Query gi|254780259|ref|YP_003064672.1| 50S ribosomal protein L23 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 110 No_of_seqs 117 out of 1550 Neff 5.4 Searched_HMMs 23785 Date Tue May 24 07:51:24 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780259.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 2zjr_Q 50S ribosomal protein L 100.0 6.7E-36 2.8E-40 226.7 7.6 93 4-109 1-93 (95) 2 3fin_X 50S ribosomal protein L 100.0 6.2E-35 2.6E-39 221.1 -1.4 92 6-110 2-93 (93) 3 3ofq_T 50S ribosomal protein L 100.0 2.3E-32 9.7E-37 206.3 -6.3 91 1-104 2-93 (93) 4 2wwb_K 60S ribosomal protein L 99.9 2.8E-27 1.2E-31 177.0 7.6 84 1-110 54-139 (142) 5 2zkr_s 60S ribosomal protein L 99.9 4.7E-27 2E-31 175.8 7.3 83 1-109 68-152 (156) 6 2go5_4 Ribosomal protein L23; 99.9 1.4E-26 5.9E-31 173.0 6.8 84 1-110 64-149 (152) 7 3bbo_V Ribosomal protein L23; 99.9 2.4E-27 1E-31 177.4 1.4 82 2-109 107-196 (198) 8 1vq8_S 50S ribosomal protein L 99.9 5.1E-25 2.2E-29 164.0 8.1 79 6-110 2-82 (85) 9 2bwf_A Ubiquitin-like protein 59.1 10 0.00043 18.2 4.2 42 25-67 13-54 (77) 10 3a9j_A Ubiquitin; protein comp 51.3 14 0.00058 17.5 4.1 40 24-64 9-48 (76) 11 1j8c_A Ubiquitin-like protein 50.1 14 0.00061 17.4 5.0 41 25-66 41-81 (125) 12 3n3k_B Ubiquitin; hydrolase, p 49.3 15 0.00063 17.3 4.1 40 24-64 12-51 (85) 13 1wx7_A Ubiquilin 3; ubiquitin- 45.0 17 0.00073 16.9 4.3 40 25-65 26-65 (106) 14 2dzm_A FAS-associated factor 1 44.4 17 0.00072 16.9 3.3 43 24-66 17-59 (100) 15 2klc_A Ubiquilin-1; ubiquitin- 43.8 18 0.00077 16.8 5.0 41 25-66 34-74 (101) 16 1v86_A DNA segment, CHR 7, way 41.5 20 0.00083 16.6 3.9 39 24-63 25-63 (95) 17 3mtn_B UBA80, ubcep1, ubiquiti 39.9 21 0.00088 16.4 4.1 42 24-66 12-53 (85) 18 1sif_A Ubiquitin; hydrophobic 39.4 21 0.0009 16.4 3.7 41 24-65 18-58 (88) 19 1wx8_A Riken cDNA 4931431F19; 38.4 22 0.00093 16.3 3.7 39 25-64 26-64 (96) 20 2kan_A Uncharacterized protein 37.1 23 0.00098 16.2 4.1 39 25-64 24-62 (94) 21 3m62_B UV excision repair prot 36.7 19 0.00079 16.7 2.5 44 23-67 9-52 (106) 22 2hj8_A Interferon-induced 17 k 36.5 24 0.001 16.1 4.1 41 24-65 13-53 (88) 23 3dbh_I NEDD8; cell cycle, acti 35.7 25 0.001 16.0 3.5 40 24-64 21-60 (88) 24 2dgv_A HnRNP M, heterogeneous 33.8 26 0.0011 15.9 5.0 39 26-66 10-48 (92) 25 1yqb_A Ubiquilin 3; structural 33.3 27 0.0011 15.8 4.3 40 25-65 31-70 (100) 26 1rk8_A CG8781-PA, CG8781-PA pr 31.3 29 0.0012 15.6 5.1 32 27-60 75-106 (165) 27 1v2y_A 3300001G02RIK protein; 30.3 27 0.0011 15.8 2.5 34 24-57 16-49 (105) 28 2g1d_A 30S ribosomal protein S 30.2 6.6 0.00028 19.3 -0.7 45 14-58 5-53 (98) 29 1yx5_B Ubiquitin; proteasome, 29.8 31 0.0013 15.5 3.9 43 23-66 8-50 (98) 30 1oqy_A HHR23A, UV excision rep 29.8 31 0.0013 15.5 3.7 45 23-67 15-61 (368) 31 3k9o_B Ubiquitin, UBB+1; E2-25 29.4 31 0.0013 15.4 4.1 42 23-65 9-50 (96) 32 2kk8_A Uncharacterized protein 29.2 32 0.0013 15.4 4.5 41 23-64 18-58 (84) 33 1v5o_A 1700011N24RIK protein; 28.8 32 0.0014 15.4 3.6 39 25-64 21-59 (102) 34 2kd0_A LRR repeats and ubiquit 27.2 35 0.0015 15.2 3.3 41 25-66 21-61 (85) 35 2d9p_A Polyadenylate-binding p 26.9 35 0.0015 15.2 4.7 42 24-67 15-56 (103) 36 2ojr_A Ubiquitin; lanthide-bin 26.3 36 0.0015 15.1 4.2 40 24-64 44-83 (111) 37 1wjn_A Tubulin-folding protein 25.8 26 0.0011 15.9 1.7 37 23-59 20-56 (97) 38 2v94_A RPS24, 30S ribosomal pr 25.2 23 0.00098 16.2 1.4 45 16-60 15-63 (107) 39 1xn9_A 30S ribosomal protein S 24.9 14 0.0006 17.4 0.3 46 14-59 5-53 (101) 40 1ywx_A 30S ribosomal protein S 24.8 16 0.00069 17.0 0.6 45 15-59 6-53 (102) 41 1ndd_A NEDD8, protein (ubiquit 24.5 39 0.0016 14.9 4.1 40 24-64 9-48 (76) 42 2err_A Ataxin-2-binding protei 23.8 39 0.0016 14.9 2.3 32 26-59 31-62 (109) 43 1ttn_A DC-UBP, dendritic cell- 23.6 40 0.0017 14.8 2.5 41 24-65 32-72 (106) 44 2dhg_A TRNA selenocysteine ass 21.9 44 0.0018 14.6 6.6 28 25-52 10-37 (104) 45 1x4b_A Heterogeneous nuclear r 21.9 44 0.0018 14.6 3.8 34 25-60 28-61 (116) 46 2kj6_A Tubulin folding cofacto 21.7 44 0.0019 14.6 4.4 37 24-60 25-61 (97) 47 1z2m_A ISG15, interferon, alph 20.4 47 0.002 14.4 4.4 36 24-59 11-46 (155) 48 3ai5_A Yeast enhanced green fl 20.3 47 0.002 14.4 4.2 36 24-59 242-277 (307) 49 2kdi_A Ubiquitin, vacuolar pro 20.3 47 0.002 14.4 4.1 41 24-65 18-58 (114) No 1 >2zjr_Q 50S ribosomal protein L23; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.12.1.1 PDB: 1sm1_R* 2aar_R 2d3o_R 2zjp_Q* 2zjq_Q 1nkw_R 3cf5_Q* 3dll_Q* 1nwy_R* 1nwx_R* 1xbp_R* 1pnu_R 1pny_R 1vor_U 1vou_U 1vow_U 1voy_U 1vp0_U Probab=100.00 E-value=6.7e-36 Score=226.69 Aligned_cols=93 Identities=38% Similarity=0.557 Sum_probs=87.9 Q ss_pred CHHHHHHHHCCCCHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCCCCC Q ss_conf 25786760032079988886489099998887898899999999968743378998518963331122466443223454 Q gi|254780259|r 4 IRFYDTIISPVIAEKSTLLAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRSSRD 83 (110) Q Consensus 4 ~~~~~vi~~P~~TEKs~~~~e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~~r~ 83 (110) |++||+|++|++||||+.+.|+|+|+|.|+++|||.|||+|||++|+|+|.+|||+|.+||.||++++ T Consensus 1 m~~ydvi~~P~vTEKs~~~~e~n~y~F~V~~~a~K~eIK~ave~~f~VkV~~Vnt~~~~gK~kr~~~~------------ 68 (95) T 2zjr_Q 1 MSHYDILQAPVISEKAYSAMERGVYSFWVSPKATKTEIKDAIQQAFGVRVIGISTMNVPGKRKRVGRF------------ 68 (95) T ss_dssp -CCSSSCCEECCTHHHHHHHTTTCCEEEECSSCTHHHHHHHHHHHHCCCCSEEEECCBCCCCCSSSSC------------ T ss_pred CCCCCEEEECCCCHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEEEEECCCEEEECCC------------ T ss_conf 98434886040288787667699899997798999999999999839964899889847953677883------------ Q ss_pred CCCCCCCCEEEEEECCCCCEECCCCC Q ss_conf 44345881389999589973133248 Q gi|254780259|r 84 MYVSRKDVKRAFVTLAKGYSIDISAG 109 (110) Q Consensus 84 ~~~k~~~~KKAiVtL~~G~~I~~~~g 109 (110) .