Query gi|254780751|ref|YP_003065164.1| ribonuclease E [Candidatus Liberibacter asiaticus str. psy62] Match_columns 723 No_of_seqs 290 out of 2083 Neff 6.5 Searched_HMMs 33803 Date Wed Jun 1 14:31:24 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780751.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >2bx2_L Ribonuclease E, RNAse 100.0 0 0 401.2 14.4 138 346-487 1-138 (138) 2 >2bx2_L Ribonuclease E, RNAse 99.8 1.8E-18 5.3E-23 147.0 9.1 96 484-579 1-97 (107) 3 >2bx2_L Ribonuclease E, RNAse 99.7 1.1E-17 3.1E-22 141.7 6.6 81 200-281 1-81 (82) 4 >2bx2_L Ribonuclease E, RNAse 99.5 3.3E-13 9.7E-18 110.4 8.8 53 293-345 43-96 (96) 5 >2bx2_L Ribonuclease E, RNAse 99.4 3.1E-13 9.2E-18 110.6 7.7 85 37-200 1-85 (94) 6 >2khi_A 30S ribosomal protein 98.2 4.6E-06 1.4E-10 60.8 6.8 96 20-204 11-106 (115) 7 >1wi5_A RRP5 protein homolog; 98.1 9.7E-06 2.9E-10 58.5 6.5 93 35-216 17-110 (119) 8 >2je6_I RRP4, exosome complex 98.1 7.8E-06 2.3E-10 59.2 5.8 40 38-79 3-42 (85) 9 >2z0s_A Probable exosome compl 98.0 1.4E-05 4.1E-10 57.4 6.2 45 33-79 60-104 (147) 10 >2ba0_A Archeal exosome RNA bi 98.0 2.2E-05 6.6E-10 56.0 7.0 40 38-79 3-42 (82) 11 >2k4k_A GSP13, general stress 98.0 2.2E-05 6.6E-10 56.0 6.8 100 36-226 4-105 (130) 12 >2nn6_H Exosome complex exonuc 98.0 3E-06 9E-11 62.0 2.3 42 37-80 2-43 (92) 13 >2ja9_A Exosome complex exonuc 97.9 3.9E-05 1.2E-09 54.3 6.8 41 37-79 5-45 (90) 14 >2khj_A 30S ribosomal protein 97.9 2.6E-05 7.8E-10 55.5 5.8 98 14-202 7-104 (109) 15 >2cqo_A Nucleolar protein of 4 97.8 7.4E-05 2.2E-09 52.4 7.4 91 31-211 14-107 (119) 16 >1go3_E DNA-directed RNA polym 97.8 5.3E-05 1.6E-09 53.4 5.8 39 39-80 1-39 (107) 17 >3cw2_C Translation initiation 97.8 8.8E-05 2.6E-09 51.9 6.7 75 34-198 6-82 (85) 18 >2nn6_G Exosome complex exonuc 97.7 7.6E-05 2.2E-09 52.3 6.3 39 37-77 3-41 (87) 19 >3go5_A Multidomain protein wi 97.7 0.0001 3.1E-09 51.4 6.2 37 37-74 3-40 (71) 20 >2k52_A Uncharacterized protei 97.7 0.00012 3.6E-09 50.9 6.4 41 37-79 3-43 (80) 21 >2nn6_I 3'-5' exoribonuclease 97.6 0.00016 4.7E-09 50.1 5.9 76 37-200 4-87 (94) 22 >2a19_A EIF-2- alpha, eukaryot 97.6 0.00014 4.2E-09 50.4 5.6 41 37-79 13-55 (88) 23 >2eqs_A ATP-dependent RNA heli 97.5 0.0003 8.8E-09 48.2 6.3 43 35-79 8-53 (103) 24 >1yz6_A Probable translation i 97.5 0.00031 9.1E-09 48.1 6.3 43 36-80 7-51 (83) 25 >3bzc_A TEX; helix-turn-helix, 97.5 5.6E-05 1.6E-09 53.3 2.3 87 35-211 9-95 (144) 26 >3cdi_A Polynucleotide phospho 97.4 2.1E-05 6.3E-10 56.2 0.0 42 36-79 250-291 (349) 27 >1kl9_A Eukaryotic translation 97.4 0.00039 1.2E-08 47.4 6.2 42 36-79 12-55 (88) 28 >1y14_B B16, RPB7, DNA-directe 97.4 0.00035 1E-08 47.8 5.9 41 39-82 1-41 (89) 29 >2id0_A Exoribonuclease 2; RNA 97.4 0.00036 1.1E-08 47.6 5.7 40 39-80 2-42 (86) 30 >2waq_E DNA-directed RNA polym 97.3 0.00032 9.5E-09 48.0 4.9 39 39-80 1-39 (100) 31 >1q8k_A Eukaryotic translation 97.3 0.00087 2.6E-08 45.0 6.8 42 36-79 10-53 (86) 32 >1hh2_P NUSA, N utilization su 97.3 0.00069 2E-08 45.7 6.0 39 36-77 3-41 (87) 33 >2b8k_G B16, DNA-directed RNA 97.1 0.0011 3.2E-08 44.3 5.8 84 39-203 1-84 (133) 34 >3h0g_G DNA-directed RNA polym 97.1 0.00058 1.7E-08 46.2 4.2 39 39-80 1-39 (89) 35 >1e3p_A Guanosine pentaphospha 97.0 0.00016 4.7E-09 50.1 0.8 42 36-79 73-114 (166) 36 >2ckz_B C25, DNA-directed RNA 97.0 0.0024 7.1E-08 41.9 6.9 91 39-206 1-92 (138) 37 >2ba1_A Archaeal exosome RNA b 96.9 0.0023 6.7E-08 42.1 6.0 40 38-79 3-52 (92) 38 >2c35_B Human RPB7, DNA-direct 96.9 0.0015 4.4E-08 43.4 5.0 38 39-79 1-38 (92) 39 >1luz_A Protein K3, protein K2 96.6 0.003 8.9E-08 41.2 4.4 42 35-79 7-50 (88) 40 >3go5_A Multidomain protein wi 96.5 0.0088 2.6E-07 38.0 6.5 39 36-76 14-53 (84) 41 >1a6f_A RNAse P protein, ribon 87.8 0.79 2.4E-05 24.4 4.2 75 203-277 27-115 (119) 42 >2asb_A Transcription elongati 87.7 0.81 2.4E-05 24.3 4.2 39 36-74 4-47 (81) 43 >2pe4_A Hyaluronidase-1; hyalu 86.4 0.74 2.2E-05 24.6 3.5 61 388-448 24-89 (147) 44 >2vf7_A UVRA2, excinuclease AB 86.2 0.36 1.1E-05 26.8 1.8 36 480-515 5-40 (70) 45 >1fcq_A Hyaluronoglucosaminida 83.8 1.1 3.2E-05 23.4 3.3 56 394-449 44-104 (159) 46 >2hl7_A Cytochrome C-type biog 83.5 1.4 4E-05 22.8 3.7 56 481-554 26-81 (84) 47 >1k0r_A NUSA; two component ar 82.1 3 8.8E-05 20.4 5.0 39 36-74 15-58 (92) 48 >2atm_A Hyaluronoglucosaminida 81.4 1.5 4.5E-05 22.4 3.3 61 387-447 37-102 (153) 49 >1d6t_A Ribonuclease P, RNAse 80.9 2.2 6.5E-05 21.3 4.0 75 202-276 25-113 (117) 50 >2bx9_A Anti-trap, AT, tryptop 73.5 1.4 4.2E-05 22.6 1.3 24 478-501 20-43 (53) 51 >2wp8_J Exosome complex exonuc 71.4 6.1 0.00018 18.3 6.4 36 42-79 2-38 (90) 52 >3lcz_A YCZA, inhibitor of tra 69.5 2 5.8E-05 21.7 1.3 30 478-509 20-49 (53) 53 >3fdr_A Tudor and KH domain-co 68.3 4.2 0.00012 19.4 2.7 42 39-82 41-87 (94) 54 >2opv_A KHSRP protein; KH doma 66.2 6.7 0.0002 18.0 3.5 46 517-562 14-59 (85) 55 >2ytv_A Cold shock domain-cont 65.5 5.9 0.00017 18.3 3.1 34 39-74 5-40 (79) 56 >2jzx_A Poly(RC)-binding prote 64.9 8.2 0.00024 17.4 4.6 42 516-557 4-45 (81) 57 >2e3u_A PH-DIM2P, hypothetical 63.6 8.6 0.00025 17.2 4.0 42 516-557 33-74 (109) 58 >2ctk_A Vigilin; K homology ty 63.3 7.9 0.00023 17.5 3.4 42 516-557 16-57 (104) 59 >1nz0_A Ribonuclease P protein 63.3 3.4 0.0001 20.0 1.5 70 202-271 28-111 (118) 60 >1dar_A EF-G, elongation facto 62.8 8.9 0.00026 17.1 6.4 74 378-467 104-177 (283) 61 >3i2z_B RNA chaperone, negativ 62.6 9 0.00026 17.1 6.0 38 40-77 3-41 (71) 62 >1tua_A Hypothetical protein A 61.1 9 0.00027 17.1 3.3 42 516-557 3-44 (79) 63 >1ec6_A RNA-binding protein NO 60.5 9.7 0.00029 16.8 4.5 42 518-559 4-45 (87) 64 >2ctm_A Vigilin; K homology ty 60.3 6.4 0.00019 18.1 2.5 50 517-566 17-66 (95) 65 >2jzx_A Poly(RC)-binding prote 60.2 9.8 0.00029 16.8 4.3 49 516-564 7-55 (79) 66 >2r6f_A Excinuclease ABC subun 60.0 3.1 9.3E-05 20.2 0.8 24 473-496 29-54 (78) 67 >1x4m_A FAR upstream element b 59.5 10 0.0003 16.7 4.3 49 516-564 14-62 (94) 68 >1wvn_A Poly(RC)-binding prote 58.8 8.3 0.00024 17.3 2.8 48 518-565 7-55 (82) 69 >2vf7_A UVRA2, excinuclease AB 58.4 3.5 0.0001 19.9 0.8 14 483-496 40-53 (77) 70 >1dtj_A RNA-binding neurooncol 57.5 8.6 0.00026 17.2 2.7 43 518-560 4-46 (76) 71 >2ctl_A Vigilin; K homology ty 56.6 7 0.00021 17.8 2.1 50 516-565 16-65 (97) 72 >1we8_A Tudor and KH domain co 56.5 11 0.00033 16.4 3.3 47 516-562 14-60 (104) 73 >2jvz_A KH type-splicing, FAR 56.5 9.1 0.00027 17.0 2.7 45 518-562 3-47 (81) 74 >2hqx_A P100 CO-activator tudo 56.2 6 0.00018 18.3 1.7 44 38-81 14-60 (183) 75 >1mhn_A SurviVal motor neuron 56.0 8.3 0.00024 17.3 2.4 34 39-74 17-53 (59) 76 >1j4w_A FUSE binding protein; 55.3 12 0.00035 16.3 3.5 48 514-561 13-60 (86) 77 >2jvz_A KH type-splicing, FAR 55.1 6.1 0.00018 18.2 1.6 50 513-562 6-55 (83) 78 >3bdl_A Staphylococcal nucleas 54.8 7.5 0.00022 17.6 2.1 34 39-74 15-50 (59) 79 >3krm_A Insulin-like growth fa 54.5 11 0.00032 16.5 2.9 49 517-565 85-133 (163) 80 >2dgr_A Ring finger and KH dom 53.6 9.1 0.00027 17.0 2.3 49 516-566 9-57 (83) 81 >2d9t_A Tudor domain-containin 53.5 8.8 0.00026 17.1 2.2 34 39-74 23-59 (78) 82 >2anr_A Neuro-oncological vent 53.2 13 0.00037 16.0 4.6 49 516-564 103-151 (178) 83 >2axy_A Poly(RC)-binding prote 51.7 13 0.0004 15.9 4.3 42 516-557 4-45 (73) 84 >2elf_A Protein translation el 51.6 13 0.0004 15.9 7.7 70 378-462 87-157 (190) 85 >1nlt_A Protein YDJ1, mitochon 51.6 5.9 0.00018 18.3 1.1 48 453-500 45-95 (102) 86 >1exk_A DNAJ protein; extended 50.9 3.8 0.00011 19.7 0.0 16 479-494 48-63 (79) 87 >1g5v_A SurviVal motor neuron 50.8 9.7 0.00029 16.8 2.1 35 38-74 23-60 (88) 88 >1j4w_A FUSE binding protein; 50.1 14 0.00042 15.7 5.4 48 518-565 4-52 (88) 89 >2cpq_A FragIle X mental retar 49.7 14 0.00042 15.7 3.5 41 516-556 14-54 (91) 90 >2p2r_A Poly(RC)-binding prote 48.7 15 0.00044 15.6 5.1 50 516-565 4-54 (76) 91 >2z0s_A Probable exosome compl 48.5 9.7 0.00029 16.8 1.8 40 518-557 2-41 (88) 92 >2equ_A PHD finger protein 20- 48.2 15 0.00045 15.5 3.3 35 39-75 22-57 (74) 93 >1x65_A UNR protein; cell-free 48.2 15 0.00045 15.5 7.1 35 39-75 5-40 (89) 94 >1zzk_A Heterogeneous nuclear 47.4 11 0.00033 16.4 2.0 45 517-561 7-51 (82) 95 >2bh8_A 1B11; transcription, m 45.5 17 0.00049 15.2 5.0 46 34-79 8-54 (71) 96 >1m1q_A Small tetraheme cytoch 44.4 7 0.00021 17.8 0.6 14 480-493 57-70 (91) 97 >2eqk_A Tudor domain-containin 44.4 15 0.00043 15.6 2.2 34 39-74 35-70 (85) 98 >2hh3_A KH-type splicing regul 43.5 17 0.00052 15.1 2.5 46 516-561 10-55 (106) 99 >1vef_A Acetylornithine/acetyl 43.1 18 0.00053 15.0 2.5 71 371-448 5-88 (122) 100 >1x4n_A FAR upstream element b 42.6 18 0.00054 14.9 4.1 47 515-561 13-59 (92) 101 >1vig_A Vigilin; RNA-binding p 41.0 11 0.00033 16.4 1.2 41 517-557 5-45 (71) 102 >2dgy_A MGC11102 protein; EIF- 40.5 17 0.0005 15.2 2.0 22 173-194 53-74 (111) 103 >1j5k_A Heterogeneous nuclear 40.1 20 0.00059 14.7 5.1 52 514-565 11-63 (89) 104 >2qnd_A FMR1 protein; KH domai 38.9 21 0.00061 14.6 2.5 40 517-556 4-43 (64) 105 >2ywe_A GTP-binding protein LE 37.8 22 0.00064 14.4 5.4 71 378-464 100-171 (187) 106 >2hh2_A KH-type splicing regul 36.3 11 0.00031 16.6 0.5 43 517-559 7-49 (107) 107 >1sff_A 4-aminobutyrate aminot 36.3 23 0.00067 14.3 4.6 78 371-452 4-97 (138) 108 >2cte_A Vigilin; K homology ty 36.3 7.4 0.00022 17.7 -0.3 41 517-557 17-57 (94) 109 >2gez_B L-asparaginase beta su 34.5 21 0.00063 14.5 1.8 26 350-375 76-101 (112) 110 >2ctt_A DNAJ homolog subfamily 33.3 14 0.00041 15.8 0.6 16 480-495 80-95 (104) 111 >2k3v_A Tetraheme cytochrome C 32.2 11 0.00032 16.5 -0.0 15 482-496 33-47 (86) 112 >3d0f_A Penicillin-binding 1 t 32.2 26 0.00078 13.8 6.0 37 39-77 2-38 (75) 113 >2r6f_A Excinuclease ABC subun 31.1 27 0.00081 13.7 2.3 35 482-516 2-36 (58) 114 >2rdo_7 EF-G, elongation facto 29.4 29 0.00086 13.5 6.4 78 378-471 109-189 (289) 115 >2wac_A CG7008-PA; unknown fun 29.1 29 0.00087 13.5 2.0 34 39-74 41-75 (83) 116 >1th8_B Anti-sigma F factor an 29.1 29 0.00087 13.5 7.3 88 414-532 5-92 (116) 117 >3cb4_D GTP-binding protein LE 28.3 30 0.0009 13.4 5.4 71 378-464 98-169 (185) 118 >3d3r_A Hydrogenase assembly c 26.7 32 0.00096 13.2 3.7 21 44-64 27-47 (73) 119 >2vnu_D Exosome complex exonuc 26.1 33 0.00098 13.1 5.6 36 42-79 2-38 (90) 120 >2hu9_A MERP, mercuric transpo 26.0 31 0.00091 13.3 1.4 20 482-501 2-21 (64) 121 >2diq_A Tudor and KH domain-co 25.5 25 0.00075 13.9 0.9 35 38-74 45-81 (110) 122 >1k3r_A Conserved protein MT00 24.3 36 0.0011 12.9 3.1 32 36-69 15-46 (76) 123 >2ba0_A Archeal exosome RNA bi 24.3 36 0.0011 12.9 2.7 39 519-557 3-41 (94) 124 >1h95_A CSD, Y-box binding pro 24.2 36 0.0011 12.9 5.8 40 38-77 4-44 (79) 125 >1w6s_A Methanol dehydrogenase 24.0 36 0.0011 12.9 1.7 16 375-390 57-72 (84) 126 >1jmx_A Amine dehydrogenase; o 23.1 38 0.0011 12.8 2.5 18 477-494 5-22 (80) 127 >2kcm_A Cold shock domain fami 23.0 38 0.0011 12.7 5.9 34 44-77 2-36 (74) 128 >3hcn_A Ferrochelatase, mitoch 22.7 38 0.0011 12.7 3.1 13 476-488 188-200 (216) 129 >2vy9_A Anti-sigma-factor anta 22.7 38 0.0011 12.7 9.1 89 413-532 4-92 (123) 130 >2je6_I RRP4, exosome complex 22.5 32 0.00095 13.2 0.9 39 519-557 2-40 (96) 131 >1p1j_A Inositol-3-phosphate s 22.4 31 0.00093 13.3 0.9 23 54-76 19-44 (44) 132 >2wjn_C Photosynthetic reactio 22.3 18 0.00052 15.0 -0.4 34 443-476 98-131 (159) 133 >1d2e_A Elongation factor TU ( 21.5 40 0.0012 12.5 6.7 76 378-468 93-174 (197) 134 >2qnd_A FMR1 protein; KH domai 21.3 41 0.0012 12.5 3.7 42 518-559 4-46 (80) 135 >2ctf_A Vigilin; K homology ty 21.0 41 0.0012 12.5 1.6 40 517-556 27-67 (102) 136 >1pby_A Quinohemoprotein amine 21.0 39 0.0012 12.6 1.1 19 477-495 4-22 (79) 137 >1zbr_A AAQ65385, conserved hy 20.8 42 0.0012 12.4 1.9 28 342-369 25-54 (59) 138 >1g8p_A Magnesium-chelatase 38 20.7 42 0.0012 12.4 3.4 34 414-447 139-172 (218) 139 >1c9o_A CSPB, cold-shock prote 20.7 42 0.0012 12.4 4.9 33 44-76 3-35 (66) 140 >3hvm_A Agmatine deiminase; hy 20.6 42 0.0012 12.4 2.0 28 342-369 25-54 (59) 141 >1c3g_A Heat shock protein 40; 20.5 29 0.00085 13.6 0.3 13 482-494 24-36 (79) 142 >2kdx_A HYPA, hydrogenase/urea 20.4 32 0.00094 13.3 0.6 90 398-491 7-100 (119) 143 >1acv_A DSBA; disulfide oxidor 20.2 16 0.00046 15.4 -1.1 15 473-487 19-33 (105) 144 >2q2g_A HSP40 protein, heat sh 20.1 17 0.00051 15.1 -0.8 19 480-498 25-43 (85) 145 >2ctj_A Vigilin; K homology ty 20.0 43 0.0013 12.3 5.0 51 516-566 16-66 (95) No 1 >>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A (L:273-410) Probab=100.00 E-value=0 Score=401.17 Aligned_cols=138 Identities=56% Similarity=0.814 Sum_probs=135.9 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 56776999999984222143678649983288069998237554445551147999999999999998731036863896 Q gi|254780751|r 346 FFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVV 425 (723) Q Consensus 346 f~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvI 425 (723) |+.|+|+.+|+.+++++||||||||||||+|||||+||||||+++++++.++|+++||+|||+||||||||||||||||| T Consensus 1 F~~~~i~~~i~~~~~~~V~L~~Gg~lvIe~TEALt~IDVNsG~~~~~~~~~~~~~~~N~eAa~eIarqlrLRnigGiIvI 80 (138) T 2bx2_L 1 FSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVI 80 (138) T ss_dssp HHHTTCHHHHHHTTCSEEECTTSCEEEEEECSSCEEEEEECCC----CCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEE T ss_pred HHHHCHHHHHHHHHHCCEECCCCEEEEEECCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE T ss_conf 78718499999986304544788089993154058985046654567777788999989999999987657516864997 Q ss_pred ECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCC Q ss_conf 03347988889999999999731278728998604861489851566630112100236754 Q gi|254780751|r 426 DFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYC 487 (723) Q Consensus 426 DFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c 487 (723) |||||+++++++.|++.|+++|++|+++++|++||+||||||||||.|+||. ++||+| T Consensus 81 DFI~m~~~~~~~~v~~~l~~~~~~D~~~~~v~~~t~lGL~EitRkR~~~sl~----e~cp~C 138 (138) T 2bx2_L 81 DFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLG----ESSHHV 138 (138) T ss_dssp ECCCCSSHHHHHHHHHHHHHHTTTCSSCEEEEEECTTSEEEEEECCCSCCHH----HHHCCC T ss_pred ECCCCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCEEEEECCCCCCCHH----HHHCCC T ss_conf 2566666789999999999998516865057456666338886144556601----220433 No 2 >>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A (L:411-517) Probab=99.77 E-value=1.8e-18 Score=147.01 Aligned_cols=96 Identities=26% Similarity=0.400 Sum_probs=90.0 Q ss_pred CCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHH-CCEEEEEECCCCCCCC Q ss_conf 675465378606114689988788999730364310135769999987302379999999984-8879998478778863 Q gi|254780751|r 484 CTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARF-GVSINVVIGIELADKL 562 (723) Q Consensus 484 c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~-~~~I~i~~d~~l~~~~ 562 (723) ||+|+|+|+|+|.+|++++|+|+|++.+.+.+...+.+.+||+||.||+|++|..|.+||.+| |+.|.|.+|++++.++ T Consensus 1 CP~C~G~G~V~s~es~a~~i~R~I~~~~~~~~~~~i~v~v~p~Va~~l~n~k~~~l~~lE~~~~g~~I~i~~d~~~~~~~ 80 (107) T 2bx2_L 1 CPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPH 80 (107) T ss_dssp CSSSSSSSCCCCHHHHHHHHHHHHHHHHHSTTEEEEEEEECHHHHHHHTTTTHHHHHHHHHHTTTCEEEEEECTTCCTTC T ss_pred CCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCC T ss_conf 88878866875789999999999999987668866999989999999973129999999998769179999579887775 Q ss_pred EEEEECCCCCCCCCCCC Q ss_conf 38971554433333211 Q gi|254780751|r 563 FYIEKGSPVQALVNTGH 579 (723) Q Consensus 563 f~Ier~~~~~~~~~~~~ 579 (723) |.|...+..+......+ T Consensus 81 f~i~~~~~~~~~~~~~~ 97 (107) T 2bx2_L 81 YHVLRVRKGEETPTLSY 97 (107) T ss_dssp CEEEEEETTCCCCCCGG T ss_pred EEEEECCCCCCCCCCCE T ss_conf 39998448986565462 No 3 >>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A (L:127-208) Probab=99.72 E-value=1.1e-17 Score=141.66 Aligned_cols=81 Identities=35% Similarity=0.640 Sum_probs=71.7 Q ss_pred CCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 34576523442278875124204688689999999998630025871699850455757999999999999999877642 Q gi|254780751|r 200 LSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELA 279 (723) Q Consensus 200 isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~ 279 (723) |||||||+||||+.+..++|||||.+.++|.+|+.+... ..|+++|+||||+|+++++++|..|+++|.++|+.|.+++ T Consensus 1 Isl~GrylVl~P~~~~ig~iSrkI~d~~~r~~l~~l~~~-~~~~~~G~IiRT~A~~a~~e~i~~e~~~L~~~w~~I~~~~ 79 (82) T 2bx2_L 1 ISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASL-ELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAA 79 (82) T ss_dssp CCEECSSEEEETTCTTCCEECTTCC------HHHHHTTS-CCCTTCEEEECGGGGGCCHHHHHHHHHHHHHHHHHHHHHH T ss_pred CCCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHH-CCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 456565279824777656522335717899999999972-5888752898610248887999988999888889888776 Q ss_pred CC Q ss_conf 01 Q gi|254780751|r 280 LN 281 (723) Q Consensus 280 ~~ 281 (723) .. T Consensus 80 ~~ 81 (82) T 2bx2_L 80 ES 81 (82) T ss_dssp HT T ss_pred HC T ss_conf 42 No 4 >>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A (L:1-42,L:219-272) Probab=99.46 E-value=3.3e-13 Score=110.44 Aligned_cols=53 Identities=30% Similarity=0.542 Sum_probs=48.9 Q ss_pred CHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHH-HHCCCCHHHHCCCCCHH Q ss_conf 588888875237663111103532036678889876-31012112201344203 Q gi|254780751|r 293 NLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLL-MPSYARIVRQYEDPHPI 345 (723) Q Consensus 293 ~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~~~~-~p~~~~~v~~~~~~~~l 345 (723) +++.|++||+++.++++|+||+++.|+.+++|++.+ +|.+..+|++|+++.|| T Consensus 43 DLi~RviRD~~t~dv~eIvVD~~e~Ye~v~~fv~~~~~P~l~~rVklY~g~~PI 96 (96) T 2bx2_L 43 NVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPL 96 (96) T ss_dssp CHHHHHHHHHCCTTEEEEEESCHHHHHHHHHHHHHTTCHHHHTTEEECCCSSCH T ss_pred CHHHHHHHHHCCCHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCH T ss_conf 489999998614143410068788999999863442287533558954799787 No 5 >>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A (L:43-126,L:209-218) Probab=99.44 E-value=3.1e-13 Score=110.59 Aligned_cols=85 Identities=55% Similarity=0.881 Sum_probs=72.8 Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 04287879899783638823135327897713022213712102898899999998886311111000000011122334 Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPN 116 (723) Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (723) +.+|+||.|+|++|.|+|.+||||||.+++||||++++.++||..+.. T Consensus 1 ~kvG~i~~G~V~~I~~f~~GaFVel~~~~~Glihis~l~~~~~~~~~~-------------------------------- 48 (94) T 2bx2_L 1 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYS-------------------------------- 48 (94) T ss_dssp CCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC------------------------------------ T ss_pred CCCCCEEEEEEEECCCCCCEEEEEECCCCCEEEEHHHCCHHHCCCCCC-------------------------------- T ss_conf 877878999995327887668995089974588858838555045533-------------------------------- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCC Q ss_conf 44334454222233445543322223432112211121100001223444421331068885799984033323456410 Q gi|254780751|r 117 DHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAV 196 (723) Q Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~l 196 (723) ..+...+.+.++.||.|+|||++....+|++.