt~tL~~qNANp~Ck~i----lk~lg~--~a~Lee~~~aCq~VG~-----p~ 225 (342)
T 3gv2_A 171 TLRAEQASQEVKNAATETLLVQNANPDCKTI----LKALGP--GATLEEMMTACQGVGG-----TR 225 (342)
T ss_dssp HHHHTTCCHHHHHHHHHTHHHHTSCHHHHHH----HHHHCT--TCCHHHHHHHTC-----------
T ss_pred HHHhhccccchhhhhhhhhhhhccCHHHHHH----HhccCC--CCCHHHHHHHccccCC-----ch
Confidence 5789999999999999999999999999999 999987 77788 9999999996 87
No 12
>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=99.23 E-value=3.7e-12 Score=98.00 Aligned_cols=42 Identities=36% Similarity=0.801 Sum_probs=38.2
Q ss_pred CcccccccCCCCcccccccCCCCCCCceecCCCcccccCCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
+...||+||+.||++++||.+.....||+||+.||++++||+
T Consensus 6 r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~ 47 (63)
T 2cqf_A 6 SGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPL 47 (63)
T ss_dssp SCCCCSSSCCSSSCTTTCCSCCCSSCCTTTCCSSSCTTTCTG
T ss_pred CCCcccccCCCCcChhhCCCCCCCCccCCcCCcCCccCcCCC
Confidence 457899999999999999988666789999999999999985
No 13
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=99.23 E-value=3.3e-12 Score=88.90 Aligned_cols=36 Identities=42% Similarity=0.912 Sum_probs=33.7
Q ss_pred cccccCCCCcccccccCCCCCCCceecCCCcccccCCCC
Q 012460 424 TCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 424 KCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
.||+||+.||++++||.+. .||+||+.||++++||+
T Consensus 2 ~C~~Cg~~GH~~~~C~~~~---~C~~Cg~~GH~a~~C~~ 37 (37)
T 2bl6_A 2 TCYNCGKPGHLSSQCRAPK---VCFKCKQPGHFSKQCRS 37 (37)
T ss_dssp CBSSSCCSSCCTTTSSCBT---TCSSCCCTTGGGGTTCC
T ss_pred cccccCCCCcchhhCcCcC---eEccCCCcCCccCcCcC
Confidence 6999999999999999874 59999999999999995
No 14
>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=99.20 E-value=6.9e-12 Score=110.23 Aligned_cols=42 Identities=36% Similarity=0.803 Sum_probs=38.7
Q ss_pred CcccccccCCCCcccccccCCCCCCCceecCCCcccccCCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
+...|||||+.||++++||.+...+.||+||+.||++++||+
T Consensus 96 ~~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp~ 137 (148)
T 3ts2_A 96 GGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPL 137 (148)
T ss_dssp CSCCCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCTT
T ss_pred CCCcccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCcC
Confidence 367899999999999999997766789999999999999996
No 15
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=99.19 E-value=6.7e-12 Score=100.09 Aligned_cols=42 Identities=36% Similarity=0.801 Sum_probs=38.4
Q ss_pred CcccccccCCCCcccccccCCCCCCCceecCCCcccccCCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
+...|||||+.||++++|+.+...+.||+||+.||++++||+
T Consensus 23 r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~ 64 (74)
T 2li8_A 23 KGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPL 64 (74)
T ss_dssp TTSCCTTTCCSSSCTTTCSSCCCCCCCTTTCCTTSCGGGCTT
T ss_pred CCCcccccCCcCcCcccCCCCCCCCccCCcCCcCCccCcCcC