|++++||||||||++|++||||+| T Consensus 69 -~g~~~~~KKAiVtL~~g~~I~~~~g 93 (95) T 2zjr_Q 69 -IGQRNDRKKAIVRLAEGQSIEALAG 93 (95) T ss_dssp -CCCCCCBEEEEEECCSSCCCSSTTT T ss_pred -CCCCCCCEEEEEECCCCCEEEECCC T ss_conf -4134898999999789696300267 No 2 >3fin_X 50S ribosomal protein L23; ribonucleoprotein, metal-binding, RNA- binding, rRNA-binding, zinc, tRNA-binding, repressor; 6.40A {Thermus thermophilus} PDB: 1n88_A 1vsa_R 1vsp_R 2hgj_W 2hgq_W 2hgu_W 2j01_X 2j03_X 2jl6_X 2jl8_X 2v47_X 2v49_X 2wdi_X 2wdj_X 2wdl_X 2wdn_X 2wh2_X 2wh4_X 2wrj_X 2wrl_X ... Probab=99.98 E-value=6.2e-35 Score=221.11 Aligned_cols=92 Identities=43% Similarity=0.593 Sum_probs=86.6 Q ss_pred HHHHHHHCCCCHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCCCCCCC Q ss_conf 78676003207998888648909999888789889999999996874337899851896333112246644322345444 Q gi|254780259|r 6 FYDTIISPVIAEKSTLLAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRSSRDMY 85 (110) Q Consensus 6 ~~~vi~~P~~TEKs~~~~e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~~r~~~ 85 (110) .||+|++|++||||+.++|+|+|+|.|+++|||+|||+|||.+|+|+|.+|||+|++||.||+|++ . T Consensus 2 ~ydii~~Pv~TEKs~~~~e~n~y~F~V~~~atK~eIK~ave~~f~VkV~~Vnt~~~~gK~kr~~~~-------------~ 68 (93) T 3fin_X 2 AYDVILAPVLSEKAYAGFAEGKYTFWVHPKATKTEIKNAVETAFKVKVVKVNTLHVRGKKKRLGRY-------------L 68 (93) T ss_dssp CSTTCCEECCSHHHHHHHTSSCCCEECCSSSCCTTCHHHHTTTTTCCCCCBCCCCCCCCCCSSCCC-------------C T ss_pred CHHEEECCCCCHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEEEEECCCEEEECCC-------------C T ss_conf 312653361188686556689899997697999999999999849960599988848962576882-------------4 Q ss_pred CCCCCCEEEEEECCCCCEECCCCCC Q ss_conf 3458813899995899731332489 Q gi|254780259|r 86 VSRKDVKRAFVTLAKGYSIDISAGV 110 (110) Q Consensus 86 ~k~~~~KKAiVtL~~G~~I~~~~gi 110 (110) |++++||||||||++|++||||||| T Consensus 69 g~~~~~KKAiVtL~~g~~I~~~~g~ 93 (93) T 3fin_X 69 GKRPDRKKAIVQVAPGQKIEALEGL 93 (93) T ss_dssp SCCCCBCCBCCSTTTCCSSSSTTC- T ss_pred CCCCCCEEEEEECCCCCEECCCCCC T ss_conf 2458978999993895981365798 No 3 >3ofq_T 50S ribosomal protein L23; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 3fik_T 2wwq_T 3ofr_T* 2j28_T 3e1b_M 3e1d_M 3iy9_T 3i1n_T 1p85_R 1p86_R 1vs8_T 1vs6_T 2aw4_T 2awb_T 1vt2_T 2i2v_T 2i2t_T* 2qao_T* 2qba_T* 2qbc_T* ... Probab=99.96 E-value=2.3e-32 Score=206.31 Aligned_cols=91 Identities=41% Similarity=0.589 Sum_probs=83.9 Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCC Q ss_conf 985257867600320799888864-8909999888789889999999996874337899851896333112246644322 Q gi|254780259|r 1 MINIRFYDTIISPVIAEKSTLLAG-QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVR 79 (110) Q Consensus 1 m~~~~~~~vi~~P~~TEKs~~~~e-~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~ 79 (110) |+++++||+|++|++||||+.+.| .|+|+|.|+++|||+|||+|||++|+|+|.+|||+|.+||.+|+++. T Consensus 2 ~~~~~~~~vi~~PvvTEKs~~~~e~~n~ytF~V~~~a~K~eIK~ave~~f~VkV~~Vnt~~~~gK~kr~~~~-------- 73 (93) T 3ofq_T 2 IREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQR-------- 73 (93) T ss_dssp CSCTTTTCCCCCCCCCSTTTSHHHHHSCCCCCCTTTCCSTTTTGGGTSSSSSCCSCCCCEEECCCEECSSSS-------- T ss_pred CCHHHHHHHHHCCCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCEEEECCC-------- T ss_conf 766789977731536888898786488899998898999999999999809976589888737953674783-------- Q ss_pred CCCCCCCCCCCCEEEEEECCCCCEE Q ss_conf 3454443458813899995899731 Q gi|254780259|r 80 SSRDMYVSRKDVKRAFVTLAKGYSI 104 (110) Q Consensus 80 ~~r~~~~k~~~~KKAiVtL~~G~~I 104 (110) .|++++||||||||++|++| T Consensus 74 -----~g~~~~~KKAiVtL~~g~~I 93 (93) T 3ofq_T 74 -----IGRRSDWKKAYVTLKEGQNL 93 (93) T ss_dssp -----CEECCCEEECCCCCCSSCCC T ss_pred -----CCCCCCCEEEEEECCCCCCC T ss_conf -----42458978999994896989 No 4 >2wwb_K 60S ribosomal protein L25; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_K 2ww9_K 1s1i_T Probab=99.94 E-value=2.8e-27 Score=176.99 Aligned_cols=84 Identities=33% Similarity=0.545 Sum_probs=76.1 Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCC Q ss_conf 985257867600320799888864-8909999888789889999999996874337899851896333112246644322 Q gi|254780259|r 1 MINIRFYDTIISPVIAEKSTLLAG-QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVR 79 (110) Q Consensus 1 m~~~~~~~vi~~P~~TEKs~~~~e-~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~ 79 (110) ++.|++|+||++|++||||+.+.| +|+|+|.||.+|||.|||+|||++|+|+|.+|||++.+| T Consensus 54 ~~kmd~y~IIk~Pl~TEKa~~~~E~~N~yvF~Vd~~AnK~qIK~AVe~lf~VkV~kVNTl~~~~---------------- 117 (142) T 2wwb_K 54 YNRLDSYKVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPN---------------- 117 (142) T ss_dssp ---CCCCCSEEEECCSHHHHHHHHHHSEEEEEECTTCCHHHHHHHHHHHHCCCEEEEEEECCTT---------------- T ss_pred CCCCCHHHCCCCCCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCEEEEEEEEECCC---------------- T ss_conf 6667743321037542888999985898999978989989999999998198342798767389---------------- Q ss_pred CCCCCCCCCCCCEEEEEECCCCC-EECCCCCC Q ss_conf 34544434588138999958997-31332489 Q gi|254780259|r 80 SSRDMYVSRKDVKRAFVTLAKGY-SIDISAGV 110 (110) Q Consensus 80 ~~r~~~~k~~~~KKAiVtL~~G~-~I~~~~gi 110 (110) +||||||+|++|+ .||++..| T Consensus 118 ----------~~KKA~V~La~d~dalDvAnki 139 (142) T 2wwb_K 118 ----------GTKKAYVRLTADYDALDIANRI 139 (142) T ss_dssp ----------SSEEEEEEECSTTCSSSSSSCC T ss_pred ----------CCEEEEEEECCCCCHHHHHHCC T ss_conf ----------9388999979998389997512 No 5 >2zkr_s 60S ribosomal protein L23A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Probab=99.94 E-value=4.7e-27 Score=175.75 Aligned_cols=83 Identities=34% Similarity=0.516 Sum_probs=74.9 Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCC Q ss_conf 985257867600320799888864-8909999888789889999999996874337899851896333112246644322 Q gi|254780259|r 1 MINIRFYDTIISPVIAEKSTLLAG-QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVR 79 (110) Q Consensus 1 m~~~~~~~vi~~P~~TEKs~~~~e-~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~ 79 (110) ++.|++|+||++|++||||+.+.| +|+|+|.||.+|||.|||+|||++|+|+|.+|||++.+ T Consensus 68 ~~~lD~y~IIk~Pl~TEKa~~~~E~~N~~vF~Vd~kAnK~qIK~AVeklf~VkV~kVNTli~~----------------- 130 (156) T 2zkr_s 68 RNKLDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRP----------------- 130 (156) T ss_dssp --------CEEEECCSHHHHHHHHHHCEEEEEECTTCCHHHHHHHHHHHHCCCEEEEEEEECS----------------- T ss_pred CCCCCHHHEEECCCCHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHCCEEEEEEEEECC----------------- T ss_conf 777886465662655077899997458059998787998999999999839843188865758----------------- Q ss_pred CCCCCCCCCCCCEEEEEECCCCCE-ECCCCC Q ss_conf 345444345881389999589973-133248 Q gi|254780259|r 80 SSRDMYVSRKDVKRAFVTLAKGYS-IDISAG 109 (110) Q Consensus 80 ~~r~~~~k~~~~KKAiVtL~~G~~-I~~~~g 109 (110) .