Query gi|254780553|ref|YP_003064966.1| Holliday junction DNA helicase RuvA [Candidatus Liberibacter asiaticus str. psy62] Match_columns 207 No_of_seqs 117 out of 1856 Neff 6.5 Searched_HMMs 33803 Date Wed Jun 1 19:36:13 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780553.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >1ixr_A Holliday junction DNA 100.0 0 0 362.4 14.6 191 1-206 1-191 (191) 2 >1cuk_A RUVA protein; DNA repa 99.9 1.3E-23 3.7E-28 177.7 7.5 74 66-139 1-74 (79) 3 >2ztd_A Holliday junction ATP- 99.9 1.4E-23 4.2E-28 177.4 6.7 73 65-137 1-73 (75) 4 >1cuk_A RUVA protein; DNA repa 99.8 1.1E-18 3.2E-23 144.9 10.5 65 1-65 1-65 (65) 5 >2ztd_A Holliday junction ATP- 99.8 7.5E-18 2.2E-22 139.2 10.2 63 1-64 17-79 (79) 6 >1ixs_A Holliday junction DNA 98.7 2.8E-08 8.1E-13 75.5 6.1 52 153-205 10-61 (62) 7 >2ztd_A Holliday junction ATP- 98.7 4.6E-08 1.4E-12 74.0 6.9 51 155-206 5-55 (58) 8 >1cuk_A RUVA protein; DNA repa 98.5 1.3E-07 3.8E-12 71.0 5.5 50 153-205 9-58 (59) 9 >3c1y_A DNA integrity scanning 97.7 2.8E-05 8.4E-10 55.4 3.7 60 69-131 8-67 (74) 10 >1z00_A DNA excision repair pr 97.5 0.00012 3.6E-09 51.1 4.6 57 71-130 17-73 (89) 11 >1pzn_A RAD51, DNA repair and 97.4 6.1E-05 1.8E-09 53.2 1.9 62 66-131 28-91 (95) 12 >1kft_A UVRC, excinuclease ABC 97.4 0.00011 3.3E-09 51.4 3.0 57 70-129 20-77 (78) 13 >1vdd_A Recombination protein 96.8 0.00071 2.1E-08 46.1 2.7 23 107-129 11-33 (66) 14 >2w9m_A Polymerase X; SAXS, DN 96.7 0.0011 3.3E-08 44.8 2.8 52 73-124 57-113 (118) 15 >2fmp_A DNA polymerase beta; n 96.3 0.0021 6.2E-08 42.9 2.3 51 75-125 59-115 (119) 16 >2ihm_A POL MU, DNA polymerase 96.2 0.0016 4.8E-08 43.7 1.3 50 75-124 63-118 (129) 17 >1wcn_A Transcription elongati 95.9 0.0071 2.1E-07 39.4 3.5 56 73-130 7-62 (70) 18 >2nrt_A Uvrabc system protein 95.9 0.0062 1.8E-07 39.8 3.1 54 69-126 7-61 (64) 19 >1jms_A Terminal deoxynucleoti 95.8 0.0044 1.3E-07 40.8 2.1 88 83-200 62-151 (154) 20 >2a1j_A DNA repair endonucleas 95.2 0.018 5.2E-07 36.8 3.5 53 74-130 5-57 (63) 21 >1z00_B DNA repair endonucleas 95.0 0.014 4.2E-07 37.4 2.4 51 72-126 17-67 (71) 22 >1a76_A Flap endonuclease-1 pr 94.9 0.021 6.2E-07 36.3 3.2 37 94-130 1-38 (65) 23 >3c65_A Uvrabc system protein 94.8 0.0058 1.7E-07 40.0 0.0 53 72-128 172-224 (226) 24 >2bcq_A DNA polymerase lambda; 94.6 0.006 1.8E-07 39.9 -0.3 72 105-201 54-127 (128) 25 >1ngn_A Methyl-CPG binding pro 94.4 0.027 8.1E-07 35.5 2.6 45 76-126 78-122 (129) 26 >1b22_A DNA repair protein RAD 94.2 0.015 4.5E-07 37.2 1.0 58 73-132 25-82 (114) 27 >1rxw_A Flap structure-specifi 93.2 0.064 1.9E-06 33.1 2.7 36 95-130 2-37 (68) 28 >1exn_A 5'-exonuclease, 5'-nuc 93.1 0.09 2.7E-06 32.0 3.4 38 93-130 5-44 (80) 29 >1b43_A Protein (FEN-1); nucle 93.0 0.064 1.9E-06 33.0 2.5 38 93-130 10-48 (77) 30 >3bz1_U Photosystem II 12 kDa 92.9 0.042 1.2E-06 34.3 1.4 48 73-129 33-80 (104) 31 >3i0w_A 8-oxoguanine-DNA-glyco 92.8 0.073 2.2E-06 32.6 2.6 35 92-126 17-51 (58) 32 >1ixr_A Holliday junction DNA 92.4 0.29 8.6E-06 28.7 5.3 60 107-188 71-131 (191) 33 >1rxw_A Flap structure-specifi 92.3 0.052 1.5E-06 33.7 1.3 30 77-106 19-49 (68) 34 >3bzc_A TEX; helix-turn-helix, 92.0 0.22 6.5E-06 29.4 4.3 25 104-128 6-30 (70) 35 >2edu_A Kinesin-like protein K 92.0 0.33 9.7E-06 28.3 5.1 33 96-128 28-60 (98) 36 >1s5l_U Photosystem II 12 kDa 92.0 0.09 2.7E-06 32.0 2.2 22 105-126 13-34 (87) 37 >2izo_A FEN1, flap structure-s 91.9 0.065 1.9E-06 33.0 1.4 37 94-130 1-38 (82) 38 >2ziu_A MUS81 protein; helix-h 91.8 0.13 3.7E-06 31.1 2.8 59 70-128 5-75 (82) 39 >2duy_A Competence protein com 91.8 0.11 3.1E-06 31.6 2.4 25 102-126 21-45 (75) 40 >1a76_A Flap endonuclease-1 pr 91.7 0.052 1.5E-06 33.6 0.8 31 76-106 19-50 (65) 41 >1m3q_A 8-oxoguanine DNA glyco 91.5 0.24 7.1E-06 29.2 4.0 20 107-126 107-126 (133) 42 >3fsp_A A/G-specific adenine g 91.3 0.11 3.2E-06 31.6 2.0 23 104-126 81-103 (110) 43 >3e1s_A Exodeoxyribonuclease V 91.1 0.077 2.3E-06 32.5 1.2 60 67-129 6-65 (149) 44 >3bz1_U Photosystem II 12 kDa 91.0 0.13 3.9E-06 30.9 2.2 25 102-126 27-51 (104) 45 >1b43_A Protein (FEN-1); nucle 90.9 0.036 1.1E-06 34.7 -0.7 40 76-126 29-69 (77) 46 >2w9m_A Polymerase X; SAXS, DN 90.9 0.12 3.7E-06 31.1 2.0 41 84-129 38-78 (118) 47 >2duy_A Competence protein com 90.9 0.14 4.3E-06 30.7 2.3 45 72-125 26-70 (75) 48 >1exn_A 5'-exonuclease, 5'-nuc 90.7 0.071 2.1E-06 32.7 0.6 38 67-104 8-54 (80) 49 >3fhf_A Mjogg, N-glycosylase/D 90.6 0.38 1.1E-05 27.9 4.3 20 107-126 87-106 (113) 50 >1ul1_X Flap endonuclease-1; p 90.0 0.19 5.5E-06 30.0 2.3 39 92-130 13-51 (89) 51 >2izo_A FEN1, flap structure-s 89.8 0.063 1.9E-06 33.1 -0.3 30 76-105 19-49 (82) 52 >2bgw_A XPF endonuclease; hydr 89.7 0.2 6E-06 29.7 2.3 22 108-129 14-35 (49) 53 >3c1y_A DNA integrity scanning 89.6 0.68 2E-05 26.2 4.9 26 105-130 9-34 (74) 54 >1orn_A Endonuclease III; DNA 89.4 0.26 7.8E-06 28.9 2.7 20 105-124 83-102 (110) 55 >3bzc_A TEX; helix-turn-helix, 89.3 0.23 6.9E-06 29.3 2.3 49 72-126 9-58 (70) 56 >1kea_A Possible G-T mismatche 89.1 0.29 8.5E-06 28.7 2.7 20 105-124 84-103 (111) 57 >2h56_A DNA-3-methyladenine gl 89.0 0.12 3.5E-06 31.3 0.7 32 97-128 50-81 (156) 58 >1z00_B DNA repair endonucleas 89.0 0.24 7.2E-06 29.2 2.2 23 108-130 18-40 (71) 59 >1s5l_U Photosystem II 12 kDa 88.8 0.18 5.2E-06 30.1 1.4 48 73-129 16-63 (87) 60 >1pu6_A 3-methyladenine DNA gl 88.8 0.44 1.3E-05 27.4 3.5 25 102-126 93-117 (123) 61 >2ziu_B Crossover junction end 88.7 0.45 1.3E-05 27.4 3.5 60 70-129 11-88 (100) 62 >2abk_A Endonuclease III; DNA- 88.6 0.31 9.3E-06 28.4 2.6 53 72-126 50-105 (111) 63 >2a1j_A DNA repair endonucleas 88.5 0.25 7.4E-06 29.1 2.1 24 107-130 3-26 (63) 64 >2edu_A Kinesin-like protein K 88.5 0.32 9.3E-06 28.4 2.6 51 72-128 39-90 (98) 65 >1mpg_A ALKA, 3-methyladenine 88.4 0.29 8.6E-06 28.7 2.3 70 95-181 10-79 (127) 66 >1kg2_A A/G-specific adenine g 87.6 0.32 9.5E-06 28.4 2.2 31 100-130 15-45 (139) 67 >1ul1_X Flap endonuclease-1; p 86.5 0.4 1.2E-05 27.7 2.1 46 77-125 33-79 (89) 68 >1z00_A DNA excision repair pr 85.9 0.51 1.5E-05 27.0 2.4 53 107-184 18-71 (89) 69 >1x2i_A HEF helicase/nuclease; 85.8 0.48 1.4E-05 27.2 2.3 21 108-128 14-34 (49) 70 >2nrt_A Uvrabc system protein 85.6 0.58 1.7E-05 26.6 2.6 24 107-130 11-34 (64) 71 >1t94_A Polymerase (DNA direct 84.9 0.46 1.4E-05 27.3 1.8 28 94-124 1-28 (70) 72 >3i0w_A 8-oxoguanine-DNA-glyco 84.5 0.46 1.4E-05 27.3 1.6 26 65-90 25-50 (58) 73 >2kp7_A Crossover junction end 84.3 0.63 1.9E-05 26.4 2.3 24 105-128 55-78 (87) 74 >1wiv_A UBP14, ubiquitin-speci 83.9 1.8 5.2E-05 23.4 4.4 30 154-183 23-52 (73) 75 >2aq4_A DNA repair protein REV 83.8 0.55 1.6E-05 26.8 1.8 17 110-126 4-20 (67) 76 >2ztd_A Holliday junction ATP- 83.6 0.69 2E-05 26.1 2.2 59 108-188 9-68 (75) 77 >1kft_A UVRC, excinuclease ABC 83.6 0.47 1.4E-05 27.3 1.4 24 107-130 23-46 (78) 78 >2zkq_m 40S ribosomal protein 83.3 0.86 2.5E-05 25.5 2.6 22 108-129 28-49 (88) 79 >2qsf_X RAD23, UV excision rep 83.2 1.6 4.8E-05 23.7 4.0 31 154-184 20-50 (67) 80 >1x2i_A HEF helicase/nuclease; 83.1 0.58 1.7E-05 26.6 1.7 33 69-101 9-43 (49) 81 >1cuk_A RUVA protein; DNA repa 82.8 0.78 2.3E-05 25.8 2.2 60 108-189 8-68 (79) 82 >2bgw_A XPF endonuclease; hydr 82.2 0.44 1.3E-05 27.4 0.8 30 66-95 6-36 (49) 83 >3fhf_A Mjogg, N-glycosylase/D 82.1 0.61 1.8E-05 26.5 1.5 31 95-134 8-38 (113) 84 >2csb_A Topoisomerase V, TOP61 81.5 2 6E-05 23.0 4.0 30 99-128 73-102 (142) 85 >2i5h_A Hypothetical protein A 80.9 1 3.1E-05 24.9 2.3 30 105-134 129-159 (205) 86 >1oqy_A HHR23A, UV excision re 80.7 1.4 4E-05 24.2 2.9 28 156-183 13-40 (60) 87 >2jhn_A ALKA, 3-methyladenine 80.3 0.86 2.6E-05 25.5 1.7 19 107-125 30-48 (55) 88 >1wgn_A UBAP1, ubiquitin assoc 80.2 1.3 3.9E-05 24.3 2.6 30 155-184 14-43 (63) 89 >2dai_A Ubadc1, ubiquitin asso 79.6 2.8 8.4E-05 22.1 4.2 29 155-183 24-52 (83) 90 >2g3q_A Protein YBL047C; endoc 79.5 2.5 7.4E-05 22.4 3.9 26 159-184 3-28 (43) 91 >1vg5_A RSGI RUH-014, rhomboid 79.3 3.4 9.9E-05 21.6 4.5 29 156-184 25-53 (73) 92 >2zbk_B Type 2 DNA topoisomera 79.0 1.3 3.7E-05 24.4 2.3 36 94-129 9-50 (82) 93 >1jx4_A DNA polymerase IV (fam 78.7 0.92 2.7E-05 25.3 1.5 13 113-125 1-13 (55) 94 >3i1m_M 30S ribosomal protein 78.4 1.3 3.8E-05 24.4 2.1 21 108-128 17-37 (63) 95 >1ify_A HHR23A, UV excision re 78.3 2.8 8.3E-05 22.1 3.9 27 157-183 5-31 (49) 96 >1oqy_A HHR23A, UV excision re 78.0 4.2 0.00012 20.9 4.7 30 155-184 38-67 (99) 97 >2vqe_M 30S ribosomal protein 76.4 1 3.1E-05 24.9 1.2 21 108-128 17-37 (64) 98 >1wji_A Tudor domain containin 76.0 3.1 9.3E-05 21.8 3.6 24 160-183 9-32 (63) 99 >1vek_A UBP14, ubiquitin-speci 75.0 4.6 0.00014 20.7 4.2 27 158-184 27-53 (84) 100 >2cpw_A CBL-interacting protei 74.3 2.3 6.8E-05 22.6 2.5 24 161-184 20-43 (64) 101 >1veg_A NEDD8 ultimate buster- 73.5 4.2 0.00012 20.9 3.7 27 157-183 26-52 (83) 102 >2w9m_A Polymerase X; SAXS, DN 71.6 4.3 0.00013 20.8 3.4 34 94-130 2-35 (123) 103 >3ihp_A Ubiquitin carboxyl-ter 70.5 5.1 0.00015 20.4 3.6 25 159-183 13-37 (75) 104 >2dak_A Ubiquitin carboxyl-ter 70.5 4.4 0.00013 20.8 3.2 25 159-183 8-32 (63) 105 >3ihp_A Ubiquitin carboxyl-ter 69.4 3.4 0.0001 21.5 2.5 25 159-183 15-39 (70) 106 >1dgs_A DNA ligase; AMP comple 67.3 1.7 5E-05 23.6 0.6 12 76-87 18-29 (116) 107 >2dag_A Ubiquitin carboxyl-ter 66.6 6 0.00018 19.9 3.3 24 161-184 10-33 (74) 108 >1dv0_A DNA repair protein HHR 62.9 3 8.9E-05 21.9 1.2 23 161-183 5-27 (47) 109 >1whc_A RSGI RUH-027, UBA/UBX 60.5 6.8 0.0002 19.5 2.6 23 162-184 11-33 (64) 110 >1fr3_A MOP, molybdate/tungsta 59.8 12 0.00037 17.8 7.0 47 3-49 7-58 (67) 111 >3h4j_B AMPK kdaid, SNF1-like 59.3 13 0.00038 17.7 4.0 40 159-200 10-50 (65) 112 >2crn_A Ubash3A protein; compa 58.1 6.4 0.00019 19.7 2.1 23 162-184 11-33 (64) 113 >3f2b_A DNA-directed DNA polym 58.0 6.4 0.00019 19.7 2.1 18 114-131 1-18 (69) 114 >2p6r_A Afuhel308 helicase; pr 55.1 11 0.00032 18.2 2.9 51 76-133 1-53 (68) 115 >1hh2_P NUSA, N utilization su 55.0 15 0.00044 17.2 8.9 64 4-67 9-72 (87) 116 >1gnl_A HCP, hybrid cluster pr 54.6 15 0.00045 17.2 6.1 36 168-203 161-197 (218) 117 >2dna_A Unnamed protein produc 54.4 15 0.00045 17.2 3.8 26 158-183 17-43 (67) 118 >3ci0_K Pseudopilin GSPK; gene 54.0 4.9 0.00015 20.5 1.0 25 65-89 16-40 (181) 119 >3bqs_A Uncharacterized protei 51.5 8.2 0.00024 19.0 1.8 17 108-124 4-20 (93) 120 >1szp_A DNA repair protein RAD 49.5 14 0.00043 17.4 2.8 32 99-130 3-34 (56) 121 >2juj_A E3 ubiquitin-protein l 48.1 16 0.00048 17.0 2.9 21 163-183 10-30 (56) 122 >2ooa_A E3 ubiquitin-protein l 48.0 16 0.00048 17.0 2.9 21 163-183 14-34 (52) 123 >1z96_A DNA-damage, UBA-domain 47.0 17 0.00051 16.9 2.9 22 163-184 7-28 (40) 124 >2oo9_A E3 ubiquitin-protein l 46.2 16 0.00047 17.1 2.6 21 163-183 7-27 (46) 125 >3go5_A Multidomain protein wi 45.2 21 0.00062 16.2 6.8 54 4-57 20-73 (84) 126 >2d9s_A CBL E3 ubiquitin prote 44.3 18 0.00052 16.8 2.6 21 163-183 12-32 (53) 127 >3bbn_M Ribosomal protein S13; 44.2 10 0.0003 18.4 1.4 26 68-93 57-82 (145) 128 >1toa_A Tromp-1, protein (peri 43.3 23 0.00067 16.1 4.3 45 94-138 39-83 (118) 129 >1bgx_T TAQ DNA polymerase; DN 42.0 2.6 7.8E-05 22.3 -1.9 12 161-172 59-70 (167) 130 >3gfk_B DNA-directed RNA polym 40.3 25 0.00074 15.8 3.1 28 103-130 43-70 (79) 131 >1wr1_B Ubiquitin-like protein 39.7 26 0.00075 15.7 3.6 27 158-184 15-42 (58) 132 >3fia_A Intersectin-1; EH 1 do 39.0 26 0.00077 15.6 4.1 39 160-198 51-89 (121) 133 >2j8s_A ACRB, acriflavine resi 36.2 24 0.0007 15.9 2.2 24 113-136 114-137 (208) 134 >3gi1_A LBP, laminin-binding p 35.6 19 0.00056 16.6 1.6 46 94-139 39-84 (109) 135 >3fe3_A MAP/microtubule affini 35.0 30 0.00089 15.2 2.7 22 162-183 118-139 (155) 136 >1nkw_E 50S ribosomal protein 33.4 21 0.00063 16.2 1.6 62 16-79 2-70 (103) 137 >2kgr_A Intersectin-1; structu 33.2 32 0.00095 15.0 4.6 43 159-201 32-74 (111) 138 >2v50_A Multidrug resistance p 31.5 34 0.001 14.8 2.5 27 92-118 14-40 (208) 139 >1qjt_A EH1, epidermal growth 30.6 35 0.001 14.7 4.7 41 161-201 31-71 (99) 140 >1zu4_A FTSY; GTPase, signal r 29.4 34 0.001 14.9 2.1 31 95-134 37-67 (117) 141 >1z3e_B DNA-directed RNA polym 29.1 37 0.0011 14.6 3.4 50 80-131 15-64 (73) 142 >1pq4_A Periplasmic binding pr 28.9 27 0.00081 15.5 1.6 42 95-136 38-79 (82) 143 >1h9m_A MODG, molybdenum-bindi 28.7 38 0.0011 14.5 7.0 47 3-49 17-69 (72) 144 >2o1e_A YCDH; alpha-beta prote 28.1 23 0.00067 16.1 1.0 42 94-135 38-79 (82) 145 >2awn_A Maltose/maltodextrin i 28.0 39 0.0012 14.5 3.5 54 3-58 4-63 (84) 146 >3go5_A Multidomain protein wi 27.2 40 0.0012 14.4 6.1 49 4-56 9-57 (64) 147 >2qpt_A EH domain-containing p 27.0 41 0.0012 14.3 4.6 41 159-199 43-83 (118) 148 >2pmy_A RAS and EF-hand domain 26.9 41 0.0012 14.3 4.1 29 160-188 46-74 (81) 149 >3hh8_A Metal ABC transporter 26.3 42 0.0012 14.2 2.3 45 94-138 41-85 (115) 150 >2qen_A Walker-type ATPase; un 26.2 42 0.0012 14.2 2.1 33 95-127 21-53 (202) 151 >1vej_A Riken cDNA 4931431F19; 26.2 42 0.0012 14.2 4.1 26 158-183 27-53 (74) 152 >3bq0_A POL IV, DBH, DNA polym 26.0 31 0.00091 15.2 1.4 11 114-124 1-11 (51) 153 >2kld_A Polycystin-2; PC2, PKD 25.9 43 0.0013 14.2 2.6 62 116-186 30-91 (123) 154 >1d8b_A SGS1 RECQ helicase; fi 25.1 44 0.0013 14.1 2.3 21 103-123 43-63 (81) 155 >3cx3_A Lipoprotein; zinc-bind 24.5 19 0.00056 16.6 0.1 44 94-137 38-81 (85) 156 >3i1n_R 50S ribosomal protein 24.1 30 0.0009 15.2 1.1 50 16-65 2-53 (103) 157 >1jr3_A DNA polymerase III sub 23.6 47 0.0014 13.9 2.3 34 95-128 25-61 (177) 158 >1gnt_A HCP, hybrid cluster pr 23.5 47 0.0014 13.9 4.6 36 168-203 166-201 (222) 159 >1iqp_A RFCS; clamp loader, ex 23.4 48 0.0014 13.9 2.1 37 94-130 33-71 (168) 160 >3fhg_A Mjogg, N-glycosylase/D 23.3 25 0.00074 15.8 0.5 11 111-121 47-57 (69) 161 >1eh2_A EPS15; calcium binding 23.1 48 0.0014 13.9 6.0 42 159-200 32-73 (106) 162 >3b9q_A Chloroplast SRP recept 22.3 50 0.0015 13.8 2.2 30 95-133 33-62 (102) 163 >1a5t_A Delta prime, HOLB; zin 21.8 51 0.0015 13.7 2.3 35 95-129 11-48 (166) 164 >1ci4_A Protein (barrier-TO-au 21.8 38 0.0011 14.5 1.2 19 108-126 18-36 (89) 165 >1ju2_A HydroxynitrIle lyase; 21.6 32 0.00096 15.0 0.8 31 74-119 7-37 (148) 166 >2chg_A Replication factor C s 20.9 53 0.0016 13.6 2.2 38 96-133 27-67 (160) 167 >2w1o_A 60S acidic ribosomal p 20.5 54 0.0016 13.5 1.8 44 159-207 20-65 (70) 168 >2z1c_A Hydrogenase expression 20.5 54 0.0016 13.5 4.9 47 4-53 4-50 (75) 169 >1kk8_A Myosin heavy chain, st 20.3 55 0.0016 13.5 5.4 29 157-185 247-278 (490) No 1 >>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} (A:) Probab=100.00 E-value=0 Score=362.38 Aligned_cols=191 Identities=25% Similarity=0.394 Sum_probs=176.5 Q ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEECHHHHHHHHHHHHHHH Q ss_conf 93258999999609979998588323897086889850247984999999997388418999706779999999850100 Q gi|254780553|r 1 MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQG 80 (207) Q Consensus 1 MI~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~Er~~F~~Li~V~G 80 (207) ||+|++|+|.