Confidence 467899999999999999987666789999999999999986
No 16
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=99.17 E-value=9.4e-12 Score=94.85 Aligned_cols=42 Identities=29% Similarity=0.759 Sum_probs=37.1
Q ss_pred CcccccccCCCCcccccccCCCC----CCCceecCCCcccccCCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQKQ----NKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaPKK----~KgCfkCGk~GH~AKDCPq 462 (463)
....||+||+.||++++||.+.. ...||+||+.||++++||+
T Consensus 3 ~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~C~~Cg~~GH~ar~C~~ 48 (61)
T 2ihx_A 3 ARGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRK 48 (61)
T ss_dssp CTTBCSSSCCBTCCGGGCTTTTSSSCCCSBCTTTCCBSSCGGGCCC
T ss_pred CCCcccccCCCCeehhhCcCCcCCCCCCCeeCCCCCCCCCcCCCcC
Confidence 35789999999999999999853 2569999999999999996
No 17
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A
Probab=99.16 E-value=6.3e-12 Score=94.79 Aligned_cols=40 Identities=33% Similarity=0.630 Sum_probs=17.7
Q ss_pred ccccccCCCCcccccccCCC-------CCCCceecCCCcccccCCCC
Q 012460 423 ETCSNCGKENHTAATCKMQK-------QNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 423 IKCFNCGKEGHiARNCPaPK-------K~KgCfkCGk~GH~AKDCPq 462 (463)
..||+||+.||++++||.+. ....||+||+.||++++||+
T Consensus 2 ~~Cf~Cg~~GH~a~~C~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~ 48 (60)
T 1cl4_A 2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKS 48 (60)
T ss_dssp ---------------------------CCCSCSSCSSCSSCSTTCCC
T ss_pred CccccCCCCCcCHhhCcCCCCCccccCCCcceeECCCCCCccCcCCC
Confidence 36999999999999999874 24679999999999999986
No 18
>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=99.06 E-value=6e-12 Score=120.85 Aligned_cols=52 Identities=6% Similarity=0.001 Sum_probs=46.5
Q ss_pred ccccccchHHHHHHHHHHhhhhccCCCCccccccccccc----ccCCCCCCcc-ccccccccC
Q 012460 303 SGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYS----LRLEDDKPLS-DMRLGRRVE 360 (463)
Q Consensus 303 q~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~Lka----Lgpe~~~tLe-mMTaCqGVg 360 (463)
.+||+||+++++++||..++++||||||||+| |++ |++ ..||+ ||++|||||
T Consensus 195 kalrae~~~~~~~~~~~~~~l~qnAnpdck~~----lraal~pl~~--~~tLee~m~aCq~VG 251 (262)
T 1d1d_A 195 KAVEGSDLPPSARAPVIIDCFRQKSQPDIQQL----IRAAPSTLTT--PGEIIKYVLDRQKIA 251 (262)
T ss_dssp HHHHTSSCCTTTTTHHHHHHHTTSSCHHHHHH----HHTSCTTCCS--TTHHHHHHHHHHCCC
T ss_pred HHHHhhccCcccchhhHHHHHHHhcCHHHHHH----HHHhhhcCCC--CCCHHHHHHHHcccC
Confidence 35999999999999996555999999999999 999 887 56777 999999998
No 19
>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=98.98 E-value=3.3e-11 Score=98.49 Aligned_cols=38 Identities=5% Similarity=-0.034 Sum_probs=35.2
Q ss_pred ccccccchHHHHHHHHHHhhhhccCCCCcccccccccccccC
Q 012460 303 SGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRL 344 (463)
Q Consensus 303 q~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgp 344 (463)
-.|+++|++++||+||+++|+|||||||||+| |++|-.