+||||||+|++|++ ||++.. T Consensus 131 ---------~~~KKAyV~La~~~~AlDvAnk 152 (156) T 2zkr_s 131 ---------DGEKKAYVRLAPDYDALDVANK 152 (156) T ss_dssp ---------SSCEEEEEEECTTSCHHHHHHH T ss_pred ---------CCCEEEEEEECCCCCHHHHHHC T ss_conf ---------9957899996899828999751 No 6 >2go5_4 Ribosomal protein L23; SR, SRP, ribosome, translation/RNA complex; 7.40A {Triticum SP} PDB: 2j37_4 Probab=99.93 E-value=1.4e-26 Score=173.00 Aligned_cols=84 Identities=29% Similarity=0.490 Sum_probs=74.8 Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCC Q ss_conf 985257867600320799888864-8909999888789889999999996874337899851896333112246644322 Q gi|254780259|r 1 MINIRFYDTIISPVIAEKSTLLAG-QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVR 79 (110) Q Consensus 1 m~~~~~~~vi~~P~~TEKs~~~~e-~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~ 79 (110) ++.|++|+||++|++||||+.+.| +|+|+|.||.+|||.|||+|||.+|+|+|.+|||++.++ T Consensus 64 ~~kld~y~IIk~Pl~TEKa~~~~E~nn~~vF~Vd~~AnK~qIK~AVe~lf~V~V~kVNTl~~~~---------------- 127 (152) T 2go5_4 64 RNKLDQYQILKYPLTTESAMKKIEDNNTLVFIVDLKADKKKIKAAVKKMYDIQAKKVNTLIRPD---------------- 127 (152) T ss_dssp -----CCCSEEEECCSHHHHHHHHHSCEEEEEECTTCCSHHHHHHHHHHHCCCEEEEEEECCSS---------------- T ss_pred CCCCCHHHEEEECCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCEEEEEEEEECCC---------------- T ss_conf 6668975645505660889998741770799972768979999999998298211888767489---------------- Q ss_pred CCCCCCCCCCCCEEEEEECCCCC-EECCCCCC Q ss_conf 34544434588138999958997-31332489 Q gi|254780259|r 80 SSRDMYVSRKDVKRAFVTLAKGY-SIDISAGV 110 (110) Q Consensus 80 ~~r~~~~k~~~~KKAiVtL~~G~-~I~~~~gi 110 (110) +||||||+|++|+ .+|++.-| T Consensus 128 ----------g~KKAyV~L~~~~dalDvAnki 149 (152) T 2go5_4 128 ----------GKKKAYVKLTPDYDALDVANKI 149 (152) T ss_dssp ----------SSEEEEEEECTTTCSHHHHHTC T ss_pred ----------CCEEEEEEECCCCCHHHHHHHC T ss_conf ----------9689999948998389997502 No 7 >3bbo_V Ribosomal protein L23; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Probab=99.93 E-value=2.4e-27 Score=177.40 Aligned_cols=82 Identities=35% Similarity=0.560 Sum_probs=74.8 Q ss_pred CCCHHHHHHHHCCCCHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCC Q ss_conf 85257867600320799888864-89099998887898899999999968743378998518963331122466443223 Q gi|254780259|r 2 INIRFYDTIISPVIAEKSTLLAG-QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRS 80 (110) Q Consensus 2 ~~~~~~~vi~~P~~TEKs~~~~e-~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~ 80 (110) ..|++|+||++|++||||+.+.| +|+|+|.||++|||.|||+|||++|+|+|.+|||++.++ T Consensus 107 k~MD~ydIIk~PviTEKAt~liE~~NqyvF~Vd~kATK~qIKkAVEkLF~VKV~kVNTli~~~----------------- 169 (198) T 3bbo_V 107 RILDVYQILQSPIITEAAIKNIADENSLLFTVDVRADKKMIREAISNFFGVKVRKVNTLIRPD----------------- 169 (198) T ss_dssp ---CCCCCBCCCCCCHHHHHHHHTSCEECCEECTTCCHHHHHHTTTTTSCCCEEECCCEEETT----------------- T ss_pred HHCCHHHEEECCCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCEEEEEEEEECCC----------------- T ss_conf 017864542135217888998987786999988999989999999998097020898668589----------------- Q ss_pred CCCCCCCCCCCEEEEEECCCCC-------EECCCCC Q ss_conf 4544434588138999958997-------3133248 Q gi|254780259|r 81 SRDMYVSRKDVKRAFVTLAKGY-------SIDISAG 109 (110) Q Consensus 81 ~r~~~~k~~~~KKAiVtL~~G~-------~I~~~~g 109 (110) +||||||+|++|+ .|.||+| T Consensus 170 ---------k~KKAyVtLa~d~dAiDVA~KIGiFeG 196 (198) T 3bbo_V 170 ---------GTKKAYIMLNKEYNASELAKKIGIFPG 196 (198) T ss_dssp ---------TEEECCEEECTTTCTTTHHHHCCCC-- T ss_pred ---------CCEEEEEEECCCCCHHHHHHHCCCCCC T ss_conf ---------927999997899747877640121048 No 8 >1vq8_S 50S ribosomal protein L23P; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: d.12.1.1 PDB: 1vq4_S* 1vq5_S* 1vq6_S* 1vq7_S* 1s72_S* 1vq9_S* 1vqk_S* 1vql_S* 1vqm_S* 1vqn_S* 1vqo_S* 1vqp_S* 1yhq_S* 1yi2_S* 1yij_S* 1yit_S* 1yj9_S* 1yjn_S* 1yjw_S* 2otj_S* ... Probab=99.91 E-value=5.1e-25 Score=163.98 Aligned_cols=79 Identities=30% Similarity=0.398 Sum_probs=70.4 Q ss_pred HHHHHHHCCCCHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCCCCCC Q ss_conf 7867600320799888864-890999988878988999999999687433789985189633311224664432234544 Q gi|254780259|r 6 FYDTIISPVIAEKSTLLAG-QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRSSRDM 84 (110) Q Consensus 6 ~~~vi~~P~~TEKs~~~~e-~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~~r~~ 84 (110) .||+|++|++||||+.+.| +|+|+|.|+++|||.|||+|||++|+|+|.+|||+|.++ T Consensus 2 ~y~iI~~P~iTEKs~~~~e~~N~y~F~V~~~a~K~eIK~Ave~~f~VkV~~Vnt~~~~~--------------------- 60 (85) T 1vq8_S 2 SWDVIKHPHVTEKAMNDMDFQNKLQFAVDDRASKGEVADAVEEQYDVTVEQVNTQNTMD--------------------- 60 (85) T ss_dssp CCCSEEEECCSHHHHHHHHHSCEEEEEECTTCCHHHHHHHHHHHHCCCEEEEEEEECTT--------------------- T ss_pred CCCEEECCCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHCCCEECEEEEEECCC--------------------- T ss_conf 72564044308988998886888999985899989999999998098325798658699--------------------- Q ss_pred CCCCCCCEEEEEECCCCCE-ECCCCCC Q ss_conf 4345881389999589973-1332489 Q gi|254780259|r 85 YVSRKDVKRAFVTLAKGYS-IDISAGV 110 (110) Q Consensus 85 ~~k~~~~KKAiVtL~~G~~-I~~~~gi 110 (110) ++|||||+|++|++ +|+++.| T Consensus 61 -----~~KKA~V~L~~~~~a~dva~kl 82 (85) T 1vq8_S 61 -----GEKKAVVRLSEDDDAQEVASRI 82 (85) T ss_dssp -----SSEEEEEEECTTSCHHHHHTTC T ss_pred -----CCEEEEEEECCCCCHHHHHHHC T ss_conf -----9478999948999689998731 No 9 >2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S Probab=59.13 E-value=10 Score=18.24 Aligned_cols=42 Identities=26% Similarity=0.355 Sum_probs=34.8 Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEE Q ss_conf 8909999888789889999999996874337899851896333 Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKR 67 (110) Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr 67 (110) .+.|++.|+++.|=.++|+.++..+|+.+...+ +...|+.=. T Consensus 13 ~~~~~v~v~~~~tV~~lK~~i~~~~gip~~~q~-Li~~Gk~L~ 54 (77) T 2bwf_A 13 QDKWEVNVAPESTVLQFKEAINKANGIPVANQR-LIYSGKILK 54 (77) T ss_dssp TEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEE-EEETTEECC T ss_pred CEEEEEEECCCCHHHHHHHHHHHHHCCCHHHEE-EEECCEECC T ss_conf 988999989989599999999988791978989-998985986 No 10 >3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 2o6v_D* 2wwz_A 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B 1s1q_B 1tbe_A 1ubi_A ... Probab=51.33 E-value=14 Score=17.49 Aligned_cols=40 Identities=13% Similarity=0.184 Sum_probs=33.3 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCC Q ss_conf 48909999888789889999999996874337899851896 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGK 64 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK 64 (110) ....