| T Consensus 49 -----------------------------------------------~~~~~~~~~~~~~Gd~V~V~V~~vd~~~~~i~l 81 (94) T 2bx2_L 49 -----------------------------------------------AHGRPNIKDVLREGQEVIVQIDKEERGNKGAAL 81 (94) T ss_dssp --------------------------------------------------CCCGGGTCCTTCEEEEEEEECCCTTCCCEE T ss_pred -----------------------------------------------CCCCCCHHHHCCCCCEEEEEECCCCCCCCCCCC T ss_conf -----------------------------------------------345656677357998888985145444557553 Q ss_pred CCCC Q ss_conf 1233 Q gi|254780751|r 197 TTYL 200 (723) Q Consensus 197 T~~i 200 (723) |... T Consensus 82 sl~~ 85 (94) T 2bx2_L 82 TTFP 85 (94) T ss_dssp ESSC T ss_pred CCCC T ss_conf 3459 No 6 >>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} (A:) Probab=98.19 E-value=4.6e-06 Score=60.75 Aligned_cols=96 Identities=11% Similarity=0.106 Sum_probs=74.3 Q ss_pred EECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 98998999996073346042878798997836388231353278977130222137121028988999999988863111 Q gi|254780751|r 20 LRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTD 99 (723) Q Consensus 20 ~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~ 99 (723) .-.-+..+..++..-....+|.||.|+|++|.|. ++||++|.+-.||||++|+..+++. T Consensus 11 ~~s~k~~~~~~~~~~~~~~~G~iv~G~V~~v~~~--G~fV~l~~~~~g~i~~~els~~~~~------------------- 69 (115) T 2khi_A 11 SSGLVPRGSHWVAIAKRYPEGTKLTGRVTNLTDY--GCFVEIEEGVEGLVHVSEMDWTNKN------------------- 69 (115) T ss_dssp ----------CCCSSCSSCSSCEEEEEEEEEETT--EEEEECSTTCEEEEETTSSSCSSTT------------------- T ss_pred CCCCCCCCCCHHHHHHHCCCCCEEEEEEEEEECC--EEEEEECCCCCEEEEEEEECCCCCC------------------- T ss_conf 2474447997899996589989999999999687--5999989857223787631344422------------------- Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCE Q ss_conf 11000000011122334443344542222334455433222234321122111211000012234444213310688857 Q gi|254780751|r 100 SEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQI 179 (723) Q Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ 179 (723) ..+.++++.||. T Consensus 70 --------------------------------------------------------------------~~~~~~~~~G~~ 81 (115) T 2khi_A 70 --------------------------------------------------------------------IHPSKVVNVGDV 81 (115) T ss_dssp --------------------------------------------------------------------CSSTTTCCTTCE T ss_pred --------------------------------------------------------------------CCCEEEEECCCE T ss_conf --------------------------------------------------------------------232048843866 Q ss_pred EEEEEECCCCCCCCCCCCCCCCCCC Q ss_conf 9998403332345641012334576 Q gi|254780751|r 180 LLVQIVKEERGNKGAAVTTYLSLAG 204 (723) Q Consensus 180 ilVQV~ke~~~~Kga~lT~~isl~G 204 (723) |.|.|.+--..++-..||..-..+. T Consensus 82 v~v~V~~vd~~~~ri~lS~k~~~~~ 106 (115) T 2khi_A 82 VEVMVLDIDEERRRISLGLKQCKAN 106 (115) T ss_dssp EEEEEEEEETTTTEEEECCCCCCSS T ss_pred EEEEEEEEECCCCEEEEEEEECCCC T ss_conf 9999999989999999998765409 No 7 >>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} (A:) Probab=98.08 E-value=9.7e-06 Score=58.54 Aligned_cols=93 Identities=17% Similarity=0.103 Sum_probs=76.5 Q ss_pred CCCCCCCEEEEEEEEECCCCCEEEEEECC-CCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 46042878798997836388231353278-97713022213712102898899999998886311111000000011122 Q gi|254780751|r 35 KKQIKGNIYLAKVTRVEPSLQAAFVDYGG-NRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVT 113 (723) Q Consensus 35 ~~~~~GnIY~G~V~~V~p~lqAAFVdiG~-~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 113 (723) .....|.||.|+|++|.|. .|||+++. +-.||||++++..+||. T Consensus 17 ~~l~~G~~v~g~V~~v~~~--G~fV~l~~~~~~g~i~~sels~~~~~--------------------------------- 61 (119) T 1wi5_A 17 EALKPGMLLTGTVSSLEDH--GYLVDIGVDGTRAFLPLLKAQEYIRQ--------------------------------- 61 (119) T ss_dssp TTCCTTCEEEEEEEEECSS--EEEEECCCSSCEEEEEHHHHHHHHHH--------------------------------- T ss_pred HHCCCCCEEEEEEEEEEEE--EEEEECCCCCCEEEEEHHHHCCCCCC--------------------------------- T ss_conf 3179997899999988401--89995145540278769993521123--------------------------------- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCC Q ss_conf 33444334454222233445543322223432112211121100001223444421331068885799984033323456 Q gi|254780751|r 114 IPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKG 193 (723) Q Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kg 193 (723) ....++++.||.|.|+|.+=-..++. T Consensus 62 ------------------------------------------------------~~~~~~~~vGd~i~v~V~~vd~~~~~ 87 (119) T 1wi5_A 62 ------------------------------------------------------KNKGAKLKVGQYLNCIVEKVKGNGGV 87 (119) T ss_dssp ------------------------------------------------------HSSSCCCCTTCEEEEEEEECCTTSCE T ss_pred ------------------------------------------------------CCCCCEEEEEEEEEEEEEEEECCCCE T ss_conf ------------------------------------------------------47300021001899999998379858 Q ss_pred CCCCCCCCCCCCCEEECCCCCCC Q ss_conf 41012334576523442278875 Q gi|254780751|r 194 AAVTTYLSLAGRYSVLMPNTSKG 216 (723) Q Consensus 194 a~lT~~isl~Gry~Vl~P~~~~~ 216 (723) ..||..-+..+..-........+ T Consensus 88 i~ls~k~~~~~~~~~~~~~~~~~ 110 (119) T 1wi5_A 88 VSLSVGHSEVSTAIATEQQSWNL 110 (119) T ss_dssp EEEECCCCCSCCCCCCSSCCCCC T ss_pred EEEECHHHHHHHHHHHHHHCCCC T ss_conf 99840197666667667642675 No 8 >>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} (I:71-155) Probab=98.07 E-value=7.8e-06 Score=59.19 Aligned_cols=40 Identities=20% Similarity=0.169 Sum_probs=36.7 Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC Q ss_conf 428787989978363882313532789771302221371210 Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723) Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723) .+|+||.|+|.+|.| .+|||+||.+..||||++|+..+|+ T Consensus 3 ~~G~~v~g~V~~v~~--~G~fV~i~~~~~Gli~~s~i~~~~~ 42 (85) T 2je6_I 3 KINDIVIGLVEDVEI--YGWVVDIKAPYKAYLPASNLLGRSI 42 (85) T ss_dssp CTTCEEEEEEEEECS--SEEEEECSSSSCEEEEHHHHHTSCC T ss_pred CCCCEEEEEEEEEEC--CEEEEECCCCCCCEEEHHHCCCCCC T ss_conf 999999999999335--4799984897222400554257542 No 9 >>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} (A:1-147) Probab=98.01 E-value=1.4e-05 Score=57.42 Aligned_cols=45 Identities=16% Similarity=0.155 Sum_probs=39.2 Q ss_pred CCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC Q ss_conf 33460428787989978363882313532789771302221371210 Q gi|254780751|r 33 EHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723) Q Consensus 33 ~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723) ......+|++|.|+|++|.+. .|||++|.+..||||++|+.++|+ T Consensus 60 ~~~~~~~G~iv~G~V~~i~~~--G~fV~i~~~~~gli~~sei~~~~~ 104 (147) T 2z0s_A 60 EIYVPQAGDVVIGLIQSVGIM--NWFVDINSPYVAVLSVQDFLGRPF 104 (147) T ss_dssp CCCCCCTTCCEEEEEEEECSS--EEEEECSSSSCEEEEHHHHHTSCC T ss_pred CCCCCCCCCEEEEEEEEEECC--EEEEECCCCCEEEECHHHCCCCCC T ss_conf 753599999999999897267--199985897203726899075332 No 10 >>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} (A:54-135) Probab=98.00 E-value=2.2e-05 Score=56.02 Aligned_cols=40 Identities=20% Similarity=0.180 Sum_probs=36.4 Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC Q ss_conf 428787989978363882313532789771302221371210 Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723) Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723) .+|.||.|+|++|.|. .|||+||.+..||||++|+.++++ T Consensus 3 ~~G~~v~g~V~~i~~~--g~~V~l~~~~~g~i~~sel~~~~~ 42 (82) T 2ba0_A 3 SVGDVVIGIIREVAAN--GWAVDIYSPYQAFLPVSENPEMKP 42 (82) T ss_dssp CTTCEEEEEEEEECSS--EEEEECSSSSCEEEEGGGCTTCCT T ss_pred CCCCEEEEEEEEECCC--EEEEECCCCCCEEEEHHHCCCCCH T ss_conf 8999999999576165--199980897337987676766101 No 11 >>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} (A:) Probab=97.98 E-value=2.2e-05 Score=56.01 Aligned_cols=100 Identities=17% Similarity=0.272 Sum_probs=78.8 Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 60428787989978363882313532789771302221371210289889999999888631111100000001112233 Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIP 115 (723) Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (723) ...+|.||.|+|++|.+. ++||+++.+-.||+|.+|+..+|+. T Consensus 4 ~~~~G~iv~g~V~~v~~~--G~~V~l~~~i~G~i~~sels~~~~~----------------------------------- 46 (130) T 2k4k_A 4 KFEVGSVYTGKVTGLQAY--GAFVALDEETQGLVHISEVTHGFVK----------------------------------- 46 (130) T ss_dssp CCCTTCEEEEEEEEEETT--EEEEEEETTEEEEEEGGGTSSSCCS----------------------------------- T ss_pred CCCCCCEEEEEEEEEECC--EEEEEECCCCEEEEEEEEECCEECC----------------------------------- T ss_conf 468999999999999787--6999979995899873010100011----------------------------------- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCC Q ss_conf 44433445422223344554332222343211221112110000122344442133106888579998403332345641 Q gi|254780751|r 116 NDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAA 195 (723) Q Consensus 116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~ 195 (723) .+.+.++.||.|.|.|..-...++... T Consensus 47 -----------------------------------------------------~~~~~~~~G~~i~~~V~~vd~~~~~i~ 73 (130) T 2k4k_A 47 -----------------------------------------------------DINEHLSVGDEVQVKVLAVDEEKGKIS 73 (130) T ss_dssp -----------------------------------------------------CGGGTCCTTCEEEEEEEEEETTTTEEE T ss_pred -----------------------------------------------------CCCCCCCCCCEEEEEEEEEECCCCEEE T ss_conf -----------------------------------------------------223345699899999999978999899 Q ss_pred CCCCCC--CCCCCEEECCCCCCCCEEEECCCCH Q ss_conf 012334--5765234422788751242046886 Q gi|254780751|r 196 VTTYLS--LAGRYSVLMPNTSKGETISRKITNP 226 (723) Q Consensus 196 lT~~is--l~Gry~Vl~P~~~~~~~iSrki~~~ 226 (723) ||.... -++......++. ...+.+.++.+. T Consensus 74 LS~k~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 105 (130) T 2k4k_A 74 LSIRATQAAPEKKESKPRKP-KAAQVSEEASTP 105 (130) T ss_dssp EESHHHHHSCCCCSCCTTTT-CTTCCSCCCSCS T ss_pred EEEEECCCCCHHHHHHHCCC-CCCCCEEEECCC T ss_conf 99677556914554311146-666423474265 No 12 >>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} (H:92-183) Probab=97.98 E-value=3e-06 Score=62.04 Aligned_cols=42 Identities=14% Similarity=0.132 Sum_probs=38.3 Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC Q ss_conf 04287879899783638823135327897713022213712102 Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ 80 (723) Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ 80 (723) ..+|+||.|+|++|.| .+||||||....||||++++..+|+. T Consensus 2 P~vGdiv~G~V~~v~~--~g~fV~i~~~~~gllhis~i~~~~~~ 43 (92) T 2nn6_H 2 GEVGDIVVGRITEVQQ--KRWKVETNSRLDSVLLLSSMNLPGGE 43 (92) T ss_dssp CCSSBCCCEEEEEEET--TEEEEECSSSSCEEEESSCCC----- T ss_pred CCCCCEEEEEEEEEEC--CEEEEECCCCCCCEECCCCCCCCCCC T ss_conf 9999999999988725--55999838865535424201367611 No 13 >>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} (A:1-90) Probab=97.90 E-value=3.9e-05 Score=54.33 Aligned_cols=41 Identities=5% Similarity=-0.075 Sum_probs=37.1 Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC Q ss_conf 0428787989978363882313532789771302221371210 Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723) Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723) ..+|.||.|+|++|.+. +|||+||.+..||||.+|+.++|+ T Consensus 5 pk~G~~v~G~V~~v~~~--g~~V~l~~~~~g~l~~s~~~~~~~ 45 (90) T 2ja9_A 5 PSVNDFVIGVIIGTFSD--SYKVSLQNFSSSVSLSYMAFPNAS 45 (90) T ss_dssp CCTTCEEEEEEEEECSS--EEEEESSTTSCCEEEETTSSTTCC T ss_pred CCCCCEEEEEEEEECCC--EEEEEECCCCHHHHCCCCCCCCCC T ss_conf 99989999999897288--089993897365407655466612 No 14 >>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} (A:) Probab=97.89 E-value=2.6e-05 Score=55.50 Aligned_cols=98 Identities=18% Similarity=0.142 Sum_probs=72.6 Q ss_pred EEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHH Q ss_conf 07999998998999996073346042878798997836388231353278977130222137121028988999999988 Q gi|254780751|r 14 ETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKES 93 (723) Q Consensus 14 e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~ 93 (723) ..|+++--...+.+. .+........|+||.|+|++|.|. ++||++|.+-.||+|.+++..+|.. T Consensus 7 ~~~~~~s~k~~~~~~-~~~~~~~~~~G~iv~g~V~~v~~~--G~~V~~~~~~~G~v~~s~l~~~~~~------------- 70 (109) T 2khj_A 7 HHHHSSGLVPRGSHM-FNNWVALNKKGAIVTGKVTAVDAK--GATVELADGVEGYLRASEASRDRVE------------- 70 (109) T ss_dssp --------------C-HHHHTTTCCSSSEEEEEEEEECSS--CEEEECSTTCBCCBCTTCCCSSSSS------------- T ss_pred CCCCCCCCCCCCCCH-HHHHHHHCCCCCEEEEEEEEEECC--EEEEEECCEEEEHEEHHHHCCCCCC------------- T ss_conf 432465731866670-999997589999999999999896--8999989818601102242445314------------- Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEC Q ss_conf 86311111000000011122334443344542222334455433222234321122111211000012234444213310 Q gi|254780751|r 94 NIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEV 173 (723) Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ 173 (723) ...+. T Consensus 71 ---------------------------------------------------------------------------~~~~~ 75 (109) T 2khj_A 71 ---------------------------------------------------------------------------DATLV 75 (109) T ss_dssp ---------------------------------------------------------------------------SGGGS T ss_pred ---------------------------------------------------------------------------CHHHH T ss_conf ---------------------------------------------------------------------------97782 Q ss_pred CCCCCEEEEEEECCCCCCCCCCCCCCCCC Q ss_conf 68885799984033323456410123345 Q gi|254780751|r 174 IKNRQILLVQIVKEERGNKGAAVTTYLSL 202 (723) Q Consensus 174 lk~gq~ilVQV~ke~~~~Kga~lT~~isl 202 (723) ++.||.|-|.|.+-...++...||..-+. T Consensus 76 ~~vG~~v~v~V~~vd~~~~~i~lSlk~~~ 104 (109) T 2khj_A 76 LSVGDEVEAKFTGVDRKNRAISLSVRAKD 104 (109) T ss_dssp CCTTCEEEEEEEEEETTTTEEEEETTSSS T ss_pred EECCCEEEEEEEEEECCCCEEEEEEEECC T ss_conf 03242799999999899999999834455 No 15 >>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Probab=97.84 E-value=7.4e-05 Score=52.40 Aligned_cols=91 Identities=15% Similarity=0.167 Sum_probs=66.7 Q ss_pred CCCCCCCCCCCEEEEEEEEECCCCCEEEEEEC-CCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 07334604287879899783638823135327-89771302221371210289889999999888631111100000001 Q gi|254780751|r 31 ESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYG-GNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTH 109 (723) Q Consensus 31 e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG-~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~ 109 (723) +.......+|.||.|+|.+|.+. .|||+++ .+..||+|++|+.++|+. T Consensus 14 ~~~~~~~~~G~vv~g~V~~I~~~--G~fV~l~~~~~~Gli~~sels~~~~~----------------------------- 62 (119) T 2cqo_A 14 ETMENLPALYTIFQGEVAMVTDY--GAFIKIPGCRKQGLVHRTHMSSCRVD----------------------------- 62 (119) T ss_dssp CCSCCSCCTTCEEEEEEEEEETT--EEEEECTTCSSCEEEEHHHHCSSCCS----------------------------- T ss_pred CHHHCCCCCCCEEEEEEEEEECC--EEEEEECCCCEEEEEEEHHCCCCCCC----------------------------- T ss_conf 11342876784799999999556--88999379743578610110455667----------------------------- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCC Q ss_conf 11223344433445422223344554332222343211221112110000122344442133106888579998403332 Q gi|254780751|r 110 GDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEER 189 (723) Q Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~ 189 (723) .+.+.++.||.|-|.|+.-.. T Consensus 63 -----------------------------------------------------------~~~~~~~vG~~v~v~V~~vd~ 83 (119) T 2cqo_A 63 -----------------------------------------------------------KPSEIVDVGDKVWVKLIGREM 83 (119) T ss_dssp -----------------------------------------------------------CHHHHCCTTCEEEEEEEEEEE T ss_pred -----------------------------------------------------------CHHHEECCCCEEEEEEEEEEC T ss_conf -----------------------------------------------------------987802799999999999977 Q ss_pred CCCCCC--CCCCCCCCCCCEEECC Q ss_conf 345641--0123345765234422 Q gi|254780751|r 190 GNKGAA--VTTYLSLAGRYSVLMP 211 (723) Q Consensus 190 ~~Kga~--lT~~isl~Gry~Vl~P 211 (723) .++.-+ ||..-..+.....+.+ T Consensus 84 ~~~~~~vsLs~k~~~~~~~~~~~~ 107 (119) T 2cqo_A 84 KNDRIKVSLSMKVVNQGTGKDLDP 107 (119) T ss_dssp CSSCEEEEEESTTBCSSSCCBSCT T ss_pred CCCCCEEEEEEEECCCCCCHHCCC T ss_conf 678648873601567796034285 No 16 >>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} (E:81-187) Probab=97.78 E-value=5.3e-05 Score=53.43 Aligned_cols=39 Identities=23% Similarity=0.318 Sum_probs=35.5 Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC Q ss_conf 287879899783638823135327897713022213712102 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ 80 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ 80 (723) +|.+|.|+|++|.|. +|||+|+ +..||+|++++..+||. T Consensus 1 VG~~~~g~V~~i~~~--G~fV~l~-g~~Glv~is~l~~~~~~ 39 (107) T 1go3_E 1 MYELIEGEVVDVVEF--GSFVRLG-PLDGLIHVSQIMDDYVS 39 (107) T ss_dssp TTCEEEEEEEEEETT--EEEEECS-SSEEEEEGGGSCSSCEE T ss_pred CCCEEEEEEEEEEEE--EEEEEEC-CCEEEEEEHHCCCCCEE T ss_conf 898999999999732--9999955-80599981132898586 No 17 >>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B (C:1-85) Probab=97.75 E-value=8.8e-05 Score=51.88 Aligned_cols=75 Identities=23% Similarity=0.454 Sum_probs=61.0 Q ss_pred CCCCCCCCEEEEEEEEECCCCCEEEEEECC--CCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 346042878798997836388231353278--977130222137121028988999999988863111110000000111 Q gi|254780751|r 34 HKKQIKGNIYLAKVTRVEPSLQAAFVDYGG--NRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGD 111 (723) Q Consensus 34 ~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~--~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~ 111 (723) -.....|+||.|+|++|.+. +|||++|. +-.||+|.+|+.++|+. T Consensus 6 ~~~~~~G~~v~g~V~~i~~~--G~~V~l~~~~~i~G~i~~s~ls~~~~~------------------------------- 52 (85) T 3cw2_C 6 SKLPSEGEILIATVKQVFDY--GSYVSLDEYGGLQAFLPWSEVSSKWVK------------------------------- 52 (85) T ss_dssp SSSCCTTCEEEEEEEECCSS--SBEEEETTTTSEECBBCGGGSSCSSCC------------------------------- T ss_pred CCCCCCCCEEEEEEEEEECC--EEEEEECCCCCCEEEEEHHHCCCCCCC------------------------------- T ss_conf 78989999999999999755--489997567990899898995886558------------------------------- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCC Q ss_conf 22334443344542222334455433222234321122111211000012234444213310688857999840333234 Q gi|254780751|r 112 VTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGN 191 (723) Q Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~ 191 (723) ...+.++.||.|-|.|.+--..+ T Consensus 53 ---------------------------------------------------------~~~~~~~vG~~V~v~V~~vd~~~ 75 (85) T 3cw2_C 53 ---------------------------------------------------------NIRDVLKENRKVIVKVIRVDRRK 75 (85) T ss_dssp ---------------------------------------------------------CHHHHSCTTCEEEEEECCCCSSS T ss_pred ---------------------------------------------------------CHHHHCCCCCEEEEEEEEEECCC T ss_conf ---------------------------------------------------------98881889999999996652557 Q ss_pred CCCCCCC Q ss_conf 5641012 Q gi|254780751|r 192 KGAAVTT 198 (723) Q Consensus 192 Kga~lT~ 198 (723) +...||. T Consensus 76 ~ri~LS~ 82 (85) T 3cw2_C 76 GTVDVSL 82 (85) T ss_dssp CCCBEES T ss_pred CCEEEEE T ss_conf 4437898 No 18 >>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} (G:123-209) Probab=97.75 E-value=7.6e-05 Score=52.33 Aligned_cols=39 Identities=26% Similarity=0.350 Sum_probs=34.6 Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC Q ss_conf 04287879899783638823135327897713022213712 Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD 77 (723) Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~ 77 (723) ..+|.|+.|+|++|.+ .+||||||.+..||||.+++..