++++++++++|+|+||+|++|.++...+ +.|+++.||||+++|||++.||||.++.||++|++|++|+| T Consensus 1 MI~~l~G~v~~~~~~~~ii~~~gvGy~i~~~~~~~~~l-~~~~~~~l~~~~~vred~~~l~GF~~~~er~~F~~L~~V~G 79 (191) T 1ixr_A 1 MIRYLRGLVLKKEAGGFVLLAGGVGFFLQAPTPFLQAL-EEGKEVGVHTHLLLKEEGLSLYGFPDEENLALFELLLSVSG 79 (191) T ss_dssp CCCEEEEEEEEECSSEEEEECSSEEEEEECCHHHHHHC-CTTSEEEEEECCCCCSSCCCEEEESSHHHHHHHHHHHSSSC T ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHC-CCCCEEEEEEEEEEEECCCEEECCCCHHHHHHHHHHHCCCC T ss_conf 95669999999839979999899899999277999746-79986999999999607866771082899999999857588 Q ss_pred CCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHH Q ss_conf 05101124431578999999985156687510457116799999999742221101133443233333445555653158 Q gi|254780553|r 81 VGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFA 160 (207) Q Consensus 81 IGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (207) ||||+|++|||++++++++++|.++|.+.|+++||||+|||+||++|||+|+.++.... ....++.. T Consensus 80 IGpk~Al~iL~~~~~~el~~aI~~~d~~~L~~ipGIG~KtA~rIi~eLk~k~~~~~~~~-------------~~~~~~~~ 146 (191) T 1ixr_A 80 VGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELKGKVPPHLLAG-------------EKVESEAA 146 (191) T ss_dssp CCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHTTTSCSCC------------------------ T ss_pred CCHHHHHHHHHCCCHHHHHHHHHCCCHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCC-------------CCCCCCCH T ss_conf 47788999985599999999998289998513888456889999999986425210011-------------23355568 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHC Q ss_conf 9999999967999899999999998516888898999999999745 Q gi|254780553|r 161 INAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAIS 206 (207) Q Consensus 161 ~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk~Ls 206 (207) +|+++||.+|||++++|++++.++..+.++ .++|++||.|||+|. T Consensus 147 ~e~~~aL~~LGy~~~ea~~ai~~~~~~~~~-~~~e~li~~aLk~l~ 191 (191) T 1ixr_A 147 EEAVMALAALGFKEAQARAVVLDLLAQNPK-ARAQDLIKEALKRLR 191 (191) T ss_dssp ---------------------------------------------- T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHCC T ss_conf 999999998699999999999999842999-999999999999639 No 2 >>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:66-144) Probab=99.89 E-value=1.3e-23 Score=177.74 Aligned_cols=74 Identities=27% Similarity=0.506 Sum_probs=70.4 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 77999999985010005101124431578999999985156687510457116799999999742221101133 Q gi|254780553|r 66 DLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVV 139 (207) Q Consensus 66 ~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~ 139 (207) ++||++|++|++|+|||||+||+|||+++|++|++||.++|.+.|+++||||+|||+||++|||||+.++.... T Consensus 1 ~~Er~~F~~L~~V~GIGpk~Al~iLs~~~~~el~~aI~~~D~~~L~~ipGIG~KtAerii~eLk~K~~~~~~~~ 74 (79) T 1cuk_A 1 KQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDL 74 (79) T ss_dssp HHHHHHHHHHHHSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHHHGGGCCSTT T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCC T ss_conf 89999999873478848999999975799999999999289999841999889999999999998887531101 No 3 >>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A (A:80-154) Probab=99.89 E-value=1.4e-23 Score=177.37 Aligned_cols=73 Identities=32% Similarity=0.452 Sum_probs=69.9 Q ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCC Q ss_conf 6779999999850100051011244315789999999851566875104571167999999997422211011 Q gi|254780553|r 65 SDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSS 137 (207) Q Consensus 65 ~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~ 137 (207) +++||++|++|++|+|||||+||+|||+++|++|++||.++|.+.|+++||||+|||+||++||+||+.++.. T Consensus 1 d~~Er~~F~~L~~V~GIGpk~Al~iLs~~~~~el~~aI~~~D~~~L~~ipGIG~KtA~rii~ELk~k~~~~~~ 73 (75) T 2ztd_A 1 DGETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKVGVAAT 73 (75) T ss_dssp SHHHHHHHHHHHTSTTCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHTTTCC---- T ss_pred CHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCC T ss_conf 8999999999854132236666232215776777788853688998508883568899999998411122233 No 4 >>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:1-65) Probab=99.79 E-value=1.1e-18 Score=144.85 Aligned_cols=65 Identities=32% Similarity=0.507 Sum_probs=63.9 Q ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEEC Q ss_conf 93258999999609979998588323897086889850247984999999997388418999706 Q gi|254780553|r 1 MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLS 65 (207) Q Consensus 1 MI~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~ 65 (207) ||+||+|++.++++++++||||||||+|++|.+++.+|++.|++++||||++||||+++||||.| T Consensus 1 Mi~~l~G~v~~~~~~~vvi~~~GvGYei~is~~~~~~l~~~g~~v~l~t~~~vrEd~~~LyGF~t 65 (65) T 1cuk_A 1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNN 65 (65) T ss_dssp CCCEEEEEEEEEETTEEEEEETTEEEEEECCHHHHTTCCCTTSEEEEEEEEEEETTEEEEEEESS T ss_pred CCCEEEEEEEEECCCEEEEEECCEEEEEEECHHHHHHCCCCCCCEEEEEEEEECCCCCEEECCCC T ss_conf 95459999999629989999589889999558999863348981599999998046865756698 No 5 >>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A (A:1-79) Probab=99.75 E-value=7.5e-18 Score=139.25 Aligned_cols=63 Identities=30% Similarity=0.519 Sum_probs=61.5 Q ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEE Q ss_conf 9325899999960997999858832389708688985024798499999999738841899970 Q gi|254780553|r 1 MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFL 64 (207) Q Consensus 1 MI~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~ 64 (207) ||+||+|++.+++++++|||||||||+|++|.++++.+ +.|++++||||++||||+++||||. T Consensus 17 MI~~i~G~i~~~~~~~ivIev~GVGYeI~is~~~~~~l-~~g~ev~lyt~~~VRED~~~LYGFS 79 (79) T 2ztd_A 17 MIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATL-RQGTEARLITAMIVREDSMTLYGFP 79 (79) T ss_dssp SCCEEEEEEEEECSSEEEEEETTEEEEEECCHHHHTTC-CTTSEEEEEEEEEEETTEEEEEEES T ss_pred CEEEEEEEEEEECCCEEEEEECCEEEEEEECHHHHHHC-CCCCEEEEEEEEEEECCHHEEEEEC T ss_conf 31689999999719989999799889998378999975-8998489999999825701067527 No 6 >>1ixs_A Holliday junction DNA helicase RUVA; heterodimeric protein complex, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.20A {Thermus thermophilus} (A:) Probab=98.71 E-value=2.8e-08 Score=75.48 Aligned_cols=52 Identities=25% Similarity=0.346 Sum_probs=46.0 Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH Q ss_conf 55653158999999996799989999999999851688889899999999974 Q gi|254780553|r 153 ICSMPSFAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAI 205 (207) Q Consensus 153 ~~~~~~~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk~L 205 (207) ....++..+||++||++|||++.+|++++.++..+.++. ++|++||.|||.| T Consensus 10 ~~~~~~~~~eAv~AL~~LGy~~~ea~kav~~i~~~~~~~-sveelIr~ALk~L 61 (62) T 1ixs_A 10 EKVESEAAEEAVMALAALGFKEAQARAVVLDLLAQNPKA-RAQDLIKEALKRL 61 (62) T ss_dssp ---CCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTC-CHHHHHHHHHTTC T ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHC T ss_conf 866661078899999996421789999999998738542-3999999998754 No 7 >>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A (A:155-212) Probab=98.69 E-value=4.6e-08 Score=73.97 Aligned_cols=51 Identities=29% Similarity=0.381 Sum_probs=45.4 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHC Q ss_conf 6531589999999967999899999999998516888898999999999745 Q gi|254780553|r 155 SMPSFAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAIS 206 (207) Q Consensus 155 ~~~~~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk~Ls 206 (207) ..++..+|+++||++|||++.|+.+++..+..++++ .+++++||.|||+|+ T Consensus 5 ~~~~~~~da~~AL~aLGy~~~ea~~av~~v~~~~~~-~~~~elIr~ALk~L~ 55 (58) T 2ztd_A 5 NGHAVRSPVVEALVGLGFAAKQAEEATDTVLAANHD-ATTSSALRSALSLLG 55 (58) T ss_dssp ---CCHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHT T ss_pred CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHH T ss_conf 653216899999997599989999999999840899-999999999999974 No 8 >>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:145-203) Probab=98.54 E-value=1.3e-07 Score=71.04 Aligned_cols=50 Identities=30% Similarity=0.370 Sum_probs=42.7 Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH Q ss_conf 55653158999999996799989999999999851688889899999999974 Q gi|254780553|r 153 ICSMPSFAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAI 205 (207) Q Consensus 153 ~~~~~~~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk~L 205 (207) ....++..+|+++||++|||++.|+.+++..+. .+..++|++||.|||.| T Consensus 9 ~~~~~~~~~eAv~AL~aLGY~~~ea~kav~~i~---~~~~s~eelIk~ALk~L 58 (59) T 1cuk_A 9 SPATDDAEQEAVARLVALGYKPQEASRMVSKIA---RPDASSETLIREALRAA 58 (59) T ss_dssp ---CCHHHHHHHHHHHHHTCCHHHHHHHHHHSC---CSSCCHHHHHHHHHHTT T ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH---CCCCCHHHHHHHHHHHC T ss_conf 767773599999999986999999999999861---68999999999999970 No 9 >>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* (A:304-377) Probab=97.72 E-value=2.8e-05 Score=55.38 Aligned_cols=60 Identities=17% Similarity=0.263 Sum_probs=51.0 Q ss_pred HHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 999999850100051011244315789999999851566875104571167999999997422 Q gi|254780553|r 69 RQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGK 131 (207) Q Consensus 69 r~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K 131 (207) +.+-+.|.+|.||||+.|-.+++.+.. ...|.+.+...|.++||||+++|+.|.--+++. T Consensus 8 ~~~~~~L~~I~giG~~~a~~L~~~fgs---l~~i~~as~~~L~~v~GiG~~~A~~i~~~~~~~ 67 (74) T 3c1y_A 8 ARGYRLLKTVARIPLSIGYNVVRMFKT---LDQISKASVEDLKKVEGIGEKRARAISESISSL 67 (74) T ss_dssp CCSHHHHHHTSCCCHHHHHHHHHHHCS---HHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHHH T ss_pred CHHHHHHHCCCCCCHHHHHHHHHHHCC---HHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 316888733999989999999998538---999985799888544784699999999999998 No 10 >>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (A:) Probab=97.52 E-value=0.00012 Score=51.13 Aligned_cols=57 Identities=21% Similarity=0.294 Sum_probs=48.2 Q ss_pred HHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 999985010005101124431578999999985156687510457116799999999742 Q gi|254780553|r 71 WFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 71 ~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) +...|.+|.||||+.|-.++..++. .+.+.+.+...|.++||||++.|+.|.--+++ T Consensus 17 ~l~~L~~I~gIG~~~a~~L~~~F~s---~~~i~~A~~~~L~~v~GiG~~~A~~i~~~~~~ 73 (89) T 1z00_A 17 VTECLTTVKSVNKTDSQTLLTTFGS---LEQLIAASREDLALCPGLGPQKARRLFDVLHE 73 (89) T ss_dssp HHHHHTTSSSCCHHHHHHHHHHTCB---HHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHS T ss_pred HHHHHCCCCCCCHHHHHHHHHHHCC---CHHHHHHHHHHHCHHCCCCHHHHHHHHHHHHC T ss_conf 9998658997699999999999099---47876654751000033279999999999818 No 11 >>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} (A:1-95) Probab=97.41 E-value=6.1e-05 Score=53.18 Aligned_cols=62 Identities=18% Similarity=0.257 Sum_probs=51.1 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHCC-C-CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 779999999850100051011244315-7-89999999851566875104571167999999997422 Q gi|254780553|r 66 DLDRQWFMLLQSVQGVGARVAMGVLSR-I-TATELVESIILQNSKVIAQIPGISMKIASRIMTELKGK 131 (207) Q Consensus 66 ~~Er~~F~~Li~V~GIGpK~AL~iLs~-l-~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K 131 (207) +.....|..+.+|+|||++.|-.++.. + +++ .|.+.+...|.++||||+++|++|+-.+++. T Consensus 28 ~~~~~~~~~ll~I~gIG~~~a~~L~~~~~~s~e----~i~~As~e~L~~i~Gig~~~A~~I~~~~~~~ 91 (95) T 1pzn_A 28 KKKEKIIRSIEDLPGVGPATAEKLREAGYDTLE----AIAVASPIELKEVAGISEGTALKIIQAARKA 91 (95) T ss_dssp -------CCSSCCTTCCHHHHHHHHTTTCCSHH----HHHTCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_pred CCHHHHHCCHHHCCCCCHHHHHHHHHCCCCCHH----HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 110233214643799799999999985997199----9982899999975498999999999999873 No 12 >>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} (A:) Probab=97.38 E-value=0.00011 Score=51.40 Aligned_cols=57 Identities=26% Similarity=0.423 Sum_probs=45.3 Q ss_pred HHHH-HHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 9999-98501000510112443157899999998515668751045711679999999974 Q gi|254780553|r 70 QWFM-LLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207) Q Consensus 70 ~~F~-~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207) +.|. .|.+|.||||+.|-.++..+.. +..|.+-+..-|.+++|||+++|++|.--|+ T Consensus 20 ~~~~~~L~~I~gIG~~~a~~L~~~Fgs---~~~i~~As~eeL~~v~gIG~~~A~~I~~~l~ 77 (78) T 1kft_A 20 HMNTSSLETIEGVGPKRRQMLLKYMGG---LQGLRNASVEEIAKVPGISQGLAEKIFWSLK 77 (78) T ss_dssp ---CCGGGGCTTCSSSHHHHHHHHHSC---HHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHCCC---HHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC T ss_conf 203284656999479999999999099---8999857899997389989999999999976 No 13 >>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} (A:1-66) Probab=96.83 E-value=0.00071 Score=46.06 Aligned_cols=23 Identities=30% Similarity=0.481 Sum_probs=20.2 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 68751045711679999999974 Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTELK 129 (207) Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ELk 129 (207) +..|+++||||+|||+|+.+.|= T Consensus 11 I~~l~~LPGIG~KsA~Rla~~lL 33 (66) T 1vdd_A 11 IRELSRLPGIGPKSAQRLAFHLF 33 (66) T ss_dssp HHHHHTSTTCCHHHHHHHHHHHS T ss_pred HHHHHHCCCCCHHHHHHHHHHHH T ss_conf 99996789988999999999997 No 14 >>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:1-118) Probab=96.67 E-value=0.0011 Score=44.75 Aligned_cols=52 Identities=13% Similarity=0.104 Sum_probs=22.1 Q ss_pred HHHHHHHHCCCHHHHHHHCCC---CHHHHHH--HHHCCCHHHHHHCCCCCHHHHHHH Q ss_conf 998501000510112443157---8999999--985156687510457116799999 Q gi|254780553|r 73 MLLQSVQGVGARVAMGVLSRI---TATELVE--SIILQNSKVIAQIPGISMKIASRI 124 (207) Q Consensus 73 ~~Li~V~GIGpK~AL~iLs~l---~~~~l~~--aI~~~D~~~L~~vpGIGkKtA~rI 124 (207) +.+.+++||||++|-.|-.-+ .+..+.. .=.-.....|.+|||||+|||+++ T Consensus 57 ~~l~~lpGIG~~~a~kI~E~l~tG~~~~le~l~~~~~~~l~~l~~i~GiGp~ta~~l 113 (118) T 2w9m_A 57 REFTGIPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLGVRGLGPKKIRSL 113 (118) T ss_dssp --CCSSTTCCHHHHHHHHHHHHHSSCHHHHHHHHHSCHHHHHHTTSTTCCHHHHHHH T ss_pred HHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHCCCCCCHHHHHHH T ss_conf 886259998789999999999849828899987025178999857898789999999 No 15 >>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} (A:1-119) Probab=96.30 E-value=0.0021 Score=42.93 Aligned_cols=51 Identities=16% Similarity=0.245 Sum_probs=20.5 Q ss_pred HHHHHHCCCHHHHHHH---CCCCHHHHHHHHHCCC---HHHHHHCCCCCHHHHHHHH Q ss_conf 8501000510112443---1578999999985156---6875104571167999999 Q gi|254780553|r 75 LQSVQGVGARVAMGVL---SRITATELVESIILQN---SKVIAQIPGISMKIASRIM 125 (207) Q Consensus 75 Li~V~GIGpK~AL~iL---s~l~~~~l~~aI~~~D---~~~L~~vpGIGkKtA~rIi 125 (207) +.