+++.|+++.|=.++|+.++...++.+...+- ...|+ T Consensus 9 ~G~t~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL-~~~Gk 48 (76) T 3a9j_A 9 TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRL-IFAGK 48 (76) T ss_dssp TSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEE-EETTE T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHCCCCHHEEE-EECCE T ss_conf 99899999879776999999988875989011999-99999 No 11 >1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Probab=50.13 E-value=14 Score=17.38 Aligned_cols=41 Identities=24% Similarity=0.323 Sum_probs=34.4 Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEE Q ss_conf 890999988878988999999999687433789985189633 Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVK 66 (110) Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~K 66 (110) .+++.|.|+++.|=.++|+.|+..+++.+..... ...|+.- T Consensus 41 ~~~~~v~V~~~~TV~~LK~~I~~~~gi~~~~qrL-i~~Gk~L 81 (125) T 1j8c_A 41 KEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVL-IFAGKIL 81 (125) T ss_dssp SCEEEEEECTTCCHHHHHHHHHHHHCSCSSSEEE-EETTEEE T ss_pred CCCEEEEECCCCCHHHHHHHHHHHHCCCHHHEEE-EECCEEC T ss_conf 9018999899991999999877776979678899-9899887 No 12 >3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} Probab=49.33 E-value=15 Score=17.30 Aligned_cols=40 Identities=15% Similarity=0.229 Sum_probs=33.8 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCC Q ss_conf 48909999888789889999999996874337899851896 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGK 64 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK 64 (110) ....|.+.|+++.+=.++|+.|++.+++.+.... +...|+ T Consensus 12 ~G~~~~i~v~~~~tV~~LK~~I~~~~~i~~~~q~-Li~~Gk 51 (85) T 3n3k_B 12 MGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQR-LIFAGK 51 (85) T ss_dssp GGCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEE-EEETBE T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHEE-EEECCE T ss_conf 9989999989988499999999888698931389-999999 No 13 >1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1 Probab=45.04 E-value=17 Score=16.91 Aligned_cols=40 Identities=18% Similarity=0.299 Sum_probs=33.8 Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE Q ss_conf 89099998887898899999999968743378998518963 Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110) Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110) .+++.|.|+++.+=.++|+.|+..+++.+..... ...|+. T Consensus 26 ~~~~~v~v~~~~tV~~lK~~i~~~~~v~~~~qrL-i~~Gk~ 65 (106) T 1wx7_A 26 KDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVL-IFAGKI 65 (106) T ss_dssp SCEEEEEEETTCCHHHHHHHHHHHHTCCTTTEEE-EETTEE T ss_pred CCCEEEEECCCCHHHHHHHHHHHCCCCCHHHEEE-EECCEE T ss_conf 9439999899891999999986201468799799-989989 No 14 >2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Probab=44.43 E-value=17 Score=16.94 Aligned_cols=43 Identities=16% Similarity=0.067 Sum_probs=35.7 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEE Q ss_conf 4890999988878988999999999687433789985189633 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVK 66 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~K 66 (110) ....|.+.|+++++=.++|+.|+...++.+....-+...|+.. T Consensus 17 ~~k~~~l~v~~~~tV~~lK~~I~~~~gip~~~Q~Li~~~g~~l 59 (100) T 2dzm_A 17 RDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDV 59 (100) T ss_dssp SSCEEEEEEETTSBHHHHHHHHHHHHCCCTTTCCEECCSSSCC T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEECCCCCC T ss_conf 9949999989989299999999987793967589981488065 No 15 >2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Probab=43.83 E-value=18 Score=16.80 Aligned_cols=41 Identities=22% Similarity=0.296 Sum_probs=34.5 Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEE Q ss_conf 890999988878988999999999687433789985189633 Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVK 66 (110) Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~K 66 (110) .+++.|.|+++.|=.++|..|+..+++.+...+. ...||.= T Consensus 34 ~~~~~i~V~~~~TV~~LK~~I~~~~~ip~~~qrL-i~~Gk~L 74 (101) T 2klc_A 34 KEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVL-IFAGKIL 74 (101) T ss_dssp SCEEEEEECSCCCHHHHHHHHHHHHTCCGGGEEE-EETTEEE T ss_pred CCCEEEEECCCCHHHHHHHHHHHHHCCCHHHEEE-EECCEEC T ss_conf 9869999899992999999999888919799884-6678098 No 16 >1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1 Probab=41.53 E-value=20 Score=16.59 Aligned_cols=39 Identities=21% Similarity=0.286 Sum_probs=32.2 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCC Q ss_conf 4890999988878988999999999687433789985189 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKG 63 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~g 63 (110) ....|.+.|++++|=.++|+.|+...++.+....-+ ..| T Consensus 25 ~~~~~~i~v~~~~TV~~LK~~I~~~~gip~~~QkLi-~~g 63 (95) T 1v86_A 25 NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVM-YKG 63 (95) T ss_dssp TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCB-SSS T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEE-ECC T ss_conf 999999998999949999999999989597788999-887 No 17 >3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} Probab=39.89 E-value=21 Score=16.44 Aligned_cols=42 Identities=12% Similarity=0.146 Sum_probs=34.0 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEE Q ss_conf 4890999988878988999999999687433789985189633 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVK 66 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~K 66 (110) ....+++.|+++.|=.++|+.++...++.+...+- ...|+.= T Consensus 12 ~G~~~~l~v~~~~TV~~lK~~I~~~~gip~~~qrL-i~~Gk~L 53 (85) T 3mtn_B 12 TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRL-IFAGKQL 53 (85) T ss_dssp TSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEE-EETTEEC T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHCCCCCEEEE-EECCEEC T ss_conf 99899999779886999999778875989850799-9999984 No 18 >1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1 Probab=39.37 E-value=21 Score=16.39 Aligned_cols=41 Identities=10% Similarity=0.110 Sum_probs=33.8 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE Q ss_conf 489099998887898899999999968743378998518963 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110) ..