+ T Consensus 3 P~~GdiV~G~V~~i~~--~g~fVdi~~~~~g~l~is~~~~~ 41 (87) T 2nn6_G 3 PVKGDHVIGIVTAKSG--DIFKVDVGGSEPASLSYLSFEGA 41 (87) T ss_dssp CCSSEEEEEEEEEEET--TEEEEECSSSSCCCEESCSSSCC T ss_pred CCCCCEEEEEEEEECC--CEEEEECCCCCCEEECCHHCCCC T ss_conf 9998999999989828--73899848985048750206770 No 19 >>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae TIGR4} (A:65-135) Probab=97.68 E-value=0.0001 Score=51.39 Aligned_cols=37 Identities=22% Similarity=0.292 Sum_probs=32.9 Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECC-CCCCCCCHHHC Q ss_conf 042878798997836388231353278-97713022213 Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGG-NRHGFLPFLEI 74 (723) Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~-~k~gFL~~~ei 74 (723) -.+|.+|.++|.++.+.+ .||||+|. +|.+|+|++|. T Consensus 3 i~vg~~~~lkVv~v~~~~-GaFvd~Glp~KD~Lvp~~e~ 40 (71) T 3go5_A 3 ATQDQFGWGRVTEVRKDL-GVFVDTGLPDKEIVVSLDIL 40 (71) T ss_dssp SCSSSCEEEEEEEEETTT-EEEEECSCTTCCEEEEGGGS T ss_pred EECCCEEEEEEEEEECCC-CEEEEECCCCCCCCCCHHHC T ss_conf 754998999999995584-08999278851033506656 No 20 >>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} (A:) Probab=97.67 E-value=0.00012 Score=50.88 Aligned_cols=41 Identities=24% Similarity=0.331 Sum_probs=36.4 Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC Q ss_conf 0428787989978363882313532789771302221371210 Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723) Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723) ..+|.||.|+|++|.+ .+|||+++.+..||||.+|+..+|+ T Consensus 3 ~~~G~~~~g~V~~v~~--~G~fV~l~~~i~Gli~~~~ls~~~~ 43 (80) T 2k52_A 3 VEPGKFYKGVVTRIEK--YGAFINLNEQVRGLLRPRDMISLRL 43 (80) T ss_dssp CCTTCEEEEEEEEEET--TEEEEEEETTEEEEECGGGCSSCCG T ss_pred CCCCCEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHCCCCCC T ss_conf 7799999999999978--7799996555789999126256423 No 21 >>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} (I:76-169) Probab=97.58 E-value=0.00016 Score=50.07 Aligned_cols=76 Identities=16% Similarity=0.115 Sum_probs=58.3 Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECC--------CCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 042878798997836388231353278--------977130222137121028988999999988863111110000000 Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGG--------NRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVT 108 (723) Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~--------~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~ 108 (723) ..+|.|+.|+|++|.+ ..|||+|+. +-.||+|.+|+.++|.. T Consensus 4 pkvG~iv~G~V~~v~~--~G~fV~i~~~~~~~l~~~i~Gli~~seis~~~v~---------------------------- 53 (94) T 2nn6_I 4 PDVGAIVTCKVSSINS--RFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKD---------------------------- 53 (94) T ss_dssp CCTTCEEEEEEEEECS--SEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSC---------------------------- T ss_pred CCCCCEEEEEEEEECC--CCEEEEEEEECCCCCCCCCCCCCCHHHCCCCCCC---------------------------- T ss_conf 8889989999989917--9889999776480157662133327520103254---------------------------- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCC Q ss_conf 11122334443344542222334455433222234321122111211000012234444213310688857999840333 Q gi|254780751|r 109 HGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEE 188 (723) Q Consensus 109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~ 188 (723) ...+.+.++.||.|-++|+.-- T Consensus 54 ----------------------------------------------------------~~~~~~~~~~Gd~V~~kV~~vd 75 (94) T 2nn6_I 54 ----------------------------------------------------------KVEIYKSFRPGDIVLAKVISLG 75 (94) T ss_dssp ----------------------------------------------------------CCCGGGTCCSSSEEEEEEEEEE T ss_pred ----------------------------------------------------------CCCHHHHCCCCCEEEEEEEEEC T ss_conf ----------------------------------------------------------3066863679999999999863 Q ss_pred CCCCCCCCCCCC Q ss_conf 234564101233 Q gi|254780751|r 189 RGNKGAAVTTYL 200 (723) Q Consensus 189 ~~~Kga~lT~~i 200 (723) ...+-..||+.- T Consensus 76 ~~~~~i~LS~k~ 87 (94) T 2nn6_I 76 DAQSNYLLTTAE 87 (94) T ss_dssp TTTTEEEEECCS T ss_pred CCCCEEEEEECC T ss_conf 889739989628 No 22 >>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha subunit; transferase, protein biosynthesis, protein synthesis/transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A (A:1-88) Probab=97.58 E-value=0.00014 Score=50.43 Aligned_cols=41 Identities=17% Similarity=0.242 Sum_probs=36.2 Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECC--CCCCCCCHHHCCCCCC Q ss_conf 042878798997836388231353278--9771302221371210 Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGG--NRHGFLPFLEIHPDYY 79 (723) Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~--~k~gFL~~~ei~~~y~ 79 (723) .-.|.||.|+|++|.+. .|||+++. +-.||||.+|+..+|+ T Consensus 13 ~~~G~i~~g~V~~i~~~--G~~V~l~~~~gi~g~i~~s~ls~~~~ 55 (88) T 2a19_A 13 PEIDDIVMVNVQQIAEM--GAYVKLLEYDNIEGMILLSELSRRRI 55 (88) T ss_dssp CCTTCEEEEEEEEEETT--EEEEEETTTTTCEEEEECC------- T ss_pred CCCCCEEEEEEEEEECC--EEEEEECCCCCEEEEEEHHHHCCCCC T ss_conf 99989999999999798--79999767798269988999286644 No 23 >>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Probab=97.49 E-value=0.0003 Score=48.21 Aligned_cols=43 Identities=26% Similarity=0.412 Sum_probs=35.9 Q ss_pred CCCCCCCEEEEEEEEECCCCCEEEEEECC---CCCCCCCHHHCCCCCC Q ss_conf 46042878798997836388231353278---9771302221371210 Q gi|254780751|r 35 KKQIKGNIYLAKVTRVEPSLQAAFVDYGG---NRHGFLPFLEIHPDYY 79 (723) Q Consensus 35 ~~~~~GnIY~G~V~~V~p~lqAAFVdiG~---~k~gFL~~~ei~~~y~ 79 (723) ....+|.+|.|+|++|.+. ++||+++. +-.||+|++|+..++| T Consensus 8 ~~~~~G~~v~g~V~~i~~~--G~fV~l~~~~~gi~Gli~~s~ls~~~~ 53 (103) T 2eqs_A 8 EEPTIGDIYNGKVTSIMQF--GCFVQLEGLRKRWEGLVHISELRREGR 53 (103) T ss_dssp SSCCTTCEEEEEEEEECSS--CEEEEECSSSSCCEEEECGGGTSSSSC T ss_pred CCCCCCCEEEEEEEEEECC--EEEEEECCCCCCEECEECHHHEECCCC T ss_conf 5688999999999999536--589994586431211001523003334 No 24 >>1yz6_A Probable translation initiation factor 2 alpha subunit; beta barrel, helical domain and alpha beta domain; 3.37A {Pyrococcus abyssi} (A:1-83) Probab=97.49 E-value=0.00031 Score=48.11 Aligned_cols=43 Identities=19% Similarity=0.413 Sum_probs=36.9 Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECC--CCCCCCCHHHCCCCCCC Q ss_conf 6042878798997836388231353278--97713022213712102 Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGG--NRHGFLPFLEIHPDYYQ 80 (723) Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~--~k~gFL~~~ei~~~y~~ 80 (723) ....|.||.|+|++|.+ .+|||+||. +..||+|.+|+..+|+. T Consensus 7 ~~~~G~~v~g~V~~i~~--~G~fV~l~~~~gv~Gli~~~~~s~~~~~ 51 (83) T 1yz6_A 7 YPEEGEFVVATVKRIHN--YGAFLELDEYPGKEAFMHISEVASTWVR 51 (83) T ss_dssp SCCTTCEEEEEEEEEET--TEEEEEETTSTTCEEEEEGGGTSSSCCS T ss_pred CCCCCCEEEEEEEEEEC--CEEEEEECCCCCCEEEEEHHHCCCCCCC T ss_conf 79999999999999972--4389997478992899898887774204 No 25 >>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} (A:642-785) Probab=97.46 E-value=5.6e-05 Score=53.26 Aligned_cols=87 Identities=21% Similarity=0.233 Sum_probs=68.8 Q ss_pred CCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 46042878798997836388231353278977130222137121028988999999988863111110000000111223 Q gi|254780751|r 35 KKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTI 114 (723) Q Consensus 35 ~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 114 (723) ....+|.||.|+|++|.|. +|||++|.+-.||+|.+|+..+|.. T Consensus 9 ~~~~~G~iv~G~V~~v~~~--G~fV~l~~~i~Glv~~sels~~~~~---------------------------------- 52 (144) T 3bzc_A 9 KDLKPGMVLEGVVTNVTNF--GAFVDIGVHQDGLVHISALSEKFVK---------------------------------- 52 (144) T ss_dssp TTCCTTCBCCCEEEEEETT--EEEEECSSSSEEEEETTTSCSSCCS---------------------------------- T ss_pred HCCCCCCEEEEEEEEECCC--CEEEEECCCCCEEEEHHHCCCCCCC---------------------------------- T ss_conf 3089998899999987578--5699806997216778854777789---------------------------------- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCC Q ss_conf 34443344542222334455433222234321122111211000012234444213310688857999840333234564 Q gi|254780751|r 115 PNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGA 194 (723) Q Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga 194 (723) ...+.++.||.|-|.|++--..+.-. T Consensus 53 ------------------------------------------------------~~~~~~~~G~~v~vkV~~vd~~~~~i 78 (144) T 3bzc_A 53 ------------------------------------------------------DPYEVVKAGDIVKVKVMEVDIPRNRV 78 (144) T ss_dssp ------------------------------------------------------CHHHHCCTTCCCCCBEEEEETTTTEE T ss_pred ------------------------------------------------------CHHHCCCCCCEEEEEEEEEECCCCEE T ss_conf ------------------------------------------------------98884999998999999986467889 Q ss_pred CCCCCCCCCCCCEEECC Q ss_conf 10123345765234422 Q gi|254780751|r 195 AVTTYLSLAGRYSVLMP 211 (723) Q Consensus 195 ~lT~~isl~Gry~Vl~P 211 (723) .||..-+.........+ T Consensus 79 ~LS~~~~~~~~~~~~~~ 95 (144) T 3bzc_A 79 GLSMRMSDTPGEKVEGQ 95 (144) T ss_dssp EECCSSCCCCC------ T ss_pred EEEECCCCCCCCCCCCC T ss_conf 98842666666666677 No 26 >>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A (A:151-239,A:464-723) Probab=97.45 E-value=2.1e-05 Score=56.18 Aligned_cols=42 Identities=31% Similarity=0.498 Sum_probs=32.1 Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC Q ss_conf 60428787989978363882313532789771302221371210 Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723) Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723) ...+|.||.|+|++|.| ..|||+++.+..||||.+++..+++ T Consensus 250 ~~~vG~i~~g~V~~I~~--fGaFV~l~~g~~GlihiSel~~~rv 291 (349) T 3cdi_A 250 EIEVGRVYTGKVTRIVD--FGAFVAIGGGKEGLVHISQIADKRV 291 (349) T ss_dssp -------------------------------------------- T ss_pred CCCCCCEEEEEEEEEEE--EEEEEEECCCCCEEEEEECCCCCCC T ss_conf 77669889999999994--3299996699944787020467565 No 27 >>1kl9_A Eukaryotic translation initiation factor 2 subunit 1; OB fold, helical domain; 1.90A {Homo sapiens} (A:1-88) Probab=97.42 E-value=0.00039 Score=47.39 Aligned_cols=42 Identities=14% Similarity=0.160 Sum_probs=35.9 Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECC--CCCCCCCHHHCCCCCC Q ss_conf 6042878798997836388231353278--9771302221371210 Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGG--NRHGFLPFLEIHPDYY 79 (723) Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~--~k~gFL~~~ei~~~y~ 79 (723) ....|.+|.|+|++|.+. ++||+++. +-.||+|++++..+|+ T Consensus 12 ~~~~G~vv~g~V~~v~~~--G~~V~l~~~~gi~G~i~~~els~~~~ 55 (88) T 1kl9_A 12 FPEVEDVVXVNVRSIAEX--GAYVSLLEYNNIEGXILLSELSRRRI 55 (88) T ss_dssp SCCTTCEEEEEEEEECSS--EEEEEETTTTTEEEEEEGGGC----- T ss_pred CCCCCCEEEEEEEEEECC--EEEEEECCCCCEEEEEEHHHHCCCCC T ss_conf 899999999999999666--68999756899089989999088865 No 28 >>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} (B:83-171) Probab=97.42 E-value=0.00035 Score=47.75 Aligned_cols=41 Identities=17% Similarity=0.091 Sum_probs=35.9 Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCC Q ss_conf 28787989978363882313532789771302221371210289 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIP 82 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip 82 (723) +|.||.|+|++|.|. +|||++| +-.||+|.+++.++|...| T Consensus 1 kG~i~~g~V~~v~~~--G~FV~l~-~~eg~v~~s~l~~d~~~~~ 41 (89) T 1y14_B 1 KGEVVDGTVVSCSQH--GFEVQVG-PMKVFVTKHLMPQDLTFNA 41 (89) T ss_dssp TTCEEEEEEEEEETT--EEEEEET-TEEEEEEGGGSCTTCEECC T ss_pred CCCEEEEEEEEEECC--CEEEEEC-CCCEEEEEEECCCCCCCCH T ss_conf 797899999998157--3899905-6217877320033211475 No 29 >>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli K12} (A:559-644) Probab=97.39 E-value=0.00036 Score=47.63 Aligned_cols=40 Identities=13% Similarity=0.190 Sum_probs=36.2 Q ss_pred CCCEEEEEEEEECCCCCEEEEEE-CCCCCCCCCHHHCCCCCCC Q ss_conf 28787989978363882313532-7897713022213712102 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDY-GGNRHGFLPFLEIHPDYYQ 80 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdi-G~~k~gFL~~~ei~~~y~~ 80 (723) .|.+|-|+|++|.|. ++||++ +.+..||+|++++..+||. T Consensus 2 ~G~~~~g~V~~I~~~--G~fV~l~~~~~eGli~~s~l~~~~~~ 42 (86) T 2id0_A 2 TDTRFAAEIVDISRG--GXRVRLVDNGAIAFIPAPFLHAVRDE 42 (86) T ss_dssp SCCCEEEEEEEEETT--EEEEEETTTCCEEEEEGGGTCSCGGG T ss_pred CCCEEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHCCCCCCE T ss_conf 973489999889706--39999826964999985664777644 No 30 >>2waq_E DNA-directed RNA polymerase RPO7 subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_E 2pmz_E 3hkz_E (E:81-180) Probab=97.33 E-value=0.00032 Score=47.98 Aligned_cols=39 Identities=21% Similarity=0.342 Sum_probs=35.6 Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC Q ss_conf 287879899783638823135327897713022213712102 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ 80 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ 80 (723) +|.+|.|+|++|.|. ++||+++ +..||+|.+++..+||. T Consensus 1 VG~~~~g~V~~v~~~--G~fV~l~-~~~Glv~~s~ls~~~~~ 39 (100) T 2waq_E 1 VQEVVEGEVLQVDNY--GIFVNLG-PMDGLVHISQITDDTLK 39 (100) T ss_dssp SSCCCCEEEEEECSS--EEEEBCS-SSBBCEESTTBCSSSSC T ss_pred CCCEEEEEEEEEECC--EEEEEEC-CCCCEEEEHHHCCCCCC T ss_conf 782999999998547--1999714-87753975232787420 No 31 >>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} (A:1-86) Probab=97.30 E-value=0.00087 Score=44.97 Aligned_cols=42 Identities=14% Similarity=0.207 Sum_probs=36.6 Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECC--CCCCCCCHHHCCCCCC Q ss_conf 6042878798997836388231353278--9771302221371210 Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGG--NRHGFLPFLEIHPDYY 79 (723) Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~--~k~gFL~~~ei~~~y~ 79 (723) ....|.+|.|+|.+|.+. .|||+++. +-.||||++|+..+|+ T Consensus 10 ~~~~G~vv~g~V~~i~~~--G~~V~l~~~~gi~g~i~~~eis~~~~ 53 (86) T 1q8k_A 10 FPEVEDVVMVNVRSIQEM--GAYVSLLEYNNIEGMIHLSELSRRRI 53 (86) T ss_dssp CCSSCCEEEEEEEEEETT--EEEEESCTTTSCCEEECGGGTSCSSC T ss_pred CCCCCCEEEEEEEEEECC--EEEEEECCCCCEEEEEEHHHCCCCCC T ss_conf 899999999999999735--49999707998189999898778544 No 32 >>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} (P:129-215) Probab=97.26 E-value=0.00069 Score=45.68 Aligned_cols=39 Identities=31% Similarity=0.319 Sum_probs=33.5 Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC Q ss_conf 604287879899783638823135327897713022213712 Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD 77 (723) Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~ 77 (723) ....|.|+.|+|.++.+. +||||+| +-.||||.+++.|. T Consensus 3 ~~~~G~iv~g~V~~i~~~--G~~V~l~-~~~g~ip~~e~~~~ 41 (87) T 1hh2_P 3 SELKGTVTTAEVIRVMGE--WADIRIG-KLETRLPKKEWIPG 41 (87) T ss_dssp TCCTTCEEEEEEEEECSS--EEEEEET-TEEEEEEGGGSCTT T ss_pred HHHCCCEEEEEEEEEECC--CEEEECC-CEEEEECHHHCCCC T ss_conf 862681899999999614--3599618-61687177886986 No 33 >>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} (G:83-215) Probab=97.12 E-value=0.0011 Score=44.31 Aligned_cols=84 Identities=13% Similarity=-0.001 Sum_probs=60.7 Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 28787989978363882313532789771302221371210289889999999888631111100000001112233444 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDH 118 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 (723) .|.+|.|+|++|.+. ++||+++ +-.||||++++..+|...+. T Consensus 1 eG~~~~G~V~~i~~~--G~fV~l~-~~~Gli~~s~l~~~~~~d~~----------------------------------- 42 (133) T 2b8k_G 1 KGEVVDGTVVSCSQH--GFEVQVG-PMKVFVTKHLMPQDLTFNAG----------------------------------- 42 (133) T ss_dssp TTEEEEEEEEEEETT--EEEEECT-TSEEEEEGGGSCSSCCCBSS----------------------------------- T ss_pred CCEEEEEEEEEECCC--EEEEEEC-CCEEEEEEEECCCCCCCCCC----------------------------------- T ss_conf 880999999976266--4899820-71689661006775421600----------------------------------- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCCC Q ss_conf 33445422223344554332222343211221112110000122344442133106888579998403332345641012 Q gi|254780751|r 119 SLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTT 198 (723) Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~ 198 (723) ..........+.++.||.|-|+|.+--...+-..|+. T Consensus 43 -------------------------------------------~~~~~~~~~~~~~~~G~~v~vkVl~vd~~~~~i~ls~ 79 (133) T 2b8k_G 43 -------------------------------------------SNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIG 79 (133) T ss_dssp -------------------------------------------CSSCEEECSSCEEETTCEEEEEEEEEEEETTEEEEEE T ss_pred -------------------------------------------CCEEEEECCCCEEECCCEEEEEEEEEECCCCEEEEEE T ss_conf -------------------------------------------0527894388299379999999999862657048999 Q ss_pred CCCCC Q ss_conf 33457 Q gi|254780751|r 199 YLSLA 203 (723) Q Consensus 199 ~isl~ 203 (723) ..... T Consensus 80 k~~~~ 84 (133) T 2b8k_G 80 SIKED 84 (133) T ss_dssp ECCST T ss_pred EECCC T ss_conf 96789 No 34 >>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (G:84-172) Probab=97.10 E-value=0.00058 Score=46.20 Aligned_cols=39 Identities=26% Similarity=0.307 Sum_probs=35.0 Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC Q ss_conf 287879899783638823135327897713022213712102 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ 80 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ 80 (723) +|+||.|+|++|.+. +|||++| +-.||+|.+++.++|.. T Consensus 1 kG~i~~G~V~~i~~~--G~FV~l~-~~eG~v~~s~l~~d~~~ 39 (89) T 3h0g_G 1 RGEVVDAIVTTVNKM--GFFANIG-PLNVFVSSHLVPPDMKF 39 (89) T ss_dssp TTCEEECCCCEEETT--EEECCBT-TBCCEEEGGGSCTTCCC T ss_pred CCCEEEEEEEEEECC--EEEEEEE-CCCEEEEHHHCCCCCCC T ss_conf 898999999688055--5999940-64157441211554311 No 35 >>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} (A:592-757) Probab=97.04 E-value=0.00016 Score=50.10 Aligned_cols=42 Identities=21% Similarity=0.200 Sum_probs=37.4 Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC Q ss_conf 60428787989978363882313532789771302221371210 Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723) Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723) ....|.||.|.|..+.+. +|||+++.+..||+|+++|..+|+ T Consensus 73 ~~~~g~i~~g~V~~i~~~--G~fv~~~~~~~g~i~is~i~~~~~ 114 (166) T 1e3p_A 73 SPEVGERILGSVVKTTTF--GAFVSLLPGKDGLLHISQIRKLAG 114 (166) T ss_dssp ---------CBEEECC-C--SCEECCC---CCCCC--------- T ss_pred CCCCCCEEEEEEEEEEEC--EEEEEECCCCCEEEEEECCCCCCC T ss_conf 356798899999999825--199996699952788322366544 No 36 >>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} (B:81-218) Probab=97.03 E-value=0.0024 Score=41.91 Aligned_cols=91 Identities=13% Similarity=0.065 Sum_probs=61.5 Q ss_pred CCCEEEEEEEEECCCCCEEEEEE-CCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 28787989978363882313532-78977130222137121028988999999988863111110000000111223344 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDY-GGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPND 117 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdi-G~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (723) +|.||.|+|++|.+ ..+||++ |....||+|.+++..+|+.-|.. T Consensus 1 VGei~~G~V~~v~~--~GifV~L~~~~~egli~~s~L~d~~~~~~~~--------------------------------- 45 (138) T 2ckz_B 1 LGEIVTGWISKCTA--EGIKVSLLGIFDDIFIPQNMLFEGCYYTPEE--------------------------------- 45 (138) T ss_dssp TTCEEEEEEEEEET--TEEEEECTTSCCCEEEETTTSCTTCEEETTT--------------------------------- T ss_pred CCCEEEEEEEEECC--CEEEEEECCCCCCEEEEHHHCCCCCEECHHC--------------------------------- T ss_conf 78599999971516--5499993387365385077678985793112--------------------------------- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCC Q ss_conf 43344542222334455433222234321122111211000012234444213310688857999840333234564101 Q gi|254780751|r 118 HSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVT 197 (723) Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT 197 (723) ..............