+++|||+++|=.|- .+-...++-..-.+.. ...|.+|+|||+|||.++. T Consensus 59 ~~~lpgiG~~ia~~I~e~l~tG~~~~le~l~~~~~~~~~~~l~~i~GvGp~~a~~~~ 115 (119) T 2fmp_A 59 AKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFV 115 (119) T ss_dssp HHTSTTCCHHHHHHHHHHHHHSSCHHHHHHHHCHHHHHHHHHTTSTTCCHHHHHHHH T ss_pred HHCCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHH T ss_conf 847999648999999999964865899998733872578898853687889999999 No 16 >>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} (A:1-129) Probab=96.20 E-value=0.0016 Score=43.69 Aligned_cols=50 Identities=20% Similarity=0.232 Sum_probs=20.1 Q ss_pred HHHHHHCCCHHHHHHHC---CCCHHHHHHHHHCC---CHHHHHHCCCCCHHHHHHH Q ss_conf 85010005101124431---57899999998515---6687510457116799999 Q gi|254780553|r 75 LQSVQGVGARVAMGVLS---RITATELVESIILQ---NSKVIAQIPGISMKIASRI 124 (207) Q Consensus 75 Li~V~GIGpK~AL~iLs---~l~~~~l~~aI~~~---D~~~L~~vpGIGkKtA~rI 124 (207) +.+++|||+++|=.|-. +-...++-..=.+. -...|++|||||+|||.++ T Consensus 63 ~~~lpgIG~~ia~~I~E~l~tG~~~~le~l~~~~~~~~l~~l~~i~GvG~~~a~~~ 118 (129) T 2ihm_A 63 LHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRW 118 (129) T ss_dssp GTTCTTCCHHHHHHHHHHHHHSCCHHHHHHHHSHHHHHHHHHHTSTTCCHHHHHHH T ss_pred HHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH T ss_conf 83599977899999999997098899998863203689999985557788999999 No 17 >>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B (A:) Probab=95.93 E-value=0.0071 Score=39.41 Aligned_cols=56 Identities=20% Similarity=0.280 Sum_probs=45.8 Q ss_pred HHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 9985010005101124431578999999985156687510457116799999999742 Q gi|254780553|r 73 MLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 73 ~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) ..|..+.||||+.|-.+-+. ... =+..++.-+..-|..++|||.++|++|+..-+. T Consensus 7 ~~L~~i~Gig~~~a~~L~~a-Gi~-TvedLa~a~~~eL~~i~Gi~~~~A~~ii~~Ar~ 62 (70) T 1wcn_A 7 DDLLNLEGVDRDLAFKLAAR-GVC-TLEDLAEQGIDDLADIEGLTDEKAGALIMAARN 62 (70) T ss_dssp HHHHSSTTCCHHHHHHHHTT-TCC-SHHHHHTSCHHHHHTSSSCCHHHHHHHHHHHHH T ss_pred HHHHHCCCCCHHHHHHHHHC-CCC-CHHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHH T ss_conf 89981789899999999996-997-599998729999976517999999999999986 No 18 >>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A (A:157-220) Probab=95.90 E-value=0.0062 Score=39.81 Aligned_cols=54 Identities=22% Similarity=0.378 Sum_probs=42.3 Q ss_pred HHHHH-HHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 99999-98501000510112443157899999998515668751045711679999999 Q gi|254780553|r 69 RQWFM-LLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 69 r~~F~-~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207) ++.|. .|.++.||||+.|..++..+.. ++.|.+-+...|.+|+|||+ +|+.|.- T Consensus 7 ~~~~~~~L~~I~gIG~~~a~~L~~~F~s---~~~i~~As~eeL~~v~gig~-~A~~I~~ 61 (64) T 2nrt_A 7 KESLRSVLDNVPGIGPIRKKKLIEHFGS---LENIRSASLEEIARVIGSTE-IARRVLD 61 (64) T ss_dssp HHHHHHHHTTSTTCCHHHHHHHHHHHCS---HHHHHTSCHHHHHHHHTCHH-HHHHHHH T ss_pred HHHHCCHHHCCCCCCHHHHHHHHHHCCC---HHHHHCCCHHHHHHCCCCHH-HHHHHHH T ss_conf 3420152220531079999999998689---99997099999986879299-9999999 No 19 >>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} (A:1-154) Probab=95.84 E-value=0.0044 Score=40.79 Aligned_cols=88 Identities=17% Similarity=0.131 Sum_probs=42.5 Q ss_pred CHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH-HHHHCCCCCCCCCCCCCCCCCCCCCCCCHHH Q ss_conf 101124431578999999985156687510457116799999999742-2211011334432333334455556531589 Q gi|254780553|r 83 ARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG-KAISLSSVVQQDMSCVNKEQAHICSMPSFAI 161 (207) Q Consensus 83 pK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~-K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (207) -+.|...|..++.. -.+...+.++||||+++|++|.--|.. ++..+.... .+... T Consensus 62 Yr~Aa~~l~~~p~~-------I~s~~~l~~lpgIG~~ia~~I~E~l~tG~l~~le~l~-----------------~~~~~ 117 (154) T 1jms_A 62 FMRASSVLKSLPFP-------ITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVL-----------------NDERY 117 (154) T ss_dssp HHHHHHHHHTCSSC-------CCSGGGGTTCSSCCHHHHHHHHHHHHHSSCHHHHHHH-----------------HCHHH T ss_pred HHHHHHHHHHCCCC-------CCCHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHH-----------------HCCCC T ss_conf 99999999859977-------7999998379996499999999999969889899987-----------------26653 Q ss_pred HHHHHHHH-CCCCHHHHHHHHHHHHHHCCCCCCHHHHHHH Q ss_conf 99999996-7999899999999998516888898999999 Q gi|254780553|r 162 NAISALVN-LGYGQDQATTAVVSVLKKEKNIADDSQIIRL 200 (207) Q Consensus 162 d~~~AL~~-LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~ 200 (207) .++.-|.. .|-.++-|++... ....+.+++.+. T Consensus 118 ~~~~~l~~i~GiGp~~a~~~~~------~Gi~sl~dL~~a 151 (154) T 1jms_A 118 KSFKLFTSVFGVGLKTAEKWFR------MGFRTLSKIQSD 151 (154) T ss_dssp HHHHHHHTSTTCCHHHHHHHHH------TTCCSHHHHHHC T ss_pred HHHHHHHHCCCCCHHHHHHHHH------CCCCCHHHHHHH T ss_conf 0788888567879999999998------598889999874 No 20 >>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} (A:) Probab=95.24 E-value=0.018 Score=36.78 Aligned_cols=53 Identities=13% Similarity=0.268 Sum_probs=38.7 Q ss_pred HHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 985010005101124431578999999985156687510457116799999999742 Q gi|254780553|r 74 LLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 74 ~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) .|.++.||||+.|-.+++.+.. .+.|.+-+..-|.++|| |+++|+.|.--|+. T Consensus 5 ~L~~IpgVG~~~a~~Ll~~f~S---i~~i~~As~eeL~~i~g-g~~~A~~i~~~l~~ 57 (63) T 2a1j_A 5 FLLKMPGVNAKNCRSLMHHVKN---IAELAALSQDELTSILG-NAANAKQLYDFIHT 57 (63) T ss_dssp HHHTSTTCCHHHHHHHHHHCSS---HHHHHTCCHHHHHHHHS-CHHHHHHHHHHHHC T ss_pred HHHCCCCCCHHHHHHHHHHHCC---HHHHHHCCHHHHHHCCC-CHHHHHHHHHHHCC T ss_conf 8851999899999999998078---99998699999977859-68999999999822 No 21 >>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (B:1-71) Probab=95.01 E-value=0.014 Score=37.40 Aligned_cols=51 Identities=14% Similarity=0.229 Sum_probs=38.4 Q ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 9998501000510112443157899999998515668751045711679999999 Q gi|254780553|r 72 FMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 72 F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207) -..|..+.|||||.+-.+|+.+.. ++.|.+-+...|..+||+ +|+|++|.- T Consensus 17 ~~~L~~ipGIg~k~~~~Ll~~f~s---i~~i~~As~eeL~~v~G~-~~~A~~i~~ 67 (71) T 1z00_B 17 QDFLLKMPGVNAKNCRSLMHHVKN---IAELAALSQDELTSILGN-AANAKQLYD 67 (71) T ss_dssp HHHHHTCSSCCHHHHHHHHHHSSC---HHHHHHSCHHHHHHHHSC-HHHHHHHHH T ss_pred HHHHHCCCCCCHHHHHHHHHHCCC---HHHHHHCCHHHHHHCCCC-HHHHHHHHH T ss_conf 999980899889999999999079---999987899999887597-899999999 No 22 >>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanococcus jannaschii} (A:210-274) Probab=94.94 E-value=0.021 Score=36.26 Aligned_cols=37 Identities=16% Similarity=0.271 Sum_probs=28.9 Q ss_pred CHHHHHH-HHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 8999999-985156687510457116799999999742 Q gi|254780553|r 94 TATELVE-SIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 94 ~~~~l~~-aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) +|++|+. ++..||..-+..|||||+|||-+++-+.++ T Consensus 1 tp~q~id~~~L~G~d~nipGV~GIGpKtA~~li~~~~~ 38 (65) T 1a76_A 1 SLDDLIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVA 38 (65) T ss_dssp CHHHHHHHHHHHCCTTSTTTTTTCCHHHHHHHHHHTCH T ss_pred CHHHHHHHHHHCCCCCCCCCCCCEEHHHHHHHHHHCCC T ss_conf 89999999985697556555685629999999997299 No 23 >>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} (A:) Probab=94.79 E-value=0.0058 Score=39.97 Aligned_cols=53 Identities=19% Similarity=0.325 Sum_probs=24.7 Q ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 999850100051011244315789999999851566875104571167999999997 Q gi|254780553|r 72 FMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTEL 128 (207) Q Consensus 72 F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~EL 128 (207) +..+.++.||||++|-.++..+..= ++|.+-....| ..-|||+++|++|.--| T Consensus 172 ~~~~~~I~~IG~~~a~~Ll~~Fgsl---~~i~~As~eeL-~~vgiG~~~A~~I~~~f 224 (226) T 3c65_A 172 HSVLDDIPGVGEKRKKALLNYFGSV---KKMKEATVEEL-QRANIPRAVAEKIYEKL 224 (226) T ss_dssp --------------------------------------------------------- T ss_pred CCHHHHHHHHCHHHHHHHHHHCCCH---HHHHHCCHHHH-HHCCCCHHHHHHHHHHH T ss_conf 1768899874799999999985899---99983999999-87799999999999996 No 24 >>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} (A:1-128) Probab=94.59 E-value=0.006 Score=39.86 Aligned_cols=72 Identities=21% Similarity=0.275 Sum_probs=40.1 Q ss_pred CCHHHHHHCCCCCHHHHHHHHHHHHHH-HHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH-CCCCHHHHHHHHH Q ss_conf 566875104571167999999997422-21101133443233333445555653158999999996-7999899999999 Q gi|254780553|r 105 QNSKVIAQIPGISMKIASRIMTELKGK-AISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVN-LGYGQDQATTAVV 182 (207) Q Consensus 105 ~D~~~L~~vpGIGkKtA~rIi~ELk~K-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL~~-LGy~~~ea~~ai~ 182 (207) .+...+.++||||+|+|++|--=|... +..+... .....++..|.+ -|-.+.-|++... T Consensus 54 ~s~~~~~~lpgIG~~ia~~I~E~l~tG~~~~le~l-------------------~~~~~~~~~~~~i~GiG~~~a~~~~~ 114 (128) T 2bcq_A 54 TSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHI-------------------SESVPVLELFSNIWGAGTKTAQMWYQ 114 (128) T ss_dssp CCHHHHHTSTTCCHHHHHHHHHHHHSSSCGGGGGC-------------------CTTHHHHHHHHTSTTCCHHHHHHHHH T ss_pred CCHHHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHH-------------------CCCCCHHHCCCCCCCCCHHHHHHHHH T ss_conf 89999827999648999999999973978888743-------------------03366133144567778899999986 Q ss_pred HHHHHCCCCCCHHHHHHHH Q ss_conf 9985168888989999999 Q gi|254780553|r 183 SVLKKEKNIADDSQIIRLA 201 (207) Q Consensus 183 ~i~~~~~~~~~~eelIk~a 201 (207) ....+.+++.+.| T Consensus 115 ------~g~~tl~dL~~~a 127 (128) T 2bcq_A 115 ------QGFRSLEDIRSQA 127 (128) T ss_dssp ------TTCCSHHHHHHHC T ss_pred ------CCCCCHHHHHHHH T ss_conf ------2826799987542 No 25 >>1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} (A:1-129) Probab=94.37 E-value=0.027 Score=35.49 Aligned_cols=45 Identities=9% Similarity=0.056 Sum_probs=30.7 Q ss_pred HHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 501000510112443157899999998515668751045711679999999 Q gi|254780553|r 76 QSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 76 i~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207) +.--|...+.|-.|. ++.+.+..+..+.|+++||||+|||+=+.+ T Consensus 78 i~~~G~~~~Ka~~i~------~~a~~~~~e~~~~L~~l~GIG~~tA~~vll 122 (129) T 1ngn_A 78 LKPLGLYDLRAKTII------KFSDEYLTKQWRYPIELHGIGKYGNDSYRI 122 (129) T ss_dssp TGGGSCHHHHHHHHH------HHHHHHHHSCCSSGGGSTTCCHHHHHHHHH T ss_pred HHCCCHHHHHHHHHH------HHHHHHHHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 812447999999999------998246663476656279966899999999 No 26 >>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; NMR {Homo sapiens} (A:) Probab=94.21 E-value=0.015 Score=37.20 Aligned_cols=58 Identities=21% Similarity=0.179 Sum_probs=46.7 Q ss_pred HHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHH Q ss_conf 998501000510112443157899999998515668751045711679999999974222 Q gi|254780553|r 73 MLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKA 132 (207) Q Consensus 73 ~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~ 132 (207) ..|..+.||||++|=.+-+ .... =+..++.-+...|.+++|+|.++|++|+-..++-. T Consensus 25 ~~l~~i~GVG~~~~~~L~~-~Gi~-Tv~~la~~~~~~L~~i~G~~~~~a~~i~~~ar~~~ 82 (114) T 1b22_A 25 ISRLEQCGINANDVKKLEE-AGFH-TVEAVAYAPKKELINIKGISEAKADKILAEAAKLV 82 (114) T ss_dssp HHHHHHTTCSHHHHHHHHT-TCCS-SGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHHHHS T ss_pred HHHHHHCCCCHHHHHHHHH-CCCC-HHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHHHC T ss_conf 8999768999899999999-6985-39999858999998620636999999999999866 No 27 >>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase/DNA complex; 2.00A {Archaeoglobus fulgidus} (A:221-288) Probab=93.17 E-value=0.064 Score=33.05 Aligned_cols=36 Identities=17% Similarity=0.269 Sum_probs=22.6 Q ss_pred HHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 999999985156687510457116799999999742 Q gi|254780553|r 95 ATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 95 ~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) |++|+..-.---...+..|||||+|||-+++-+..+ T Consensus 2 ~~q~~d~~~L~GsD~~pGV~GIG~ktA~~li~~~~s 37 (68) T 1rxw_A 2 REQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGD 37 (68) T ss_dssp HHHHHHHHHHHCBTTBCCCTTCCHHHHHHHHHHHSS T ss_pred HHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCC T ss_conf 999989998339743589999578999999999499 No 28 >>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} (A:182-261) Probab=93.08 E-value=0.09 Score=32.04 Aligned_cols=38 Identities=18% Similarity=0.268 Sum_probs=27.0 Q ss_pred CCHHHHHHH-HHCCC-HHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 789999999-85156-687510457116799999999742 Q gi|254780553|r 93 ITATELVES-IILQN-SKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 93 l~~~~l~~a-I~~~D-~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) ++|++++.. +..|| ..-+-.|||||+|||.+++-+..+ T Consensus 5 v~p~q~~d~~~L~GD~sD~ipGV~GIG~ktA~~Li~~~gs 44 (80) T 1exn_A 5 DDVEQFISLKAIXGDLGDNIRGVEGIGAKRGYNIIREFGN 44 (80) T ss_dssp SSHHHHHHHHHHHCBGGGTBCCCTTCCHHHHHHHHHHHCS T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCC T ss_conf 9899999999971983136899997679999999999599 No 29 >>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication; 2.00A {Pyrococcus furiosus} (A:212-288) Probab=92.98 E-value=0.064 Score=33.04 Aligned_cols=38 Identities=29% Similarity=0.394 Sum_probs=31.2 Q ss_pred CCHHHHHH-HHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 78999999-985156687510457116799999999742 Q gi|254780553|r 93 ITATELVE-SIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 93 l~~~~l~~-aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) ++|++++. ++..||.--+..|||||+|||-+++-+..+ T Consensus 10 ~~~~q~id~~~L~G~d~ni~GV~GiG~ktA~kli~~~gs 48 (77) T 1b43_A 10 LTREKLIELAILVGTDYNPGGIKGIGLKKALEIVRHSKD 48 (77) T ss_dssp CCHHHHHHHHHHHCCTTSTTCSTTCCHHHHHHHHHTCSS T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCC T ss_conf 789999999997286656565896249999999999599 No 30 >>3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3a0b_U* 3a0h_U* (U:) Probab=92.87 E-value=0.042 Score=34.25 Aligned_cols=48 Identities=13% Similarity=0.227 Sum_probs=33.9 Q ss_pred HHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 998501000510112443157899999998515668751045711679999999974 Q gi|254780553|r 73 MLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207) Q Consensus 73 ~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207) ..