+.+++.|+++.|=.++|+.|+...++.+....- ...|+. T Consensus 18 ~Gkt~~l~V~~~~tV~~lK~~I~~~~gi~~~~qrL-~~~Gk~ 58 (88) T 1sif_A 18 TGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRL-IFAGKQ 58 (88) T ss_dssp TSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGCEE-EETTEE T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEE-EECCEE T ss_conf 99999999789686999888789887989679388-879768 No 19 >1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Probab=38.42 E-value=22 Score=16.30 Aligned_cols=39 Identities=18% Similarity=0.211 Sum_probs=32.3 Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCC Q ss_conf 8909999888789889999999996874337899851896 Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGK 64 (110) Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK 64 (110) .+++.|.|++++|=.++|+.|+..+++.+...+. ...|| T Consensus 26 ~~~~~~~v~~~~TV~~lK~~I~~~~~ip~~~qrL-i~~Gk 64 (96) T 1wx8_A 26 QDCHEFFLAENSNVRRFKKQISKYLHCNADRLVL-IFTGK 64 (96) T ss_dssp SSEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCC-EETTE T ss_pred CCEEEEEECCCCHHHHHHHHHHHHHCCCHHHEEE-EECCC T ss_conf 9129999899991999999998787959578787-85783 No 20 >2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Probab=37.11 E-value=23 Score=16.18 Aligned_cols=39 Identities=13% Similarity=0.216 Sum_probs=33.1 Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCC Q ss_conf 8909999888789889999999996874337899851896 Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGK 64 (110) Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK 64 (110) .+.|.+.|+++.|=.++|+.|+...++.+...+- ...|+ T Consensus 24 ~~~~~l~V~~~dTV~~lK~~I~~~~gip~~~Q~L-i~~Gk 62 (94) T 2kan_A 24 SKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQL-YYSGI 62 (94) T ss_dssp SCEEEEEECTTCBHHHHHHHHHHHSSSCTTTEEE-EETTE T ss_pred CEEEEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-EECCE T ss_conf 9899999899694999999998887989021899-99998 No 21 >3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Probab=36.67 E-value=19 Score=16.72 Aligned_cols=44 Identities=18% Similarity=0.255 Sum_probs=35.9 Q ss_pred HHCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEE Q ss_conf 648909999888789889999999996874337899851896333 Q gi|254780259|r 23 AGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKR 67 (110) Q Consensus 23 ~e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr 67 (110) ...+.+++.|+++.|=.++|+.|++.+++.+...+. ...|+.-. T Consensus 9 ~~~~~~~l~v~~~~TV~~lK~~i~~~~gi~~~~~rL-i~~Gk~L~ 52 (106) T 3m62_B 9 FKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKL-IYSGKVLQ 52 (106) T ss_dssp TTCCEEEECCCTTSBHHHHHHHHHHTTTSCGGGCEE-EETTEECC T ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEE-EECCEECC T ss_conf 899999999899890999999999884989568066-88999834 No 22 >2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens} Probab=36.49 E-value=24 Score=16.12 Aligned_cols=41 Identities=20% Similarity=0.184 Sum_probs=33.9 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE Q ss_conf 489099998887898899999999968743378998518963 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110) +-..+++.|+++.|=.++|+.|+...++.+...+ +...||. T Consensus 13 ~G~~~~~~V~~~~tV~~LK~~I~~~~gip~~~qr-Li~~Gk~ 53 (88) T 2hj8_A 13 KGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFW-LTFEGKP 53 (88) T ss_dssp TSCEEEEEEESSSBHHHHHHHHHHHTCSCTTTEE-EESSSSC T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCEE-EEECCEE T ss_conf 9999999989979099999999998699912289-9989988 No 23 >3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: k.45.1.1 PDB: 3dbr_I 3dbl_I Probab=35.66 E-value=25 Score=16.04 Aligned_cols=40 Identities=18% Similarity=0.212 Sum_probs=33.3 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCC Q ss_conf 48909999888789889999999996874337899851896 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGK 64 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK 64 (110) ..+.+++.|+++.|=.++|+.|+..+++.+...+- ...|+ T Consensus 21 ~G~~~~l~v~~~~TV~~lK~~I~~~~~i~~~~qrL-i~~Gk 60 (88) T 3dbh_I 21 TGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRL-IYSGK 60 (88) T ss_dssp TSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCE-EETTE T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCEEE-EECCE T ss_conf 99899999889692999999777762988642399-89997 No 24 >2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Probab=33.79 E-value=26 Score=15.86 Aligned_cols=39 Identities=21% Similarity=0.213 Sum_probs=28.1 Q ss_pred CEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEE Q ss_conf 90999988878988999999999687433789985189633 Q gi|254780259|r 26 NQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVK 66 (110) Q Consensus 26 n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~K 66 (110) +.|+-.++.+++..++++.++. || .|.+|....-.|+.+ T Consensus 10 ~l~V~nLp~~~t~~~l~~~F~~-~G-~v~~~~i~~~~g~~~ 48 (92) T 2dgv_A 10 QIFVRNLPFDFTWKMLKDKFNE-CG-HVLYADIKMENGKSK 48 (92) T ss_dssp EEEECSCCTTCCHHHHHHHHHT-TS-CEEEEEEEESSSCEE T ss_pred EEEEECCCCCCCHHHHHHHHHH-HC-CCEEEEEECCCCCCC T ss_conf 9999499986999999999997-39-964999973389746 No 25 >1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin, ubiquitin-like domain, structural genomics, signaling protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1 Probab=33.29 E-value=27 Score=15.82 Aligned_cols=40 Identities=20% Similarity=0.343 Sum_probs=33.3 Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE Q ss_conf 89099998887898899999999968743378998518963 Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110) Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110) ..++.+.|+++.+=.++|+.|+..+++.+.... +...|+. T Consensus 31 ~~~~~i~V~~~~TV~~LK~~I~~~~gip~~~qr-Li~~Gk~ 70 (100) T 1yqb_A 31 KDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLV-LIFAGKI 70 (100) T ss_dssp SCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEE-EEETTEE T ss_pred CCCEEEEECCCCHHHHHHHHHHHHHCCCHHHEE-EEECCEE T ss_conf 977999989989399999999988793967979-6888898 No 26 >1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A Probab=31.26 E-value=29 Score=15.62 Aligned_cols=32 Identities=9% Similarity=0.300 Sum_probs=26.0 Q ss_pred EEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEE Q ss_conf 0999988878988999999999687433789985 Q gi|254780259|r 27 QVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLI 60 (110) Q Consensus 27 ~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~ 60 (110) .