T Consensus 24 kal~~e~~~~~vk~~m~~tLl~QNANpdCk~i----lk~l~~ 61 (77)
T 3g21_A 24 KAVEGSDLPPSARAPVIIDCFRQKSQPDIQQL----IRTAPS 61 (77)
T ss_dssp HHHHTSSSCHHHHHHHHHHHHHHHSCHHHHHH----HTTSCT
T ss_pred HHHHHhhChHHHHHHHHHHHHHHhcCHHHHHH----HHhCCC
Confidence 35899999999999999999999999999999 999854
No 20
>1u57_A GAG polyprotein, HIV-1; particle assembly, viral protein; NMR {Human immunodeficiency virus 1}
Probab=98.85 E-value=8.2e-10 Score=81.47 Aligned_cols=42 Identities=21% Similarity=0.192 Sum_probs=32.0
Q ss_pred cccccccccCCccccCcchhhhHHhhhhhhhhhhhhhhcchHHhhhhhhhhhH-HHHHhhCCCC
Q 012460 351 SDMRLGRRVEDTVSVGPIVGERQQKKRRKKTRVIEAKDKVEDARKENEAKYNV-VLRMLLRKPR 413 (463)
Q Consensus 351 emMTaCqGVgGgv~~gPs~~Em~QKkkthKaRVLAEamsmEdtmsqv~~n~NI-MmRknfRGpR 413 (463)
||||+|||||| |+ ||+||+||+|++ ++.++++ |+|.+|+++|
T Consensus 3 em~~acqgvgg-----p~----------hKarvlAEAMsq------~~~~~~immqr~nf~g~r 45 (48)
T 1u57_A 3 EMMTACQGVGG-----PG----------HKARVLAEAMSQ------VTNSATIMMQRGNFRNQR 45 (48)
T ss_dssp THHHHBTTTSB-----CT----------THHHHHHHHHHH------HHHHHHHHHHTTTTTTCS
T ss_pred hhhhhccCCCC-----Cc----------chhhHHHHHHHH------hccccchhhhcccccCCC
Confidence 49999999995 99 999999999843 3322344 5588888875
No 21
>3g1g_A GAG polyprotein, capsid protein; alpha-helical bundle, virion, viral protein, retrovirus; 2.01A {Rous sarcoma virus}
Probab=98.84 E-value=1.5e-10 Score=96.39 Aligned_cols=38 Identities=5% Similarity=-0.034 Sum_probs=35.2
Q ss_pred ccccccchHHHHHHHHHHhhhhccCCCCcccccccccccccC
Q 012460 303 SGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRL 344 (463)
Q Consensus 303 q~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgp 344 (463)
-.|+++|++++||+||++||+|||||||||+| |++|-.
T Consensus 23 kal~~eq~~~~vK~~m~~tLlvQNANpdCk~I----l~~~~~ 60 (87)
T 3g1g_A 23 KAVEGSDLPPSARAPVIIDCFRQKSQPDIQQL----IRTAPS 60 (87)
T ss_dssp HHHHHSSSCGGGHHHHHHHHHHHHSCHHHHHH----HHTSCT
T ss_pred HHHHHhhchHHHHHHHHHHHHHHhcCHHHHHH----HHhCCC
Confidence 35789999999999999999999999999999 999865
No 22
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=98.77 E-value=1.8e-09 Score=87.92 Aligned_cols=39 Identities=21% Similarity=0.320 Sum_probs=21.3
Q ss_pred cccccCCCCcccccccCCCCCCCceecCCCcccccCCCC
Q 012460 424 TCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 424 KCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
.||+|+..||++++|+.|...+.||+||+.||++++||+
T Consensus 26 rcY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~ 64 (83)
T 3nyb_B 26 RAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKE 64 (83)
T ss_dssp CCCCBC-------------CCCBCSSSSCBSSCGGGCSS
T ss_pred cccccccCCcccccccCCCCCCeecccCCCCcCcccCCc
Confidence 455555555555555555445789999999999999996
No 23
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=98.72 E-value=8.7e-09 Score=86.52 Aligned_cols=41 Identities=29% Similarity=0.630 Sum_probs=37.1
Q ss_pred cccccccCCCCcccccccCCCCCCCceecCCCcccccCCCC
Q 012460 422 SETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
...||+||+.||++++||.+.+...||+||+.||++++||+
T Consensus 42 ~~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~~~~Cp~ 82 (124)
T 2lli_A 42 AIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPS 82 (124)
T ss_dssp SSCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCCTTTCCC
T ss_pred cccccccCCCCCccccCcCcccCccCCCCCcCCcchhhCCC
Confidence 47899999999999999988655789999999999999996
No 24
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=98.69 E-value=6.7e-09 Score=87.19 Aligned_cols=42 Identities=24% Similarity=0.575 Sum_probs=36.6
Q ss_pred cccccccCCCCcccccccCCCC-------------------CCCceecCCCcccccCCCCC
Q 012460 422 SETCSNCGKENHTAATCKMQKQ-------------------NKPCFLCGSFKHRWKNCKQV 463 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPaPKK-------------------~KgCfkCGk~GH~AKDCPqV 463 (463)
...||+||+.||++++||...+ ...||+||+.||+++|||+.