|..+.||||+.|-+|+..-+. ....-|.+++|||.++-++|---++ T Consensus 33 ~~L~~ipGig~~~A~~Iv~~gpf---------~s~~dL~~v~gi~~~~~~~i~~~l~ 80 (104) T 3bz1_U 33 AAFIQYRGLYPTLAKLIVKNAPY---------ESVEDVLNIPGLTERQKQILRENLE 80 (104) T ss_dssp GGGGGSTTTTHHHHHHHHHSCCC---------SSGGGGGGCTTCCHHHHHHHHHHGG T ss_pred HHHHHCCCCCHHHHHHHHHCCCC---------CCHHHHHCCCCCCHHHHHHHHHHHC T ss_conf 99977758699999999970897---------8799996179989999999998761 No 31 >>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A (A:111-127,A:196-236) Probab=92.78 E-value=0.073 Score=32.64 Aligned_cols=35 Identities=11% Similarity=0.104 Sum_probs=24.5 Q ss_pred CCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 57899999998515668751045711679999999 Q gi|254780553|r 92 RITATELVESIILQNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 92 ~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207) .++.+.+...=..+=.+.|+++||||+|||+=+.+ T Consensus 17 ~Ldl~~L~~l~~eea~~~L~~i~GIGpwTAdciLL 51 (58) T 3i0w_A 17 NLNLEYIKSLNDNECHEELKKFMGVGPQVADCIML 51 (58) T ss_dssp TSCHHHHHHSCHHHHHHHHTTSTTCCHHHHHHHHH T ss_pred HCCHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 57989973135446789998268812999999999 No 32 >>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} (A:) Probab=92.44 E-value=0.29 Score=28.66 Aligned_cols=60 Identities=17% Similarity=0.297 Sum_probs=36.1 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHC-CCCHHHHHHHHHHHH Q ss_conf 6875104571167999999997422211011334432333334455556531589999999967-999899999999998 Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNL-GYGQDQATTAVVSVL 185 (207) Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL~~L-Gy~~~ea~~ai~~i~ 185 (207) -..|.+|||||+|+|.+|+-.+.-.- +...+.. .-..+|..+ |-.++-|++.+.... T Consensus 71 F~~L~~V~GIGpk~Al~iL~~~~~~e--l~~aI~~--------------------~d~~~L~~ipGIG~KtA~rIi~eLk 128 (191) T 1ixr_A 71 FELLLSVSGVGPKVALALLSALPPRL--LARALLE--------------------GDARLLTSASGVGRRLAERIALELK 128 (191) T ss_dssp HHHHHSSSCCCHHHHHHHHHHSCHHH--HHHHHHT--------------------TCHHHHTTSTTCCHHHHHHHHHHHT T ss_pred HHHHHCCCCCCHHHHHHHHHCCCHHH--HHHHHHC--------------------CCHHHHCCCCCCCHHHHHHHHHHHH T ss_conf 99985758847788999985599999--9999982--------------------8999851388845688999999998 Q ss_pred HHC Q ss_conf 516 Q gi|254780553|r 186 KKE 188 (207) Q Consensus 186 ~~~ 188 (207) .+. T Consensus 129 ~k~ 131 (191) T 1ixr_A 129 GKV 131 (191) T ss_dssp TTS T ss_pred HHC T ss_conf 642 No 33 >>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase/DNA complex; 2.00A {Archaeoglobus fulgidus} (A:221-288) Probab=92.28 E-value=0.052 Score=33.66 Aligned_cols=30 Identities=17% Similarity=0.337 Sum_probs=24.9 Q ss_pred HHHHCCCHHHHHHHCCC-CHHHHHHHHHCCC Q ss_conf 01000510112443157-8999999985156 Q gi|254780553|r 77 SVQGVGARVAMGVLSRI-TATELVESIILQN 106 (207) Q Consensus 77 ~V~GIGpK~AL~iLs~l-~~~~l~~aI~~~D 106 (207) +|.|||||+|+.+++.+ +.+.+.+.+..-. T Consensus 19 GV~GIG~ktA~~li~~~~sle~i~~~~~~~~ 49 (68) T 1rxw_A 19 GVKGVGVKKALNYIKTYGDIFRALKALKVNI 49 (68) T ss_dssp CCTTCCHHHHHHHHHHHSSHHHHHHHHTC-- T ss_pred CCCCCCHHHHHHHHHHHCCHHHHHHHHHHCH T ss_conf 9999578999999999499999999876142 No 34 >>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} (A:499-568) Probab=92.04 E-value=0.22 Score=29.45 Aligned_cols=25 Identities=20% Similarity=0.429 Sum_probs=14.1 Q ss_pred CCCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 1566875104571167999999997 Q gi|254780553|r 104 LQNSKVIAQIPGISMKIASRIMTEL 128 (207) Q Consensus 104 ~~D~~~L~~vpGIGkKtA~rIi~EL 128 (207) .-+...|.++||||++.|++|+-.. T Consensus 6 ~A~~~~L~~lpgig~~~A~~Ii~~R 30 (70) T 3bzc_A 6 TASAALLARISGLNSTLAQNIVAHR 30 (70) T ss_dssp TCCHHHHHTSTTCCHHHHHHHHHHH T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHH T ss_conf 7548888660697889999999999 No 35 >>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=92.04 E-value=0.33 Score=28.31 Aligned_cols=33 Identities=12% Similarity=0.102 Sum_probs=24.7 Q ss_pred HHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 999999851566875104571167999999997 Q gi|254780553|r 96 TELVESIILQNSKVIAQIPGISMKIASRIMTEL 128 (207) Q Consensus 96 ~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~EL 128 (207) ....--|.+.+...|.++||||++.|++|+-.= T Consensus 28 ~~~~idiNtAs~~eL~~lpgig~~~A~~Ii~~R 60 (98) T 2edu_A 28 QKILDLLNEGSARDLRSLQRIGPKKAQLIVGWR 60 (98) T ss_dssp HHHHHHHHHSCHHHHHHSTTCCHHHHHHHHHHH T ss_pred CCCCCCCCCCCHHHHHHCCCCCHHHHHHHHHHH T ss_conf 422441357999999757898999999999999 No 36 >>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} (U:48-134) Probab=92.00 E-value=0.09 Score=32.04 Aligned_cols=22 Identities=23% Similarity=0.259 Sum_probs=11.7 Q ss_pred CCHHHHHHCCCCCHHHHHHHHH Q ss_conf 5668751045711679999999 Q gi|254780553|r 105 QNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 105 ~D~~~L~~vpGIGkKtA~rIi~ 126 (207) -+...|.++||||+++|+||+- T Consensus 13 A~~~~L~~ipGig~~~A~~Iv~ 34 (87) T 1s5l_U 13 TNIAAFIQYRGLYPTLAKLIVK 34 (87) T ss_dssp SCGGGGGGSTTCTHHHHHHHHH T ss_pred CCHHHHHHHHHHHHHHHHHHHH T ss_conf 7899997710346999999998 No 37 >>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-binding, excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} (A:219-300) Probab=91.86 E-value=0.065 Score=32.99 Aligned_cols=37 Identities=22% Similarity=0.310 Sum_probs=29.0 Q ss_pred CHHHHHH-HHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 8999999-985156687510457116799999999742 Q gi|254780553|r 94 TATELVE-SIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 94 ~~~~l~~-aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) +|++|+. ++..||..-+..|||||+|||-+++-+..+ T Consensus 1 Tp~q~~d~~~L~G~d~ni~GV~GiG~ktA~~li~~~g~ 38 (82) T 2izo_A 1 TREQLIDIGILIGTDYNPDGIRGIGPERALKIIKKYGK 38 (82) T ss_dssp CHHHHHHHHHHHCCSSSTTCSTTCCHHHHHHHHHHSSC T ss_pred CHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCC T ss_conf 99999999986288654334799448899999998399 No 38 >>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A (A:230-311) Probab=91.83 E-value=0.13 Score=31.09 Aligned_cols=59 Identities=17% Similarity=0.223 Sum_probs=45.5 Q ss_pred HHHHHHHHHHHCCCHHHHHHHCCC-CHHHHHHHHHCCC-----HHHHHHCCC------CCHHHHHHHHHHH Q ss_conf 999998501000510112443157-8999999985156-----687510457------1167999999997 Q gi|254780553|r 70 QWFMLLQSVQGVGARVAMGVLSRI-TATELVESIILQN-----SKVIAQIPG------ISMKIASRIMTEL 128 (207) Q Consensus 70 ~~F~~Li~V~GIGpK~AL~iLs~l-~~~~l~~aI~~~D-----~~~L~~vpG------IGkKtA~rIi~EL 128 (207) -|.++|+.|+||++-.|.+|...+ +|..|.+|-.+.+ ...|..++. ||+...+||..=+ T Consensus 5 ~~~~~L~qi~gvs~~~A~aI~~~yPTp~~L~~ay~~~~~~~e~~~lL~~l~~~~~~r~iG~~lS~~Iy~~f 75 (82) T 2ziu_A 5 VFARQLMQISGVSGDKAAAVLEHYSTVSSLLQAYDKCSSETEKEKLLSSVKYGKLKRNLGPALSRTIYQLY 75 (82) T ss_dssp HHHHHHTTBTTCCHHHHHHHHHHCSSHHHHHHHHHHCSSHHHHTTTTTTCEETTTTEECHHHHHHHHHHHH T ss_pred HHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH T ss_conf 99999980899999999999997699999999998578677899998645356566765899999999997 No 39 >>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} (A:) Probab=91.81 E-value=0.11 Score=31.59 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=14.3 Q ss_pred HHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 8515668751045711679999999 Q gi|254780553|r 102 IILQNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 102 I~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207) |.+-+...|.++||||++.|++|+- T Consensus 21 iNtA~~~~L~~lpGig~~~A~~Ii~ 45 (75) T 2duy_A 21 LNEASLEELXALPGIGPVLARRIVE 45 (75) T ss_dssp TTTCCHHHHTTSTTCCHHHHHHHHH T ss_pred CCCCCHHHHHHCCCCCHHHHHHHHH T ss_conf 6128799997778989999999998 No 40 >>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanococcus jannaschii} (A:210-274) Probab=91.73 E-value=0.052 Score=33.62 Aligned_cols=31 Identities=19% Similarity=0.262 Sum_probs=23.6 Q ss_pred HHHHHCCCHHHHHHHCCCCH-HHHHHHHHCCC Q ss_conf 50100051011244315789-99999985156 Q gi|254780553|r 76 QSVQGVGARVAMGVLSRITA-TELVESIILQN 106 (207) Q Consensus 76 i~V~GIGpK~AL~iLs~l~~-~~l~~aI~~~D 106 (207) -+|.|||||+|..+++.+.- +.+.+.+..=+ T Consensus 19 pGV~GIGpKtA~~li~~~~~le~i~~~l~~~~ 50 (65) T 1a76_A 19 GGVKGIGFKRAYELVRSGVAKDVLKKEVEYYD 50 (65) T ss_dssp TTTTTCCHHHHHHHHHHTCHHHHHHHHSTTHH T ss_pred CCCCCEEHHHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 55685629999999997299999999765268 No 41 >>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} (A:123-255) Probab=91.53 E-value=0.24 Score=29.21 Aligned_cols=20 Identities=30% Similarity=0.554 Sum_probs=14.4 Q ss_pred HHHHHHCCCCCHHHHHHHHH Q ss_conf 68751045711679999999 Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ 126 (207) .+.|+++||||+|||+=+.+ T Consensus 107 ~~~L~~lpGIG~~tA~~ill 126 (133) T 1m3q_A 107 HKALCILPGVGTKVADCICL 126 (133) T ss_dssp HHHHTTSTTCCHHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHHH T ss_conf 99998468837999999999 No 42 >>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A* (A:34-143) Probab=91.25 E-value=0.11 Score=31.55 Aligned_cols=23 Identities=4% Similarity=0.261 Sum_probs=13.3 Q ss_pred CCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 15668751045711679999999 Q gi|254780553|r 104 LQNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 104 ~~D~~~L~~vpGIGkKtA~rIi~ 126 (207) ..+.+.|+++||||+|||+=+.+ T Consensus 81 ~~~~~~L~~lpGIG~~tA~~vll 103 (110) T 3fsp_A 81 PDDPDEFSRLKGVGPYTVGAVLS 103 (110) T ss_dssp CCSHHHHHTSTTCCHHHHHHHHH T ss_pred CCCHHHHHHHHHHHHHHHHHHHH T ss_conf 98899995111268999999999 No 43 >>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, hydrolase; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A* (A:1-149) Probab=91.15 E-value=0.077 Score=32.49 Aligned_cols=60 Identities=13% Similarity=0.162 Sum_probs=46.8 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 799999998501000510112443157899999998515668751045711679999999974 Q gi|254780553|r 67 LDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207) Q Consensus 67 ~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207) ..|+++.- ++=-||+|+.|..|...+..+ ...+..+|.=.|+.++|||-|+|.+|...+. T Consensus 6 ~~~~~~~~-L~~~Gi~~~~a~ki~~~yg~~--a~~~i~~nPY~L~~i~gigF~~aD~iA~~~g 65 (149) T 3e1s_A 6 LERRLLAG-LQGLGLTINQAQRAVKHFGAD--ALDRLEKDLFTLTEVEGIGFLTADKLWQARG 65 (149) T ss_dssp -----------------------------------------CGGGTSSSCCHHHHHTTC---- T ss_pred HHHHHHHH-HHHCCCCHHHHHHHHHHHHHH--HHHHHHHCCCEEEECCCCCHHHHHHHHHHCC T ss_conf 99999999-987799999999999998499--9999994993554158999599999999769 No 44 >>3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3a0b_U* 3a0h_U* (U:) Probab=91.01 E-value=0.13 Score=30.94 Aligned_cols=25 Identities=20% Similarity=0.188 Sum_probs=21.7 Q ss_pred HHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 8515668751045711679999999 Q gi|254780553|r 102 IILQNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 102 I~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207) |.+-+...|.++||||++.|++|+- T Consensus 27 IN~As~~~L~~ipGig~~~A~~Iv~ 51 (104) T 3bz1_U 27 LNNTNIAAFIQYRGLYPTLAKLIVK 51 (104) T ss_dssp TTSSCGGGGGGSTTTTHHHHHHHHH T ss_pred CCCCCHHHHHHCCCCCHHHHHHHHH T ss_conf 7228999997775869999999997 No 45 >>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication; 2.00A {Pyrococcus furiosus} (A:212-288) Probab=90.92 E-value=0.036 Score=34.67 Aligned_cols=40 Identities=8% Similarity=0.258 Sum_probs=28.0 Q ss_pred HHHHHCCCHHHHHHHCCC-CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 501000510112443157-899999998515668751045711679999999 Q gi|254780553|r 76 QSVQGVGARVAMGVLSRI-TATELVESIILQNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 76 i~V~GIGpK~AL~iLs~l-~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207) -+|+|||||+|+.++..+ +.+. .+..+.-++++.++++.. T Consensus 29 ~GV~GiG~ktA~kli~~~gsle~-----------i~~~~~~~~~~~~~~~~~ 69 (77) T 1b43_A 29 GGIKGIGLKKALEIVRHSKDPLA-----------KFQKQSDVDLYAIKEFFL 69 (77) T ss_dssp TCSTTCCHHHHHHHHHTCSSGGG-----------GTGGGCSSCHHHHHHHHH T ss_pred CCCCCCCHHHHHHHHHHHCCHHH-----------HHCCCCCCCHHHHHHHHC T ss_conf 65896249999999999599999-----------752210016899999843 No 46 >>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:1-118) Probab=90.88 E-value=0.12 Score=31.09 Aligned_cols=41 Identities=17% Similarity=0.179 Sum_probs=28.5 Q ss_pred HHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 0112443157899999998515668751045711679999999974 Q gi|254780553|r 84 RVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207) Q Consensus 84 K~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207) +.|.+.+..++. .|.+...+.+.++||||+++|++|.-=+. T Consensus 38 r~Aa~~i~~l~~-----~i~~~~~~~l~~lpGIG~~~a~kI~E~l~ 78 (118) T 2w9m_A 38 RSAARSLEELNE-----ETPELLAREFTGIPKVGKGIAAELSDFAR 78 (118) T ss_dssp HHHHHHHHSCC---------------CCSSTTCCHHHHHHHHHHHH T ss_pred HHHHHHHHHCCC-----HHHHHHHHHHHCCCCCCHHHHHHHHHHHH T ss_conf 999999996882-----36675498862599987899999999998 No 47 >>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} (A:) Probab=90.88 E-value=0.14 Score=30.68 Aligned_cols=45 Identities=16% Similarity=0.261 Sum_probs=37.0 Q ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHH Q ss_conf 999850100051011244315789999999851566875104571167999999 Q gi|254780553|r 72 FMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIM 125 (207) Q Consensus 72 F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi 125 (207) .+.|..+.||||+.|=+|+..=+. .+..-|.+++|||+++-++|- T Consensus 26 ~~~L~~lpGig~~~A~~Ii~~R~f---------~s~~dL~~v~gl~~~~~~~l~ 70 (75) T 2duy_A 26 LEELXALPGIGPVLARRIVEGRPY---------ARVEDLLKVKGIGPATLERLR 70 (75) T ss_dssp HHHHTTSTTCCHHHHHHHHHTCCC---------SSGGGGGGSTTCCHHHHHHHG T ss_pred HHHHHHCCCCCHHHHHHHHHCCCC---------CCHHHHHHCCCCCHHHHHHHH T ss_conf 999977789899999999986898---------989999618898999999998 No 48 >>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} (A:182-261) Probab=90.70 E-value=0.071 Score=32.74 Aligned_cols=38 Identities=13% Similarity=0.349 Sum_probs=27.0 Q ss_pred HHHHHHHHHHH--------HHHCCCHHHHHHHCCC-CHHHHHHHHHC Q ss_conf 79999999850--------1000510112443157-89999999851 Q gi|254780553|r 67 LDRQWFMLLQS--------VQGVGARVAMGVLSRI-TATELVESIIL 104 (207) Q Consensus 67 ~Er~~F~~Li~--------V~GIGpK~AL~iLs~l-~~~~l~~aI~~ 104 (207) +.---|..|.+ |.|||||+|+.++..+ +.+.+..++.. T Consensus 8 ~q~~d~~~L~GD~sD~ipGV~GIG~ktA~~Li~~~gsle~i~~~~~~ 54 (80) T 1exn_A 8 EQFISLKAIXGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPL 54 (80) T ss_dssp HHHHHHHHHHCBGGGTBCCCTTCCHHHHHHHHHHHCSHHHHHHHCSC T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHH T ss_conf 99999999719831368999976799999999995999999997865 No 49 >>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} (A:38-150) Probab=90.65 E-value=0.38 Score=27.90 Aligned_cols=20 Identities=30% Similarity=0.424 Sum_probs=16.0 Q ss_pred HHHHHHCCCCCHHHHHHHHH Q ss_conf 68751045711679999999 Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ 126 (207) ...