|+=.++.++|..+|+++++. || .|..|..+. T Consensus 75 lfV~nLp~~~te~~L~~~F~~-~G-~i~~v~i~~ 106 (165) T 1rk8_A 75 LFVTSIHEEAQEDEIQEKFCD-YG-EIKNIHLNL 106 (165) T ss_dssp EEEESCCTTCCHHHHHHHHGG-GS-CEEEEEEEE T ss_pred EEECCCCCCCCHHHHHHHHHH-HC-CCEEEEEEE T ss_conf 998189985889999999998-69-952886652 No 27 >1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Probab=30.29 E-value=27 Score=15.81 Aligned_cols=34 Identities=12% Similarity=0.159 Sum_probs=29.7 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEE Q ss_conf 4890999988878988999999999687433789 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVN 57 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vn 57 (110) +...+.+.|++++|=.++|..|+..+++.+..-+ T Consensus 16 ~G~~~~v~V~~~~TV~dLK~~I~~~~~i~~~~Qr 49 (105) T 1v2y_A 16 DGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREG 49 (105) T ss_dssp SSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTT T ss_pred CCCEEEEEECCCCHHHHHHHHHHHHHCCCHHHHC T ss_conf 9999988989989699999999998794978824 No 28 >2g1d_A 30S ribosomal protein S24E; complete proteome, ribosome; NMR {Thermoplasma acidophilum} SCOP: d.12.1.3 Probab=30.16 E-value=6.6 Score=19.34 Aligned_cols=45 Identities=16% Similarity=0.235 Sum_probs=32.8 Q ss_pred CCCHHHHHHHHCCEEEEEEC----CCCCHHHHHHHHHHHHCCCEEEEEE Q ss_conf 20799888864890999988----8789889999999996874337899 Q gi|254780259|r 14 VIAEKSTLLAGQNQVVFNVK----KDSSKSEIKSAVEALFSVKVVSVNT 58 (110) Q Consensus 14 ~~TEKs~~~~e~n~y~F~V~----~~atK~eIK~ave~~f~V~V~~Vnt 58 (110) ++++|...|+.-.++.|.|. +..++.||+..+.+.|++++.-|=+ T Consensus 5 I~~~k~N~LL~R~Ei~~~v~h~g~~Tpsr~ei~~kla~~~~~~~~~vvv 53 (98) T 2g1d_A 5 IKEKRDNPILKRKEIKYVLKFDSSRTPSREEIKELIAKHEGVDKELVIV 53 (98) T ss_dssp EEEEEECSSSCEEEEEEEEECCTTSCCCHHHHHHHHHHHHHSCSTTEEC T ss_pred EEECCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEEE T ss_conf 9863407770638999999838999989999999999997989787999 No 29 >1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B Probab=29.83 E-value=31 Score=15.47 Aligned_cols=43 Identities=12% Similarity=0.134 Sum_probs=35.2 Q ss_pred HHCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEE Q ss_conf 64890999988878988999999999687433789985189633 Q gi|254780259|r 23 AGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVK 66 (110) Q Consensus 23 ~e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~K 66 (110) .....+.+.|+++.+=.++|+.|+...|+.+...+- ...|+.= T Consensus 8 l~G~~~~l~v~~~~tV~~LK~~I~~~~gip~~~qrL-i~~Gk~L 50 (98) T 1yx5_B 8 LTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRL-IFAGKQL 50 (98) T ss_dssp TTSCEEEEECCTTCBHHHHHHHHHHHTCCCGGGEEE-EETTEEC T ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEE-EECCEEC T ss_conf 899899999889887999997440451999799788-8799883 No 30 >1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A 1p98_A 1p9d_U 1p1a_A Probab=29.79 E-value=31 Score=15.47 Aligned_cols=45 Identities=22% Similarity=0.226 Sum_probs=35.8 Q ss_pred HHCCEEEEEECCCCCHHHHHHHHHHHHCCC--EEEEEEEECCCCEEE Q ss_conf 648909999888789889999999996874--337899851896333 Q gi|254780259|r 23 AGQNQVVFNVKKDSSKSEIKSAVEALFSVK--VVSVNTLIRKGKVKR 67 (110) Q Consensus 23 ~e~n~y~F~V~~~atK~eIK~ave~~f~V~--V~~Vnt~~~~gK~Kr 67 (110) ....+|++.|+++.|=.++|+.|+..|+.+ +.+--.|++.||.=+ T Consensus 15 ~~~~~~~i~v~~~~tV~~lK~~i~~~~~~~~~p~~~q~LIy~Gk~L~ 61 (368) T 1oqy_A 15 LQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILS 61 (368) T ss_dssp TTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEEC T ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCHHHEEEEECCEECC T ss_conf 89998999969979199999999987289889744248888982767 No 31 >3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A Probab=29.38 E-value=31 Score=15.43 Aligned_cols=42 Identities=12% Similarity=0.154 Sum_probs=34.7 Q ss_pred HHCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE Q ss_conf 6489099998887898899999999968743378998518963 Q gi|254780259|r 23 AGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110) Q Consensus 23 ~e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110) .....|.+.|++..+=.++|+.|+...|+.+...+- ...|+. T Consensus 9 ~~G~t~~l~v~~~~tV~~lK~~i~~~~gip~~~qrL-~~~Gk~ 50 (96) T 3k9o_B 9 LTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRL-IFAGKQ 50 (96) T ss_dssp TTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEE-EETTEE T ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCEEE-EECCEE T ss_conf 899999999788472999998778761999660799-999999 No 32 >2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana} Probab=29.18 E-value=32 Score=15.41 Aligned_cols=41 Identities=15% Similarity=0.122 Sum_probs=34.0 Q ss_pred HHCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCC Q ss_conf 648909999888789889999999996874337899851896 Q gi|254780259|r 23 AGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGK 64 (110) Q Consensus 23 ~e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK 64 (110) ...+.+.+.|++..|=.++|..|+...|+.+...+- ...|+ T Consensus 18 l~G~~~~l~V~~~dTV~~lK~~I~~~~gip~~~QrL-iy~Gk 58 (84) T 2kk8_A 18 LNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTL-IVDGI 58 (84) T ss_dssp TTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEE-EETTE T ss_pred CCCCEEEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-EECCE T ss_conf 899999999899486999999999871989766899-99998 No 33 >1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Probab=28.78 E-value=32 Score=15.37 Aligned_cols=39 Identities=13% Similarity=0.077 Sum_probs=31.9 Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCC Q ss_conf 8909999888789889999999996874337899851896 Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGK 64 (110) Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK 64 (110) ...|+++|+++++=.++|+.||...++.+..-+- ...|+ T Consensus 21 ~~t~~l~V~~~~tV~~lK~~I~~~~gip~~~qrL-i~~G~ 59 (102) T 1v5o_A 21 EVTFSLQVNPDFELSNFRVLCELESGVPAEEAQI-VYMEQ 59 (102) T ss_dssp CCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCE-EETTE T ss_pred CCEEEEEECCCCHHHHHHHHHHHHHCCCHHHEEE-EECCE T ss_conf 9899999788044999999997776849021898-75886 No 34 >2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana} Probab=27.15 E-value=35 Score=15.20 Aligned_cols=41 Identities=22% Similarity=0.307 Sum_probs=33.9 Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEE Q ss_conf 890999988878988999999999687433789985189633 Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVK 66 (110) Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~K 66 (110) .