T Consensus 64 ~~~C~~Cg~~GH~~~~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~~ 124 (124)
T 2lli_A 64 KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 124 (124)
T ss_dssp CCSSSSSCSSCCCTTTCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCCC
T ss_pred CccCCCCCcCCcchhhCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcCC
Confidence 4789999999999999997532 35799999999999999973
No 25
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=98.36 E-value=9.4e-08 Score=77.87 Aligned_cols=38 Identities=13% Similarity=0.280 Sum_probs=23.6
Q ss_pred CcccccccCCCCcccccccCCCCCCCceecCCCcccccCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCK 461 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH~AKDCP 461 (463)
..+.||+||+.||++++||...+ ||+|+..||++++|+
T Consensus 4 k~~~C~~Cg~~GH~~~~Cp~~~r---cY~c~~~gh~~~~c~ 41 (83)
T 3nyb_B 4 KKVQCTLCKSKKHSKERCPSIWR---AYILVDDNEKAKPKV 41 (83)
T ss_dssp ---CCSSSCCSSSCGGGCGGGTC---CCCBC----------
T ss_pred ccCCCCCCCCCCCccccCCCccc---ccccccCCccccccc
Confidence 46899999999999999999764 999999999999996
No 26
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A
Probab=98.14 E-value=9.2e-07 Score=59.19 Aligned_cols=23 Identities=39% Similarity=0.884 Sum_probs=20.8
Q ss_pred CcccccccCCCCcccccccCCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQKQ 443 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaPKK 443 (463)
+.+.|||||++||++++|+.|++
T Consensus 5 ~~~~C~nCgk~GH~ar~C~~prk 27 (29)
T 1nc8_A 5 KVIRCWNCGKEGHSARQCRAPRR 27 (29)
T ss_dssp CCCBCTTTSCBSSCGGGCCSSSS
T ss_pred CCCEEEECCccccCHhHCccccc
Confidence 46899999999999999999875
No 27
>3tir_A ROUS sarcoma virus capsid protein P27; viral capsid protein, viral protein; 4.10A {Rous sarcoma virus} PDB: 2x8q_A
Probab=98.05 E-value=3.8e-07 Score=86.27 Aligned_cols=37 Identities=5% Similarity=-0.036 Sum_probs=34.3
Q ss_pred cccccchHHHHHHHHHHhhhhccCCCCcccccccccccccC
Q 012460 304 GVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRL 344 (463)
Q Consensus 304 ~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgp 344 (463)
.++++++.+++|+||+++|++||||||||+| |++|-.
T Consensus 174 a~~~~~~~~~~~~~~~~~l~~qNAN~~ck~i----l~~~~~ 210 (226)
T 3tir_A 174 AVEGSDLPPSARAPVIIDCFRQKSQPDIQQL----IRTAPS 210 (226)
T ss_dssp HHHTSSSCHHHHHHHHHHHHHHHSCHHHHHH----HHTSCT
T ss_pred HHHHHcCcHHHHHHHHHHHHHHhCCHHHHHH----HHhCCC
Confidence 4788999999999999999999999999999 999854
No 28
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}
Probab=97.97 E-value=2.1e-06 Score=68.39 Aligned_cols=32 Identities=28% Similarity=0.616 Sum_probs=18.3
Q ss_pred CCcccccccCCCC---------CCCceecCCCcccccCCCC
Q 012460 431 ENHTAATCKMQKQ---------NKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 431 EGHiARNCPaPKK---------~KgCfkCGk~GH~AKDCPq 462 (463)
.||++++|+.++. ...||+||+.||++++||.