|+++||||+|||+=+.. T Consensus 87 ~~~L~~l~GIG~~tA~~~l~ 106 (113) T 3fhf_A 87 EFLVRNIKGIGYKEASHFLR 106 (113) T ss_dssp HHHHHHSTTCCHHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHHH T ss_conf 99998785832999999999 No 50 >>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} (X:1-14,X:218-292) Probab=90.04 E-value=0.19 Score=29.95 Aligned_cols=39 Identities=26% Similarity=0.283 Sum_probs=31.2 Q ss_pred CCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 578999999985156687510457116799999999742 Q gi|254780553|r 92 RITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 92 ~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) ..++++|+..-.---...+..|||||+|||-+++-+..+ T Consensus 13 ~~tp~q~id~~~L~GsDy~pGV~GIG~KtA~kLI~~ygs 51 (89) T 1ul1_X 13 APNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKS 51 (89) T ss_dssp CTCHHHHHHHHHHHHCSSSCCCTTCCHHHHHHHHHHSSS T ss_pred CCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCC T ss_conf 859899999999639965355788569999999998099 No 51 >>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-binding, excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} (A:219-300) Probab=89.79 E-value=0.063 Score=33.06 Aligned_cols=30 Identities=13% Similarity=0.349 Sum_probs=23.6 Q ss_pred HHHHHCCCHHHHHHHCCC-CHHHHHHHHHCC Q ss_conf 501000510112443157-899999998515 Q gi|254780553|r 76 QSVQGVGARVAMGVLSRI-TATELVESIILQ 105 (207) Q Consensus 76 i~V~GIGpK~AL~iLs~l-~~~~l~~aI~~~ 105 (207) -+|.|||||+|+.++..+ +.+.+.+++..- T Consensus 19 ~GV~GiG~ktA~~li~~~g~le~i~~~~~~~ 49 (82) T 2izo_A 19 DGIRGIGPERALKIIKKYGKIEKAMEYGEIS 49 (82) T ss_dssp TCSTTCCHHHHHHHHHHSSCC---------- T ss_pred CCCCCCCHHHHHHHHHHCCCHHHHHHHHHHH T ss_conf 3479944889999999839999999999985 No 52 >>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} (A:149-197) Probab=89.67 E-value=0.2 Score=29.69 Aligned_cols=22 Identities=27% Similarity=0.593 Sum_probs=15.2 Q ss_pred HHHHHCCCCCHHHHHHHHHHHH Q ss_conf 8751045711679999999974 Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELK 129 (207) Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk 129 (207) +.|..+||||+|++++++-... T Consensus 14 s~L~~IpGIG~k~~~~LL~~Fg 35 (49) T 2bgw_A 14 YILQSFPGIGRRTAERILERFG 35 (49) T ss_dssp HHHHTSTTCCHHHHHHHHHHHS T ss_pred HHHHCCCCCCHHHHHHHHHHCC T ss_conf 8885356899789999999869 No 53 >>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* (A:304-377) Probab=89.63 E-value=0.68 Score=26.17 Aligned_cols=26 Identities=12% Similarity=0.336 Sum_probs=21.3 Q ss_pred CCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 56687510457116799999999742 Q gi|254780553|r 105 QNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 105 ~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) .-...|+.+||||+++|++|+-..+. T Consensus 9 ~~~~~L~~I~giG~~~a~~L~~~fgs 34 (74) T 3c1y_A 9 RGYRLLKTVARIPLSIGYNVVRMFKT 34 (74) T ss_dssp CSHHHHHHTSCCCHHHHHHHHHHHCS T ss_pred HHHHHHHCCCCCCHHHHHHHHHHHCC T ss_conf 16888733999989999999998538 No 54 >>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} (A:28-137) Probab=89.41 E-value=0.26 Score=28.92 Aligned_cols=20 Identities=20% Similarity=0.526 Sum_probs=9.3 Q ss_pred CCHHHHHHCCCCCHHHHHHH Q ss_conf 56687510457116799999 Q gi|254780553|r 105 QNSKVIAQIPGISMKIASRI 124 (207) Q Consensus 105 ~D~~~L~~vpGIGkKtA~rI 124 (207) .+.+.|+++||||+|||+=+ T Consensus 83 ~~~~~L~~l~GIG~~ta~~~ 102 (110) T 1orn_A 83 RDRDELMKLPGVGRKTANVV 102 (110) T ss_dssp SCHHHHTTSTTCCHHHHHHH T ss_pred CCHHHHHHCCCCCHHHHHHH T ss_conf 88999975879752589999 No 55 >>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} (A:499-568) Probab=89.28 E-value=0.23 Score=29.30 Aligned_cols=49 Identities=10% Similarity=0.243 Sum_probs=37.6 Q ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHHHH-HCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 9998501000510112443157899999998-515668751045711679999999 Q gi|254780553|r 72 FMLLQSVQGVGARVAMGVLSRITATELVESI-ILQNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 72 F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI-~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207) ...|..+.||||+.|-+|+.. .+.- .-.+..-|.++||+|+++.+++.- T Consensus 9 ~~~L~~lpgig~~~A~~Ii~~------R~~~G~f~s~~dL~~v~gl~~~~~~~l~~ 58 (70) T 3bzc_A 9 AALLARISGLNSTLAQNIVAH------RDANGAFRTRDELKKVSRLGEKTFEQAAG 58 (70) T ss_dssp HHHHHTSTTCCHHHHHHHHHH------HHHHCCCSSGGGGGGSTTCCHHHHHHHGG T ss_pred HHHHHHCCCCCHHHHHHHHHH------HHHCCCCCCHHHHHHCCCCCHHHHHHCCE T ss_conf 888866069788999999999------99669957799998567888128987180 No 56 >>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} (A:29-139) Probab=89.06 E-value=0.29 Score=28.67 Aligned_cols=20 Identities=25% Similarity=0.544 Sum_probs=9.3 Q ss_pred CCHHHHHHCCCCCHHHHHHH Q ss_conf 56687510457116799999 Q gi|254780553|r 105 QNSKVIAQIPGISMKIASRI 124 (207) Q Consensus 105 ~D~~~L~~vpGIGkKtA~rI 124 (207) +....|+++||||+|||+=+ T Consensus 84 ~~~~~L~~l~GIG~~tA~~~ 103 (111) T 1kea_A 84 RNRKAILDLPGVGKYTCAAV 103 (111) T ss_dssp SCHHHHHTSTTCCHHHHHHH T ss_pred CHHHHHHCCCCCCHHHHHHH T ss_conf 30467650898761689999 No 57 >>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} (A:1-49,A:127-233) Probab=89.02 E-value=0.12 Score=31.26 Aligned_cols=32 Identities=19% Similarity=0.073 Sum_probs=24.6 Q ss_pred HHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 99999851566875104571167999999997 Q gi|254780553|r 97 ELVESIILQNSKVIAQIPGISMKIASRIMTEL 128 (207) Q Consensus 97 ~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~EL 128 (207) ++...-..++.+.|.++||||+|||+-++.-- T Consensus 50 el~~g~~pe~~~~LlsLPGIGpkTA~~ILlfa 81 (156) T 2h56_A 50 ELEGAEATTVIEKLTAIKGIGQWTAEXFXXFS 81 (156) T ss_dssp HHTTSCHHHHHHHHHTSTTCCHHHHHHHHHHT T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC T ss_conf 26665355788888873897878999999851 No 58 >>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (B:1-71) Probab=89.00 E-value=0.24 Score=29.18 Aligned_cols=23 Identities=22% Similarity=0.534 Sum_probs=19.7 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 87510457116799999999742 Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) ..|.++||||+|+|.+++-..+. T Consensus 18 ~~L~~ipGIg~k~~~~Ll~~f~s 40 (71) T 1z00_B 18 DFLLKMPGVNAKNCRSLMHHVKN 40 (71) T ss_dssp HHHHTCSSCCHHHHHHHHHHSSC T ss_pred HHHHCCCCCCHHHHHHHHHHCCC T ss_conf 99980899889999999999079 No 59 >>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} (U:48-134) Probab=88.80 E-value=0.18 Score=30.12 Aligned_cols=48 Identities=13% Similarity=0.227 Sum_probs=38.2 Q ss_pred HHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 998501000510112443157899999998515668751045711679999999974 Q gi|254780553|r 73 MLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207) Q Consensus 73 ~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207) ..|..+.||||+.|=.|+..=+. .+..-|.+++|||+++-++|---++ T Consensus 16 ~~L~~ipGig~~~A~~Iv~~g~f---------~s~~dL~~v~gi~~~~~~~i~~~l~ 63 (87) T 1s5l_U 16 AAFIQYRGLYPTLAKLIVKNAPY---------ESVEDVLNIPGLTERQKQILRENLE 63 (87) T ss_dssp GGGGGSTTCTHHHHHHHHHTCCC---------SSGGGGGGCTTCCHHHHHHHHHHHT T ss_pred HHHHHHHHHHHHHHHHHHHCCCC---------CCHHHHHCCCCCCHHHHHHHHHHHC T ss_conf 99977103469999999982784---------8799996177579999999998653 No 60 >>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} (A:23-145) Probab=88.77 E-value=0.44 Score=27.43 Aligned_cols=25 Identities=16% Similarity=0.112 Sum_probs=15.2 Q ss_pred HHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 8515668751045711679999999 Q gi|254780553|r 102 IILQNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 102 I~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207) -..+....|.++||||+|||+=+.+ T Consensus 93 ~~~~~~~~L~~l~GIG~~tA~~ill 117 (123) T 1pu6_A 93 KQEVTREWLLDQKGIGKESADAILC 117 (123) T ss_dssp HHHCCHHHHHTSTTCCHHHHHHHHH T ss_pred CCHHHHHHHHCCCCCCHHHHHHHHH T ss_conf 9467999998489966999999999 No 61 >>2ziu_B Crossover junction endonuclease EME1; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Homo sapiens} PDB: 2ziw_B 2zix_B 2ziv_B (B:242-341) Probab=88.68 E-value=0.45 Score=27.37 Aligned_cols=60 Identities=20% Similarity=0.303 Sum_probs=44.4 Q ss_pred HHHHHHHHHHHCCCHHHHHHHCCC-CHHHHHHHHHCCC-----HHHHHHCC------------CCCHHHHHHHHHHHH Q ss_conf 999998501000510112443157-8999999985156-----68751045------------711679999999974 Q gi|254780553|r 70 QWFMLLQSVQGVGARVAMGVLSRI-TATELVESIILQN-----SKVIAQIP------------GISMKIASRIMTELK 129 (207) Q Consensus 70 ~~F~~Li~V~GIGpK~AL~iLs~l-~~~~l~~aI~~~D-----~~~L~~vp------------GIGkKtA~rIi~ELk 129 (207) -|-++|+.|+||.+-.|.+|.+.+ +|..|.+|-...+ ...|..++ -||+..++||--=+. T Consensus 11 ~~~~~L~qI~gvs~~kA~aI~~~YPTp~~L~~ay~~~~~~~e~~~lL~~i~~~~~~~~~~~~r~iG~~lS~~Iy~~f~ 88 (100) T 2ziu_B 11 VWRRQIQQLNRVSLEMASAVVNAYPSPQLLVQAYQQCFSDKERQNLLADIQVRRGEGVTSTSRRIGPELSRRIYLQMT 88 (100) T ss_dssp HHHHHHTTSTTCCHHHHHHHHHHSCSHHHHHHHHHTCSCHHHHTTTTTTCBTTTTC----CCCBCCHHHHHHHHHHHH T ss_pred HHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHEECCCCCCCCCCCCCCHHHHHHHHHHHH T ss_conf 999999865799999999999978999999999984567245678776510022578764556146999999999983 No 62 >>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} (A:23-133) Probab=88.56 E-value=0.31 Score=28.42 Aligned_cols=53 Identities=13% Similarity=0.256 Sum_probs=26.3 Q ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHH---HHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 9998501000510112443157899999---998515668751045711679999999 Q gi|254780553|r 72 FMLLQSVQGVGARVAMGVLSRITATELV---ESIILQNSKVIAQIPGISMKIASRIMT 126 (207) Q Consensus 72 F~~Li~V~GIGpK~AL~iLs~l~~~~l~---~aI~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207) +..++.--|.....|-.|.+. .+.+. ..-...+...|.++||||+|||.=+.. T Consensus 50 ~~~~l~~~g~~~~ka~~i~~~--a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~vll 105 (111) T 2abk_A 50 VKTYIKTIGLYNSKAENIIKT--CRILLEQHNGEVPEDRAALEALPGVGRKTANVVLN 105 (111) T ss_dssp HHHHHTTSTTHHHHHHHHHHH--HHHHHHHTTTSCCSCHHHHHHSTTCCHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHH T ss_conf 777767411567788899999--99999860411367799999898606359999999 No 63 >>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} (A:) Probab=88.54 E-value=0.25 Score=29.07 Aligned_cols=24 Identities=21% Similarity=0.515 Sum_probs=20.2 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 687510457116799999999742 Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) .+.|..+||||+|+|++++-..+. T Consensus 3 ~s~L~~IpgVG~~~a~~Ll~~f~S 26 (63) T 2a1j_A 3 QDFLLKMPGVNAKNCRSLMHHVKN 26 (63) T ss_dssp CHHHHTSTTCCHHHHHHHHHHCSS T ss_pred HHHHHCCCCCCHHHHHHHHHHHCC T ss_conf 888851999899999999998078 No 64 >>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=88.50 E-value=0.32 Score=28.41 Aligned_cols=51 Identities=18% Similarity=0.177 Sum_probs=39.1 Q ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHHHH-HCCCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 9998501000510112443157899999998-51566875104571167999999997 Q gi|254780553|r 72 FMLLQSVQGVGARVAMGVLSRITATELVESI-ILQNSKVIAQIPGISMKIASRIMTEL 128 (207) Q Consensus 72 F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI-~~~D~~~L~~vpGIGkKtA~rIi~EL 128 (207) ...|..+.||||+.|=+|+.. .+.- .-.++.-|.+++|||+++.+++.--+ T Consensus 39 ~~eL~~lpgig~~~A~~Ii~~------R~~~G~f~siedL~~v~gi~~~~~~~l~~~~ 90 (98) T 2edu_A 39 ARDLRSLQRIGPKKAQLIVGW------RELHGPFSQVEDLERVEGITGKQMESFLKAN 90 (98) T ss_dssp HHHHHHSTTCCHHHHHHHHHH------HHHHCCCSSGGGGGGSTTCCHHHHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHHHH------HHHCCCCCCHHHHHCCCCCCHHHHHHHHHHC T ss_conf 999975789899999999999------9985895889998258898999999999828 No 65 >>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} (A:105-231) Probab=88.42 E-value=0.29 Score=28.66 Aligned_cols=70 Identities=14% Similarity=0.073 Sum_probs=34.9 Q ss_pred HHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCH Q ss_conf 99999998515668751045711679999999974222110113344323333344555565315899999999679998 Q gi|254780553|r 95 ATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQ 174 (207) Q Consensus 95 ~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL~~LGy~~ 174 (207) .+.++.+|..++.+ -+.|.++.-.|..++........... .........+...+.+..+||.. T Consensus 10 fe~lv~~Il~Qq~~---------~~~a~~~~~~l~~~~g~~~~~~~~~~--------~~p~~~~~~~~~~~~~~~~g~~~ 72 (127) T 1mpg_A 10 FEQGVRAILGQLVS---------VAMAAKLTARVAQLYGERLDDFPEYI--------CFPTPQRLAAADPQALKALGMPL 72 (127) T ss_dssp HHHHHHHHHTTTSC---------HHHHHHHHHHHHHHHCCBCSSCTTCB--------CCCCHHHHHTCCHHHHHHTTSCH T ss_pred HHHHHHHHHHCHHH---------HHHHHHHHHHHHHHHCCCCCCCCCCC--------CCCCHHHHHCCCHHHHHHCCCCH T ss_conf 99999999967232---------99999999999998588767687656--------79989999769999997528866 Q ss_pred HHHHHHH Q ss_conf 9999999 Q gi|254780553|r 175 DQATTAV 181 (207) Q Consensus 175 ~ea~~ai 181 (207) ..+.... T Consensus 73 ~ka~~i~ 79 (127) T 1mpg_A 73 KRAEALI 79 (127) T ss_dssp HHHHHHH T ss_pred HHHHHHH T ss_conf 5899999 No 66 >>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} (A:1-23,A:110-225) Probab=87.62 E-value=0.32 Score=28.36 Aligned_cols=31 Identities=19% Similarity=0.287 Sum_probs=22.1 Q ss_pred HHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 9985156687510457116799999999742 Q gi|254780553|r 100 ESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 100 ~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) .---....-.|.++||||+|||.-|++--=+ T Consensus 15 ~~~~~~~~~eL~~LpGIG~ktAd~Illfa~~ 45 (139) T 1kg2_A 15 DKYGRKTLPEVAALPGVGRSTAGAILSLSLG 45 (139) T ss_dssp HHHCCCCSGHHHTSTTCCHHHHHHHHHHHHC T ss_pred HHCCCCCCCHHHCCCCCCHHHHHHHHHHHCC T ss_conf 9819987999862898727899999998449 No 67 >>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} (X:1-14,X:218-292) Probab=86.47 E-value=0.4 Score=27.74 Aligned_cols=46 Identities=17% Similarity=0.302 Sum_probs=27.5 Q ss_pred HHHHCCCHHHHHHHCCC-CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHH Q ss_conf 01000510112443157-89999999851566875104571167999999 Q gi|254780553|r 77 SVQGVGARVAMGVLSRI-TATELVESIILQNSKVIAQIPGISMKIASRIM 125 (207) Q Consensus 77 ~V~GIGpK~AL~iLs~l-~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi 125 (207) +|.|||||+|+.++..+ +.+.+.+++. ......-+..-.+-|+.+. T Consensus 33 GV~GIG~KtA~kLI~~ygsle~ii~~l~---~~~~~~~~~~~~~~~~~~f 79 (89) T 1ul1_X 33 SIRGIGPKRAVDLIQKHKSIEEIVRRLD---PNKYPVPENWLHKEAHQLF 79 (89) T ss_dssp CCTTCCHHHHHHHHHHSSSHHHHHTTCC---CTTSCCCSSCCHHHHHHHH T ss_pred CCCCCCHHHHHHHHHHCCCHHHHHHHHH---HHCCCCCCCCCHHHHHHHH T ss_conf 5788569999999998099999999998---6077554123699999984 No 68 >>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (A:) Probab=85.88 E-value=0.51 Score=27.00 Aligned_cols=53 Identities=11% Similarity=0.185 Sum_probs=34.5 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHC-CCCHHHHHHHHHHH Q ss_conf 6875104571167999999997422211011334432333334455556531589999999967-99989999999999 Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNL-GYGQDQATTAVVSV 184 (207) Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL~~L-Gy~~~ea~~ai~~i 184 (207) ...