++.||.|-|+|..--..+.-..|+ T Consensus 46 ------------------------------------------~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~ls 83 (138) T 2ckz_B 46 ------------------------------------------SAWIWPMDEETKLYFDVNEKIRFRIEREVFVDVKPKSP 83 (138) T ss_dssp ------------------------------------------TEEEEECC--CEEEECTTCEEEEEEEEEEECCCCC--- T ss_pred ------------------------------------------CEEEEECCCCCCEEECCCCEEEEEEEEEEEECCCCCCC T ss_conf ------------------------------------------55997248745609758998999999999642799873 Q ss_pred CCCCCCCCC Q ss_conf 233457652 Q gi|254780751|r 198 TYLSLAGRY 206 (723) Q Consensus 198 ~~isl~Gry 206 (723) ..=...... T Consensus 84 l~~~~~~~~ 92 (138) T 2ckz_B 84 KERELEERA 92 (138) T ss_dssp --------- T ss_pred CCCCCCCCC T ss_conf 100123223 No 37 >>2ba1_A Archaeal exosome RNA binding protein CSL4; RNAse PH, RNA degradation, exoribonuclease, RNA binding, S1 domain, Zn-ribbon, phosphorolytic; 2.70A {Archaeoglobus fulgidus} (A:54-145) Probab=96.93 E-value=0.0023 Score=42.08 Aligned_cols=40 Identities=23% Similarity=0.470 Sum_probs=33.9 Q ss_pred CCCCEEEEEEEEECCCCCEEEEEEC----------CCCCCCCCHHHCCCCCC Q ss_conf 4287879899783638823135327----------89771302221371210 Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYG----------GNRHGFLPFLEIHPDYY 79 (723) Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG----------~~k~gFL~~~ei~~~y~ 79 (723) .+|.+|.|+|++|.+- .|||++. .+..||+|.+++...+. T Consensus 3 ~vG~~v~G~V~~I~~f--G~fVel~~~~~~~~~~~~~~~gli~~s~~s~~~~ 52 (92) T 2ba1_A 3 VKGDVVLGRVVDLRNS--IALIEVSSKKGENRGPSNRGIGILHVSNVDEGYV 52 (92) T ss_dssp CTTCEEEEEEEEEETT--EEEEEEEEETTCCSCCTTCEEEEEEHHHHCSSCC T ss_pred CCCCEEEEEEEEECCC--CEEEEEEECCCCCCCCCCCCCCEEEECCCCHHHH T ss_conf 7899999999896168--3899997125863555545523068423315666 No 38 >>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} (B:81-172) Probab=96.92 E-value=0.0015 Score=43.36 Aligned_cols=38 Identities=26% Similarity=0.330 Sum_probs=34.0 Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC Q ss_conf 28787989978363882313532789771302221371210 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723) +|.||.|+|++|.+ .++||++| +-.||+|.+++..+|. T Consensus 1 kG~i~~G~V~~v~~--~G~FV~l~-~~eGli~~s~l~~~~~ 38 (92) T 2c35_B 1 KGEVVDAVVTQVNK--VGLFTEIG-PMSCFISRHSIPSEME 38 (92) T ss_dssp TTCEEEEEEEEEET--TEEEEEET-TEEEEEEGGGSCTTEE T ss_pred CCEEEEEEEEEECC--CEEEEEEE-CCCEEECCHHCCCEEE T ss_conf 63599999998727--86999960-6311201011023032 No 39 >>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus WR} (A:) Probab=96.56 E-value=0.003 Score=41.21 Aligned_cols=42 Identities=10% Similarity=-0.013 Sum_probs=34.6 Q ss_pred CCCCCCCEEEEEEEEECCCCCEEEEEECC--CCCCCCCHHHCCCCCC Q ss_conf 46042878798997836388231353278--9771302221371210 Q gi|254780751|r 35 KKQIKGNIYLAKVTRVEPSLQAAFVDYGG--NRHGFLPFLEIHPDYY 79 (723) Q Consensus 35 ~~~~~GnIY~G~V~~V~p~lqAAFVdiG~--~k~gFL~~~ei~~~y~ 79 (723) .....|.|+.|+|+-.. .+|||.++. +..||+|.+++.++|. T Consensus 7 ~~~~~G~iv~g~V~v~~---~G~fV~l~~~~gv~Gli~~s~is~~~~ 50 (88) T 1luz_A 7 SLPNAGDVIKGRVYEKD---YALYIYLFDYPHFEAILAESVKXHXDR 50 (88) T ss_dssp CCCCTTCEEEEEEEEET---TEEEEEETTCTTSEEEEGGGSSCCHHH T ss_pred ECCCCCCEEEEEEEEEC---CEEEEEECCCCCCEEEEEEHHHHHHHH T ss_conf 06987721324899968---899999368898238877343551589 No 40 >>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae TIGR4} (A:136-219) Probab=96.50 E-value=0.0088 Score=37.97 Aligned_cols=39 Identities=26% Similarity=0.255 Sum_probs=32.6 Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECCCC-CCCCCHHHCCC Q ss_conf 604287879899783638823135327897-71302221371 Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNR-HGFLPFLEIHP 76 (723) Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k-~gFL~~~ei~~ 76 (723) ....|.+|.|+|++|.|. ++||++.... .||||.+|+.. T Consensus 14 ~~~~G~~~~g~V~~i~~~--G~fV~l~~~~~eGlv~~sel~~ 53 (84) T 3go5_A 14 NNXQNQNWPAIVYRLKLS--GTFVYLPENNXLGFIHPSERYA 53 (84) T ss_dssp SCCTTCEEEEEEEEEETT--EEEEEETTTTEEEEECGGGCSS T ss_pred HCCCCCEEEEEEEEEECC--CCEEEECCCCEEEEECCCCCCC T ss_conf 325999999999999748--7189843787899963541244 No 41 >>1a6f_A RNAse P protein, ribonuclease P protein; endonuclease, subunit; 2.60A {Bacillus subtilis} (A:) Probab=87.79 E-value=0.79 Score=24.39 Aligned_cols=75 Identities=27% Similarity=0.278 Sum_probs=53.4 Q ss_pred CCCCEEEC--CCC-----CCCCEEEECCCCHHHHHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHHHH Q ss_conf 76523442--278-----875124204688689999999998630-------0258716998504557579999999999 Q gi|254780751|r 203 AGRYSVLM--PNT-----SKGETISRKITNPVDRKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFEYL 268 (723) Q Consensus 203 ~Gry~Vl~--P~~-----~~~~~iSrki~~~~~r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~~L 268 (723) .|.|+++. |+. --|+.+|+|+...-.|.+.+..+.+.. .+.++-+|+|..+...+..++..|+..| T Consensus 27 ~~~~~~l~~~~~~~~~~~R~gi~vsKKvg~AV~RNriKR~lRe~~R~~~~~l~~~d~v~i~r~~~~~~~~~~l~~~l~~l 106 (119) T 1a6f_A 27 ANRQFVLYTLDQPENDELRVGLSVSKKIGNAVMRNRIKRLIRQAFLEEKERLKEKDYIIIARKPASQLTYEETKKSLQHL 106 (119) T ss_dssp ECSSEEEEECCCTTCSSCEEEEEECSTTCCHHHHHHHHHHHHHHHHHHTTTBCSSEEEEEECGGGTTCCHHHHHHHHHHH T ss_pred ECCCEEEEEECCCCCCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHHHHH T ss_conf 48978999973898998269999931025568889999999999998641289974999966876769999999999999 Q ss_pred HHHHHHHHH Q ss_conf 999998776 Q gi|254780751|r 269 MRLWDNVRE 277 (723) Q Consensus 269 ~~~w~~i~~ 277 (723) ++.+..+.. T Consensus 107 l~k~~~~~~ 115 (119) T 1a6f_A 107 FRKSSLYKK 115 (119) T ss_dssp HHHTTCBC- T ss_pred HHHHHHHHC T ss_conf 998242311 No 42 >>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} (A:1-81) Probab=87.69 E-value=0.81 Score=24.35 Aligned_cols=39 Identities=21% Similarity=0.271 Sum_probs=31.0 Q ss_pred CCCCCCEEEEEEEEECCCC--CEEEEEECCC---CCCCCCHHHC Q ss_conf 6042878798997836388--2313532789---7713022213 Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSL--QAAFVDYGGN---RHGFLPFLEI 74 (723) Q Consensus 36 ~~~~GnIY~G~V~~V~p~l--qAAFVdiG~~---k~gFL~~~ei 74 (723) ....|.|--|.|.++.+.= -..+||+|.+ -.|+||-+|. T Consensus 4 ~~~~geivtg~V~r~~~~~~~~~v~v~lg~~~~~~EaiLp~~eq 47 (81) T 2asb_A 4 STREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQ 47 (81) T ss_dssp CCCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGS T ss_pred CCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCCEEEECCHHHC T ss_conf 11279589999999805897258999868877660695897886 No 43 >>2pe4_A Hyaluronidase-1; hyaluronan, EGF-like domain, alternative splicing, hydrolase; HET: NAG BMA MAN; 2.00A {Homo sapiens} (A:48-194) Probab=86.44 E-value=0.74 Score=24.62 Aligned_cols=61 Identities=15% Similarity=0.269 Sum_probs=40.1 Q ss_pred CCCCCCCCHHHHHHHHHH-HHHHHHHHHHHHCCCCEEEEECCCCCCHH----HHHHHHHHHHHHHH Q ss_conf 544455511479999999-99999998731036863896033479888----89999999999731 Q gi|254780751|r 388 RSTREHCIEDTALQTNLE-AAEEIARQLRLRDLAGLIVVDFIDMEEKK----NNRSVEKKLKESLK 448 (723) Q Consensus 388 ~~~~~~~~e~t~l~tNle-AA~EIaRQlRLRnlgGiIvIDFIdM~~~~----~~~~v~~~l~~~l~ 448 (723) ..+-++=.....|...|+ |.+.|.+.|.-+|-+||-||||=.=+.-= ..+.|++.....|- T Consensus 24 ~~~NGGiPQ~g~L~~HL~k~~~dI~~~ip~~~f~GLaVIDwE~WRP~w~rNw~~k~iYr~~S~~lv 89 (147) T 2pe4_A 24 EPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALV 89 (147) T ss_dssp CEETTSSGGGSCHHHHHHHHHHHHHHHCCCTTCCSEEEECCCSSCSSGGGCCGGGHHHHHHHHHHH T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCCHHHCCCCCHHHHHHHHHHH T ss_conf 851588898577999999999889975779999841798764636653433776388999999999 No 44 >>2vf7_A UVRA2, excinuclease ABC, subunit A.; DNA-binding protein, nucleotide-binding, zinc-binding domain, SOS response, metal-binding; HET: ADP; 2.30A {Deinococcus radiodurans} PDB: 2vf8_A* (A:143-168,A:257-300) Probab=86.22 E-value=0.36 Score=26.78 Aligned_cols=36 Identities=19% Similarity=0.339 Sum_probs=26.4 Q ss_pred HCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCC Q ss_conf 002367546537860611468998878899973036 Q gi|254780751|r 480 TTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYT 515 (723) Q Consensus 480 ~~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~ 515 (723) -+-.||.|+|.|.+...+.-.+-|+..|++...... T Consensus 5 ~~g~cp~c~g~g~~~~~~~~~~Gvi~~Ler~y~et~ 40 (70) T 2vf7_A 5 PEGACPECHGLGRVYTVTEDSMSARRHVLHTFANTE 40 (70) T ss_dssp TTTBCTTTTSSSEEEECCHHHHCHHHHHHHHHHHCC T ss_pred CCCCCCCCCCCCCEEEECHHHEHHHHHHHHHHHCCC T ss_conf 111184258885355537655456678998761125 No 45 >>1fcq_A Hyaluronoglucosaminidase; 7-stranded (beta/alpha) TIM barrel, glycosidase family 56, allergen, hydrolase; 1.60A {Apis mellifera} (A:35-193) Probab=83.81 E-value=1.1 Score=23.43 Aligned_cols=56 Identities=18% Similarity=0.199 Sum_probs=39.2 Q ss_pred CCHHHHHHHHHHHHHH-HHHHHHHHCCCCEEEEECCCCCCHH----HHHHHHHHHHHHHHH Q ss_conf 5114799999999999-9998731036863896033479888----899999999997312 Q gi|254780751|r 394 CIEDTALQTNLEAAEE-IARQLRLRDLAGLIVVDFIDMEEKK----NNRSVEKKLKESLKK 449 (723) Q Consensus 394 ~~e~t~l~tNleAA~E-IaRQlRLRnlgGiIvIDFIdM~~~~----~~~~v~~~l~~~l~~ 449 (723) =.....|...|+.|++ |.+.|.-+|.+||-||||=.=+.-= +.+.|++.+...|-+ T Consensus 44 iPQ~~~L~~HL~k~~~dI~~~ip~~~f~GLaVIDwE~WRP~w~rNw~~k~iYr~~S~elv~ 104 (159) T 1fcq_A 44 VPQLGNLTKHLQVFRDHLINQIPDKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVR 104 (159) T ss_dssp SGGGCCHHHHHHHHHHHHHHHCCCTTCCSEEEEECCSCCSSGGGCCGGGHHHHHHHHHHHH T ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCCHHHCCCCCHHHHHHHHHHHH T ss_conf 7871669999999999899848898998537987556366444337763899999999999 No 46 >>2hl7_A Cytochrome C-type biogenesis protein CCMH; three-helices bundle, oxidoreductase; HET: PG4; 1.70A {Pseudomonas aeruginosa} (A:) Probab=83.47 E-value=1.4 Score=22.79 Aligned_cols=56 Identities=16% Similarity=0.211 Sum_probs=44.6 Q ss_pred CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEE Q ss_conf 02367546537860611468998878899973036431013576999998730237999999998488799984 Q gi|254780751|r 481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVI 554 (723) Q Consensus 481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~ 554 (723) .-.||+|.|.-.--|.-.+|..+.+.|++....+.+ +..-+..|..+||-.|...+ T Consensus 26 ~lRC~~Cqnqsi~dSna~~A~dmR~~i~~~i~~G~s------------------d~eI~~~lv~RYG~~Vl~~P 81 (84) T 2hl7_A 26 ELRCPKCQNQDIADSNAPIAADLRKQIYGQLQQGKS------------------DGEIVDYMVARYGDFVRYKP 81 (84) T ss_dssp HEECTTSSSCBTTTCCSHHHHHHHHHHHHHHHHTCC------------------HHHHHHHHHHHHTTTCEECC T ss_pred HCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCC------------------HHHHHHHHHHHCCCEEEEEC T ss_conf 378887699683006778899999999999995999------------------89999999997088386319 No 47 >>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} (A:113-204) Probab=82.07 E-value=3 Score=20.39 Aligned_cols=39 Identities=21% Similarity=0.261 Sum_probs=29.7 Q ss_pred CCCCCCEEEEEEEEECCCC--CEEEEEECC---CCCCCCCHHHC Q ss_conf 6042878798997836388--231353278---97713022213 Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSL--QAAFVDYGG---NRHGFLPFLEI 74 (723) Q Consensus 36 ~~~~GnIY~G~V~~V~p~l--qAAFVdiG~---~k~gFL~~~ei 74 (723) ....|.|--|.|.++.+.- -..+||+|. +-.|+||-+|. T Consensus 15 ~~~~geiVtg~V~r~~~~~~~~~v~~~L~~~~~~~ea~Lp~~eq 58 (92) T 1k0r_A 15 STREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQ 58 (92) T ss_dssp CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGS T ss_pred HHHCCCEEEEEEEEEECCCCCEEEEEECCCCCCCCEEECCHHHC T ss_conf 87439778899999736886159999737767564594687775 No 48 >>2atm_A Hyaluronoglucosaminidase; beta-alpha-barrels, hydrolase; HET: MES; 2.00A {Vespula vulgaris} (A:31-183) Probab=81.38 E-value=1.5 Score=22.41 Aligned_cols=61 Identities=15% Similarity=0.213 Sum_probs=38.6 Q ss_pred CCCCCCCCCHHHHHHHHHHHHH-HHHHHHHHHCCCCEEEEECCCCCCHH----HHHHHHHHHHHHH Q ss_conf 5544455511479999999999-99998731036863896033479888----8999999999973 Q gi|254780751|r 387 GRSTREHCIEDTALQTNLEAAE-EIARQLRLRDLAGLIVVDFIDMEEKK----NNRSVEKKLKESL 447 (723) Q Consensus 387 G~~~~~~~~e~t~l~tNleAA~-EIaRQlRLRnlgGiIvIDFIdM~~~~----~~~~v~~~l~~~l 447 (723) |...-++=.....|...|+.|+ .|...|.-.|-+||-||||=.=+.-= +.+.|++.+...| T Consensus 37 g~~~nGGiPQ~~~L~~HL~k~~~dI~~~ip~~~f~GLaVIDwE~WRP~w~rNw~~k~iYr~~S~el 102 (153) T 2atm_A 37 YKKRNGGVPQEGNITIHLQKFIENLDKIYPNRNFSGIGVIDFERWRPIFRQNWGNMKIHKNFSIDL 102 (153) T ss_dssp EEEETTSSGGGCCHHHHHHHHHHHHHHHCCCTTCCSEEEEECCSCCSSGGGCCGGGTHHHHHHHHH T ss_pred CCEECCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCCHHHCCCCCHHHHHHHHHH T ss_conf 431058859757699999999998998577988884279874342653554266408899999999 No 49 >>1d6t_A Ribonuclease P, RNAse P protein; endonuclease, subunit; NMR {Staphylococcus aureus} (A:) Probab=80.92 E-value=2.2 Score=21.33 Aligned_cols=75 Identities=24% Similarity=0.323 Sum_probs=53.1 Q ss_pred CCCCCEEEC--CCC-----CCCCEEEECCCCHHHHHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHHH Q ss_conf 576523442--278-----875124204688689999999998630-------025871699850455757999999999 Q gi|254780751|r 202 LAGRYSVLM--PNT-----SKGETISRKITNPVDRKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFEY 267 (723) Q Consensus 202 l~Gry~Vl~--P~~-----~~~~~iSrki~~~~~r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~~ 267 (723) +.|+|+++. |+. --|+.+|+|+...-.|.+.+..+.+.. .+.++-+|++..+..++..++..|+.. T Consensus 25 ~~~~~~~l~~~~~~~~~~~Rvgi~vsKKvg~AV~RNriKR~lRe~~R~~~~~l~~~d~vii~~~~~~~~~~~~l~~~l~~ 104 (117) T 1d6t_A 25 VANRQFVVYTCNNKEIDHFRLGISVSKKLGNAVLRNKIKRAIRENFKVHKSHILAKDIIVIARQPAKDMTTLQIQNSLEH 104 (117) T ss_dssp CCSSSEECEECSTTCCSSCCEEEECCSSSCSTTHHHHHHHHHHHHHHHGGGTCCSSCEEEEECSGGGGCCTTHHHHHHTT T ss_pred EECCCEEEEEECCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCHHHHHHHHHH T ss_conf 75897899997189888856999993356554788999999999999710248996499997577565999999999999 Q ss_pred HHHHHHHHH Q ss_conf 999999877 Q gi|254780751|r 268 LMRLWDNVR 276 (723) Q Consensus 268 L~~~w~~i~ 276 (723) |+..+.... T Consensus 105 ll~k~~~~~ 113 (117) T 1d6t_A 105 VLKIAKVFN 113 (117) T ss_dssp HHHHHTCSS T ss_pred HHHHHHHHH T ss_conf 999976666 No 50 >>2bx9_A Anti-trap, AT, tryptophan RNA-binding attenuator protein-inhibitory protein; transcription regulation, Trp RNA-binding attenuation protein; 2.8A {Bacillus subtilis} PDB: 2zp8_E* 2zp9_C* (A:) Probab=73.46 E-value=1.4 Score=22.62 Aligned_cols=24 Identities=29% Similarity=0.540 Sum_probs=16.9 Q ss_pred HHHCCCCCCCCCEEEEECCHHHHH Q ss_conf 210023675465378606114689 Q gi|254780751|r 478 ESTTKVCTYCKGAGYIRSQSSVAL 501 (723) Q Consensus 478 e~~~~~c~~c~g~g~~~~~~~~~~ 501 (723) ....++|+.|+|.|+++...++.. T Consensus 20 ~ii~~~C~~C~G~G~v~~~~~i~V 43 (53) T 2bx9_A 20 EIEGTPCPACSGKGVILTAQGYTL 43 (53) T ss_dssp EETTEECTTTTTSSEEECHHHHHH T ss_pred CCCCCCCCCCCCCEEEEECCCCHH T ss_conf 627983876677557997355369 No 51 >>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, cytoplasm, RNA-binding, RNA binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} (J:888-977) Probab=71.42 E-value=6.1 Score=18.26 Aligned_cols=36 Identities=14% Similarity=0.005 Sum_probs=30.4 Q ss_pred EEEEEEEEECCCCCEEEEEEC-CCCCCCCCHHHCCCCCC Q ss_conf 879899783638823135327-89771302221371210 Q gi|254780751|r 42 IYLAKVTRVEPSLQAAFVDYG-GNRHGFLPFLEIHPDYY 79 (723) Q Consensus 42 IY~G~V~~V~p~lqAAFVdiG-~~k~gFL~~~ei~~~y~ 79 (723) -|-|.|++|-+ .++||.+- .+-.|+.|++++.-||| T Consensus 2 ~f~g~I~~V~~--~G~fV~l~~~g~EGlV~~~~l~~d~~ 38 (90) T 2wp8_J 2 TETGYVIKVFN--NGIVVLVPKFGVEGLIRLDNLTEDPN 38 (90) T ss_dssp EEEEEEEEECS--SEEEEECTTTCCEEEEEGGGTCSCGG T ss_pred EEEEEEEEEEE--CCEEEEECCCCCEEEEEHHHCCCCCC T ss_conf 48899999995--71999970897189998200799754 No 52 >>3lcz_A YCZA, inhibitor of trap, regulated by T-box (Trp) sequence RTPA; anti-trap, tryptophan RNA-binding attenuation protein; 2.06A {Bacillus licheniformis} PDB: 3ld0_A (A:) Probab=69.51 E-value=2 Score=21.65 Aligned_cols=30 Identities=20% Similarity=0.500 Sum_probs=19.8 Q ss_pred HHHCCCCCCCCCEEEEECCHHHHHHHHHHHHH Q ss_conf 21002367546537860611468998878899 Q gi|254780751|r 478 ESTTKVCTYCKGAGYIRSQSSVALSILRSVEE 509 (723) Q Consensus 478 e~~~~~c~~c~g~g~~~~~~~~~~~~~r~i~~ 509 (723) +.-.+|||.|.|.|.|.+..-. .+|.-|+. T Consensus 20 ~~e~~pcp~c~~kgviltaqg~--tll~fi~k 49 (53) T 3lcz_A 20 REEPEPCPKCLGKGVILTAQGS--TLLHFIKK 49 (53) T ss_dssp EETTEECTTTTTSSEEECHHHH--HHHHHHHH T ss_pred CCCCCCCCCCCCCEEEEECCCC--HHHHHHHH T ss_conf 6279838634575369973553--69999998 No 53 >>3fdr_A Tudor and KH domain-containing protein; TDRD2, structural genomics, structural genomics consortium, SGC, alternative splicing, RNA-binding; 1.75A {Homo sapiens} (A:) Probab=68.27 E-value=4.2 Score=19.40 Aligned_cols=42 Identities=33% Similarity=0.660 Sum_probs=29.0 Q ss_pred CCCEEEEEEEEECCC--CCEEEEEECCCCCCCCCHHHC---CCCCCCCC Q ss_conf 287879899783638--823135327897713022213---71210289 Q gi|254780751|r 39 KGNIYLAKVTRVEPS--LQAAFVDYGGNRHGFLPFLEI---HPDYYQIP 82 (723) Q Consensus 39 ~GnIY~G~V~~V~p~--lqAAFVdiG~~k~gFL~~~ei---~~~y~~ip 82 (723) -|..|.|+|.++.++ ..--|||||.- ..+++++| .++|.++| T Consensus 41 d~~wyRa~I~~~~~~~~~~V~fiDyG~~--~~v~~~~l~~l~~~~~~lP 87 (94) T 3fdr_A 41 NGSWYRARVLGTLENGNLDLYFVDFGDN--GDCPLKDLRALRSDFLSLP 87 (94) T ss_dssp TTEEEEEEEEEECTTSCEEEEETTTCCE--EEECGGGCEECCGGGGCSC T ss_pred CCEEEEEEEEEECCCCEEEEEEEEECCE--EEEEHHHHHHHCHHHHCCC T ss_conf 9929999999988999599999961997--9986799660189876085 No 54 >>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} (A:) Probab=66.22 E-value=6.7 Score=17.96 Aligned_cols=46 Identities=11% Similarity=0.093 Sum_probs=39.1 Q ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCC Q ss_conf 3101357699999873023799999999848879998478778863 Q gi|254780751|r 517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKL 562 (723) Q Consensus 517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~ 562 (723) -.+.+.+|...+.+|.+.+-..|.+|++.+|++|.|..+.....+. T Consensus 14 ~~~~i~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~ 59 (85) T 2opv_A 14 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV 59 (85) T ss_dssp EEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTS T ss_pred EEEEEEECHHHCCEEECCCCHHHHHHHHHHCCEEEECCCCCCCCCC T ss_conf 6899997967637549989701799999709369985788888888 No 55 >>2ytv_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding; NMR {Homo sapiens} (A:) Probab=65.54 E-value=5.9 Score=18.34 Aligned_cols=34 Identities=21% Similarity=0.381 Sum_probs=27.5 Q ss_pred CCCEEEEEEEEECCCCCEEEEE--ECCCCCCCCCHHHC Q ss_conf 2878798997836388231353--27897713022213 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVD--YGGNRHGFLPFLEI 74 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVd--iG~~k~gFL~~~ei 74 (723) .+..+.|+|+-...|-. ||. =+.++.-|+|+++| T Consensus 5 ~~~~~~G~Vk~fdkGfG--FI~~~d~~g~dvF~H~s~i 40 (79) T 2ytv_A 5 SSGLRRATVECVKDQFG--FINYEVGDSKKLFFHVKEV 40 (79) T ss_dssp CCSBCCEEEEECCSSEE--EESCCCSSSSSEEEETTTC T ss_pred CCCCEEEEEEEECCCCE--EEEECCCCCCEEEEEHHHC T ss_conf 67535899989338820--8881489983788895674 No 56 >>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, cytoplasm, DNA-binding, nucleus, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Homo sapiens} (A:1-81) Probab=64.87 E-value=8.2 Score=17.37 Aligned_cols=42 Identities=19% Similarity=0.226 Sum_probs=36.7 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC Q ss_conf 431013576999998730237999999998488799984787 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723) .-...+.+|.+.+.++.+.+-..|.+|++.+|+.|.|..