+.|.+.|+++.+=.++|+.|+...++.+....-+ ..|+.- T Consensus 21 g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~Q~Li-~~Gk~L 61 (85) T 2kd0_A 21 GKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLI-FKGKVL 61 (85) T ss_dssp TEEEEEEECTTSBHHHHHHHHHHHHCCCTTTCEEE-ETTEEC T ss_pred CEEEEEEECCCCCHHHHHHHHHHHHCCCCCCEEEE-ECCEEC T ss_conf 99999999999909999999857778296446999-999998 No 35 >2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Probab=26.91 E-value=35 Score=15.17 Aligned_cols=42 Identities=19% Similarity=0.321 Sum_probs=29.7 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEE Q ss_conf 48909999888789889999999996874337899851896333 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKR 67 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr 67 (110) ..|.|+=.++.+++..++++.++. || .|.+|..+.-.++.+. T Consensus 15 ~~~lfV~nLp~~~te~~L~~~F~~-~G-~i~~~~i~~~~~~~~g 56 (103) T 2d9p_A 15 VVNLYVKNLDDGIDDERLRKAFSP-FG-TITSAKVMMEGGRSKG 56 (103) T ss_dssp CCCEEEECCCTTCCHHHHHHTTTT-TS-CEEEEEEEECSSSEEE T ss_pred CCEEEEECCCCCCCHHHHHHHHHH-CC-CCEEEEEECCCCCCCC T ss_conf 988999699998989999999997-09-9518999743898576 No 36 >2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens} Probab=26.27 E-value=36 Score=15.10 Aligned_cols=40 Identities=10% Similarity=0.174 Sum_probs=33.3 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCC Q ss_conf 48909999888789889999999996874337899851896 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGK 64 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK 64 (110) .-+.+.+.|++..+=.++|+.|+...++.+....-+ ..|+ T Consensus 44 ~Gkt~~l~V~~~~tV~~LK~~I~~~~gip~~~qrLi-y~Gk 83 (111) T 2ojr_A 44 TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI-FAGK 83 (111) T ss_dssp SSCEEEEEECTTCBHHHHHHHHHHHHCCCTTTEEEE-ETTE T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHCCCCHHEEEE-ECCE T ss_conf 999999998997909999999999888791045787-7887 No 37 >1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1 Probab=25.78 E-value=26 Score=15.95 Aligned_cols=37 Identities=11% Similarity=0.118 Sum_probs=32.4 Q ss_pred HHCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEE Q ss_conf 6489099998887898899999999968743378998 Q gi|254780259|r 23 AGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTL 59 (110) Q Consensus 23 ~e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~ 59 (110) .+...+.+.|+...|=.++|.-++.+||+.+...+-. T Consensus 20 ~~~~~~~~kl~~~~TV~~LK~~i~~~~gip~~~q~L~ 56 (97) T 1wjn_A 20 PERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLS 56 (97) T ss_dssp SSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEE T ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEE T ss_conf 7775799990999989999999999879796895999 No 38 >2v94_A RPS24, 30S ribosomal protein S24E; ribonucleoprotein; 1.90A {Pyrococcus abyssi} SCOP: d.12.1.3 Probab=25.18 E-value=23 Score=16.17 Aligned_cols=45 Identities=16% Similarity=0.307 Sum_probs=32.4 Q ss_pred CHHHHHHHHCCEEEEEEC----CCCCHHHHHHHHHHHHCCCEEEEEEEE Q ss_conf 799888864890999988----878988999999999687433789985 Q gi|254780259|r 16 AEKSTLLAGQNQVVFNVK----KDSSKSEIKSAVEALFSVKVVSVNTLI 60 (110) Q Consensus 16 TEKs~~~~e~n~y~F~V~----~~atK~eIK~ave~~f~V~V~~Vnt~~ 60 (110) .++-..|..-.++.|.|. +..++.+|+.++...|+++..-|=+.. T Consensus 15 ~~k~NpLL~RkEi~~~v~h~g~~TPsr~ei~~kla~~~~~~~~~vvv~~ 63 (107) T 2v94_A 15 EVKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDLNPETTVIQY 63 (107) T ss_dssp EEEEETTTTEEEEEEEEECTTSCCCCHHHHHHHHHHHHTCCGGGEEEEE T ss_pred ECCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEEEEC T ss_conf 7111788475899999971899998999999999997795978899975 No 39 >1xn9_A 30S ribosomal protein S24E; beta+alpha, GFT structural genomics, protein structure initiative, PSI, NESG, MAR11; NMR {Methanosarcina mazei} SCOP: d.12.1.3 Probab=24.86 E-value=14 Score=17.39 Aligned_cols=46 Identities=17% Similarity=0.327 Sum_probs=32.5 Q ss_pred CCCHHHHHHHHCCEEEEEECC---CCCHHHHHHHHHHHHCCCEEEEEEE Q ss_conf 207998888648909999888---7898899999999968743378998 Q gi|254780259|r 14 VIAEKSTLLAGQNQVVFNVKK---DSSKSEIKSAVEALFSVKVVSVNTL 59 (110) Q Consensus 14 ~~TEKs~~~~e~n~y~F~V~~---~atK~eIK~ave~~f~V~V~~Vnt~ 59 (110) ++.++-..|+.-.+++|.|.- .-++.+|+..+-+.|++++.-|=+. T Consensus 5 I~~~k~N~LL~R~Ei~~~v~h~g~Tpsr~ei~~kla~~~~~~~~~vvv~ 53 (101) T 1xn9_A 5 IIKDKKNPLLNRRELDFIVKYEGSTPSRNDVRNKLAAMLNAPLELLVIQ 53 (101) T ss_dssp EEEEEEETTTTEEEEEEEEECSSSCCCHHHHHHHHHHHTTCCTTTEEEE T ss_pred EEECCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEEEE T ss_conf 9862448772638999999889999899999999999679296889997 No 40 >1ywx_A 30S ribosomal protein S24E; GFT MRR16, nesgc, structural genomics, PSI, protein structure initiative; NMR {Methanococcus maripaludis} SCOP: d.12.1.3 Probab=24.79 E-value=16 Score=17.05 Aligned_cols=45 Identities=16% Similarity=0.254 Sum_probs=32.2 Q ss_pred CCHHHHHHHHCCEEEEEEC---CCCCHHHHHHHHHHHHCCCEEEEEEE Q ss_conf 0799888864890999988---87898899999999968743378998 Q gi|254780259|r 15 IAEKSTLLAGQNQVVFNVK---KDSSKSEIKSAVEALFSVKVVSVNTL 59 (110) Q Consensus 15 ~TEKs~~~~e~n~y~F~V~---~~atK~eIK~ave~~f~V~V~~Vnt~ 59 (110) +.++-..|+.-.+++|.|. ...++.+|+..+-.+|+++..-|=+. T Consensus 6 ~~~k~N~LL~R~Ei~~~v~h~g~tpsr~ei~~kla~~~~~~~~~vvv~ 53 (102) T 1ywx_A 6 ISDRNNPLLQRREIKFTVSFDAATPSIKDVKMKLVAVLNANKQVLVVD 53 (102) T ss_dssp EEEEEETTTTEEEEEEEEECSSCCCCHHHHHHHHHHHHTSCSTTEEEE T ss_pred EECCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEEEE T ss_conf 863558772638999999889999899999999999779397889998 No 41 >1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protein; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A Probab=24.50 E-value=39 Score=14.91 Aligned_cols=40 Identities=18% Similarity=0.212 Sum_probs=33.0 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCC Q ss_conf 48909999888789889999999996874337899851896 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGK 64 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK 64 (110) .