|+.+||||+++|++++-...+- ..+.. --.+-|... |..+.-|+...... T Consensus 18 l~~L~~I~gIG~~~a~~L~~~F~s~-~~i~~------------------------A~~~~L~~v~GiG~~~A~~i~~~~ 71 (89) T 1z00_A 18 TECLTTVKSVNKTDSQTLLTTFGSL-EQLIA------------------------ASREDLALCPGLGPQKARRLFDVL 71 (89) T ss_dssp HHHHTTSSSCCHHHHHHHHHHTCBH-HHHHH------------------------CCHHHHHTSTTCCHHHHHHHHHHH T ss_pred HHHHCCCCCCCHHHHHHHHHHHCCC-HHHHH------------------------HHHHHHCHHCCCCHHHHHHHHHHH T ss_conf 9986589976999999999990994-78766------------------------547510000332799999999998 No 69 >>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} (A:1-49) Probab=85.84 E-value=0.48 Score=27.17 Aligned_cols=21 Identities=19% Similarity=0.550 Sum_probs=11.0 Q ss_pred HHHHHCCCCCHHHHHHHHHHH Q ss_conf 875104571167999999997 Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTEL 128 (207) Q Consensus 108 ~~L~~vpGIGkKtA~rIi~EL 128 (207) ..|..+||||+++|+++.-.. T Consensus 14 ~~L~~I~gVG~~~ak~Ll~~F 34 (49) T 1x2i_A 14 LIVEGLPHVSATLARRLLKHF 34 (49) T ss_dssp HHHTTSTTCCHHHHHHHHHHH T ss_pred HHHCCCCCCCHHHHHHHHHHC T ss_conf 998589997899999999970 No 70 >>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A (A:157-220) Probab=85.60 E-value=0.58 Score=26.64 Aligned_cols=24 Identities=17% Similarity=0.426 Sum_probs=20.0 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 687510457116799999999742 Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) ...|..+||||+++|++++-..++ T Consensus 11 ~~~L~~I~gIG~~~a~~L~~~F~s 34 (64) T 2nrt_A 11 RSVLDNVPGIGPIRKKKLIEHFGS 34 (64) T ss_dssp HHHHTTSTTCCHHHHHHHHHHHCS T ss_pred CCHHHCCCCCCHHHHHHHHHHCCC T ss_conf 152220531079999999998689 No 71 >>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family DNA polymerase, translesion DNA synthesis, lesion bypass; 2.40A {Homo sapiens} (A:271-340) Probab=84.92 E-value=0.46 Score=27.30 Aligned_cols=28 Identities=14% Similarity=0.186 Sum_probs=18.9 Q ss_pred CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH Q ss_conf 8999999985156687510457116799999 Q gi|254780553|r 94 TATELVESIILQNSKVIAQIPGISMKIASRI 124 (207) Q Consensus 94 ~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207) +|+++.+-+.+=+ ++.+||||+||++|+ T Consensus 1 d~~~~~~~l~~lp---i~~i~GIG~~~~~~L 28 (70) T 1t94_A 1 NRQAVMDFIKDLP---IRKVSGIGKVTEKML 28 (70) T ss_dssp SHHHHHHHHTTCB---GGGCTTSCHHHHHHH T ss_pred CHHHHHHHHHHCC---CCCCCCCCCCCHHHH T ss_conf 2789999997397---140257631100454 No 72 >>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A (A:111-127,A:196-236) Probab=84.47 E-value=0.46 Score=27.32 Aligned_cols=26 Identities=31% Similarity=0.332 Sum_probs=21.6 Q ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHH Q ss_conf 67799999998501000510112443 Q gi|254780553|r 65 SDLDRQWFMLLQSVQGVGARVAMGVL 90 (207) Q Consensus 65 ~~~Er~~F~~Li~V~GIGpK~AL~iL 90 (207) +....+.-+.|+++.|||||+|=-+| T Consensus 25 ~l~~eea~~~L~~i~GIGpwTAdciL 50 (58) T 3i0w_A 25 SLNDNECHEELKKFMGVGPQVADCIM 50 (58) T ss_dssp HSCHHHHHHHHTTSTTCCHHHHHHHH T ss_pred HCCCHHHHHHHHHCCCCHHHHHHHHH T ss_conf 13544678999826881299999999 No 73 >>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} (A:) Probab=84.31 E-value=0.63 Score=26.41 Aligned_cols=24 Identities=8% Similarity=0.135 Sum_probs=19.4 Q ss_pred CCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 566875104571167999999997 Q gi|254780553|r 105 QNSKVIAQIPGISMKIASRIMTEL 128 (207) Q Consensus 105 ~D~~~L~~vpGIGkKtA~rIi~EL 128 (207) .+.+-+..+||||+|+|.+|-=-| T Consensus 55 ~s~~~l~~lpgiG~~ia~kI~e~l 78 (87) T 2kp7_A 55 RSGKEAKILQHFGDRLCRMLDEKL 78 (87) T ss_dssp CSHHHHHTCTTTCHHHHHHHHHHH T ss_pred CCHHHHHCCCCCCHHHHHHHHHHH T ss_conf 889998738998789999999999 No 74 >>1wiv_A UBP14, ubiquitin-specific protease 14; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Arabidopsis thaliana} (A:) Probab=83.89 E-value=1.8 Score=23.44 Aligned_cols=30 Identities=17% Similarity=0.400 Sum_probs=24.3 Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 565315899999999679998999999999 Q gi|254780553|r 154 CSMPSFAINAISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 154 ~~~~~~~~d~~~AL~~LGy~~~ea~~ai~~ 183 (207) ........+++..|+.+||++..+++|+.. T Consensus 23 ~~~~~~~~~~i~~L~~MGF~~~~a~~AL~~ 52 (73) T 1wiv_A 23 HQTSDIDQSSVDTLLSFGFAEDVARKALKA 52 (73) T ss_dssp CSSCSSCHHHHHHHHHHTCCHHHHHHHHHH T ss_pred CCCCCCCHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 788998999999999469999999999999 No 75 >>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A* (A:240-306) Probab=83.83 E-value=0.55 Score=26.78 Aligned_cols=17 Identities=24% Similarity=0.591 Sum_probs=14.2 Q ss_pred HHHCCCCCHHHHHHHHH Q ss_conf 51045711679999999 Q gi|254780553|r 110 IAQIPGISMKIASRIMT 126 (207) Q Consensus 110 L~~vpGIGkKtA~rIi~ 126 (207) +.++||||+||++|+-- T Consensus 4 i~~i~GVG~~t~~kL~~ 20 (67) T 2aq4_A 4 LDDLPGVGHSTLSRLES 20 (67) T ss_dssp GGGSTTCCHHHHHHHHH T ss_pred CCCHHCCCHHHHHHHHH T ss_conf 23012027899999998 No 76 >>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A (A:80-154) Probab=83.61 E-value=0.69 Score=26.15 Aligned_cols=59 Identities=19% Similarity=0.321 Sum_probs=34.7 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH-CCCCHHHHHHHHHHHHH Q ss_conf 87510457116799999999742221101133443233333445555653158999999996-79998999999999985 Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVN-LGYGQDQATTAVVSVLK 186 (207) Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL~~-LGy~~~ea~~ai~~i~~ 186 (207) ..|.+|+|||+|+|-+|+..+.-. .+...+.. +=..+|.. =|-.++-|++.+-+... T Consensus 9 ~~L~~V~GIGpk~Al~iLs~~~~~--el~~aI~~--------------------~D~~~L~~ipGIG~KtA~rii~ELk~ 66 (75) T 2ztd_A 9 LTLLSVSGVGPRLAMAALAVHDAP--ALRQVLAD--------------------GNVAALTRVPGIGKRGAERMVLELRD 66 (75) T ss_dssp HHHHTSTTCCHHHHHHHHHHSCHH--HHHHHHHT--------------------TCHHHHHTSTTCCHHHHHHHHHHHTT T ss_pred HHHHCCCCCCHHHHHHHHCCCCHH--HHHHHHHC--------------------CCHHHHHCCCCCCHHHHHHHHHHHHC T ss_conf 998541322366662322157767--77788853--------------------68899850888356889999999841 Q ss_pred HC Q ss_conf 16 Q gi|254780553|r 187 KE 188 (207) Q Consensus 187 ~~ 188 (207) .. T Consensus 67 k~ 68 (75) T 2ztd_A 67 KV 68 (75) T ss_dssp TC T ss_pred CC T ss_conf 11 No 77 >>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} (A:) Probab=83.61 E-value=0.47 Score=27.26 Aligned_cols=24 Identities=17% Similarity=0.343 Sum_probs=19.7 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 687510457116799999999742 Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) ...|+.+||||+++|++|+-...+ T Consensus 23 ~~~L~~I~gIG~~~a~~L~~~Fgs 46 (78) T 1kft_A 23 TSSLETIEGVGPKRRQMLLKYMGG 46 (78) T ss_dssp CCGGGGCTTCSSSHHHHHHHHHSC T ss_pred CCCCCCCCCCCHHHHHHHHHHCCC T ss_conf 284656999479999999999099 No 78 >>2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M (m:1-88) Probab=83.26 E-value=0.86 Score=25.50 Aligned_cols=22 Identities=18% Similarity=0.326 Sum_probs=19.5 Q ss_pred HHHHHCCCCCHHHHHHHHHHHH Q ss_conf 8751045711679999999974 Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELK 129 (207) Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk 129 (207) -+|+++.|||+++|.+|+-.|. T Consensus 28 ~ALt~I~GIG~~~A~~Ic~~lg 49 (88) T 2zkq_m 28 FAITAIKGVGRRYAHVVLRKAD 49 (88) T ss_dssp HHGGGSTTCCHHHHHHHHHHHT T ss_pred EEHHCCCCCCHHHHHHHHHHCC T ss_conf 6030246628999999999829 No 79 >>2qsf_X RAD23, UV excision repair protein RAD23; alpha-beta structure, beta hairpin, transglutaminase fold, DNA-damage recognition, DNA repair; HET: DNA; 2.35A {Saccharomyces cerevisiae} PDB: 2qsg_X* 2qsh_X* 1x3z_B* 1x3w_B* 3esw_B* (X:105-171) Probab=83.20 E-value=1.6 Score=23.70 Aligned_cols=31 Identities=23% Similarity=0.277 Sum_probs=24.8 Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 5653158999999996799989999999999 Q gi|254780553|r 154 CSMPSFAINAISALVNLGYGQDQATTAVVSV 184 (207) Q Consensus 154 ~~~~~~~~d~~~AL~~LGy~~~ea~~ai~~i 184 (207) ........++++-|+++||++..+++|+..- T Consensus 20 ~~~~~~~~~~i~~L~~MGF~~~~a~~AL~~~ 50 (67) T 2qsf_X 20 VDYTPEDDQAISRLCELGFERDLVIQVYFAC 50 (67) T ss_dssp CCCCHHHHHHHHHHHTTTCCHHHHHHHHHHT T ss_pred CCCCCCCHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 6788114999999998499999999999990 No 80 >>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} (A:1-49) Probab=83.12 E-value=0.58 Score=26.63 Aligned_cols=33 Identities=12% Similarity=0.197 Sum_probs=23.2 Q ss_pred HHHHH-HHHHHHHCCCHHHHHHHCCCC-HHHHHHH Q ss_conf 99999-985010005101124431578-9999999 Q gi|254780553|r 69 RQWFM-LLQSVQGVGARVAMGVLSRIT-ATELVES 101 (207) Q Consensus 69 r~~F~-~Li~V~GIGpK~AL~iLs~l~-~~~l~~a 101 (207) ++.|. .|-+|.||||++|-.+|..+. .+.+.+| T Consensus 9 ~~~~~~~L~~I~gVG~~~ak~Ll~~Fgsi~~i~~A 43 (49) T 1x2i_A 9 AERQRLIVEGLPHVSATLARRLLKHFGSVERVFTA 43 (49) T ss_dssp HHHHHHHHTTSTTCCHHHHHHHHHHHCSHHHHHHC T ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHCCHHHHHHHC T ss_conf 99999998589997899999999970628888626 No 81 >>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:66-144) Probab=82.78 E-value=0.78 Score=25.79 Aligned_cols=60 Identities=23% Similarity=0.416 Sum_probs=35.9 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH-CCCCHHHHHHHHHHHHH Q ss_conf 87510457116799999999742221101133443233333445555653158999999996-79998999999999985 Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVN-LGYGQDQATTAVVSVLK 186 (207) Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL~~-LGy~~~ea~~ai~~i~~ 186 (207) ..|.+|+|||+|+|-+|+.-+.-. .+...+.. +=..+|.. =|-.++-|++.+-++.. T Consensus 8 ~~L~~V~GIGpk~Al~iLs~~~~~--el~~aI~~--------------------~D~~~L~~ipGIG~KtAerii~eLk~ 65 (79) T 1cuk_A 8 KELIKTNGVGPKLALAILSGMSAQ--QFVNAVER--------------------EEVGALVKLPGIGKKTAERLIVEMKD 65 (79) T ss_dssp HHHHHSSSCCHHHHHHHHHHSCHH--HHHHHHHT--------------------TCHHHHHTSTTCCHHHHHHHHHHHHH T ss_pred HHHHCCCCCCHHHHHHHHCCCCHH--HHHHHHHH--------------------CCHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 987347884899999997579999--99999992--------------------89999841999889999999999998 Q ss_pred HCC Q ss_conf 168 Q gi|254780553|r 187 KEK 189 (207) Q Consensus 187 ~~~ 189 (207) ... T Consensus 66 K~~ 68 (79) T 1cuk_A 66 RFK 68 (79) T ss_dssp HGG T ss_pred HHH T ss_conf 887 No 82 >>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} (A:149-197) Probab=82.23 E-value=0.44 Score=27.42 Aligned_cols=30 Identities=37% Similarity=0.654 Sum_probs=24.1 Q ss_pred HHHHHHHH-HHHHHHHCCCHHHHHHHCCCCH Q ss_conf 77999999-9850100051011244315789 Q gi|254780553|r 66 DLDRQWFM-LLQSVQGVGARVAMGVLSRITA 95 (207) Q Consensus 66 ~~Er~~F~-~Li~V~GIGpK~AL~iLs~l~~ 95 (207) ...+.++. .|-+|.|||||.+-.+|..|.. T Consensus 6 ~r~k~~~~s~L~~IpGIG~k~~~~LL~~FgS 36 (49) T 2bgw_A 6 SDVREWQLYILQSFPGIGRRTAERILERFGS 36 (49) T ss_dssp CHHHHHHHHHHHTSTTCCHHHHHHHHHHHSS T ss_pred CCHHHHHHHHHHCCCCCCHHHHHHHHHHCCC T ss_conf 9888988888853568997899999998699 No 83 >>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} (A:38-150) Probab=82.12 E-value=0.61 Score=26.50 Aligned_cols=31 Identities=23% Similarity=0.198 Sum_probs=18.1 Q ss_pred HHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 9999999851566875104571167999999997422211 Q gi|254780553|r 95 ATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAIS 134 (207) Q Consensus 95 ~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~ 134 (207) .+.++.+|..+.+ .-+.|.++.-.|..++.. T Consensus 8 fe~Lv~~Il~Qq~---------s~~~a~~~~~~l~~~~~~ 38 (113) T 3fhf_A 8 FKELCFCILTANF---------TAEGGIRIQKEIGDGFLT 38 (113) T ss_dssp HHHHHHHHHHTTS---------CHHHHHHHHHHHTTHHHH T ss_pred HHHHHHHHHCCCC---------CHHHHHHHHHHHHHHHHC T ss_conf 9999999961458---------699999999999999871 No 84 >>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix- hairpin-helix, HHH motif, three helix bundle; 2.30A {Methanopyrus kandleri} (A:181-225,A:375-471) Probab=81.53 E-value=2 Score=23.02 Aligned_cols=30 Identities=13% Similarity=0.249 Sum_probs=20.1 Q ss_pred HHHHHCCCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 999851566875104571167999999997 Q gi|254780553|r 99 VESIILQNSKVIAQIPGISMKIASRIMTEL 128 (207) Q Consensus 99 ~~aI~~~D~~~L~~vpGIGkKtA~rIi~EL 128 (207) ++|...-...-|++-.|+|.|||+|++-.. T Consensus 73 yraaveiqlaeltkkegvgrktaerllraf 102 (142) T 2csb_A 73 YRAAVEIQLAELTKKEGVGRKTAERLLRAF 102 (142) T ss_dssp HHHHHHHHHHHHHTSTTCCHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 988898779977654064565799999970 No 85 >>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} (A:) Probab=80.91 E-value=1 Score=24.94 Aligned_cols=30 Identities=23% Similarity=0.290 Sum_probs=22.9 Q ss_pred CCHHHHHHCCCCCHHHHHHHHHHH-HHHHHH Q ss_conf 566875104571167999999997-422211 Q gi|254780553|r 105 QNSKVIAQIPGISMKIASRIMTEL-KGKAIS 134 (207) Q Consensus 105 ~D~~~L~~vpGIGkKtA~rIi~EL-k~K~~~ 134 (207) ...-.|..+||||+++|++|+-+= ++.+.+ T Consensus 129 ~i~~~L~~I~GiG~~~a~~Iie~Re~g~F~S 159 (205) T 2i5h_A 129 TRMHQLELLPGVGKKMMWAIIEERKKRPFES 159 (205) T ss_dssp SSSBGGGGSTTCCHHHHHHHHHHHHHSCCCS T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHCCCCCCC T ss_conf 8789887444515899999999975489889 No 86 >>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} (A:309-368) Probab=80.69 E-value=1.4 Score=24.17 Aligned_cols=28 Identities=21% Similarity=0.275 Sum_probs=22.6 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 5315899999999679998999999999 Q gi|254780553|r 156 MPSFAINAISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 156 ~~~~~~d~~~AL~~LGy~~~ea~~ai~~ 183 (207) .....++.+..|+.|||++..+++|+.. T Consensus 13 ~~~~~e~~i~~L~~MGF~~~~a~~AL~~ 40 (60) T 1oqy_A 13 VTPQEKEAIERLKALGFPESLVIQAYFA 40 (60) T ss_dssp CCTTTHHHHHHHHHHTCCSHHHHHHTSS T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 9989999999999849998999999998 No 87 >>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A (A:112-130,A:199-234) Probab=80.28 E-value=0.86 Score=25.50 Aligned_cols=19 Identities=16% Similarity=0.242 Sum_probs=15.3 Q ss_pred HHHHHHCCCCCHHHHHHHH Q ss_conf 6875104571167999999 Q gi|254780553|r 107 SKVIAQIPGISMKIASRIM 125 (207) Q Consensus 107 ~~~L~~vpGIGkKtA~rIi 125 (207) .+.|++++|||+.||+-.. T Consensus 30 i~~Lt~IkGIG~WTAem~L 48 (55) T 2jhn_A 30 YEYLTSFKGIGRWTAELVL 48 (55) T ss_dssp HHHHHTSTTCCHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHH T ss_conf 8898753782899999999 No 88 >>1wgn_A UBAP1, ubiquitin associated protein; ubiquitin associated protein 1 (UBAP1), UBA domain, structural genomics; NMR {Homo sapiens} (A:) Probab=80.16 E-value=1.3 Score=24.29 Aligned_cols=30 Identities=17% Similarity=0.297 Sum_probs=24.8 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 653158999999996799989999999999 Q gi|254780553|r 155 SMPSFAINAISALVNLGYGQDQATTAVVSV 184 (207) Q Consensus 155 ~~~~~~~d~~~AL~~LGy~~~ea~~ai~~i 184 (207) ......