+.. T Consensus 4 ~~~~~i~Vp~~~~g~iIG~~G~~I~~i~~~tg~~I~i~~~~~ 45 (81) T 2jzx_A 4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC 45 (81) T ss_dssp EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECCTT T ss_pred CEEEEEEECHHHCCEEECCCCHHHHHHHHHHCCCEEECCCCC T ss_conf 289999985345051488998779999998679557546665 No 57 >>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii OT3} (A:1-109) Probab=63.56 E-value=8.6 Score=17.20 Aligned_cols=42 Identities=21% Similarity=0.176 Sum_probs=37.3 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC Q ss_conf 431013576999998730237999999998488799984787 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723) ...+.+.+|.+.+.++.+..-..|.+|++.+|++|.|..++. T Consensus 33 ~~~~~i~Ip~~~~g~iIGk~G~~Ik~I~~~tg~~I~i~~~~~ 74 (109) T 2e3u_A 33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETG 74 (109) T ss_dssp CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTTTC T ss_pred CCCEEEECCHHHHHHHCCCCCHHHHHHHHHHCCCEEECCCCC T ss_conf 743798777687123007874889999999697743114567 No 58 >>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=63.31 E-value=7.9 Score=17.48 Aligned_cols=42 Identities=26% Similarity=0.244 Sum_probs=36.8 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC Q ss_conf 431013576999998730237999999998488799984787 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723) ...+.+.+|.....+|.+.+...|.+|++.+|++|.|-.+.. T Consensus 16 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~ 57 (104) T 2ctk_A 16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL 57 (104) T ss_dssp CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT T ss_pred CEEEEEEECHHHHHHHCCCCCCCHHHHHHHHCCEEEECCCCC T ss_conf 789999989899988518999517899997297799789999 No 59 >>1nz0_A Ribonuclease P protein component; endonuclease, RNAse, ALFA-beta sandwich, dimer, structural genomics, BSGC structure funded by NIH; HET: MSE; 1.20A {Thermotoga maritima} (A:) Probab=63.28 E-value=3.4 Score=20.00 Aligned_cols=70 Identities=23% Similarity=0.241 Sum_probs=46.3 Q ss_pred CCCCCEEEC--CCC----CCCCEEEECCCCHHHHHHHHHHHHHHH------CCCC--CEEEEEEECCCCCHHHHHHHHHH Q ss_conf 576523442--278----875124204688689999999998630------0258--71699850455757999999999 Q gi|254780751|r 202 LAGRYSVLM--PNT----SKGETISRKITNPVDRKNLKEIARGLE------VPAG--MGVILRTAGASRTKIEIKRDFEY 267 (723) Q Consensus 202 l~Gry~Vl~--P~~----~~~~~iSrki~~~~~r~~l~~~~~~~~------~~~~--~G~IiRT~a~~~~~~~l~~d~~~ 267 (723) +.|.|+++. |+. --|+.+|+|+...-.|.+++.++.+.. .+.+ +-+|++..+..++..++..++.. T Consensus 28 ~~~~~~~l~~~~~~~~~~R~g~~vsKKvg~AV~RNriKR~lRe~~R~~~~~l~~~~d~vii~~~~~~~~~~~~l~~~l~~ 107 (118) T 1nz0_A 28 LQNEYFVVLFRKNGXDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVRE 107 (118) T ss_dssp EECSSEEEEEEECSSSSCEEEECCCGGGCSHHHHHHHHHHHHHHHHHHTTTSCSSEEEEEEECHHHHHHGGGSCHHHHHH T ss_pred EECCCEEEEEECCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCHHHHHH T ss_conf 86897899998089998569999815455505789999999999998775178888799996432011331045999999 Q ss_pred HHHH Q ss_conf 9999 Q gi|254780751|r 268 LMRL 271 (723) Q Consensus 268 L~~~ 271 (723) |+.. T Consensus 108 ~l~k 111 (118) T 1nz0_A 108 KLLN 111 (118) T ss_dssp HHHH T ss_pred HHHH T ss_conf 9999 No 60 >>1dar_A EF-G, elongation factor G; ribosomal translocase, translational GTPase; HET: GDP; 2.40A {Thermus thermophilus HB8} (A:1-283) Probab=62.80 E-value=8.9 Score=17.11 Aligned_cols=74 Identities=16% Similarity=0.152 Sum_probs=60.3 Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 06999823755444555114799999999999999873103686389603347988889999999999731278728998 Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVG 457 (723) Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~ 457 (723) |+.+||.+.|-. ...+++.+|++.+++--|++|-=||.. ..+...+...+++.|......+++. T Consensus 104 ailVvda~~G~~---------------~qt~~~~~~~~~~~~p~ii~iNKiD~~-~~~~~~~~~~~~~~l~~~~~~~~~~ 167 (283) T 1dar_A 104 AIVVFDSSQGVE---------------PQSETVWRQAEKYKVPRIAFANKMDKT-GADLWLVIRTMQERLGARPVVMQLP 167 (283) T ss_dssp EEEEEETTTCSC---------------HHHHHHHHHHHHTTCCEEEEEECTTST-TCCHHHHHHHHHHTTCCCEEECEEE T ss_pred EEEEEECCCCCC---------------HHHHHHHHHHHHCCCCEEEEEECCCCC-CCCHHHHHHHHHHHHCCCEEEEECC T ss_conf 899997898862---------------779999999997499849998634645-5899999999999848962688657 Q ss_pred EECCCCEEEE Q ss_conf 6048614898 Q gi|254780751|r 458 AISNFGLLEM 467 (723) Q Consensus 458 ~it~lGLlEl 467 (723) -++..+...+ T Consensus 168 i~~~~~~~~~ 177 (283) T 1dar_A 168 IGREDTFSGI 177 (283) T ss_dssp ESCGGGCCEE T ss_pred CCCCCCEEEE T ss_conf 6667750058 No 61 >>3i2z_B RNA chaperone, negative regulator of CSPA transcription; beta barrel, DNA binding protein/transcription, cytoplasm, gene regulation; 1.10A {Salmonella typhimurium} PDB: 1mjc_A 3mef_A (B:) Probab=62.57 E-value=9 Score=17.08 Aligned_cols=38 Identities=18% Similarity=0.239 Sum_probs=31.8 Q ss_pred CCEEEEEEEEECCCCCEEEEEEC-CCCCCCCCHHHCCCC Q ss_conf 87879899783638823135327-897713022213712 Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYG-GNRHGFLPFLEIHPD 77 (723) Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG-~~k~gFL~~~ei~~~ 77 (723) ...|.|+|+...+.-.=-||.-. .+..-|+|++.+... T Consensus 3 ~~~~~G~Vk~f~~~kGyGFI~~~~g~~dif~h~s~l~~~ 41 (71) T 3i2z_B 3 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN 41 (71) T ss_dssp --CEEEEEEEEETTTTEEEEEETTCCCCEEEEGGGBCCS T ss_pred CCCCEEEEEEECCCCCEEEEEECCCCCCEEEEHHHHCCC T ss_conf 750047999990999848998689981299991880613 No 62 >>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} (A:1-79) Probab=61.12 E-value=9 Score=17.06 Aligned_cols=42 Identities=17% Similarity=0.136 Sum_probs=37.1 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC Q ss_conf 431013576999998730237999999998488799984787 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723) +..+.+.+|++...++.+.+-..+.+|++.+|+.|.|..++. T Consensus 3 ap~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~ 44 (79) T 1tua_A 3 KPRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENS 44 (79) T ss_dssp CCCEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTT T ss_pred CCEEEEECCHHHCCCCCCCCCHHHHHHHHHHCCEEEEECCCC T ss_conf 974998888887322668872769999999898589952655 No 63 >>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} (A:) Probab=60.45 E-value=9.7 Score=16.83 Aligned_cols=42 Identities=21% Similarity=0.265 Sum_probs=37.1 Q ss_pred CCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCC Q ss_conf 101357699999873023799999999848879998478778 Q gi|254780751|r 518 NIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELA 559 (723) Q Consensus 518 ~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~ 559 (723) .+.+.+|...+.++.+.+-..|.+|++.+|++|.|..+.... T Consensus 4 ~~~~~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~ 45 (87) T 1ec6_A 4 LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL 45 (87) T ss_dssp EEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBS T ss_pred EEEEEECHHHCCEEECCCCHHHHHHHHHCCCEEEEECCCCCC T ss_conf 999980976658569979754999999729789980577889 No 64 >>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=60.35 E-value=6.4 Score=18.12 Aligned_cols=50 Identities=12% Similarity=0.026 Sum_probs=42.8 Q ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEE Q ss_conf 31013576999998730237999999998488799984787788633897 Q gi|254780751|r 517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE 566 (723) Q Consensus 517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ie 566 (723) -...+.+|.....+|.+.+-..|.+|+..++++|.|-.++.-....+.|. T Consensus 17 ~~~~i~vp~~~~g~iIGk~G~~i~~I~~~tg~~I~i~~~~~~~~~~i~I~ 66 (95) T 2ctm_A 17 VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVT 66 (95) T ss_dssp CCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEE T ss_pred EEEEEEECHHHHHHHCCCCCCCHHHHHHHHCCEEEECCCCCCCCCEEEEE T ss_conf 78999999899977518898339999998298699687656665504676 No 65 >>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, cytoplasm, DNA-binding, nucleus, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Homo sapiens} (A:82-160) Probab=60.21 E-value=9.8 Score=16.81 Aligned_cols=49 Identities=10% Similarity=0.012 Sum_probs=41.6 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEE Q ss_conf 4310135769999987302379999999984887999847877886338 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFY 564 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~ 564 (723) .-...+.+|...+.++.+.+-..|.+|++.+|.+|.|..++.-..++-. T Consensus 7 ~~~~~i~Vp~~~vg~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~r~ 55 (79) T 2jzx_A 7 PVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERA 55 (79) T ss_dssp SEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEE T ss_pred EEEEEEECCHHHHHHEECCCCHHHHHHHHHHCCEEEECCCCCCCCCCEE T ss_conf 0468872788885022268985899999985996998888899998338 No 66 >>2r6f_A Excinuclease ABC subunit A; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, ATP-binding cassette, cytoplasm; HET: ADP; 3.20A {Geobacillus stearothermophilus 10} (A:715-792) Probab=59.97 E-value=3.1 Score=20.25 Aligned_cols=24 Identities=21% Similarity=0.530 Sum_probs=13.9 Q ss_pred CCCHHHHHC--CCCCCCCCEEEEECC Q ss_conf 630112100--236754653786061 Q gi|254780751|r 473 RSSVLESTT--KVCTYCKGAGYIRSQ 496 (723) Q Consensus 473 r~sl~e~~~--~~c~~c~g~g~~~~~ 496 (723) .+++....+ --||.|.|+|.|... T Consensus 29 ~~~~FSfNs~~G~C~~C~G~G~i~~~ 54 (78) T 2r6f_A 29 KKGRFSFNVKGGRCEACHGDGIIKIE 54 (78) T ss_dssp CTTTTCTTSTTTBCTTTTTCSEEEEC T ss_pred CCCCCCCCCCCCCEECCCCCCEEECC T ss_conf 64443412455410101376245134 No 67 >>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} (A:) Probab=59.53 E-value=10 Score=16.73 Aligned_cols=49 Identities=10% Similarity=0.005 Sum_probs=41.4 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEE Q ss_conf 4310135769999987302379999999984887999847877886338 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFY 564 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~ 564 (723) ...+.+.+|...+.+|.+..-..|.+|++.+|++|.|..+........+ T Consensus 14 ~~~~~i~ip~~~vg~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r 62 (94) T 1x4m_A 14 NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADK 62 (94) T ss_dssp CEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCE T ss_pred CEEEEEEECHHHHCCEECCCCHHHHHHHHHCCCEEEECCCCCCCCCCCE T ss_conf 7799999786750504897973599999872926997568878899830 No 68 >>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} (A:) Probab=58.76 E-value=8.3 Score=17.33 Aligned_cols=48 Identities=15% Similarity=0.167 Sum_probs=38.4 Q ss_pred CCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCC-CEEE Q ss_conf 10135769999987302379999999984887999847877886-3389 Q gi|254780751|r 518 NIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADK-LFYI 565 (723) Q Consensus 518 ~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~-~f~I 565 (723) .+.+.+|.+...++.+.+...|.+|++.+|++|.|..++.-... .+.| T Consensus 7 ~~~i~ip~~~~~~iIG~~G~~i~~I~~~tga~I~i~~~~~~~~~~~i~I 55 (82) T 1wvn_A 7 THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTI 55 (82) T ss_dssp EEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEE T ss_pred EEEEEECHHHCCEEECCCCCCHHHHHHHCCCEEEEECCCCCCCCEEEEE T ss_conf 9999988563343799598525899997595899954789998228999 No 69 >>2vf7_A UVRA2, excinuclease ABC, subunit A.; DNA-binding protein, nucleotide-binding, zinc-binding domain, SOS response, metal-binding; HET: ADP; 2.30A {Deinococcus radiodurans} PDB: 2vf8_A* (A:601-677) Probab=58.38 E-value=3.5 Score=19.94 Aligned_cols=14 Identities=29% Similarity=0.942 Sum_probs=9.9 Q ss_pred CCCCCCCEEEEECC Q ss_conf 36754653786061 Q gi|254780751|r 483 VCTYCKGAGYIRSQ 496 (723) Q Consensus 483 ~c~~c~g~g~~~~~ 496 (723) -||.|.|+|.+... T Consensus 40 rCp~C~G~G~i~~~ 53 (77) T 2vf7_A 40 RCEHCQGEGWVMVE 53 (77) T ss_dssp BCTTTTTCSEEEET T ss_pred CCEECCCCCCCCHH T ss_conf 41000146620002 No 70 >>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif; 2.00A {Homo sapiens} (A:) Probab=57.50 E-value=8.6 Score=17.20 Aligned_cols=43 Identities=21% Similarity=0.242 Sum_probs=37.1 Q ss_pred CCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCC Q ss_conf 1013576999998730237999999998488799984787788 Q gi|254780751|r 518 NIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELAD 560 (723) Q Consensus 518 ~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~ 560 (723) .+.+.+|...+..+.+.+-..|.+|++.+|.+|.|..+..... T Consensus 4 ~~~i~vp~~~vg~iIG~~G~~I~~I~~~tga~I~i~~~~~~~~ 46 (76) T 1dtj_A 4 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP 46 (76) T ss_dssp EEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCST T ss_pred EEEEEECHHHCCEEECCCCHHHHHHHHHCCCEEEEECCCCCCC T ss_conf 9999939887373599697259999987197999972888899 No 71 >>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=56.58 E-value=7 Score=17.83 Aligned_cols=50 Identities=14% Similarity=0.066 Sum_probs=41.1 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEE Q ss_conf 43101357699999873023799999999848879998478778863389 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYI 565 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~I 565 (723) .-.+.+.+|...+.+|.+.+-..|..|++.+++.|.|..+.....++-.| T Consensus 16 ~~~~~i~Vp~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~i 65 (97) T 2ctl_A 16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQI 65 (97) T ss_dssp TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEE T ss_pred CEEEEEEECHHHHHHCCCCCCCCHHHHHHHHCCEEEECCCCCCCCCCCEE T ss_conf 65799998989996613889741999999869869946877789876645 No 72 >>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} (A:) Probab=56.46 E-value=11 Score=16.39 Aligned_cols=47 Identities=15% Similarity=-0.060 Sum_probs=40.2 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCC Q ss_conf 43101357699999873023799999999848879998478778863 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKL 562 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~ 562 (723) ...+.+.+|.....+|.+.+-..|.+|++.+|++|.|..+.....+. T Consensus 14 ~~~~~i~vp~~~v~~iIGk~G~~ik~I~~~tga~I~i~~~~~~~~~~ 60 (104) T 1we8_A 14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLL 60 (104) T ss_dssp EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSS T ss_pred CEEEEEEECHHHHHHEECCCCCCHHHHHHHCCCEEEECCCCCCCCCC T ss_conf 88999998978760436929988119898659889978888888888 No 73 >>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} (A:1-81) Probab=56.46 E-value=9.1 Score=17.02 Aligned_cols=45 Identities=11% Similarity=0.097 Sum_probs=38.5 Q ss_pred CCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCC Q ss_conf 101357699999873023799999999848879998478778863 Q gi|254780751|r 518 NIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKL 562 (723) Q Consensus 518 ~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~ 562 (723) .+.+.+|...+.++.+..-..|.+|+..+++.|.|..+.....+. T Consensus 3 t~~i~Vp~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~~ 47 (81) T 2jvz_A 3 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV 47 (81) T ss_dssp EEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSS T ss_pred EEEEECCHHHHCEEECCCCHHHHHHHHHHCCEEEEECCCCCCCCC T ss_conf 899984736718468999876999999879889995054555566 No 74 >>2hqx_A P100 CO-activator tudor domain; human P100 tudor domain, proteolytic fragment, PSI, structural genomics; 1.42A {Homo sapiens} (A:64-246) Probab=56.16 E-value=6 Score=18.30 Aligned_cols=44 Identities=23% Similarity=0.483 Sum_probs=27.9 Q ss_pred CCCCEEEEEEEEECCC--CCEEEEEECCCCC-CCCCHHHCCCCCCCC Q ss_conf 4287879899783638--8231353278977-130222137121028 Q gi|254780751|r 38 IKGNIYLAKVTRVEPS--LQAAFVDYGGNRH-GFLPFLEIHPDYYQI 81 (723) Q Consensus 38 ~~GnIY~G~V~~V~p~--lqAAFVdiG~~k~-gFL~~~ei~~~y~~i 81 (723) .-|.-|.|+|++|.++ +.--|||+|..-. .+..+..+..++..+ T Consensus 14 ~d~~wyRa~V~~v~~~~~~~V~~iD~G~~~~v~~~~l~~~~~~~~~~ 60 (183) T 2hqx_A 14 VDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTR 60 (183) T ss_dssp TTSCEEEEEEEEEEETTEEEEEETTTCCEEEECGGGEECCCGGGSTT T ss_pred CCCCEEEEEEEEECCCCEEEEEEEECCCCEEEEHHHCCCCCHHHCCC T ss_conf 69979899999955898099999966981999989971578344214 No 75 >>1mhn_A SurviVal motor neuron protein; SMN, SMA, spinal muscular atrophy, RNA binding protein; 1.80A {Homo sapiens} (A:) Probab=55.97 E-value=8.3 Score=17.33 Aligned_cols=34 Identities=18% Similarity=0.373 Sum_probs=24.4 Q ss_pred CCCEEEEEEEEECCCC---CEEEEEECCCCCCCCCHHHC Q ss_conf 2878798997836388---23135327897713022213 Q gi|254780751|r 39 KGNIYLAKVTRVEPSL---QAAFVDYGGNRHGFLPFLEI 74 (723) Q Consensus 39 ~GnIY~G~V~~V~p~l---qAAFVdiG~~k~gFL~~~ei 74 (723) =|.-|.|+|..+.+.- .--|||||.- .-+++++| T Consensus 17 D~~wYRa~I~~i~~~~~~~~V~fvDyGn~--e~v~~~~l 53 (59) T 1mhn_A 17 DGCIYPATIASIDFKRETCVVVYTGYGNR--EEQNLSDL 53 (59) T ss_dssp TSCEEEEEEEEEETTTTEEEEEETTTTEE--EEEEGGGC T ss_pred CCCEEEEEEEEECCCCCEEEEEEECCCCE--EEEEHHHC T ss_conf 89898999999838899999999817999--99889997 No 76 >>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} (A:89-174) Probab=55.33 E-value=12 Score=16.26 Aligned_cols=48 Identities=8% Similarity=-0.005 Sum_probs=40.6 Q ss_pred CCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCC Q ss_conf 364310135769999987302379999999984887999847877886 Q gi|254780751|r 514 YTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADK 561 (723) Q Consensus 514 ~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~ 561 (723) .....+.+.+|.+.+.++.+..-..|.+|++.+|++|.|..+...... T Consensus 13 ~~~~~~~i~Ip~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~ 60 (86) T 1j4w_A 13 GGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNAD 60 (86) T ss_dssp ---CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSC T ss_pred CCCCCEEEEECHHHHHHEECCCCCHHHHHHHHHCCEEEECCCCCCCCC T ss_conf 566426999887875243789995799999973998997788888899 No 77 >>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} (A:82-164) Probab=55.14 E-value=6.1 Score=18.24 Aligned_cols=50 Identities=14% Similarity=0.046 Sum_probs=40.7 Q ss_pred CCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCC Q ss_conf 03643101357699999873023799999999848879998478778863 Q gi|254780751|r 513 QYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKL 562 (723) Q Consensus 513 ~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~ 562 (723) ......+.+.+|.....++.+.+-..|.+|++.+|+.|.|..++.-.... T Consensus 6 ~~~~~~~~i~vp~~~~g~iIG~~G~~I~~I~~~tga~I~i~~~~~~~~~~ 55 (83) T 2jvz_A 6 SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEK 55 (83) T ss_dssp TSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEE T ss_pred CCCCEEEEECCCHHHHHHHCCCCCCEEEHHHHHCCCEEEECCCCCCCCCE T ss_conf 44320245315587888751899842212466079679834888899843 No 78 >>3bdl_A Staphylococcal nuclease domain-containing protein 1; staphylococcal nuclease OB fold, tudor domain, cytoplasm, HOST-virus interaction, nucleus; HET: CIT; 1.90A {Homo sapiens} (A:410-468) Probab=54.78 E-value=7.5 Score=17.63 Aligned_cols=34 Identities=32% Similarity=0.683 Sum_probs=25.2 Q ss_pred CCCEEEEEEEEECCC--CCEEEEEECCCCCCCCCHHHC Q ss_conf 287879899783638--823135327897713022213 Q gi|254780751|r 39 KGNIYLAKVTRVEPS--LQAAFVDYGGNRHGFLPFLEI 74 (723) Q Consensus 39 ~GnIY~G~V~~V~p~--lqAAFVdiG~~k~gFL~~~ei 74 (723) -|..|.|+|..+.++ ..--|||||.-.. +++++| T Consensus 15 Dg~wYRa~I~~i~~~~~~~V~fvDyGn~~~--v~~~~l 50 (59) T 3bdl_A 15 DGEWYRARVEKVESPAKIHVFYIDYGNREV--LPSTRL 50 (59) T ss_dssp TSCEEEEEEEEEEETTEEEEEETTTCCEEE--ECGGGE T ss_pred CCCEEEEEEEEECCCCCEEEEEEECCCEEE--EEHHHE T ss_conf 897899999985689955899994486299--887992 No 79 >>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} (A:) Probab=54.49 E-value=11 Score=16.48 Aligned_cols=49 Identities=8% Similarity=-0.007 Sum_probs=39.6 Q ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEE Q ss_conf 3101357699999873023799999999848879998478778863389 Q gi|254780751|r 517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYI 565 (723) Q Consensus 517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~I 565 (723) ..