T Consensus 2 ~gh~~rdc~~~~~~~~~~~~~r~~~C~~Cg~~GH~a~~C~~ 42 (74)
T 2li8_A 2 SGLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKL 42 (74)
T ss_dssp ----------CCCCCCCSCCSTTSCCTTTCCSSSCTTTCSS
T ss_pred CccccCcCCCCCcCccccccCCCCcccccCCcCcCcccCCC
Confidence 5999999998852 2469999999999999984
No 29
>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=97.81 E-value=6.2e-06 Score=54.11 Aligned_cols=21 Identities=33% Similarity=0.775 Sum_probs=16.7
Q ss_pred ccccccCCCCcccccccCCCC
Q 012460 423 ETCSNCGKENHTAATCKMQKQ 443 (463)
Q Consensus 423 IKCFNCGKEGHiARNCPaPKK 443 (463)
..||+||+.||++++||.+..
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 579999999999999988753
No 30
>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=97.59 E-value=2.8e-05 Score=56.40 Aligned_cols=23 Identities=22% Similarity=0.660 Sum_probs=20.3
Q ss_pred CcccccccCCCCcccccccCCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQKQ 443 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaPKK 443 (463)
...+||+||+.||++++||.+.+
T Consensus 9 ~~~~C~~Cgk~GH~ardCP~~~~ 31 (40)
T 1a6b_B 9 DRDQCAYCKEKGHWAKDCPKKPR 31 (40)
T ss_dssp CSSSCSSSCCTTCCTTSCSSSCC
T ss_pred CCCeeeECCCCCcchhhCcCCcc
Confidence 46899999999999999999853
No 31
>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=97.49 E-value=3.2e-05 Score=50.71 Aligned_cols=18 Identities=39% Similarity=0.931 Sum_probs=16.6
Q ss_pred CCceecCCCcccccCCCC
Q 012460 445 KPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 445 KgCfkCGk~GH~AKDCPq 462 (463)
..||+||+.||++++||+
T Consensus 3 ~~Cf~CG~~GH~ardC~~ 20 (26)
T 1dsq_A 3 PVCFSCGKTGHIKRDCKE 20 (26)
T ss_dssp CBCTTTCCBSSCTTTTTC
T ss_pred CeeEeCCCCCcccccCCC
Confidence 469999999999999986
No 32
>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=97.33 E-value=0.00013 Score=56.13 Aligned_cols=24 Identities=21% Similarity=0.623 Sum_probs=20.6
Q ss_pred CCcccccccCCCCcccccccCCCC
Q 012460 420 WNSETCSNCGKENHTAATCKMQKQ 443 (463)
Q Consensus 420 kg~IKCFNCGKEGHiARNCPaPKK 443 (463)
.....||+||+.||++++||.+.+
T Consensus 21 ~~~~~C~~Cge~GH~ardCp~~~~ 44 (56)
T 1u6p_A 21 LDRDQCAYCKEKGHWAKDCPKKPR 44 (56)
T ss_dssp CCTTBCSSSCCBSSCGGGCTTCCC
T ss_pred CCCCcceeCCCCCcccccCcCCcc
Confidence 346899999999999999998753
No 33
>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=97.29 E-value=0.00015 Score=55.68 Aligned_cols=32 Identities=25% Similarity=0.421 Sum_probs=27.7
Q ss_pred CcccccccCCCCcccccccCCCCCCCceecCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQKQNKPCFLCGSF 453 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaPKK~KgCfkCGk~ 453 (463)
....||+||+.||++++||.... .+++.||++
T Consensus 28 ~~~~C~~Cg~~GH~ar~Cp~~~~-~~~~~~g~~ 59 (63)
T 2cqf_A 28 QPKKCHFCQSISHMVASCPLKAQ-QGPSAQGSG 59 (63)
T ss_dssp CSSCCTTTCCSSSCTTTCTGGGC-SCCCCSCCC
T ss_pred CCCccCCcCCcCCccCcCCCccc-cCCccCCCC
Confidence 46799999999999999999764 579999875
No 34
>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=97.21 E-value=0.00011 Score=48.97 Aligned_cols=21 Identities=24% Similarity=0.697 Sum_probs=17.6
Q ss_pred CCCCCceecCCCcccccCCCC
Q 012460 442 KQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 442 KK~KgCfkCGk~GH~AKDCPq 462 (463)
++...||+||+.||++++|+.