++.+..|+.+||++..+++|+... T Consensus 14 ~~~~~~~~~i~~L~~MGF~~~~a~~AL~~~ 43 (63) T 1wgn_A 14 MLSPSERQCVETVVNMGYSYECVLRAMKKK 43 (63) T ss_dssp TCCHHHHHHHHHHHHHHCCHHHHHHHHHHH T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 468057999999998699899999999992 No 89 >>2dai_A Ubadc1, ubiquitin associated domain containing 1; UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=79.60 E-value=2.8 Score=22.07 Aligned_cols=29 Identities=21% Similarity=0.311 Sum_probs=23.7 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 65315899999999679998999999999 Q gi|254780553|r 155 SMPSFAINAISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 155 ~~~~~~~d~~~AL~~LGy~~~ea~~ai~~ 183 (207) .....-++++..|+.+||++..+++|+.. T Consensus 24 ~~~~~~~~~i~~L~~MGF~~~~a~~AL~~ 52 (83) T 2dai_A 24 EDERVDEAALRQLTEMGFPENRATKALQL 52 (83) T ss_dssp CSSSCCHHHHHHHHHHTCCHHHHHHHHHH T ss_pred CCCCCCHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 23567999999999969999999999999 No 90 >>2g3q_A Protein YBL047C; endocytosis, solution structure, UBA domain, endocytosis/signaling protein complex; NMR {Saccharomyces cerevisiae} (A:) Probab=79.46 E-value=2.5 Score=22.42 Aligned_cols=26 Identities=19% Similarity=0.317 Sum_probs=22.2 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 58999999996799989999999999 Q gi|254780553|r 159 FAINAISALVNLGYGQDQATTAVVSV 184 (207) Q Consensus 159 ~~~d~~~AL~~LGy~~~ea~~ai~~i 184 (207) ..++.+.-|+.+||++.++.+|+..- T Consensus 3 ~~~~~v~~L~~MGF~~~~a~~AL~~~ 28 (43) T 2g3q_A 3 PKSLAVEELSGMGFTEEEAHNALEKC 28 (43) T ss_dssp HHHHHHHHHHTTTSCHHHHHHHHHHH T ss_pred CCHHHHHHHHHCCCCHHHHHHHHHHC T ss_conf 84999999997699999999999992 No 91 >>1vg5_A RSGI RUH-014, rhomboid family protein; UBA domain, cDNA, structural genomics, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} (A:) Probab=79.32 E-value=3.4 Score=21.57 Aligned_cols=29 Identities=21% Similarity=0.342 Sum_probs=23.9 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 53158999999996799989999999999 Q gi|254780553|r 156 MPSFAINAISALVNLGYGQDQATTAVVSV 184 (207) Q Consensus 156 ~~~~~~d~~~AL~~LGy~~~ea~~ai~~i 184 (207) .....++.+..|+.+||++.++++|+... T Consensus 25 ~~~~~e~~i~~L~~MGF~~~~a~~AL~~~ 53 (73) T 1vg5_A 25 RVAASEEQIQKLVAMGFDRTQVEVALAAA 53 (73) T ss_dssp CSCCCHHHHHHHHTTTCCHHHHHHHHHHH T ss_pred CCCCCHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 87868999999999399999999999995 No 92 >>2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae} (B:229-310) Probab=79.00 E-value=1.3 Score=24.39 Aligned_cols=36 Identities=14% Similarity=0.082 Sum_probs=25.0 Q ss_pred CHHHHHHHHHCC-C-----HHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 899999998515-6-----68751045711679999999974 Q gi|254780553|r 94 TATELVESIILQ-N-----SKVIAQIPGISMKIASRIMTELK 129 (207) Q Consensus 94 ~~~~l~~aI~~~-D-----~~~L~~vpGIGkKtA~rIi~ELk 129 (207) +...+.+....+ + .-+|+.+.|||+++|.+|+-.+. T Consensus 9 d~~~~~ri~~~~~~~~k~i~~aLt~i~GIG~~~A~~I~~~~g 50 (82) T 2zbk_B 9 DREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAG 50 (82) T ss_dssp CHHHHHHHHTTCSSCCBHHHHHHTTSTTCCHHHHHHHHHHTT T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC T ss_conf 267778877502321013345515764676087776665523 No 93 >>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family, transferase/DNA complex; HET: DNA MSE ADI; 1.70A {Sulfolobus solfataricus} (A:183-237) Probab=78.70 E-value=0.92 Score=25.33 Aligned_cols=13 Identities=31% Similarity=0.603 Sum_probs=11.0 Q ss_pred CCCCCHHHHHHHH Q ss_conf 4571167999999 Q gi|254780553|r 113 IPGISMKIASRIM 125 (207) Q Consensus 113 vpGIGkKtA~rIi 125 (207) +||||++|++|+- T Consensus 1 i~GIG~~t~~kL~ 13 (55) T 1jx4_A 1 VPGIGNITAEKLK 13 (55) T ss_dssp STTCCHHHHHHHH T ss_pred CCCCCHHHHHHHH T ss_conf 2599667999999 No 94 >>3i1m_M 30S ribosomal protein S13; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ... (M:1-63) Probab=78.44 E-value=1.3 Score=24.37 Aligned_cols=21 Identities=14% Similarity=0.251 Sum_probs=17.9 Q ss_pred HHHHHCCCCCHHHHHHHHHHH Q ss_conf 875104571167999999997 Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTEL 128 (207) Q Consensus 108 ~~L~~vpGIGkKtA~rIi~EL 128 (207) -+|+.+.|||+++|.+|+-.+ T Consensus 17 ~aLt~i~GIG~~~A~~Ic~~~ 37 (63) T 3i1m_M 17 IALTSIYGVGKTRSKAILAAA 37 (63) T ss_dssp HHGGGSTTCCHHHHHHHHTTT T ss_pred EEEECEECCCHHHHHHHHHHC T ss_conf 875344573899999999991 No 95 >>1ify_A HHR23A, UV excision repair protein RAD23 homolog A; ubiquitin associated domain, UBA domain, ubiquitin proteosome pathway, DNA binding protein; NMR {Homo sapiens} (A:) Probab=78.33 E-value=2.8 Score=22.08 Aligned_cols=27 Identities=15% Similarity=0.338 Sum_probs=22.9 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 315899999999679998999999999 Q gi|254780553|r 157 PSFAINAISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 157 ~~~~~d~~~AL~~LGy~~~ea~~ai~~ 183 (207) ++..++.+.-|+.+||++..+++|+.. T Consensus 5 ~~~~e~~v~~L~~MGF~~~~a~~AL~~ 31 (49) T 1ify_A 5 GSEYETMLTEIMSMGYERERVVAALRA 31 (49) T ss_dssp SHHHHHHHHHHHHTTCCHHHHHHHHHT T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 216999999999800279999999998 No 96 >>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} (A:126-224) Probab=77.97 E-value=4.2 Score=20.93 Aligned_cols=30 Identities=13% Similarity=0.276 Sum_probs=24.6 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 653158999999996799989999999999 Q gi|254780553|r 155 SMPSFAINAISALVNLGYGQDQATTAVVSV 184 (207) Q Consensus 155 ~~~~~~~d~~~AL~~LGy~~~ea~~ai~~i 184 (207) ......++.+.-|+.+||++..+++|+... T Consensus 38 ~~~~~~e~~i~~L~eMGF~~~~a~~AL~~~ 67 (99) T 1oqy_A 38 VTGSEYETMLTEIMSMGYERERVVAALRAS 67 (99) T ss_dssp CCTTTHHHHHHHHHTTTCCSHHHHHHHHHS T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHHHH T ss_conf 123157788999985063779999999987 No 97 >>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (M:1-64) Probab=76.38 E-value=1 Score=24.94 Aligned_cols=21 Identities=19% Similarity=0.200 Sum_probs=17.8 Q ss_pred HHHHHCCCCCHHHHHHHHHHH Q ss_conf 875104571167999999997 Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTEL 128 (207) Q Consensus 108 ~~L~~vpGIGkKtA~rIi~EL 128 (207) -+|+++.|||+++|.+||-.| T Consensus 17 ~aLt~I~GIG~~~A~~Ic~~l 37 (64) T 2vqe_M 17 VALTYIYGIGKARAKEALEKT 37 (64) T ss_dssp HHHTTSSSCCSHHHHHHTTTT T ss_pred EEEEEEECCCHHHHHHHHHHC T ss_conf 873306581899999999982 No 98 >>1wji_A Tudor domain containing protein 3; UBA domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} (A:) Probab=75.98 E-value=3.1 Score=21.75 Aligned_cols=24 Identities=13% Similarity=0.447 Sum_probs=21.3 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 899999999679998999999999 Q gi|254780553|r 160 AINAISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 160 ~~d~~~AL~~LGy~~~ea~~ai~~ 183 (207) -++.+..|+.+||++..+++|+.. T Consensus 9 ~~~~i~~L~~MGF~~~~a~~AL~~ 32 (63) T 1wji_A 9 DEKALKHITEMGFSKEASRQALMD 32 (63) T ss_dssp CHHHHHHHHTTTCCHHHHHHHHHH T ss_pred CHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 999999999969999999999999 No 99 >>1vek_A UBP14, ubiquitin-specific protease 14, putative; UBA domain, three helix bundle, ubiquitin associated domain, structural genomics; NMR {Arabidopsis thaliana} (A:) Probab=75.03 E-value=4.6 Score=20.67 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=22.4 Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 158999999996799989999999999 Q gi|254780553|r 158 SFAINAISALVNLGYGQDQATTAVVSV 184 (207) Q Consensus 158 ~~~~d~~~AL~~LGy~~~ea~~ai~~i 184 (207) ..-.+++..|+.+||++..+++|+... T Consensus 27 ~~d~~~l~~L~~MGF~~~~a~kAL~~t 53 (84) T 1vek_A 27 VANEEIVAQLVSMGFSQLHCQKAAINT 53 (84) T ss_dssp CCCHHHHHHHHHHTCCHHHHHHHHHHT T ss_pred CCCHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 899999999999599999999999998 No 100 >>2cpw_A CBL-interacting protein STS-1 variant; ubiquitin associated domain, UBA, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=74.34 E-value=2.3 Score=22.65 Aligned_cols=24 Identities=25% Similarity=0.466 Sum_probs=20.8 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 999999996799989999999999 Q gi|254780553|r 161 INAISALVNLGYGQDQATTAVVSV 184 (207) Q Consensus 161 ~d~~~AL~~LGy~~~ea~~ai~~i 184 (207) .+.++.|+.+||++..|++|+... T Consensus 20 ~~~v~~L~~MGF~~~~a~kAL~~t 43 (64) T 2cpw_A 20 GSALDVLLSMGFPRARAQKALAST 43 (64) T ss_dssp CCHHHHHHHHTCCHHHHHHHHHHT T ss_pred HHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 999999999699899999999997 No 101 >>1veg_A NEDD8 ultimate buster-1; ubiquitin associated domain, UBA domain, three helix bundle, structural genomics; NMR {Mus musculus} (A:) Probab=73.49 E-value=4.2 Score=20.91 Aligned_cols=27 Identities=26% Similarity=0.309 Sum_probs=22.8 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 315899999999679998999999999 Q gi|254780553|r 157 PSFAINAISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 157 ~~~~~d~~~AL~~LGy~~~ea~~ai~~ 183 (207) ...-.+.+.-|+.+||++..+++|+.. T Consensus 26 ~~~~~~~i~~L~~MGF~~~~a~~AL~~ 52 (83) T 1veg_A 26 ASPSQESINQLVYMGFDTVVAEAALRV 52 (83) T ss_dssp CCCCHHHHHHHHHHSCCHHHHHHHHHH T ss_pred CCCCHHHHHHHHHHCCCHHHHHHHHHH T ss_conf 797788899999834238889999999 No 102 >>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:119-241) Probab=71.58 E-value=4.3 Score=20.85 Aligned_cols=34 Identities=21% Similarity=0.222 Sum_probs=26.3 Q ss_pred CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 8999999985156687510457116799999999742 Q gi|254780553|r 94 TATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 94 ~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) +.++|..|..++- +.++||+|.||.++|..-++- T Consensus 2 tleeL~~a~~~~~---i~~l~gfG~K~~~~il~gl~~ 35 (123) T 2w9m_A 2 SLERLREAAESGE---LAGLKGFGAKSAATILENVVF 35 (123) T ss_dssp SHHHHHHHHHHTT---TTTSTTCCHHHHHHHHHHHHH T ss_pred CHHHHHHHHHCCC---HHHHHCCCHHHHHHHHHHHHH T ss_conf 8999999876088---012110138899999987878 No 103 >>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens} (A:707-781) Probab=70.52 E-value=5.1 Score=20.35 Aligned_cols=25 Identities=24% Similarity=0.496 Sum_probs=21.5 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 5899999999679998999999999 Q gi|254780553|r 159 FAINAISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 159 ~~~d~~~AL~~LGy~~~ea~~ai~~ 183 (207) ...+++..|+.+||++..+++|+.. T Consensus 13 ~~~~~i~~L~~MGF~~~~a~~AL~~ 37 (75) T 3ihp_A 13 PPEDCVTTIVSMGFSRDQALKALRA 37 (75) T ss_dssp CCHHHHHHHHTTTCCHHHHHHHHHH T ss_pred CCHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 5477651045416799999999986 No 104 >>2dak_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5, USP 5, UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=70.45 E-value=4.4 Score=20.78 Aligned_cols=25 Identities=24% Similarity=0.496 Sum_probs=21.5 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 5899999999679998999999999 Q gi|254780553|r 159 FAINAISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 159 ~~~d~~~AL~~LGy~~~ea~~ai~~ 183 (207) ...+.+..|+++||++..+++|+.. T Consensus 8 ~~~~~i~~L~~MGF~~~~a~~AL~~ 32 (63) T 2dak_A 8 PPEDCVTTIVSMGFSRDQALKALRA 32 (63) T ss_dssp CCHHHHHHHHHHTCCHHHHHHHHHH T ss_pred CCHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 8999999999969999999999999 No 105 >>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens} (A:637-706) Probab=69.45 E-value=3.4 Score=21.49 Aligned_cols=25 Identities=28% Similarity=0.400 Sum_probs=21.5 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 5899999999679998999999999 Q gi|254780553|r 159 FAINAISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 159 ~~~d~~~AL~~LGy~~~ea~~ai~~ 183 (207) .-.++++.|+.+||++..|++|+.. T Consensus 15 ~d~~~i~~L~~MGF~~~~a~kAL~~ 39 (70) T 3ihp_A 15 LDESVIIQLVEMGFPMDACRKAVYY 39 (70) T ss_dssp --CHHHHHHHHHTCCHHHHHHHHHH T ss_pred CCHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 4415565676438887875666652 No 106 >>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} (A:427-542) Probab=67.31 E-value=1.7 Score=23.57 Aligned_cols=12 Identities=17% Similarity=0.584 Sum_probs=6.3 Q ss_pred HHHHHCCCHHHH Q ss_conf 501000510112 Q gi|254780553|r 76 QSVQGVGARVAM 87 (207) Q Consensus 76 i~V~GIGpK~AL 87 (207) +.+.|+|+++-- T Consensus 18 l~i~glg~~~i~ 29 (116) T 1dgs_A 18 MDIEGLGEKLIE 29 (116) T ss_dssp SCCTTCCHHHHH T ss_pred CCCCCCCHHHHH T ss_conf 585665999999 No 107 >>2dag_A Ubiquitin carboxyl-terminal hydrolase 5; isopeptidase T, ubiquitin specific protease 5 (USP 5), UBA domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=66.57 E-value=6 Score=19.90 Aligned_cols=24 Identities=29% Similarity=0.393 Sum_probs=21.2 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 999999996799989999999999 Q gi|254780553|r 161 INAISALVNLGYGQDQATTAVVSV 184 (207) Q Consensus 161 ~d~~~AL~~LGy~~~ea~~ai~~i 184 (207) .+.+..|+.+||++..+++|+..- T Consensus 10 ~~~l~~L~eMGF~~~~a~kAL~~t 33 (74) T 2dag_A 10 ESVIIQLVEMGFPMDACRKAVYYT 33 (74) T ss_dssp HHHHHHHHHHSCCHHHHHHHHHHH T ss_pred HHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 999999999599999999999997 No 108 >>1dv0_A DNA repair protein HHR23A; helical bundle, DNA binding protein; HET: DNA; NMR {Homo sapiens} (A:) Probab=62.93 E-value=3 Score=21.90 Aligned_cols=23 Identities=26% Similarity=0.342 Sum_probs=19.9 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 99999999679998999999999 Q gi|254780553|r 161 INAISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 161 ~d~~~AL~~LGy~~~ea~~ai~~ 183 (207) +++++-|+++||++..+++|+.. T Consensus 5 e~~i~~L~~MGF~~~~a~~AL~~ 27 (47) T 1dv0_A 5 KEAIERLKALGFPESLVIQAYFA 27 (47) T ss_dssp HHHHTTTTTTTCCHHHHHHHHTT T ss_pred HHHHHHHHHCCCCHHHHHHHHHH T ss_conf 99999999839988899999998 No 109 >>1whc_A RSGI RUH-027, UBA/UBX 33.3 kDa protein; UBA domain, structural genomics, riken structural genomics/proteomics initiative, unknown function; NMR {Mus musculus} (A:) Probab=60.50 E-value=6.8 Score=19.52 Aligned_cols=23 Identities=22% Similarity=0.517 Sum_probs=20.3 Q ss_pred HHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 99999996799989999999999 Q gi|254780553|r 162 NAISALVNLGYGQDQATTAVVSV 184 (207) Q Consensus 162 d~~~AL~~LGy~~~ea~~ai~~i 184 (207) +.+..|+.+||++..|++|+..- T Consensus 11 ~~l~~L~eMGF~~~~a~kAL~~t 33 (64) T 1whc_A 11 TALESLIEMGFPRGRAEKALALT 33 (64) T ss_dssp CHHHHHHTTTCCHHHHHHHHHHH T ss_pred HHHHHHHHCCCCHHHHHHHHHHH T ss_conf 99999999599999999999997 No 110 >>1fr3_A MOP, molybdate/tungstate binding protein; molybdate homeostasis, metal binding protein; 1.50A {Sporomusa ovata} (A:) Probab=59.85 E-value=12 Score=17.77 Aligned_cols=47 Identities=19% Similarity=0.339 Sum_probs=38.9 Q ss_pred CEEEEEEEEEECC----EEEEEECCEEEEEECCHHHHHHCC-CCCCEEEEEE Q ss_conf 2589999996099----799985883238970868898502-4798499999 Q gi|254780553|r 3 GKIKGNIEGLYED----YVLIDVQGVCYIIYCPIRTLSCLG-KIGDFCTLFV 49 (207) Q Consensus 3 ~~i~G~i~~~~~~----~ivi~v~GvGY~i~vs~~~~~~l~-~~g~~v~l~~ 49 (207) ..