-..+.+.|+++.|=.++|+.|+...++.+...+- ...|+ T Consensus 9 ~G~~~~l~v~~~~tV~~lK~~I~~~~~ip~~~qrL-i~~Gk 48 (76) T 1ndd_A 9 TGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRL-IYSGK 48 (76) T ss_dssp TSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEE-EETTE T ss_pred CCCEEEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-EECCE T ss_conf 99899999789792999999997775768744599-99998 No 42 >2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Probab=23.77 E-value=39 Score=14.91 Aligned_cols=32 Identities=16% Similarity=0.285 Sum_probs=24.5 Q ss_pred CEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEE Q ss_conf 9099998887898899999999968743378998 Q gi|254780259|r 26 NQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTL 59 (110) Q Consensus 26 n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~ 59 (110) ..|+-.++.+.+..+|++.++. || .|.+|+.+ T Consensus 31 ~l~V~nLp~~~te~~l~~~f~~-~G-~I~~v~i~ 62 (109) T 2err_A 31 RLHVSNIPFRFRDPDLRQMFGQ-FG-KILDVEII 62 (109) T ss_dssp EEEEESCCTTCCHHHHHHHGGG-TC-CCSCEEEC T ss_pred EEEEECCCCCCCHHHHHHHHHH-CC-CEEEEEEE T ss_conf 8999798986999999999986-49-98999773 No 43 >1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1 Probab=23.60 E-value=40 Score=14.81 Aligned_cols=41 Identities=15% Similarity=0.113 Sum_probs=34.2 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE Q ss_conf 489099998887898899999999968743378998518963 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110) .-+.+.+.|++..|=.++|..|+...++.+...+ +...|+. T Consensus 32 ~G~~~~l~V~~~dTV~~lK~~I~~~~~ip~~~qr-Li~~Gk~ 72 (106) T 1ttn_A 32 TGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQR-WFFSGRP 72 (106) T ss_dssp TTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCE-EEETTEE T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHEE-EEECCEE T ss_conf 9999999988968099999999998895968978-7766718 No 44 >2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Probab=21.93 E-value=44 Score=14.61 Aligned_cols=28 Identities=7% Similarity=0.031 Sum_probs=23.5 Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCC Q ss_conf 8909999888789889999999996874 Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVK 52 (110) Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~ 52 (110) .+.|+=.++.+++..+|++.+...+++- T Consensus 10 ~~lfV~nLp~~~te~~l~~~F~~~g~~~ 37 (104) T 2dhg_A 10 YSLFVGDLTPDVDDGMLYEFFVKVYPSC 37 (104) T ss_dssp CCEEEECCCTTCCHHHHHHHHHHHCTTE T ss_pred CEEEEECCCCCCCHHHHHHHHHHHCCCC T ss_conf 8999948998488999999986533563 No 45 >1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Probab=21.88 E-value=44 Score=14.60 Aligned_cols=34 Identities=6% Similarity=0.190 Sum_probs=27.6 Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEE Q ss_conf 890999988878988999999999687433789985 Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLI 60 (110) Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~ 60 (110) .+.|+-.++.++|..++++.++. || .|.+|+.+. T Consensus 28 ~~lfV~nL~~~~te~~L~~~F~~-~G-~i~~v~i~~ 61 (116) T 1x4b_A 28 RKLFIGGLSFETTEESLRNYYEQ-WG-KLTDCVVMR 61 (116) T ss_dssp TEEEEECCTTCCCHHHHHHHHTS-SC-CCSEEEEEC T ss_pred CEEEEECCCCCCCHHHHHHHHHH-CC-CEEEEEEEC T ss_conf 88999089986889999999986-09-778888502 No 46 >2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Probab=21.69 E-value=44 Score=14.58 Aligned_cols=37 Identities=11% Similarity=-0.039 Sum_probs=32.3 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEE Q ss_conf 4890999988878988999999999687433789985 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLI 60 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~ 60 (110) +.....+.|+++.|=.++|.-+|..+|+.+...+..- T Consensus 25 ~~~~~e~~v~~~~TV~~LK~kIe~~~gip~~~QrL~~ 61 (97) T 2kj6_A 25 KSFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALEL 61 (97) T ss_dssp SCCCEEEEECTTCCHHHHHHHHHHHHCCCTTSEEEEE T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEE T ss_conf 8759999989818099999999998799868989999 No 47 >1z2m_A ISG15, interferon, alpha-inducible protein (clone IFI- 15K); ubiquitin cross reactive protein, signaling protein; 2.50A {Homo sapiens} SCOP: d.15.1.1 d.15.1.1 Probab=20.42 E-value=47 Score=14.42 Aligned_cols=36 Identities=17% Similarity=0.203 Sum_probs=30.3 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEE Q ss_conf 489099998887898899999999968743378998 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTL 59 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~ 59 (110) ....|++.|++++|=.++|..|+..+++.+..-+.. T Consensus 11 ~g~~~~l~v~~~~tV~~lK~~I~~~~~i~~~~q~L~ 46 (155) T 1z2m_A 11 AGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLA 46 (155) T ss_dssp SSCEEEEECCSSCCHHHHHHHHHHHHCCCGGGEEEE T ss_pred CCCEEEEEECCCCHHHHHHHHHHHHHCCCHHHEEEE T ss_conf 997999997997929999999998879697992999 No 48 >3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} Probab=20.30 E-value=47 Score=14.41 Aligned_cols=36 Identities=6% Similarity=0.135 Sum_probs=31.8 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEE Q ss_conf 489099998887898899999999968743378998 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTL 59 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~ 59 (110) ..+.+.+.|++++|=.++|+.||...++.+...+.+ T Consensus 242 ~Gkt~~L~V~~~~TV~dLK~~Ie~k~gIP~e~QrLi 277 (307) T 3ai5_A 242 TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 277 (307) T ss_dssp TSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEE T ss_pred CCCEEEEEECCCCHHHHHHHHHHHHHCCCHHHEEEE T ss_conf 998999997997919999999999879896896999 No 49 >2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae} Probab=20.27 E-value=47 Score=14.40 Aligned_cols=41 Identities=12% Similarity=0.187 Sum_probs=33.6 Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE Q ss_conf 489099998887898899999999968743378998518963 Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110) Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110) .-..+.+.|+++.|=.++|..|+...++.+....-+ ..|+. T Consensus 18 ~G~t~~l~V~~~~tV~~LK~~I~~~~gip~~~qrL~-~~Gk~ 58 (114) T 2kdi_A 18 TGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLI-WAGKQ 58 (114) T ss_dssp TCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEE-ETTEE T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEE-ECCEE T ss_conf 998999997995939999999999879791267999-89878 Done!