T Consensus 4 r~~~~C~nCgk~GH~ar~C~~ 24 (29)
T 1nc8_A 4 RKVIRCWNCGKEGHSARQCRA 24 (29)
T ss_dssp CCCCBCTTTSCBSSCGGGCCS
T ss_pred CCCCEEEECCccccCHhHCcc
Confidence 334569999999999999985
No 35
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=97.07 E-value=0.00016 Score=55.49 Aligned_cols=21 Identities=33% Similarity=0.725 Sum_probs=17.8
Q ss_pred CcccccccCCCCcccccccCC
Q 012460 421 NSETCSNCGKENHTAATCKMQ 441 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaP 441 (463)
..-.||.||++||++++||..
T Consensus 6 ~~~~C~kCGk~GH~~k~Cp~~ 26 (55)
T 2ysa_A 6 SGYTCFRCGKPGHYIKNCPTN 26 (55)
T ss_dssp SSCCCTTTCCTTSCGGGCSGG
T ss_pred CCCccccCCCcCcccccCCCC
Confidence 345899999999999999943
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=96.99 E-value=0.00031 Score=50.90 Aligned_cols=18 Identities=28% Similarity=0.636 Sum_probs=16.7
Q ss_pred CCceecCCCcccccCCCC
Q 012460 445 KPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 445 KgCfkCGk~GH~AKDCPq 462 (463)
..||.||+.||++++||+
T Consensus 11 ~~C~~Cgk~GH~ardCP~ 28 (40)
T 1a6b_B 11 DQCAYCKEKGHWAKDCPK 28 (40)
T ss_dssp SSCSSSCCTTCCTTSCSS
T ss_pred CeeeECCCCCcchhhCcC
Confidence 569999999999999996
No 37
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=96.73 E-value=0.00085 Score=46.87 Aligned_cols=25 Identities=32% Similarity=0.503 Sum_probs=20.1
Q ss_pred CCCCCCcccccccCCCCcccccccC
Q 012460 416 DPPGWNSETCSNCGKENHTAATCKM 440 (463)
Q Consensus 416 dgPkkg~IKCFNCGKEGHiARNCPa 440 (463)
+.+..+...||+||+.||++++||.
T Consensus 15 ~C~~~~~~~C~~Cg~~GH~~~~C~~ 39 (39)
T 2a51_A 15 MCRQPRQEGCWNCGSKEHRFAQCPK 39 (39)
T ss_dssp TCCSCCCSSCTTTCCSSSCTTTSCC
T ss_pred cCCCCCCCccccCCCCCCccCcCcC
Confidence 3444346799999999999999984
No 38
>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=0.00061 Score=52.38 Aligned_cols=18 Identities=28% Similarity=0.636 Sum_probs=16.6
Q ss_pred CCceecCCCcccccCCCC
Q 012460 445 KPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 445 KgCfkCGk~GH~AKDCPq 462 (463)
..||.||+.||++++||.