+.+.+|.....++.+.+-..|.+|+..+|+.|.|..+.....+.-.+ T Consensus 85 ~~~~~~ip~~~~g~iIG~~G~~ik~I~~~tg~~I~i~~~~~~~~~~~~~ 133 (163) T 3krm_A 85 LETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVI 133 (163) T ss_dssp EEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEE T ss_pred CEEEECCCHHHHHHCCCCCCHHHHHHHHHHCCEEEECCCCCCCCCCEEE T ss_conf 1256339778786435799779999999849889988888899898048 No 80 >>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Probab=53.59 E-value=9.1 Score=17.03 Aligned_cols=49 Identities=22% Similarity=0.154 Sum_probs=39.4 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEE Q ss_conf 431013576999998730237999999998488799984787788633897 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE 566 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ie 566 (723) .-...+.+|.....+|.+.+-..|.+|++.++++|.|..+.. ...+.|. T Consensus 9 ~~~~~i~vp~~~~~~iIGk~G~~i~~I~~~tg~~I~i~~~~~--~~~i~I~ 57 (83) T 2dgr_A 9 QTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK--EPVFAVT 57 (83) T ss_dssp SEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSSS--CCEEEEE T ss_pred EEEEEEEECHHHHHHEECCCCCCHHHHHHHHCCEEEECCCCC--CCEEEEC T ss_conf 089999999787503389689129999998799899657888--5489964 No 81 >>2d9t_A Tudor domain-containing protein 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} (A:) Probab=53.50 E-value=8.8 Score=17.14 Aligned_cols=34 Identities=26% Similarity=0.404 Sum_probs=25.5 Q ss_pred CCCEEEEEEEEECCC---CCEEEEEECCCCCCCCCHHHC Q ss_conf 287879899783638---823135327897713022213 Q gi|254780751|r 39 KGNIYLAKVTRVEPS---LQAAFVDYGGNRHGFLPFLEI 74 (723) Q Consensus 39 ~GnIY~G~V~~V~p~---lqAAFVdiG~~k~gFL~~~ei 74 (723) -|..|.|+|..|.+. ..--|||||.. ..+++++| T Consensus 23 d~~wyRa~I~~i~~~~~~~~V~fvDyG~~--e~v~~~~l 59 (78) T 2d9t_A 23 DNKFYRAEVEALHSSGMTAVVKFTDYGNY--EEVLLSNI 59 (78) T ss_dssp TCCEEEEEEEEECSSSSEEEEEETTTTEE--EEEEGGGE T ss_pred CCCEEEEEEEEECCCCCEEEEEEEECCCE--EEEEHHHE T ss_conf 99699999999648999899999968985--99887990 No 82 >>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein/RNA complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* (A:) Probab=53.24 E-value=13 Score=16.04 Aligned_cols=49 Identities=8% Similarity=0.039 Sum_probs=38.5 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEE Q ss_conf 4310135769999987302379999999984887999847877886338 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFY 564 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~ 564 (723) ...+.+.+|.....++.+.+-..+.+|++.+|++|.|..++......-+ T Consensus 103 ~~~~~i~Vp~~~~g~iIG~~G~~i~~i~~~tg~~I~i~~~~~~~~~~~r 151 (178) T 2anr_A 103 ANQVKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPDGINLQNR 151 (178) T ss_dssp GGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEE T ss_pred CEEEEEEECHHHHHHEECCCCCCHHHHHHHHCCEEEEECCCCCCCCCCE T ss_conf 4479997176871012268995569988863987998078888899830 No 83 >>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein/DNA complex; 1.70A {Homo sapiens} (A:) Probab=51.68 E-value=13 Score=15.87 Aligned_cols=42 Identities=19% Similarity=0.233 Sum_probs=36.2 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC Q ss_conf 431013576999998730237999999998488799984787 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723) .-.+.+.+|.....++.+.+-..|..|++.+|++|.|..+.+ T Consensus 4 ~~~~~i~vp~~~~g~iIG~~G~~Ik~i~~~tg~~I~i~~~~~ 45 (73) T 2axy_A 4 TLTIRLLXHGKEVGSIIGKKGESVKKXREESGARINISEGNC 45 (73) T ss_dssp CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCC T ss_pred CEEEEEEECHHHCCEEECCCCCCHHHHHHHHCCEEEECCCCC T ss_conf 489999988788195899998009999998699699748999 No 84 >>2elf_A Protein translation elongation factor 1A; tRNA, pyrrolysine, structural genomics, NPPSFA; HET: CIT; 1.70A {Methanosarcina mazei} (A:1-190) Probab=51.62 E-value=13 Score=15.87 Aligned_cols=70 Identities=16% Similarity=0.036 Sum_probs=55.4 Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHH-CCCCEEE Q ss_conf 069998237554445551147999999999999998731036863896033479888899999999997312-7872899 Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKK-DRARVQV 456 (723) Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~-D~~~~~v 456 (723) |+.+||.+.|-. +-..++.++.++...-.||+|-=||+.+......+.+.+++.+.. ....+.| T Consensus 87 ailVvda~~g~~---------------~~t~~~~~~~~~~~~p~Iv~iNKiD~~~~~~~~~~~~~~~~~~~~~~~~~~pi 151 (190) T 2elf_A 87 AVLCIPPQGLDA---------------HTGECIIALDLLGFKHGIIALTRSDSTHXHAIDELKAKLKVITSGTVLQDWEC 151 (190) T ss_dssp EEEEECTTCCCH---------------HHHHHHHHHHHTTCCEEEEEECCGGGSCHHHHHHHHHHHHHHTTTSTTTTCEE T ss_pred EEEEECCCCCCH---------------HHHHHHHHHHHCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCE T ss_conf 999941554322---------------56789998874156641231245543214443456544555402655445650 Q ss_pred EEECCC Q ss_conf 860486 Q gi|254780751|r 457 GAISNF 462 (723) Q Consensus 457 ~~it~l 462 (723) +++|.+ T Consensus 152 vpiSA~ 157 (190) T 2elf_A 152 ISLNTN 157 (190) T ss_dssp EECCCC T ss_pred EEEECC T ss_conf 366555 No 85 >>1nlt_A Protein YDJ1, mitochondrial protein import protein MAS5; beta-strands, chaperone, heat shock, mitochondrion; 2.70A {Saccharomyces cerevisiae} (A:21-122) Probab=51.60 E-value=5.9 Score=18.33 Aligned_cols=48 Identities=8% Similarity=0.017 Sum_probs=27.5 Q ss_pred CEEEEEECCCCEEEEECCCCCC-CHHHHH--CCCCCCCCCEEEEECCHHHH Q ss_conf 2899860486148985156663-011210--02367546537860611468 Q gi|254780751|r 453 RVQVGAISNFGLLEMSRQRIRS-SVLEST--TKVCTYCKGAGYIRSQSSVA 500 (723) Q Consensus 453 ~~~v~~it~lGLlEltRkR~r~-sl~e~~--~~~c~~c~g~g~~~~~~~~~ 500 (723) .+.....+.+|.+++...--.- .-...+ ..+|+.|+|.|++....++. T Consensus 45 ~~~~~~~~~~g~~q~~~~c~~C~G~G~~~~~~~~C~~C~G~g~v~~~~~~~ 95 (102) T 1nlt_A 45 IKFVTRQMGPMIQRFQTECDVCHGTGDIIDPKDRCKSCNGKKVENERKILE 95 (102) T ss_dssp CEEEEEESSSEEEEEECSCTTCSSSSSCCCTTSBCSSSTTSCEEEEEEEEE T ss_pred EEEEEEECCCCCEEEEEECCCCCCCCEEECCCCCCCCCCCCEEEEEEEEEE T ss_conf 699887627762155665677789764834677650037955898889999 No 86 >>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} (A:) Probab=50.92 E-value=3.8 Score=19.68 Aligned_cols=16 Identities=25% Similarity=0.752 Sum_probs=7.2 Q ss_pred HHCCCCCCCCCEEEEE Q ss_conf 1002367546537860 Q gi|254780751|r 479 STTKVCTYCKGAGYIR 494 (723) Q Consensus 479 ~~~~~c~~c~g~g~~~ 494 (723) .+..+|+.|+|+|.+. T Consensus 48 ~~~~~C~~C~G~G~~i 63 (79) T 1exk_A 48 AVQQTCPHCQGRGTLI 63 (79) T ss_dssp EEEEECTTTTTSSEEC T ss_pred EEEEECCCCCCEEEEC T ss_conf 7457998687672481 No 87 >>1g5v_A SurviVal motor neuron protein 1; mRNA processing, translation; NMR {Homo sapiens} (A:) Probab=50.84 E-value=9.7 Score=16.84 Aligned_cols=35 Identities=17% Similarity=0.343 Sum_probs=26.3 Q ss_pred CCCCEEEEEEEEECCC---CCEEEEEECCCCCCCCCHHHC Q ss_conf 4287879899783638---823135327897713022213 Q gi|254780751|r 38 IKGNIYLAKVTRVEPS---LQAAFVDYGGNRHGFLPFLEI 74 (723) Q Consensus 38 ~~GnIY~G~V~~V~p~---lqAAFVdiG~~k~gFL~~~ei 74 (723) .-|..|.|+|..+.++ .+--|||||.. ..++.++| T Consensus 23 ~d~~wyRa~I~~~~~~~~~~~V~fvDyG~~--e~V~~~~l 60 (88) T 1g5v_A 23 EDGCIYPATIASIDFKRETCVVVYTGYGNR--EEQNLSDL 60 (88) T ss_dssp TTCCEEEEEEEEEETTTTEEEEEETTTCCE--EEEEGGGC T ss_pred CCCCEEEEEEEEEEECCCCEEEEEECCCCH--HHHHHHHH T ss_conf 578471356777773156079998036856--66317888 No 88 >>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} (A:1-88) Probab=50.14 E-value=14 Score=15.71 Aligned_cols=48 Identities=17% Similarity=0.023 Sum_probs=39.7 Q ss_pred CCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCC-EEE Q ss_conf 101357699999873023799999999848879998478778863-389 Q gi|254780751|r 518 NIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKL-FYI 565 (723) Q Consensus 518 ~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~-f~I 565 (723) .+.+.+|.+...+|.+.+-..|.+|++.+|+.|.|..+..-.... +.| T Consensus 4 ~~~i~vp~~~vg~iIG~~G~~i~~i~~~tg~~I~i~~~~~~~~~~~v~i 52 (88) T 1j4w_A 4 MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQI 52 (88) T ss_dssp EEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEE T ss_pred EEEEECCHHHEEEEECCCCHHHHHHHHHHCCEEEEECCCCCCCCEEEEE T ss_conf 6999808346005799897799999997698999971688887406885 No 89 >>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=49.72 E-value=14 Score=15.67 Aligned_cols=41 Identities=12% Similarity=-0.001 Sum_probs=36.8 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECC Q ss_conf 43101357699999873023799999999848879998478 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGI 556 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~ 556 (723) ...+.+.+|++...++.+.+-..+.+|++.+|++|.|..+. T Consensus 14 ~~~~~i~Vp~~~~~~iIGk~G~~Ik~I~~~tga~I~i~~~~ 54 (91) T 2cpq_A 14 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED 54 (91) T ss_dssp SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT T ss_pred CEEEEEEECHHHHHHHCCCCCHHHHHHHHHCCCEEEECCCC T ss_conf 60699998989987881896089999999629779630577 No 90 >>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} (A:) Probab=48.71 E-value=15 Score=15.56 Aligned_cols=50 Identities=16% Similarity=0.193 Sum_probs=40.1 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCC-EEE Q ss_conf 43101357699999873023799999999848879998478778863-389 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKL-FYI 565 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~-f~I 565 (723) .-.+.+.+|.....++.+.+-..|.+|++.+|..|.|..++.-.... +.| T Consensus 4 ~~~~~i~vp~~~~g~iIG~~G~~I~~I~~~tga~I~i~~~~~~~~~~~i~I 54 (76) T 2p2r_A 4 TTSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTI 54 (76) T ss_dssp CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEE T ss_pred CEEEEEEECHHHCCEEECCCCCHHHHHHHHCCCEEEECCCCCCCCCEEEEE T ss_conf 478999998676584599598528999987697899707899999458999 No 91 >>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} (A:148-235) Probab=48.48 E-value=9.7 Score=16.83 Aligned_cols=40 Identities=18% Similarity=0.120 Sum_probs=34.8 Q ss_pred CCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC Q ss_conf 1013576999998730237999999998488799984787 Q gi|254780751|r 518 NIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723) Q Consensus 518 ~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723) ...+.+|++....+.+.+-..+.+|++.++++|.|..+.. T Consensus 2 t~~i~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~ 41 (88) T 2z0s_A 2 GKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGR 41 (88) T ss_dssp SEEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETTTE T ss_pred CEEEEECHHHHHHHHCCCHHHHHHHHHCCCEEEEEECCCE T ss_conf 1796526688323025752268877507785999918908 No 92 >>2equ_A PHD finger protein 20-like 1; tudor domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Probab=48.17 E-value=15 Score=15.51 Aligned_cols=35 Identities=20% Similarity=0.148 Sum_probs=26.4 Q ss_pred CCCEEEEEEEEECCCCC-EEEEEECCCCCCCCCHHHCC Q ss_conf 28787989978363882-31353278977130222137 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQ-AAFVDYGGNRHGFLPFLEIH 75 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lq-AAFVdiG~~k~gFL~~~ei~ 75 (723) =|.-|.|+|+.|.++-. ..|+|||.... +++.+|. T Consensus 22 Dg~~Yra~I~~v~~~~~~~v~fDyGn~e~--V~~~~i~ 57 (74) T 2equ_A 22 DCRYYPAKIEAINKEGTFTVQFYDGVIRC--LKRMHIK 57 (74) T ss_dssp SSSEEEEEEEEESTTSSEEEEETTSCEEE--ECGGGEE T ss_pred CCCEEEEEEEEECCCCEEEEEEECCCEEE--ECHHHCE T ss_conf 99899689999867988999997299799--8689987 No 93 >>1x65_A UNR protein; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding, QB fold, greek- KEY topology; NMR {Homo sapiens} (A:) Probab=48.16 E-value=15 Score=15.51 Aligned_cols=35 Identities=14% Similarity=0.270 Sum_probs=27.2 Q ss_pred CCCEEEEEEEEECCCCCEEEEEE-CCCCCCCCCHHHCC Q ss_conf 28787989978363882313532-78977130222137 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDY-GGNRHGFLPFLEIH 75 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdi-G~~k~gFL~~~ei~ 75 (723) ...-|.|+|+..-.|-. ||.- ..++.-|+|++++. T Consensus 5 ~~~r~~G~Vk~~~kGfG--FI~~~~~~~diFfH~s~~~ 40 (89) T 1x65_A 5 SSGREMGVIAAMRDGFG--FIKCVDRDVRMFFHFSEIL 40 (89) T ss_dssp CCCCEEEEEEECCTTBC--EEEESSSSSCCCCBTTGGG T ss_pred CCCCEEEEEEEECCCEE--EEECCCCCCCEEEEHHHCC T ss_conf 78857799999708714--7862899940899934605 No 94 >>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} (A:) Probab=47.38 E-value=11 Score=16.43 Aligned_cols=45 Identities=16% Similarity=0.143 Sum_probs=38.1 Q ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCC Q ss_conf 310135769999987302379999999984887999847877886 Q gi|254780751|r 517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADK 561 (723) Q Consensus 517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~ 561 (723) -.+.+.+|.+...++.+.+-..|.+|++.+|+.|.|..+...... T Consensus 7 ~~~~i~vp~~~~~~iIG~~G~~i~~I~~~tga~I~i~~~~~~~~~ 51 (82) T 1zzk_A 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSED 51 (82) T ss_dssp EEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSE T ss_pred EEEEEEECHHHCCEEECCCCCHHHHHHHHCCCEEEECCCCCCCCC T ss_conf 789999886762815996982389999754987996478899984 No 95 >>2bh8_A 1B11; transcription, molecular evolution, unique architecture, activator, transcription regulation, phosphorylation; 1.9A {Escherichia coli} (A:1-71) Probab=45.48 E-value=17 Score=15.23 Aligned_cols=46 Identities=11% Similarity=0.126 Sum_probs=35.9 Q ss_pred CCCCCCCCEEEEEEEEECCCCCEEEEEECC-CCCCCCCHHHCCCCCC Q ss_conf 346042878798997836388231353278-9771302221371210 Q gi|254780751|r 34 HKKQIKGNIYLAKVTRVEPSLQAAFVDYGG-NRHGFLPFLEIHPDYY 79 (723) Q Consensus 34 ~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~-~k~gFL~~~ei~~~y~ 79 (723) ......+.+|.|+|+---..=.--||.-.. +..-|+|++.|..++| T Consensus 8 ~~~~~~~~~~~G~Vk~fn~~kGfGFI~~~d~~~dvFvH~s~i~~~g~ 54 (71) T 2bh8_A 8 HGSRLQSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAA 54 (71) T ss_dssp --------CEEEEEEEEEGGGTEEEEEESSSSCEEEEECCCSCSSSC T ss_pred CCCCCCCCCEEEEEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCC T ss_conf 42304468458889998689987998836899504666300121220 No 96 >>1m1q_A Small tetraheme cytochrome C; atomic structure of oxidized tetraheme cytochrome C, electron transport; HET: HEM; 0.97A {Shewanella oneidensis mr-1} (A:) Probab=44.44 E-value=7 Score=17.83 Aligned_cols=14 Identities=7% Similarity=0.003 Sum_probs=5.6 Q ss_pred HCCCCCCCCCEEEE Q ss_conf 00236754653786 Q gi|254780751|r 480 TTKVCTYCKGAGYI 493 (723) Q Consensus 480 ~~~~c~~c~g~g~~ 493 (723) +..+|+.|+|+|.+ T Consensus 57 ~~~~C~~C~G~G~~ 70 (91) T 1m1q_A 57 VCADCHAVHDMNVG 70 (91) T ss_dssp CGGGTCCTTTSBTT T ss_pred CCCCCCCCCCCCCC T ss_conf 21558777676874 No 97 >>2eqk_A Tudor domain-containing protein 4; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Probab=44.39 E-value=15 Score=15.62 Aligned_cols=34 Identities=12% Similarity=0.117 Sum_probs=24.2 Q ss_pred CCCEEEEEEEEECCC--CCEEEEEECCCCCCCCCHHHC Q ss_conf 287879899783638--823135327897713022213 Q gi|254780751|r 39 KGNIYLAKVTRVEPS--LQAAFVDYGGNRHGFLPFLEI 74 (723) Q Consensus 39 ~GnIY~G~V~~V~p~--lqAAFVdiG~~k~gFL~~~ei 74 (723) -|.-|.|+|..+.++ ..--|||||..-. ++.++| T Consensus 35 d~~wyRa~I~~~~~~~~~~V~fvD~G~~~~--v~~~~l 70 (85) T 2eqk_A 35 KNQWRRGQIIRMVTDTLVEVLLYDVGVELV--VNVDCL 70 (85) T ss_dssp SCCEEEEEEEEECSSSEEEEECTTTCCEEE--EETTTE T ss_pred CCEEEEEEEEEECCCCCEEEEEEEECCEEE--ECHHHH T ss_conf 998867899997189968999981010587--517876 No 98 >>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} (A:) Probab=43.54 E-value=17 Score=15.08 Aligned_cols=46 Identities=15% Similarity=0.081 Sum_probs=38.6 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCC Q ss_conf 4310135769999987302379999999984887999847877886 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADK 561 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~ 561 (723) ...+.+.+|...+.++.+.+-..|.+|++.++++|.|..+..-... T Consensus 10 ~~t~~i~Ip~~~vg~iIG~~G~~I~~i~~~tg~~I~i~~~~~~~~~ 55 (106) T 2hh3_A 10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE 55 (106) T ss_dssp --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSE T ss_pred CCEEEEEECHHHCCEEECCCCCCHHHHHHHCCEEEEEEECCCCCCC T ss_conf 8749999686767857998973279998758618999856899983 No 99 >>1vef_A Acetylornithine/acetyl-lysine aminotransferase; PLP, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: PLP; 1.35A {Thermus thermophilus} (A:25-57,A:307-395) Probab=43.05 E-value=18 Score=14.98 Aligned_cols=71 Identities=10% Similarity=0.093 Sum_probs=44.6 Q ss_pred EEEECCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-------------HHCCCCEEEEECCCCCCHHHHH Q ss_conf 998328806999823755444555114799999999999999873-------------1036863896033479888899 Q gi|254780751|r 371 VIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLR-------------LRDLAGLIVVDFIDMEEKKNNR 437 (723) Q Consensus 371 lvIe~TEALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlR-------------LRnlgGiIvIDFIdM~~~~~~~ 437 (723) +||++-|-.+..|+|.=+|.-- -....+|++-|.++..+++ .|+.|-|+-|||-. ....+ T Consensus 5 ~~~~~g~g~~l~d~~g~~ylD~----~~g~~vnle~v~~~g~~l~~~L~~l~~~~v~~vRg~Glm~giel~~---~~~~~ 77 (122) T 1vef_A 5 LLIVRGQGARVWDAEGNEYIDC----VGGYGVAWERAAELGPWFMEKLRAIPSPKIREVRGMGLMVGLELKE---KAAPY 77 (122) T ss_dssp SCEEEEEBTEEEETTSCEEEES----SHHHHTCHHHHHHHHHHHHHHHHTSCCTTEEEEEEETTEEEEEESS---CSHHH T ss_pred CEEEEEECCEEEECCCCEEEEC----CCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECC---CCHHH T ss_conf 3399836699997997999985----6078766147999748999999961798579852454899999717---75689 Q ss_pred HHHHHHHHHHH Q ss_conf 99999999731 Q gi|254780751|r 438 SVEKKLKESLK 448 (723) Q Consensus 438 ~v~~~l~~~l~ 448 (723) .+...++..+- T Consensus 78 i~~~~~~~Gll 88 (122) T 1vef_A 78 IARLEKEHRVL 88 (122) T ss_dssp HHHHHHHHCEE T ss_pred HHHHHHHCCCE T ss_conf 99999978976 No 100 >>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} (A:) Probab=42.64 E-value=18 Score=14.94 Aligned_cols=47 Identities=9% Similarity=0.085 Sum_probs=39.6 Q ss_pred CCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCC Q ss_conf 64310135769999987302379999999984887999847877886 Q gi|254780751|r 515 TAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADK 561 (723) Q Consensus 515 ~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~ 561 (723) ....+.+.+|.....++.+.+-..|.+|++.+++.|.|..+..-... T Consensus 13 ~~~~~~i~ip~~~vg~iIG~~G~~I~~I~~~tga~I~i~~~~~~~~~ 59 (92) T 1x4n_A 13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPE 59 (92) T ss_dssp CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSE T ss_pred CCEEEEEEECHHHCCEEECCCCHHHHHHHHHCCCEEEECCCCCCCCC T ss_conf 85899999996752703997973189999970968998788999983 No 101 >>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} (A:) Probab=41.01 E-value=11 Score=16.41 Aligned_cols=41 Identities=15% Similarity=0.211 Sum_probs=35.6 Q ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC Q ss_conf 31013576999998730237999999998488799984787 Q gi|254780751|r 517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723) Q Consensus 517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723) -...+.+|.....++.+.+-..+.+|++.+|++|.|..+.. T Consensus 5 ~t~~i~Vp~~~~~~iIG~~G~~I~~I~~~tg~~I~i~~~~~ 45 (71) T 1vig_A 5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE 45 (71) T ss_dssp EEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCS T ss_pred EEEEEEECHHHHHHCCCCCCHHHHHHHHHHCCEEEECCCCC T ss_conf 89999999887423279999029999997099899689878 No 102 >>2dgy_A MGC11102 protein; EIF-1A, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Probab=40.54 E-value=17 Score=15.18 Aligned_cols=22 Identities=27% Similarity=0.338 Sum_probs=14.4 Q ss_pred CCCCCCEEEEEEECCCCCCCCC Q ss_conf 0688857999840333234564 Q gi|254780751|r 173 VIKNRQILLVQIVKEERGNKGA 194 (723) Q Consensus 173 ~lk~gq~ilVQV~ke~~~~Kga 194 (723) -|++|+.