T Consensus 24 ~~C~~Cge~GH~ardCp~ 41 (56)
T 1u6p_A 24 DQCAYCKEKGHWAKDCPK 41 (56)
T ss_dssp TBCSSSCCBSSCGGGCTT
T ss_pred CcceeCCCCCcccccCcC
Confidence 469999999999999985
No 39
>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=96.56 E-value=0.0015 Score=47.70 Aligned_cols=27 Identities=26% Similarity=0.536 Sum_probs=21.5
Q ss_pred CCCCCCcccccccCCCCcccccccCCC
Q 012460 416 DPPGWNSETCSNCGKENHTAATCKMQK 442 (463)
Q Consensus 416 dgPkkg~IKCFNCGKEGHiARNCPaPK 442 (463)
+++..+...||+||+.||++++||...
T Consensus 21 ~C~~~~~~~C~~Cg~~GH~~~~C~~~~ 47 (49)
T 2ec7_A 21 QCRAPRRQGCWKCGKTGHVMAKCPERQ 47 (49)
T ss_dssp TCCCSSCCSCSSSCCSSCCGGGCCSSC
T ss_pred hCcCCCCCeeCcCCCcCCccCCCcCCC
Confidence 444444578999999999999999754
No 40
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=96.50 E-value=0.0015 Score=45.17 Aligned_cols=19 Identities=21% Similarity=0.705 Sum_probs=17.4
Q ss_pred cccccccCCCCcccccccC
Q 012460 422 SETCSNCGKENHTAATCKM 440 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPa 440 (463)
...||+||+.||++++||+
T Consensus 19 ~~~C~~Cg~~GH~a~~C~~ 37 (37)
T 2bl6_A 19 PKVCFKCKQPGHFSKQCRS 37 (37)
T ss_dssp BTTCSSCCCTTGGGGTTCC
T ss_pred cCeEccCCCcCCccCcCcC
Confidence 4789999999999999985
No 41
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=96.43 E-value=0.0012 Score=50.53 Aligned_cols=18 Identities=44% Similarity=0.886 Sum_probs=16.6
Q ss_pred CCceecCCCcccccCCCC
Q 012460 445 KPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 445 KgCfkCGk~GH~AKDCPq 462 (463)
..||+||++||++++||.
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 579999999999999993
No 42
>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=96.43 E-value=0.0015 Score=48.28 Aligned_cols=26 Identities=27% Similarity=0.562 Sum_probs=21.0
Q ss_pred CCCCCcccccccCCCCcccccccCCC
Q 012460 417 PPGWNSETCSNCGKENHTAATCKMQK 442 (463)
Q Consensus 417 gPkkg~IKCFNCGKEGHiARNCPaPK 442 (463)
++..+...||+||+.||++++||...
T Consensus 28 C~~~~~~~C~~Cg~~GH~~~~C~~~~ 53 (55)
T 1a1t_A 28 CRAPRKKGCWKCGKEGHQMKDCTERQ 53 (55)
T ss_dssp CSSCSCCBCTTTCCBSSCGGGCSSSC
T ss_pred cCCCCCCEeCCCCCcCCccCCCcCcC
Confidence 33334578999999999999999864
No 43
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=96.14 E-value=0.002 Score=48.91 Aligned_cols=22 Identities=27% Similarity=0.658 Sum_probs=19.2
Q ss_pred cccccccCCCCcccccccCCCC
Q 012460 422 SETCSNCGKENHTAATCKMQKQ 443 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPaPKK 443 (463)
...||+||+.||++++||.++.
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 4789999999999999998753
No 44
>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=96.13 E-value=0.0024 Score=47.87 Aligned_cols=21 Identities=29% Similarity=0.683 Sum_probs=19.3
Q ss_pred cccccccCCCCcccccccCCC
Q 012460 422 SETCSNCGKENHTAATCKMQK 442 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPaPK 442 (463)
...||+||+.||++++|+...
T Consensus 30 ~~~C~~Cg~~GH~ar~C~~~~ 50 (60)
T 1cl4_A 30 PGLCPRCKRGKHWANECKSKT 50 (60)
T ss_dssp CCSCSSCSSCSSCSTTCCCTT
T ss_pred CcceeECCCCCCccCcCCCcc
Confidence 578999999999999999875
No 45
>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=94.59 E-value=0.012 Score=51.61 Aligned_cols=18 Identities=39% Similarity=1.006 Sum_probs=16.4
Q ss_pred CCceecCCCcccccCCCC
Q 012460 445 KPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 445 KgCfkCGk~GH~AKDCPq 462 (463)
..||+||+.||++++||.
T Consensus 98 ~~C~~Cg~~GH~a~~C~~ 115 (148)
T 3ts2_A 98 DRCYNCGGLDHHAKECKL 115 (148)
T ss_dssp CCCTTTCCSSCCGGGCCS
T ss_pred CcccEeCCccchhhhCCC
Confidence 459999999999999985
No 46
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=45.07 E-value=6.7 Score=33.94 Aligned_cols=30 Identities=30% Similarity=0.613 Sum_probs=24.7
Q ss_pred Cccccc------ccCCCCCCCceecCCCc---ccccCCCC
Q 012460 432 NHTAAT------CKMQKQNKPCFLCGSFK---HRWKNCKQ 462 (463)
Q Consensus 432 GHiARN------CPaPKK~KgCfkCGk~G---H~AKDCPq 462 (463)
.|..++ ||..+. -.|-.||..| |..+-||.
T Consensus 54 SH~LKd~~G~V~CPvLR~-Y~CpiCGATGd~AHT~kYCP~ 92 (106)
T 3alr_A 54 SHYLKNRDGDVMCPYLRQ-YKCPLCGATGAKAHTKRFCPM 92 (106)
T ss_dssp SBCSBCTTSCBCCTTGGG-CCCTTTCCCGGGCCCGGGCTT
T ss_pred cceeECCCCCCcCCCccc-ccCCCCCCcCCcccceecCCC
Confidence 487777 888765 5799999999 99999985
No 47
>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=21.58 E-value=83 Score=23.29 Aligned_cols=40 Identities=28% Similarity=0.585 Sum_probs=29.3
Q ss_pred Ccccc-cccCC-------CCcccccccCCCCCCCceecCCCc-------ccccCCCCC
Q 012460 421 NSETC-SNCGK-------ENHTAATCKMQKQNKPCFLCGSFK-------HRWKNCKQV 463 (463)
Q Consensus 421 g~IKC-FNCGK-------EGHiARNCPaPKK~KgCfkCGk~G-------H~AKDCPqV 463 (463)
..+.| ..||. .-|....||... ..|-.|+... |. ..||.+
T Consensus 15 ~~v~C~~~C~~~v~r~~l~~H~~~~C~~r~--v~C~~C~~~~~~~~l~~H~-~~Cp~~ 69 (76)
T 2yuc_A 15 NVIPCPNRCPMKLSRRDLPAHLQHDCPKRR--LKCEFCGCDFSGEAYESHE-GMCPQE 69 (76)
T ss_dssp SCCBCTTCCSCBCCSSSSTTTTTTSCTTSC--CCCSSSCCCCCHHHHHHTT-TSCTTS
T ss_pred cccCCCccccHHhhHhHHHhhCHhhCCCcc--eECCCCCCccCHHHHHHHH-hHCCCC
Confidence 46788 67873 348888999865 4588898877 88 578864
No 48
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}
Probab=20.92 E-value=27 Score=23.74 Aligned_cols=18 Identities=28% Similarity=0.512 Sum_probs=13.0
Q ss_pred ccccccCCCCcccccccC
Q 012460 423 ETCSNCGKENHTAATCKM 440 (463)
Q Consensus 423 IKCFNCGKEGHiARNCPa 440 (463)
+.|-+|...||...+|..
T Consensus 4 pYCe~CE~FGH~t~~C~d 21 (26)
T 2hqh_E 4 PYCEICEMFGHWATNCND 21 (26)
T ss_dssp CEETTTTEESSCGGGCCT
T ss_pred ccchHHHHhCcccccCCc
Confidence 467777777777777754
Done!