|||+...+....||- T Consensus 53 WIk~GD~VlV~~~~~~~k~k~d 74 (111) T 2dgy_A 53 WIKRGDFLIVDPIEEGEKVKAE 74 (111) T ss_dssp CCCSSCEEEEEECSSCSSCCEE T ss_pred EEECCCEEEEEEHHHCCCCEEE T ss_conf 7945999999873546873499 No 103 >>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} (A:) Probab=40.12 E-value=20 Score=14.68 Aligned_cols=52 Identities=15% Similarity=0.100 Sum_probs=41.6 Q ss_pred CCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCC-EEE Q ss_conf 3643101357699999873023799999999848879998478778863-389 Q gi|254780751|r 514 YTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKL-FYI 565 (723) Q Consensus 514 ~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~-f~I 565 (723) .....+.+.+|...+.+|.+.+-..|.+|++.+|++|.|..+..-..+. +.| T Consensus 11 ~~~~~~~i~Vp~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~~~v~i 63 (89) T 1j5k_A 11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 63 (89) T ss_dssp CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEE T ss_pred CCEEEEEEEECHHHCCEEECCCCHHHHHHHHHHCCEEEECCCCCCCCCCEEEE T ss_conf 98489999998675682499797189999998799899747889998536999 No 104 >>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I KH domains, fragIle X mental retardation protein, RNA binding protein; 1.90A {Homo sapiens} PDB: 2fmr_A (A:1-64) Probab=38.88 E-value=21 Score=14.55 Aligned_cols=40 Identities=13% Similarity=-0.027 Sum_probs=35.4 Q ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECC Q ss_conf 3101357699999873023799999999848879998478 Q gi|254780751|r 517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGI 556 (723) Q Consensus 517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~ 556 (723) ....+.+|++...++.+..-..|.+|.+.+|++|.+..++ T Consensus 4 ~t~~i~Vp~~~vg~iIGkgG~~I~~I~~~tga~I~i~d~~ 43 (64) T 2qnd_A 4 FHEQFIVREDLXGLAIGTHGANIQQARKVPGVTAIDLDED 43 (64) T ss_dssp CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEETT T ss_pred EEEEEEECHHHHHHHHCCCCHHHHHHHHHCCEEEEECCCC T ss_conf 0799999988986655876088999998567368723787 No 105 >>2ywe_A GTP-binding protein LEPA; G domain, beta-barrel, ferredoxin-like domain, structural genomics, NPPSFA; 2.05A {Aquifex aeolicus VF5} PDB: 2ywf_A* 2ywg_A* 2ywh_A* (A:1-187) Probab=37.76 E-value=22 Score=14.43 Aligned_cols=71 Identities=24% Similarity=0.293 Sum_probs=54.0 Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 06999823755444555114799999999999999873103686389603347988889999999999731278728998 Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVG 457 (723) Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~ 457 (723) ||.+||.+.|-. ..-.++.+|++..++-=|+||-=||.. ..+...+.+.+++.++.+.+.+... T Consensus 100 allvvda~~g~~---------------~~t~~~~~~~~~~~~p~ivviNKiD~~-~~~~~~~~~~~~~~~~~~~~~ii~i 163 (187) T 2ywe_A 100 ALLLIDASQGIE---------------AQTVANFWKAVEQDLVIIPVINKIDLP-SADVDRVKKQIEEVLGLDPEEAILA 163 (187) T ss_dssp EEEEEETTTBCC---------------HHHHHHHHHHHHTTCEEEEEEECTTST-TCCHHHHHHHHHHTSCCCGGGCEEC T ss_pred EEEEEECCCCCC---------------CCHHHHHHHHHHCCCCEEEEEECCCCC-CCCHHHHHHHHHHHHCCCCHHEEEE T ss_conf 999995899865---------------012999999998799779999896578-7799999999999868992352676 Q ss_pred -EECCCCE Q ss_conf -6048614 Q gi|254780751|r 458 -AISNFGL 464 (723) Q Consensus 458 -~it~lGL 464 (723) ..+..|+ T Consensus 164 SA~~g~gi 171 (187) T 2ywe_A 164 SAKEGIGI 171 (187) T ss_dssp BTTTTBSH T ss_pred ECCCCCCH T ss_conf 62058498 No 106 >>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} (A:) Probab=36.32 E-value=11 Score=16.57 Aligned_cols=43 Identities=2% Similarity=0.059 Sum_probs=36.9 Q ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCC Q ss_conf 3101357699999873023799999999848879998478778 Q gi|254780751|r 517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELA 559 (723) Q Consensus 517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~ 559 (723) -.+.+.+|.....+|.+.+-..|.+|++.++++|.|..+.... T Consensus 7 ~t~~i~Vp~~~~g~iIGk~G~~ik~I~~~tg~~I~i~~~~~~~ 49 (107) T 2hh2_A 7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPN 49 (107) T ss_dssp CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTT T ss_pred CEEEEEECHHHCCEEECCCCHHHHHHHHHCCEEEEEECCCCCC T ss_conf 7699998956502247939703888752437399983267888 No 107 >>1sff_A 4-aminobutyrate aminotransferase; enzyme complexes; HET: IK2; 1.90A {Escherichia coli} (A:22-53,A:321-426) Probab=36.30 E-value=23 Score=14.28 Aligned_cols=78 Identities=12% Similarity=0.282 Sum_probs=49.9 Q ss_pred EEEECCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH---------------HHCCCCEEEEECCCCCCHHH Q ss_conf 998328806999823755444555114799999999999999873---------------10368638960334798888 Q gi|254780751|r 371 VIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLR---------------LRDLAGLIVVDFIDMEEKKN 435 (723) Q Consensus 371 lvIe~TEALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlR---------------LRnlgGiIvIDFIdM~~~~~ 435 (723) +||++-|-.+..|+|--+|.-- -..+.+|+|-+.++..+|+ .|+.|-++-|+|.+-+..+. T Consensus 4 ~~~~~~~g~~~~d~~g~ryld~----~~g~~~~~e~v~~~g~~l~~~L~~l~~~~p~V~dvRG~GLm~~iel~~~~~~~~ 79 (138) T 1sff_A 4 IFADRAENCRVWDVEGREYLDF----AGGIAVLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNK 79 (138) T ss_dssp EEEEEEEBTEEEETTCCEEEES----SHHHHTCHHHHHHHHHHHHHHHHHHHHTCTTEEEEEEETTEEEEEEBGGGCTTS T ss_pred CEEEEEECCEEEECCCCEEEEC----CCCHHHHCHHHHCCHHHHHHHHHHHHHHCCCEEEEEEECEEEEEEEECCCCCCC T ss_conf 4299976399996997999985----728886401221001234566678898689637897445499999942666677 Q ss_pred -HHHHHHHHHHHHHHCCC Q ss_conf -99999999997312787 Q gi|254780751|r 436 -NRSVEKKLKESLKKDRA 452 (723) Q Consensus 436 -~~~v~~~l~~~l~~D~~ 452 (723) ...+...+...+..-.. T Consensus 80 ~~~~~~~~i~~~~~~~Gv 97 (138) T 1sff_A 80 PDAKLTAEIVARARDKGL 97 (138) T ss_dssp BCHHHHHHHHHHHHHTTE T ss_pred CCHHHHHHHHHHHHHCCC T ss_conf 569999999999997898 No 108 >>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=36.27 E-value=7.4 Score=17.65 Aligned_cols=41 Identities=7% Similarity=0.133 Sum_probs=35.7 Q ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC Q ss_conf 31013576999998730237999999998488799984787 Q gi|254780751|r 517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723) Q Consensus 517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723) -.+.+.+|.....+|.+.+...|.+|++.+|+.|.|..+.. T Consensus 17 ~~~~i~Vp~~~~g~iIG~~G~~I~~I~~~tg~~I~i~~~~~ 57 (94) T 2cte_A 17 ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD 57 (94) T ss_dssp EEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTS T ss_pred EEEEEEECHHHHHHHCCCCCHHHHHHHHHHCCEEEECCCCC T ss_conf 78999999899967608896519999998298899789999 No 109 >>2gez_B L-asparaginase beta subunit; isoaspartyl aminopeptidase, NTN-hydrolase, autoproteolysis, taspase, sodium binding; 2.60A {Lupinus luteus} (B:1-112) Probab=34.51 E-value=21 Score=14.47 Aligned_cols=26 Identities=8% Similarity=0.165 Sum_probs=11.1 Q ss_pred HHHHHHHHHHCCCCCCCCCCEEEEEC Q ss_conf 69999999842221436786499832 Q gi|254780751|r 350 GIEVQLDSLHQTEVTLPSRGYVIINQ 375 (723) Q Consensus 350 ~ie~~i~~~~~~~V~L~sGG~lvIe~ 375 (723) ..++.++.++++...--.||-|+++. T Consensus 76 ~~~~A~~~~i~~~~~~~~~G~Ia~~~ 101 (112) T 2gez_B 76 SLKEAADFVIHERTPKGTVGLIAVSA 101 (112) T ss_dssp CHHHHHHHHHHTSSCTTSEEEEEEET T ss_pred CHHHHHHHHHHHHCCCCCEEEEEECC T ss_conf 98999999998407578607999927 No 110 >>2ctt_A DNAJ homolog subfamily A member 3; ZING finger, beta-hairpin, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=33.31 E-value=14 Score=15.79 Aligned_cols=16 Identities=31% Similarity=0.785 Sum_probs=6.2 Q ss_pred HCCCCCCCCCEEEEEC Q ss_conf 0023675465378606 Q gi|254780751|r 480 TTKVCTYCKGAGYIRS 495 (723) Q Consensus 480 ~~~~c~~c~g~g~~~~ 495 (723) ...+|+.|+|.|+++. T Consensus 80 ~~~~C~~C~G~G~v~~ 95 (104) T 2ctt_A 80 IISPCVVCRGAGQAKQ 95 (104) T ss_dssp CSSCCSSSSSCSEECC T ss_pred CCCCCCCCCCCEEEEE T ss_conf 7898989889606873 No 111 >>2k3v_A Tetraheme cytochrome C-type; multihaem cytochromes, redox proteins, electron transport, iron, metal-binding, periplasm, transport; HET: HEM; NMR {Shewanella frigidimarina} (A:) Probab=32.25 E-value=11 Score=16.50 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=7.4 Q ss_pred CCCCCCCCEEEEECC Q ss_conf 236754653786061 Q gi|254780751|r 482 KVCTYCKGAGYIRSQ 496 (723) Q Consensus 482 ~~c~~c~g~g~~~~~ 496 (723) +.|+.|+|+|++... T Consensus 33 ~~C~~C~G~G~~~~~ 47 (86) T 2k3v_A 33 EQCQSCHGSLAEMDD 47 (86) T ss_dssp HHTSSSSCCGGGSCT T ss_pred CHHHHHHHHHHHCCC T ss_conf 340776616876034 No 112 >>3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, structural genomics, PSI-2, protein structure initiative; 1.64A {Nitrosomonas europaea atcc 19718} (A:32-106) Probab=32.21 E-value=26 Score=13.84 Aligned_cols=37 Identities=14% Similarity=-0.041 Sum_probs=28.7 Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC Q ss_conf 287879899783638823135327897713022213712 Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD 77 (723) Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~ 77 (723) +|+.+.|.|+.|.+ +.|=|=+..+..+.|+.+.+.+- T Consensus 2 ~~~l~~AvV~~v~~--~~a~v~~~~g~~~~l~~~~l~wa 38 (75) T 3d0f_A 2 SDDILAAVVLSATP--GAVEAFRKNGETIRITGDGLKAA 38 (75) T ss_dssp TTTCEEEEEEEEET--TEEEEEETTSCEEEECGGGGSTT T ss_pred CCCEEEEEEEEECC--CEEEEEECCCCEEEEEHHHHHHH T ss_conf 58906899999668--81899976997799808996678 No 113 >>2r6f_A Excinuclease ABC subunit A; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, ATP-binding cassette, cytoplasm; HET: ADP; 3.20A {Geobacillus stearothermophilus 10} (A:291-311,A:394-430) Probab=31.09 E-value=27 Score=13.72 Aligned_cols=35 Identities=17% Similarity=0.308 Sum_probs=22.9 Q ss_pred CCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCC Q ss_conf 23675465378606114689988788999730364 Q gi|254780751|r 482 KVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTA 516 (723) Q Consensus 482 ~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~ 516 (723) -.||.|.|.|.-.-++.-..-|+..|++......+ T Consensus 2 ~~~~~~~~~~~~~~~~~~~~GII~~LeRRY~ET~S 36 (58) T 2r6f_A 2 GACPDCDGLGAKLEVDLDLVGVIPNVERRYRETSS 36 (58) T ss_dssp TBCTTTTSCCEEEEECHHHHCHHHHHHHHHHHCCC T ss_pred CCCCHHHCCCCEEEECHHHCCCCCCHHHHHHHHCC T ss_conf 63842332541687358880652327888887307 No 114 >>2rdo_7 EF-G, elongation factor G; elongation factor G, EF-G, RRF, GDPNP, 50S subunit, cryo-EM, REAL-space refinement, ribonucleoprotein; 9.10A {Escherichia coli} (7:1-289) Probab=29.44 E-value=29 Score=13.53 Aligned_cols=78 Identities=17% Similarity=0.206 Sum_probs=57.9 Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 06999823755444555114799999999999999873103686389603347988889999999999731278728998 Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVG 457 (723) Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~ 457 (723) |+.+||-..|-. ...++..+|++.+++.=+++|-=||.. ..+...+...+++.|..+...+++. T Consensus 109 ailVVdA~~Gv~---------------~qT~~~~~~a~~~~~p~i~~iNK~D~~-~~~~~~~~~ei~~~l~~~~~~~~~p 172 (289) T 2rdo_7 109 AVMVYCAVGGVQ---------------PQSETVWRQANKYKVPRIAFVNKMDRM-GANFLKVVNQIKTRLGANPVPLQLA 172 (289) T ss_pred EEEEEECCCCCC---------------HHHHHHHHHHHHCCCCEEEEEECCCCC-CCCHHHHHHHHHHHHCCCCCCEECC T ss_conf 799997898864---------------758999999987699869997330245-7778999999999868983211523 Q ss_pred EECCC---CEEEEECCC Q ss_conf 60486---148985156 Q gi|254780751|r 458 AISNF---GLLEMSRQR 471 (723) Q Consensus 458 ~it~l---GLlEltRkR 471 (723) -...- |++.+...+ T Consensus 173 i~~~~~~~g~v~~~~~~ 189 (289) T 2rdo_7 173 IGAEEHFTGVVDLVKMK 189 (289) T ss_pred CCCCCCEEEEEEEHHHH T ss_conf 34566516999713331 No 115 >>2wac_A CG7008-PA; unknown function, tudor, beta-barrel, nuclease domain, tudor-SN, SND1, methylated arginine, SDMA, splicing; 2.10A {Drosophila melanogaster} (A:25-107) Probab=29.15 E-value=29 Score=13.50 Aligned_cols=34 Identities=35% Similarity=0.564 Sum_probs=23.0 Q ss_pred CCCEEEEEEEEECCC-CCEEEEEECCCCCCCCCHHHC Q ss_conf 287879899783638-823135327897713022213 Q gi|254780751|r 39 KGNIYLAKVTRVEPS-LQAAFVDYGGNRHGFLPFLEI 74 (723) Q Consensus 39 ~GnIY~G~V~~V~p~-lqAAFVdiG~~k~gFL~~~ei 74 (723) -|.-|.|+|.+|.++ .+-=|||||.- ...+.++| T Consensus 41 d~~wyRa~I~~i~~~~~~V~fvDyGn~--~~v~~~~l 75 (83) T 2wac_A 41 DNQWYRAKVERVQGSNATVLYIDYGNK--ETLPTNRL 75 (83) T ss_dssp TCCEEEEEEEEEETTEEEEEETTTCCE--EEEEGGGE T ss_pred CCCEEEEEEEEECCCCEEEEEEECCCE--EEEEHHHH T ss_conf 892889999981699569999812982--99878998 No 116 >>1th8_B Anti-sigma F factor antagonist; SPOIIAB, SPOIIAA, anti-ANTI-sigma, sporulation, serine kinase, transcription; HET: ADP; 2.40A {Geobacillus stearothermophilus} (B:) Probab=29.07 E-value=29 Score=13.49 Aligned_cols=88 Identities=9% Similarity=0.131 Sum_probs=68.4 Q ss_pred HHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCCEEEE Q ss_conf 73103686389603347988889999999999731278728998604861489851566630112100236754653786 Q gi|254780751|r 414 LRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYI 493 (723) Q Consensus 414 lRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g~g~~ 493 (723) +.....+|+.||.+..--...+-..+.+.+.+++.....+.-|..+|.. T Consensus 5 ~~~~~~~~~~vi~~~g~L~~~~~~~~~~~l~~~~~~~~~~~vilDls~v------------------------------- 53 (116) T 1th8_B 5 IDLEVKQDVLIVRLSGELDHHTAEELREQVTDVLENRAIRHIVLNLGQL------------------------------- 53 (116) T ss_dssp EEEEEETTEEEEEEEEEESHHHHHHHHHHHHHHHHSSCCCEEEEEEEEE------------------------------- T ss_pred EEEEEECCEEEEEEEEEEEHHHHHHHHHHHHHHHHHCCCCEEEEEECCC------------------------------- T ss_conf 8899989999999999998799999999999999608996899997798------------------------------- Q ss_pred ECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHH Q ss_conf 061146899887889997303643101357699999873 Q gi|254780751|r 494 RSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLL 532 (723) Q Consensus 494 ~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~ll 532 (723) ...++.+...+..+.+........-+.+.+++.+...+. T Consensus 54 ~~iDssg~~~L~~~~~~~~~~g~~l~l~~~~~~v~~~l~ 92 (116) T 1th8_B 54 TFMDSSGLGVILGRYKQIKNVGGQMVVCAVSPAVKRLFD 92 (116) T ss_dssp EEECHHHHHHHHHHHHHHHHTTCCEEEESCCHHHHHHHH T ss_pred CCCCHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHH T ss_conf 623879999999999999968998999978999999999 No 117 >>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane, nucleotide-binding, periplasm, translation; 2.80A {Escherichia coli K12} PDB: 3deg_C* (D:1-185) Probab=28.31 E-value=30 Score=13.40 Aligned_cols=71 Identities=18% Similarity=0.252 Sum_probs=52.4 Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCE-EE Q ss_conf 06999823755444555114799999999999999873103686389603347988889999999999731278728-99 Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARV-QV 456 (723) Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~-~v 456 (723) |+.+||...|-. ....++.++++..++-=+++|-=+|.. ..+...+.+.+++.++...+.+ -+ T Consensus 98 ailVvda~~g~~---------------~qt~~~~~~~~~~~~p~ivviNK~D~~-~~~~~~~~~~i~~~~~~~~~~vv~i 161 (185) T 3cb4_D 98 ALLVVDAGQGVE---------------AQTLANCYTAMEMDLEVVPVLNKIDLP-AADPERVAEEIEDIVGIDATDAVRC 161 (185) T ss_dssp EEEEEETTTCCC---------------THHHHHHHHHHHTTCEEEEEEECTTST-TCCHHHHHHHHHHHTCCCCTTCEEE T ss_pred EEEEEECCCCCC---------------CCHHHHHHHHHHCCCCEEEEEECCCCC-CCCHHHHHHHHHHHHCCCCCCEEEE T ss_conf 899997998855---------------221999999998799879998887588-8899999999999868994110234 Q ss_pred EEECCCCE Q ss_conf 86048614 Q gi|254780751|r 457 GAISNFGL 464 (723) Q Consensus 457 ~~it~lGL 464 (723) +..+.-|+ T Consensus 162 SA~~g~gi 169 (185) T 3cb4_D 162 SAKTGVGV 169 (185) T ss_dssp CTTTCTTH T ss_pred ECCCCCCH T ss_conf 32068296 No 118 >>3d3r_A Hydrogenase assembly chaperone HYPC/HUPF; small beta-barrel, structural genomics, PSI-2, protein structure initiative; 1.85A {Shewanella oneidensis mr-1} (A:1-73) Probab=26.73 E-value=32 Score=13.21 Aligned_cols=21 Identities=29% Similarity=0.227 Sum_probs=17.4 Q ss_pred EEEEEEECCCCCEEEEEECCC Q ss_conf 989978363882313532789 Q gi|254780751|r 44 LAKVTRVEPSLQAAFVDYGGN 64 (723) Q Consensus 44 ~G~V~~V~p~lqAAFVdiG~~ 64 (723) -|+|..|.+..+-|.||++.- T Consensus 27 P~kIveI~~~~~~A~Vd~~Gv 47 (73) T 3d3r_A 27 PSQVVAVDNERQSVTVDTLGV 47 (73) T ss_dssp CEEEEEEETTTTEEEEEETTE T ss_pred CEEEEEECCCCCEEEEECCCE T ss_conf 549999919988899967995 No 119 >>2vnu_D Exosome complex exonuclease RRP44; rRNA processing, RNA degradation, cytoplasm, RNA-binding, RNA processing, DIS3P, nucleus, hydrolase; HET: 1PE; 2.30A {Saccharomyces cerevisiae} (D:671-760) Probab=26.07 E-value=33 Score=13.13 Aligned_cols=36 Identities=14% Similarity=0.007 Sum_probs=28.9 Q ss_pred EEEEEEEEECCCCCEEEEEEC-CCCCCCCCHHHCCCCCC Q ss_conf 879899783638823135327-89771302221371210 Q gi|254780751|r 42 IYLAKVTRVEPSLQAAFVDYG-GNRHGFLPFLEIHPDYY 79 (723) Q Consensus 42 IY~G~V~~V~p~lqAAFVdiG-~~k~gFL~~~ei~~~y~ 79 (723) +|-|.|+.|-+. +.||.+- .+-.|+.|++++.-||+ T Consensus 2 ~~~g~Is~V~~~--Gi~V~l~~~giEG~V~l~~l~~d~~ 38 (90) T 2vnu_D 2 TETGYVIKVFNN--GIVVLVPKFGVEGLIRLDNLTEDPN 38 (90) T ss_dssp EEEEEEEEEETT--EEEEEETTTTEEEEEEHHHHCSCGG T ss_pred EEEEEEEEEEEC--EEEEEEECCCCEEEEECCCCCCCCC T ss_conf 489999999957--2999980897489998011799854 No 120 >>2hu9_A MERP, mercuric transport protein periplasmic component; copper chaperone, iron-sufur protein, COPZ, ATX1, ATOX1, metal transport; 1.78A {Archaeoglobus fulgidus} (A:1-64) Probab=25.98 E-value=31 Score=13.34 Aligned_cols=20 Identities=20% Similarity=0.370 Sum_probs=15.6 Q ss_pred CCCCCCCCEEEEECCHHHHH Q ss_conf 23675465378606114689 Q gi|254780751|r 482 KVCTYCKGAGYIRSQSSVAL 501 (723) Q Consensus 482 ~~c~~c~g~g~~~~~~~~~~ 501 (723) ..||.|+..|.--...++-. T Consensus 2 ~~CP~Cg~~G~~V~~~TVk~ 21 (64) T 2hu9_A 2 MRCPECSTEGWRVLPLTVGA 21 (64) T ss_dssp CBCTTTCCBCEEECHHHHHH T ss_pred CCCCCCCCCCEEECHHHHHH T ss_conf 75887887675810888998 No 121 >>2diq_A Tudor and KH domain-containing protein; tudor domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Probab=25.51 E-value=25 Score=13.94 Aligned_cols=35 Identities=31% Similarity=0.557 Sum_probs=23.3 Q ss_pred CCCCEEEEEEEEECCC--CCEEEEEECCCCCCCCCHHHC Q ss_conf 4287879899783638--823135327897713022213 Q gi|254780751|r 38 IKGNIYLAKVTRVEPS--LQAAFVDYGGNRHGFLPFLEI 74 (723) Q Consensus 38 ~~GnIY~G~V~~V~p~--lqAAFVdiG~~k~gFL~~~ei 74 (723) .-|..|.|+|..+.++ ..--|||||.... .++++| T Consensus 45 ~d~~w~Ra~I~~~~~~~~~~V~~iD~G~~~~--v~~~~l 81 (110) T 2diq_A 45 TNGSWYRARVLGTLENGNLDLYFVDFGDNGD--CPLKDL 81 (110) T ss_dssp TTCSCEEEEECCCCSSSCEEEEETTTCCEEE--ECGGGC T ss_pred CCCCEEEEEEEEECCCCEEEEEEEEECCEEE--EEHHHH T ss_conf 7991999999997799979999995199899--878998 No 122 >>1k3r_A Conserved protein MT0001; beta barrel, structural genomics, PSI, protein structure initiative; 2.30A {Methanothermobacterthermautotrophicus} (A:85-160) Probab=24.34 E-value=36 Score=12.92 Aligned_cols=32 Identities=16% Similarity=0.307 Sum_probs=23.1 Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCC Q ss_conf 6042878798997836388231353278977130 Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFL 69 (723) Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL 69 (723) ..-.|.+=-|.|.+-.. ..+|||+|..+.+.+ T Consensus 15 ~~e~~~yREGvv~~~~~--~gt~VdvGl~~~v~i 46 (76) T 1k3r_A 15 KPVTGEYRQGLTVKRVK--KGTLVDIGADKLALC 46 (76) T ss_dssp SCCTTCEEEEEEEEECS--SSEEEESSSSCEEEC T ss_pred CCCCCCCCCEEEEECCC--CCEEEECCCCCEECC T ss_conf 76744642358875268--963785798740214 No 123 >>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} (A:136-229) Probab=24.26 E-value=36 Score=12.91 Aligned_cols=39 Identities=21% Similarity=0.108 Sum_probs=33.7 Q ss_pred CCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC Q ss_conf 013576999998730237999999998488799984787 Q gi|254780751|r 519 IIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723) Q Consensus 519 i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723) ..+.+|++....+.+..-..+.+|++++|++|.+..+.. T Consensus 3 ~~i~vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~ 41 (94) T 2ba0_A 3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGL 41 (94) T ss_dssp EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECTTSE T ss_pred EEEEECCCEECEEEECCCEEEHHHCCCCCEEEEEECCCE T ss_conf 685144535450550684520012146686999967858 No 124 >>1h95_A CSD, Y-box binding protein; translation factor, transcription factor, OB-fold, 5- stranded anti-parallel beta-barrel, single stranded DNA binding; NMR {Homo sapiens} (A:) Probab=24.15 E-value=36 Score=12.89 Aligned_cols=40 Identities=13% Similarity=0.141 Sum_probs=32.4 Q ss_pred CCCCEEEEEEEEECCCCCEEEEEEC-CCCCCCCCHHHCCCC Q ss_conf 4287879899783638823135327-897713022213712 Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYG-GNRHGFLPFLEIHPD 77 (723) Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG-~~k~gFL~~~ei~~~ 77 (723) .....+.|+|+.--+.=.=-||.-. .++.-|+|++.|+.+ T Consensus 4 ~~~~~~~G~Vk~f~~~kGfGFI~~~~g~~dif~h~s~i~~~ 44 (79) T 1h95_A 4 VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKN 44 (79) T ss_dssp CCEEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSC T ss_pred HHCCCCEEEEEEEECCCCEEEEEECCCCCCEEEEHHHHCCC T ss_conf 21475108999997999989998689986799984993346 No 125 >>1w6s_A Methanol dehydrogenase subunit 1; anisotropic, electron transfer, oxidoreductase, calcium- binding, methanol utilization, PQQ; HET: PQQ; 1.2A {Methylobacterium extorquens} (A:220-303) Probab=23.97 E-value=36 Score=12.87 Aligned_cols=16 Identities=19% Similarity=0.335 Sum_probs=11.8 Q ss_pred CCCEEEEEEECCCCCC Q ss_conf 2880699982375544 Q gi|254780751|r 375 QTEALVSIDVNSGRST 390 (723) Q Consensus 375 ~TEALt~IDVNSG~~~ 390 (723) .|.+++++|+.||+.. T Consensus 57 ~s~sivAld~~TG~~~ 72 (84) T 1w6s_A 57 WTMTIFGRDADTGEAK 72 (84) T ss_dssp TSSEEEEEETTTCCEE T ss_pred CCCCCEEECCCCCCEE T ss_conf 4354121243552003 No 126 >>1jmx_A Amine dehydrogenase; oxidoreductase; HET: TRQ HEC; 1.90A {Pseudomonas putida} (A:1-80) Probab=23.07 E-value=38 Score=12.75 Aligned_cols=18 Identities=11% Similarity=0.012 Sum_probs=14.0 Q ss_pred HHHHCCCCCCCCCEEEEE Q ss_conf 121002367546537860 Q gi|254780751|r 477 LESTTKVCTYCKGAGYIR 494 (723) Q Consensus 477 ~e~~~~~c~~c~g~g~~~ 494 (723) .+.+...|..||+.++|. T Consensus 5 ~~lv~~~C~~CHs~~~i~ 22 (80) T 1jmx_A 5 PSLLQNKCMGCHIPEGND 22 (80) T ss_dssp HHHHHHHHBTTBCEEETT T ss_pred HHHHHHHHHHCCCCCCCC T ss_conf 899984433303855577 No 127 >>2kcm_A Cold shock domain family protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Shewanella oneidensis mr-1} (A:) Probab=23.02 E-value=38 Score=12.75 Aligned_cols=34 Identities=12% Similarity=-0.017 Sum_probs=27.7 Q ss_pred EEEEEEECCCCCEEEEEE-CCCCCCCCCHHHCCCC Q ss_conf 989978363882313532-7897713022213712 Q gi|254780751|r 44 LAKVTRVEPSLQAAFVDY-GGNRHGFLPFLEIHPD 77 (723) Q Consensus 44 ~G~V~~V~p~lqAAFVdi-G~~k~gFL~~~ei~~~ 77 (723) .|+|+..-+.-.--||.- +.+..-|+|++.+..+ T Consensus 2 ~G~Vk~f~~~kGfGFI~~d~~~~dif~h~s~l~~~ 36 (74) T 2kcm_A 2 KGKVVSYLAAKKYGFIQGDDGESYFLHFSELLDKK 36 (74) T ss_dssp EEEEEEEETTTTEEEEEETTSCEECCCGGGSSCSG T ss_pred EEEEEEEECCCCEEEEECCCCCEEEEEHHHHCCCC T ss_conf 38999998999866783699967999947703478 No 128 >>3hcn_A Ferrochelatase, mitochondrial; metal selectivity, 2Fe-2S, disease mutation, heme biosynthesis, iron, iron-sulfur, lyase, membrane, metal-binding; HET: CHD HEM GOL; 1.60A {Homo sapiens} PDB: 2qd3_A* 2qd5_A* 2qd4_A* 3hco_A* 3hcr_A* 2qd1_A* 2hre_A* 3hcp_A* 2qd2_A* 2hrc_A* 1hrk_A* 2pnj_A* 2po5_A* 2po7_A* (A:1-164,A:308-359) Probab=22.71 E-value=38 Score=12.71 Aligned_cols=13 Identities=23% Similarity=0.483 Sum_probs=8.2 Q ss_pred HHHHHCCCCCCCC Q ss_conf 1121002367546 Q gi|254780751|r 476 VLESTTKVCTYCK 488 (723) Q Consensus 476 l~e~~~~~c~~c~ 488 (723) ....++..||.|. T Consensus 188 ~~~~~~~~~~~~~ 200 (216) T 3hcn_A 188 CSKQLTLSCPLCV 200 (216) T ss_dssp SCGGGGSCCTTCC T ss_pred CCCCCCCCCCCCC T ss_conf 7745688899988 No 129 >>2vy9_A Anti-sigma-factor antagonist; gene regulation, RSBS, stressosome, STAS domain, bacillus subtilis; 2.3A {Moorella thermoacetica} (A:) Probab=22.67 E-value=38 Score=12.70 Aligned_cols=89 Identities=11% Similarity=0.087 Sum_probs=62.9 Q ss_pred HHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCCEEE Q ss_conf 87310368638960334798888999999999973127872899860486148985156663011210023675465378 Q gi|254780751|r 413 QLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGY 492 (723) Q Consensus 413 QlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g~g~ 492 (723) .+.+...+|+.||.|-.=-...+-..+.+.+.+.+...+.+.-|..+|..- T Consensus 4 ~~~~~~~~~~~ii~~~g~l~~~~~~~~~~~l~~~~~~~~~~~vilD~s~v~----------------------------- 54 (123) T 2vy9_A 4 RVPILKVDDYWVVAIEETLHDQSVIQFKEELLHNITGVAGKGLVIDISALE----------------------------- 54 (123) T ss_dssp --CCEEETTEEEEECCCCSCSHHHHHHHHHHHHHHTTSCCSEEEEECTTCS----------------------------- T ss_pred CCEEEEECCEEEEEEEEEECHHHHHHHHHHHHHHHCCCCCCEEEEECCCCC----------------------------- T ss_conf 303899899999996789878999999999987531579869999755787----------------------------- Q ss_pred EECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHH Q ss_conf 6061146899887889997303643101357699999873 Q gi|254780751|r 493 IRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLL 532 (723) Q Consensus 493 ~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~ll 532 (723) ..++.++..+..+.+........-+.+.+++.+...|. T Consensus 55 --~iDss~~~~L~~l~~~~~~~g~~l~l~~~~~~v~~~l~ 92 (123) T 2vy9_A 55 --VVDSFVTRVLIEISRLAELLGLPFVLTGIKPAVAITLT 92 (123) T ss_dssp --SCCHHHHHHHHHHHHHHHHTTCCEEEECCCHHHHHHHH T ss_pred --CCCHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHH T ss_conf --55989999999999999735985999948989999999 No 130 >>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} (I:156-251) Probab=22.54 E-value=32 Score=13.22 Aligned_cols=39 Identities=15% Similarity=0.166 Sum_probs=33.6 Q ss_pred CCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC Q ss_conf 013576999998730237999999998488799984787 Q gi|254780751|r 519 IIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723) Q Consensus 519 i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723) ..+.+|++...++.+..-..|..|++.+|++|.+.-+.. T Consensus 2 e~i~vp~~~vg~iIGkgG~~Ik~I~~~tg~~I~i~~~~~ 40 (96) T 2je6_I 2 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGR 40 (96) T ss_dssp CEEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTTSE T ss_pred EEEEEECCCCCEEEECCCEEEEEECCCCCEEEEECCCCE T ss_conf 626652565660575486888980577368999766357 No 131 >>1p1j_A Inositol-3-phosphate synthase; 1L-MYO-inositol 1-phosphate, NADH, isomerase, rossmann fold; HET: NAI; 1.70A {Saccharomyces cerevisiae} (A:92-135) Probab=22.37 E-value=31 Score=13.29 Aligned_cols=23 Identities=26% Similarity=0.551 Sum_probs=16.8 Q ss_pred CCEEEEEECCCCCC---CCCHHHCCC Q ss_conf 82313532789771---302221371 Q gi|254780751|r 54 LQAAFVDYGGNRHG---FLPFLEIHP 76 (723) Q Consensus 54 lqAAFVdiG~~k~g---FL~~~ei~~ 76 (723) .||+=|-+|.+.+| |.||+++-| T Consensus 19 tqaSTv~lG~d~~G~ev~vPf~~lLP 44 (44) T 1p1j_A 19 TQCSTLKLGIDAEGNDVYAPFNSLLP 44 (44) T ss_dssp HHHCEEEEEECTTSCEEEEEGGGSSC T ss_pred HHCCEEEECCCCCCCCCCCCHHHCCC T ss_conf 10022420346678724663776178 No 132 >>2wjn_C Photosynthetic reaction center cytochrome C subunit; bacteriochlorophyll, lipidic-sponge phase, photosynthesis, electron transport, cell membrane; HET: HEM FME BCB BPB MPG MQ7 NS5; 1.86A {Rhodopseudomonas viridis} PDB: 1prc_C* 1r2c_C* 1dxr_C* 2prc_C* 2i5n_C* 2wjm_C* 3d38_C* 3g7f_C* 3prc_C* 5prc_C* 6prc_C* 7prc_C* 2jbl_C* 1vrn_C* (C:93-251) Probab=22.27 E-value=18 Score=15.02 Aligned_cols=34 Identities=24% Similarity=0.337 Sum_probs=13.3 Q ss_pred HHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCH Q ss_conf 9997312787289986048614898515666301 Q gi|254780751|r 443 LKESLKKDRARVQVGAISNFGLLEMSRQRIRSSV 476 (723) Q Consensus 443 l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl 476 (723) |...|-.|..-+.|.+.+.|-+++.+++--++++ T Consensus 98 ~~~fLl~d~~~irV~~~~alP~~~v~~~~~~~~i 131 (159) T 2wjn_C 98 FTMFLANDKRQVRVVPQTALPLVGVSRGKERRPL 131 (159) T ss_dssp HHHHTSCSCSCCCCSCSSSSCBTTSSSGGGSCCT T ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHH T ss_conf 2666435853210047767876666666665316 No 133 >>1d2e_A Elongation factor TU (EF-TU); G-protein, beta-barrel, RNA binding protein; HET: GDP; 1.94A {Bos taurus} (A:1-197) Probab=21.53 E-value=40 Score=12.55 Aligned_cols=76 Identities=16% Similarity=0.125 Sum_probs=44.8 Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC-CEEEEECCCCCCHH-HHHHHHHHHHHHH---HHCCC Q ss_conf 0699982375544455511479999999999999987310368-63896033479888-8999999999973---12787 Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLA-GLIVVDFIDMEEKK-NNRSVEKKLKESL---KKDRA 452 (723) Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlg-GiIvIDFIdM~~~~-~~~~v~~~l~~~l---~~D~~ 452 (723) |+.+||...|-. +...|..++++..++. -||+|-=+|.-... .+..+...+.+.+ ..... T Consensus 93 ailVvda~~g~~---------------~qT~e~~~~~~~~~i~~iiv~iNKmD~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (197) T 1d2e_A 93 CILVVAANDGPM---------------PQTREHLLLARQIGVEHVVVYVNKADAVQDSEMVELVELEIRELLTEFGYKGE 157 (197) T ss_dssp EEEEEETTTCSC---------------HHHHHHHHHHHHTTCCCEEEEEECGGGCSCHHHHHHHHHHHHHHHHHTTSCTT T ss_pred EEEEEECCCCCC---------------HHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCH T ss_conf 899988577875---------------63899999999729985899850566678489999999999999986099801 Q ss_pred CEEEEEECCC-CEEEEE Q ss_conf 2899860486-148985 Q gi|254780751|r 453 RVQVGAISNF-GLLEMS 468 (723) Q Consensus 453 ~~~v~~it~l-GLlElt 468 (723) .+.+.++|.+ |+.+.. T Consensus 158 ~v~~ipiSa~~G~~~~~ 174 (197) T 1d2e_A 158 ETPIIVGSALCALEQRD 174 (197) T ss_dssp TSCEEECCHHHHHTTCC T ss_pred HEEEEECCCCCCEECCC T ss_conf 20189610542201358 No 134 >>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I KH domains, fragIle X mental retardation protein, RNA binding protein; 1.90A {Homo sapiens} PDB: 2fmr_A (A:65-144) Probab=21.34 E-value=41 Score=12.52 Aligned_cols=42 Identities=14% Similarity=0.184 Sum_probs=34.6 Q ss_pred CCCCCCCHHHHHHHHCCHHHHHHHHHHHHCC-EEEEEECCCCC Q ss_conf 1013576999998730237999999998488-79998478778 Q gi|254780751|r 518 NIIVHTHSDVVLYLLNQKRATIVEYEARFGV-SINVVIGIELA 559 (723) Q Consensus 518 ~i~v~~~~~va~~lln~kr~~l~~lE~~~~~-~I~i~~d~~l~ 559 (723) .+.+.+|...+..|.+..-..|.+|.+.+|+ .|.|..+.+.. T Consensus 4 t~~~~Ip~~~vg~iIGk~G~~I~~I~~~tGa~~i~i~~~~~~~ 46 (80) T 2qnd_A 4 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKN 46 (80) T ss_dssp EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTC T ss_pred EEEECCCHHHHHHHCCCCCHHHHHHHHHHCCEEEEECCCCCCC T ss_conf 6776055777766405686589998886198799964887788 No 135 >>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=21.04 E-value=41 Score=12.48 Aligned_cols=40 Identities=15% Similarity=0.166 Sum_probs=28.3 Q ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHC-CEEEEEECC Q ss_conf 3101357699999873023799999999848-879998478 Q gi|254780751|r 517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFG-VSINVVIGI 556 (723) Q Consensus 517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~-~~I~i~~d~ 556 (723) ....+.+|+....++.+.+...|.+|++.+| +.|.|-.+. T Consensus 27 ~~~~i~Vp~~~~~~iIG~~G~~Ik~I~~~tg~~~I~~~~~~ 67 (102) T 2ctf_A 27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGE 67 (102) T ss_dssp EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSSS T ss_pred EEEEEEECHHHHHHHCCCCHHHHHHHHHHCCCEEEECCCCC T ss_conf 79999808898847238862789999998398287469998 No 136 >>1pby_A Quinohemoprotein amine dehydrogenase 60 kDa subunit; oxidoreductase; HET: TRW HEM; 1.70A {Paracoccus denitrificans} (A:1-79) Probab=21.01 E-value=39 Score=12.63 Aligned_cols=19 Identities=16% Similarity=0.156 Sum_probs=14.1 Q ss_pred HHHHCCCCCCCCCEEEEEC Q ss_conf 1210023675465378606 Q gi|254780751|r 477 LESTTKVCTYCKGAGYIRS 495 (723) Q Consensus 477 ~e~~~~~c~~c~g~g~~~~ 495 (723) .+.+...|..||+.++|-. T Consensus 4 ~~lv~~~C~~CHs~~~i~~ 22 (79) T 1pby_A 4 EEVLQNACAACHVQHEDGR 22 (79) T ss_dssp HHHHHHTGGGTSCBCTTSC T ss_pred HHHHHHHHHHCCCCCCCCC T ss_conf 8999744344138666876 No 137 >>1zbr_A AAQ65385, conserved hypothetical protein; alpha-beta protein., structural genomics, PSI, protein structure initiative; 2.60A {Porphyromonas gingivalis W83} (A:146-204) Probab=20.77 E-value=42 Score=12.44 Aligned_cols=28 Identities=14% Similarity=0.061 Sum_probs=20.4 Q ss_pred CCHHHHHHHHHHHHHHHH--CCCCCCCCCC Q ss_conf 420356776999999984--2221436786 Q gi|254780751|r 342 PHPIFFRSGIEVQLDSLH--QTEVTLPSRG 369 (723) Q Consensus 342 ~~~lf~~y~ie~~i~~~~--~~~V~L~sGG 369 (723) .-|-+.+-.|+..+...| ++.+||+.|+ T Consensus 25 RNp~ls~~~ie~~L~~~lG~~kviWL~~G~ 54 (59) T 1zbr_A 25 RNAGLSRTAIIDTLKESLGVSRVLSLRHGA 54 (59) T ss_dssp TSTTSCHHHHHHHHHHHSCCSEEEEESSCC T ss_pred CCCCCCHHHHHHHHHHHCCCCEEEEECCCC T ss_conf 788756789999999861976478606888 No 138 >>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} (A:1-218) Probab=20.68 E-value=42 Score=12.43 Aligned_cols=34 Identities=15% Similarity=0.080 Sum_probs=28.4 Q ss_pred HHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHH Q ss_conf 7310368638960334798888999999999973 Q gi|254780751|r 414 LRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESL 447 (723) Q Consensus 414 lRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l 447 (723) +.-+.-+|+..||.|++-....+..++..|.+.- T Consensus 139 ~~~~a~~gil~iDEi~~~~~~~~~~ll~~le~~~ 172 (218) T 1g8p_A 139 LLARANRGYLYIDECNLLEDHIVDLLLDVAQSGE 172 (218) T ss_dssp HHHHHTTEEEEETTGGGSCHHHHHHHHHHHHHSE T ss_pred CEECCCCCEEEECCHHHHCHHHHHHHHHHHHHCE T ss_conf 3230569878615587757999999999986143 No 139 >>1c9o_A CSPB, cold-shock protein; beta barrel, homodimer; 1.17A {Bacillus caldolyticus} (A:) Probab=20.68 E-value=42 Score=12.43 Aligned_cols=33 Identities=21% Similarity=0.312 Sum_probs=28.1 Q ss_pred EEEEEEECCCCCEEEEEECCCCCCCCCHHHCCC Q ss_conf 989978363882313532789771302221371 Q gi|254780751|r 44 LAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHP 76 (723) Q Consensus 44 ~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~ 76 (723) .|+|+..-+.-.=-||.--.+..-|+|.+.+.. T Consensus 3 ~G~Vk~f~~~kGfGFI~~d~g~d~~f~~~~~~~ 35 (66) T 1c9o_A 3 RGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQG 35 (66) T ss_dssp EEEEEEEETTTTEEEEEETTEEEEEEEGGGBCS T ss_pred CEEEEEEECCCCEEEEEECCCCEEEEEEHHCCC T ss_conf 819999979999899977699349999045450 No 140 >>3hvm_A Agmatine deiminase; hydrolase; 2.10A {Helicobacter pylori J99} PDB: 2cmu_A (A:140-198) Probab=20.57 E-value=42 Score=12.42 Aligned_cols=28 Identities=18% Similarity=0.139 Sum_probs=20.8 Q ss_pred CCHHHHHHHHHHHHHHHH--CCCCCCCCCC Q ss_conf 420356776999999984--2221436786 Q gi|254780751|r 342 PHPIFFRSGIEVQLDSLH--QTEVTLPSRG 369 (723) Q Consensus 342 ~~~lf~~y~ie~~i~~~~--~~~V~L~sGG 369 (723) .-|-+.+-.|+..+...| ++.+||+.|. T Consensus 25 RNp~lt~~~ie~~L~~~lG~~kviWL~~G~ 54 (59) T 3hvm_A 25 RNPHLNQNGIETMLKKELGAKQVLWYSYGY 54 (59) T ss_dssp TSTTSCHHHHHHHHHHHHCCSEEEEECCCC T ss_pred CCCCCCHHHHHHHHHHHHCCCEEEEECCCC T ss_conf 387879999999999974997699967887 No 141 >>1c3g_A Heat shock protein 40; beta sheets, short helices; 2.70A {Saccharomyces cerevisiae} (A:1-79) Probab=20.52 E-value=29 Score=13.57 Aligned_cols=13 Identities=15% Similarity=-0.243 Sum_probs=4.9 Q ss_pred CCCCCCCCEEEEE Q ss_conf 2367546537860 Q gi|254780751|r 482 KVCTYCKGAGYIR 494 (723) Q Consensus 482 ~~c~~c~g~g~~~ 494 (723) .+|+.|+|.|..+ T Consensus 24 ~~c~~c~g~~~~~ 36 (79) T 1c3g_A 24 IGRKGPHGASEKT 36 (79) T ss_dssp EEEEETTTEEEEE T ss_pred EEEECCCCCEEEE T ss_conf 9961688740269 No 142 >>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori} (A:) Probab=20.42 E-value=32 Score=13.27 Aligned_cols=90 Identities=12% Similarity=0.044 Sum_probs=44.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCEEEE-ECCCCCCHHHHHHHHHHHHHHHH-HCCCCEEEEEECCCCEEEEECCCCCC- Q ss_conf 7999999999999998731036863896-03347988889999999999731-27872899860486148985156663- Q gi|254780751|r 398 TALQTNLEAAEEIARQLRLRDLAGLIVV-DFIDMEEKKNNRSVEKKLKESLK-KDRARVQVGAISNFGLLEMSRQRIRS- 474 (723) Q Consensus 398 t~l~tNleAA~EIaRQlRLRnlgGiIvI-DFIdM~~~~~~~~v~~~l~~~l~-~D~~~~~v~~it~lGLlEltRkR~r~- 474 (723) .+..-=++++.+.|+.-..+-+..+.|. -=.-.-.+..-+--...+.+.-. -..++..|-.+...+- =+.=+. T Consensus 7 si~~~iv~~v~~~a~~~~~~~V~~V~l~IG~ls~V~p~~L~faf~~~~~~T~l~ega~L~i~~~p~~~~----C~~Cg~~ 82 (119) T 2kdx_A 7 SVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELE----CKDCSHV 82 (119) T ss_dssp HHHHHHHHHHHHHHHHTTCCCCCEEEEEEETTSCCCHHHHHHHHHHHGGGCTTTSSCCEEEEEECCEEE----CSSSSCE T ss_pred HHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEEEECCCEEE----CCCCCCE T ss_conf 999999999999999859958999999988756408999999999996798445376899996386689----7789988 Q ss_pred -CHHHHHCCCCCCCCCEE Q ss_conf -01121002367546537 Q gi|254780751|r 475 -SVLESTTKVCTYCKGAG 491 (723) Q Consensus 475 -sl~e~~~~~c~~c~g~g 491 (723) ++.+..+..||+|++.. T Consensus 83 ~~~~~~~~~~CP~Cgs~~ 100 (119) T 2kdx_A 83 FKPNALDYGVCEKCHSKN 100 (119) T ss_dssp ECSCCSTTCCCSSSSSCC T ss_pred ECCCCCCCCCCCCCCCCC T ss_conf 534775177490978988 No 143 >>1acv_A DSBA; disulfide oxidoreductase, thioredoxin fold, redox-active center; 1.90A {Escherichia coli} (A:1-64,A:149-189) Probab=20.19 E-value=16 Score=15.42 Aligned_cols=15 Identities=33% Similarity=0.567 Sum_probs=9.2 Q ss_pred CCCHHHHHCCCCCCC Q ss_conf 630112100236754 Q gi|254780751|r 473 RSSVLESTTKVCTYC 487 (723) Q Consensus 473 r~sl~e~~~~~c~~c 487 (723) .+.+.|.|+-.|||| T Consensus 19 kpeVvEFFSy~CpHC 33 (105) T 1acv_A 19 APQVLEFFSFFCPSC 33 (105) T ss_dssp CCSEEEEECTTCHHH T ss_pred CCEEEEEECCCCCCH T ss_conf 977999988889340 No 144 >>2q2g_A HSP40 protein, heat shock 40 kDa protein, putative (fragment); malaria, structural genomics, structural genomics consortium, SGC; 1.90A {Cryptosporidium parvum iowa II} (A:1-85) Probab=20.09 E-value=17 Score=15.08 Aligned_cols=19 Identities=0% Similarity=-0.241 Sum_probs=8.8 Q ss_pred HCCCCCCCCCEEEEECCHH Q ss_conf 0023675465378606114 Q gi|254780751|r 480 TTKVCTYCKGAGYIRSQSS 498 (723) Q Consensus 480 ~~~~c~~c~g~g~~~~~~~ 498 (723) +..+|+.|.|.|++....+ T Consensus 25 i~~~c~~c~g~g~~~~~~~ 43 (85) T 2q2g_A 25 IKVTRKRFIEHKVRNEENI 43 (85) T ss_dssp EEEEEEEEETTEEEEEEEE T ss_pred EEEEEEEECCCCEEEEEEE T ss_conf 9986688779966877799 No 145 >>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=20.05 E-value=43 Score=12.34 Aligned_cols=51 Identities=12% Similarity=-0.051 Sum_probs=38.9 Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEE Q ss_conf 431013576999998730237999999998488799984787788633897 Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE 566 (723) Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ie 566 (723) ...+.+.+|+....++.+.+-..|.+|++.++..+...+++.-....+.|. T Consensus 16 ~~~~~i~Vp~~~~g~iIG~~G~~I~~I~~~tg~~~I~~~~~~~~~~~i~I~ 66 (95) T 2ctj_A 16 IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIR 66 (95) T ss_dssp SCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEE T ss_pred CEEEEEEECHHHHHHHCCCCCHHHHHHHHHCCCEEEEECCCCCCCCEEEEE T ss_conf 589999989898735089984689999997299189957988877537984 Done!