+.|+|.++.++ .+.++++|.-....++......|. +.|+.+...+ T Consensus 7 N~l~g~V~~i~~~~~~~~V~l~~~g~~l~a~IT~~s~~~L~L~~G~~v~a~i 58 (67) T 1fr3_A 7 NKLEATVKEIVKGTVMAKIVMDYKGTELVAAITIDSVADLDLVPGDKVTALV 58 (67) T ss_dssp EEEEEEEEEEEECSSEEEEEEEETTEEEEEEEEHHHHHHHTCCTTCEEEEEE T ss_pred CEEEEEEEEEEECCCEEEEEEEECCCEEEEECCHHHHHHCCCCCCCEEEEEE T ss_conf 2999999999989971999999289699999198999767999999999999 No 111 >>3h4j_B AMPK kdaid, SNF1-like protein kinase SSP2; ATP-binding, nucleotide-binding, phosphoprotein, serine/threonine-protein kinase; 2.80A {Schizosaccharomyces pombe} (B:272-336) Probab=59.33 E-value=13 Score=17.71 Aligned_cols=40 Identities=15% Similarity=0.276 Sum_probs=27.0 Q ss_pred HHHHHHHHHHH-CCCCHHHHHHHHHHHHHHCCCCCCHHHHHHH Q ss_conf 58999999996-7999899999999998516888898999999 Q gi|254780553|r 159 FAINAISALVN-LGYGQDQATTAVVSVLKKEKNIADDSQIIRL 200 (207) Q Consensus 159 ~~~d~~~AL~~-LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~ 200 (207) +.++++.+|.. +||.+.++..|+..- +..++.|.=.++|+ T Consensus 10 id~~vv~kLs~tMGY~rdeI~eAL~~~--e~neIkDAY~likE 50 (65) T 3h4j_B 10 ADSRIVSKLGEAMGFSEDYIVEALRSD--ENNEVKEAYNLLHE 50 (65) T ss_dssp CCHHHHHHHHHTTCCCHHHHHHHTTSS--SCCSSTTHHHHHHH T ss_pred CCHHHHHHHHHHHCCCHHHHHHHHHCC--CCCHHHHHHHHHHH T ss_conf 689999999988299999999998676--74099999999987 No 112 >>2crn_A Ubash3A protein; compact three-helix bundle, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Probab=58.10 E-value=6.4 Score=19.72 Aligned_cols=23 Identities=17% Similarity=0.391 Sum_probs=20.1 Q ss_pred HHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 99999996799989999999999 Q gi|254780553|r 162 NAISALVNLGYGQDQATTAVVSV 184 (207) Q Consensus 162 d~~~AL~~LGy~~~ea~~ai~~i 184 (207) +.+.-|+.+||++..+++|+... T Consensus 11 ~~l~~L~eMGF~~~~a~kAL~~t 33 (64) T 2crn_A 11 SLLEPLLAMGFPVHTALKALAAT 33 (64) T ss_dssp SSHHHHHHTSCCHHHHHHHHHHH T ss_pred HHHHHHHHCCCHHHHHHHHHHHH T ss_conf 88889998367389999999985 No 113 >>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C; HET: DGT; 2.39A {Geobacillus kaustophilus} PDB: 3f2c_A* 3f2d_A* (A:973-1041) Probab=57.96 E-value=6.4 Score=19.69 Aligned_cols=18 Identities=22% Similarity=0.468 Sum_probs=15.9 Q ss_pred CCCCHHHHHHHHHHHHHH Q ss_conf 571167999999997422 Q gi|254780553|r 114 PGISMKIASRIMTELKGK 131 (207) Q Consensus 114 pGIGkKtA~rIi~ELk~K 131 (207) ||||.+.|++|+-+-+.+ T Consensus 1 pGig~~~a~~Iv~~R~~g 18 (69) T 3f2b_A 1 PGLGTNVAQAIVRAREEG 18 (69) T ss_dssp TTCCHHHHHHHHHHHHTS T ss_pred CCCCHHHHHHHHHHHCCC T ss_conf 898999999999986579 No 114 >>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} (A:635-702) Probab=55.05 E-value=11 Score=18.20 Aligned_cols=51 Identities=18% Similarity=0.238 Sum_probs=32.4 Q ss_pred HHHHHCCCHHHHHHHCCC--CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHH Q ss_conf 501000510112443157--8999999985156687510457116799999999742221 Q gi|254780553|r 76 QSVQGVGARVAMGVLSRI--TATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAI 133 (207) Q Consensus 76 i~V~GIGpK~AL~iLs~l--~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~ 133 (207) +.|.|||-+-|-.+-+.- ++++|+.+ +. .+ +.-+|+|+|++|+-+++-++. T Consensus 1 v~i~gVGR~RAR~Ly~aGiks~~dla~a----p~-~l--~~~iG~k~A~~I~~~a~~~~~ 53 (68) T 2p6r_A 1 VRIRHIGRVRARKLYNAGIRNAEDIVRH----RE-KV--ASLIGRGIAERVVEGISVKSL 53 (68) T ss_dssp HTSTTCCHHHHHHHHTTTCCSHHHHHHT----HH-HH--HHHHCHHHHHHHHHHHHHHC- T ss_pred CCCCCCCHHHHHHHHHCCCCCHHHHHCC----CH-HH--HHHHCCCHHHHHHHHHHHHHH T ss_conf 5889999999999998799999999749----88-78--977634638999999878762 No 115 >>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} (P:129-215) Probab=54.96 E-value=15 Score=17.24 Aligned_cols=64 Identities=6% Similarity=-0.018 Sum_probs=49.8 Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEECHH Q ss_conf 5899999960997999858832389708688985024798499999999738841899970677 Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDL 67 (207) Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~ 67 (207) -+.|++..+.+..+.++.+|+-=.+..+.-.....-+.|+.+..++...-++..-.-....... T Consensus 9 iv~g~V~~i~~~G~~V~l~~~~g~ip~~e~~~~~~~~~G~~i~~~v~~vd~~~~~i~ls~k~~~ 72 (87) T 1hh2_P 9 VTTAEVIRVMGEWADIRIGKLETRLPKKEWIPGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRV 72 (87) T ss_dssp EEEEEEEEECSSEEEEEETTEEEEEEGGGSCTTCCCCTTCEEEEEEEEEEEETTEEEEEEESSS T ss_pred EEEEEEEEEECCCEEEECCCEEEEECHHHCCCCCCCCCCCEEEEEEEEEEECCCCCEEEEECCC T ss_conf 8999999996143599618616871778869865679999899999999874889779998898 No 116 >>1gnl_A HCP, hybrid cluster protein; anaerobic desulfovibrio desulfuricans, iron anomalous; HET: FSO; 1.25A {Desulfovibrio desulfuricans} (A:1-218) Probab=54.57 E-value=15 Score=17.20 Aligned_cols=36 Identities=17% Similarity=0.199 Sum_probs=30.2 Q ss_pred HHCCCCHHHHHHHHHHHHHHCC-CCCCHHHHHHHHHH Q ss_conf 9679998999999999985168-88898999999999 Q gi|254780553|r 168 VNLGYGQDQATTAVVSVLKKEK-NIADDSQIIRLALR 203 (207) Q Consensus 168 ~~LGy~~~ea~~ai~~i~~~~~-~~~~~eelIk~aLk 203 (207) ..|||...++..-+.+++.... +..+.+++|..+|+ T Consensus 161 ~~Lg~~d~eI~~F~~~aL~~~~~~~~~~~eli~l~le 197 (218) T 1gnl_A 161 DVLGKHENSLDAFMQEALAKTLDDSLSVADLVALTLE 197 (218) T ss_dssp HHTTCCCHHHHHHHHHHHHHTTCTTCCHHHHHHHHHH T ss_pred HHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH T ss_conf 8745552388999999999848995237899999988 No 117 >>2dna_A Unnamed protein product; ubiquitin associated domain, DSK2 protein, proteasome, structural genomics, NPPSFA; NMR {Mus musculus} (A:) Probab=54.45 E-value=15 Score=17.18 Aligned_cols=26 Identities=12% Similarity=0.210 Sum_probs=20.6 Q ss_pred CHHHHHHHHHHHCCCC-HHHHHHHHHH Q ss_conf 1589999999967999-8999999999 Q gi|254780553|r 158 SFAINAISALVNLGYG-QDQATTAVVS 183 (207) Q Consensus 158 ~~~~d~~~AL~~LGy~-~~ea~~ai~~ 183 (207) ....+.++.|..+||. +..+.+|+.. T Consensus 17 ~~~~~~l~~L~~MGF~d~~~~~~AL~~ 43 (67) T 2dna_A 17 VRFSKEMECLQAMGFVNYNANLQALIA 43 (67) T ss_dssp HHTHHHHHHHHHHTCCCHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHH T ss_conf 889999999999389969999999999 No 118 >>3ci0_K Pseudopilin GSPK; general secretory pathway, pseudopilus, type 4 pilin biogenesis, methylation, protein transport; 2.20A {Escherichia coli} (K:76-256) Probab=53.96 E-value=4.9 Score=20.47 Aligned_cols=25 Identities=28% Similarity=0.061 Sum_probs=17.4 Q ss_pred CHHHHHHHHHHHHHHHCCCHHHHHH Q ss_conf 6779999999850100051011244 Q gi|254780553|r 65 SDLDRQWFMLLQSVQGVGARVAMGV 89 (207) Q Consensus 65 ~~~Er~~F~~Li~V~GIGpK~AL~i 89 (207) +..-.++|..|+...|+.+..|-.+ T Consensus 16 ~~~~~~~~~~ll~~~~~~~~~a~~~ 40 (181) T 3ci0_K 16 RPLAVQQLIALISRLDVPAYRAELI 40 (181) T ss_dssp SCHHHHHHHHHHHTTTCCHHHHHHH T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHH T ss_conf 6799999999999849986789999 No 119 >>3bqs_A Uncharacterized protein; 10114F, NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.42A {Listeria monocytogenes str} PDB: 3bqt_A (A:) Probab=51.50 E-value=8.2 Score=18.98 Aligned_cols=17 Identities=12% Similarity=0.405 Sum_probs=13.9 Q ss_pred HHHHHCCCCCHHHHHHH Q ss_conf 87510457116799999 Q gi|254780553|r 108 KVIAQIPGISMKIASRI 124 (207) Q Consensus 108 ~~L~~vpGIGkKtA~rI 124 (207) ..|+.+|+||+++++.+ T Consensus 4 ~~l~~LPNiG~~~e~~L 20 (93) T 3bqs_A 4 ANLSELPNIGKVLEQDL 20 (93) T ss_dssp SCGGGSTTCCHHHHHHH T ss_pred HHHHHCCCCCHHHHHHH T ss_conf 77856899999999999 No 120 >>1szp_A DNA repair protein RAD51; homologous recombination, asymmetry, RAD51 filament, DNA binding protein; HET: DNA; 3.25A {Saccharomyces cerevisiae} (A:26-81) Probab=49.51 E-value=14 Score=17.35 Aligned_cols=32 Identities=25% Similarity=0.353 Sum_probs=26.2 Q ss_pred HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 99985156687510457116799999999742 Q gi|254780553|r 99 VESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 99 ~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) +++|+.--.+.|+.+.||+.-+|++|+-+=+. T Consensus 3 ve~ia~at~k~L~~ikGisE~ka~KIi~aA~k 34 (56) T 1szp_A 3 AEAVAYAPRKDLLEIKGISEAKADKLLNEAAR 34 (56) T ss_dssp HHHHHHSCSHHHHTSTTCCHHHHHHHHHHHHH T ss_pred HHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 99997389999987639999999999999998 No 121 >>2juj_A E3 ubiquitin-protein ligase CBL; alpha helix, UBA domain, calcium, cytoplasm, metal- binding, phosphorylation, proto-oncogene, SH2 domain; NMR {Homo sapiens} (A:) Probab=48.14 E-value=16 Score=17.03 Aligned_cols=21 Identities=29% Similarity=0.458 Sum_probs=17.9 Q ss_pred HHHHHHHCCCCHHHHHHHHHH Q ss_conf 999999679998999999999 Q gi|254780553|r 163 AISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 163 ~~~AL~~LGy~~~ea~~ai~~ 183 (207) -++-|.+.||+..++.+|+.- T Consensus 10 eI~~Lm~~GYs~~~V~rAL~I 30 (56) T 2juj_A 10 EIENLMSQGYSYQDIQKALVI 30 (56) T ss_dssp HHHHHHTTTCCHHHHHHHHHH T ss_pred HHHHHHHCCCCHHHHHHHHHH T ss_conf 999999866659999999999 No 122 >>2ooa_A E3 ubiquitin-protein ligase CBL-B; alpha-helical domain; 1.56A {Homo sapiens} PDB: 2oob_A 2jnh_A 2do6_A (A:) Probab=47.96 E-value=16 Score=17.02 Aligned_cols=21 Identities=24% Similarity=0.368 Sum_probs=17.9 Q ss_pred HHHHHHHCCCCHHHHHHHHHH Q ss_conf 999999679998999999999 Q gi|254780553|r 163 AISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 163 ~~~AL~~LGy~~~ea~~ai~~ 183 (207) -++-|.+.||+..++.+|+.- T Consensus 14 eI~~Lm~~GYs~~dv~rAL~I 34 (52) T 2ooa_A 14 KIAKLXGEGYAFEEVKRALEI 34 (52) T ss_dssp HHHHHHHTTCCHHHHHHHHHH T ss_pred HHHHHHHCCCCHHHHHHHHHH T ss_conf 999999855439999999999 No 123 >>1z96_A DNA-damage, UBA-domain protein MUD1; ubiquitin, three-helix bundle, protein transport; 1.80A {Schizosaccharomyces pombe} (A:) Probab=46.97 E-value=17 Score=16.86 Aligned_cols=22 Identities=27% Similarity=0.462 Sum_probs=18.2 Q ss_pred HHHHHHHCCCCHHHHHHHHHHH Q ss_conf 9999996799989999999999 Q gi|254780553|r 163 AISALVNLGYGQDQATTAVVSV 184 (207) Q Consensus 163 ~~~AL~~LGy~~~ea~~ai~~i 184 (207) -+.-|+++||++-|+.+++... T Consensus 7 kiaqlvsmgfdpleaaqaldaa 28 (40) T 1z96_A 7 KIAQLVSMGFDPLEAAQALDAA 28 (40) T ss_dssp HHHHHHHTTCCHHHHHHHHHHT T ss_pred HHHHHHHCCCCHHHHHHHHHHH T ss_conf 9999998178878999887540 No 124 >>2oo9_A E3 ubiquitin-protein ligase CBL; alpha-helical domain, homodimer; 2.10A {Homo sapiens} (A:) Probab=46.22 E-value=16 Score=17.07 Aligned_cols=21 Identities=29% Similarity=0.433 Sum_probs=17.7 Q ss_pred HHHHHHHCCCCHHHHHHHHHH Q ss_conf 999999679998999999999 Q gi|254780553|r 163 AISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 163 ~~~AL~~LGy~~~ea~~ai~~ 183 (207) -++-|.++||+..++.+|+.- T Consensus 7 eI~~Lm~~GYs~~~v~rAL~I 27 (46) T 2oo9_A 7 EIENLXSQGYSYQDIQKALVI 27 (46) T ss_dssp HHHHHHHTTBCHHHHHHHHHH T ss_pred HHHHHHHCCCCHHHHHHHHHH T ss_conf 999999867769999999999 No 125 >>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=45.23 E-value=21 Score=16.25 Aligned_cols=54 Identities=7% Similarity=-0.055 Sum_probs=44.5 Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCC Q ss_conf 589999996099799985883238970868898502479849999999973884 Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQ 57 (207) Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~ 57 (207) -..|+|..+.+-.+.++..+...+-++|.+.++.--+.|+.++..+-..=.++. T Consensus 20 ~~~g~V~~i~~~G~fV~l~~~~~eGlv~~sel~~~~~vGd~v~v~v~~vd~~~~ 73 (84) T 3go5_A 20 NWPAIVYRLKLSGTFVYLPENNXLGFIHPSERYAEPRLGQVLDARVIGFREVDR 73 (84) T ss_dssp EEEEEEEEEETTEEEEEETTTTEEEEECGGGCSSCCCTTCEEEEEEEEEETTTT T ss_pred EEEEEEEEEECCCCEEEECCCCEEEEECCCCCCCCCCCCCEEEEEEEEEECCCC T ss_conf 999999999748718984378789996354124446757489999999984376 No 126 >>2d9s_A CBL E3 ubiquitin protein ligase; UBA domain, dimer, protein binding, structural genomics, NPPSFA; NMR {Mus musculus} (A:) Probab=44.29 E-value=18 Score=16.78 Aligned_cols=21 Identities=29% Similarity=0.453 Sum_probs=17.8 Q ss_pred HHHHHHHCCCCHHHHHHHHHH Q ss_conf 999999679998999999999 Q gi|254780553|r 163 AISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 163 ~~~AL~~LGy~~~ea~~ai~~ 183 (207) -++-|.+.||+..++.+|+.- T Consensus 12 eI~~Lm~~GYs~~~v~rAL~I 32 (53) T 2d9s_A 12 EIERLMSQGYSYQDIQKALVI 32 (53) T ss_dssp HHHHHHHHTCCHHHHHHHHHH T ss_pred HHHHHHHCCCCHHHHHHHHHH T ss_conf 999999855339999999999 No 127 >>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa} (M:) Probab=44.20 E-value=10 Score=18.37 Aligned_cols=26 Identities=19% Similarity=0.313 Sum_probs=12.3 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHCCC Q ss_conf 99999998501000510112443157 Q gi|254780553|r 68 DRQWFMLLQSVQGVGARVAMGVLSRI 93 (207) Q Consensus 68 Er~~F~~Li~V~GIGpK~AL~iLs~l 93 (207) .+.++--|..+.|||++.|..|+..+ T Consensus 57 ~K~i~~ALt~IyGIG~~~A~~Ic~~l 82 (145) T 3bbn_M 57 HKRVEYSLQYIHGIGRSRSRQILLDL 82 (145) T ss_dssp SSBTTTGGGGSTTCCSSTTTGGGTTT T ss_pred CCEEEEEEEEEECCCHHHHHHHHHHC T ss_conf 97889986537550899999999986 No 128 >>1toa_A Tromp-1, protein (periplasmic binding protein TROA); zinc binding protein, ABC transporter; 1.80A {Treponema pallidum} (A:196-313) Probab=43.27 E-value=23 Score=16.05 Aligned_cols=45 Identities=13% Similarity=0.065 Sum_probs=38.0 Q ss_pred CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCC Q ss_conf 899999998515668751045711679999999974222110113 Q gi|254780553|r 94 TATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSV 138 (207) Q Consensus 94 ~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~ 138 (207) ...++++.|...+++.+-.=|...+|.+++|.-+++-++..++.. T Consensus 39 ~l~~l~~~ik~~~v~~if~e~~~~~~~~~~ia~~~~~~~~~l~p~ 83 (118) T 1toa_A 39 DMQELAAFIAQRKLPAIFIESSIPHKNVEALRDAVQARGHVVQIG 83 (118) T ss_dssp HHHHHHHHHHHTTCSEEEEETTSCTHHHHHHHHHHHTTTCCCEEE T ss_pred HHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHCCCCEEECCC T ss_conf 999999999864996899848999089999999857884132557 No 129 >>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} (T:1-19,T:58-205) Probab=42.05 E-value=2.6 Score=22.28 Aligned_cols=12 Identities=17% Similarity=-0.031 Sum_probs=5.0 Q ss_pred HHHHHHHHHCCC Q ss_conf 999999996799 Q gi|254780553|r 161 INAISALVNLGY 172 (207) Q Consensus 161 ~d~~~AL~~LGy 172 (207) ..+...|..+|+ T Consensus 59 ~~~~~~l~~~gi 70 (167) T 1bgx_T 59 ALIKELVDLLGL 70 (167) T ss_dssp GTHHHHHHHTTC T ss_pred HHHHHHHHHCCC T ss_conf 999999997899 No 130 >>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} (B:) Probab=40.29 E-value=25 Score=15.75 Aligned_cols=28 Identities=7% Similarity=0.154 Sum_probs=21.0 Q ss_pred HCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 5156687510457116799999999742 Q gi|254780553|r 103 ILQNSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 103 ~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) ..-...-|.++||+|+|+.+.|.--|+. T Consensus 43 ~~~s~~dLl~i~nlG~ksl~EI~~~L~~ 70 (79) T 3gfk_B 43 ANKTEEDMMKVRNLGRKSLEEVKAKLEE 70 (79) T ss_dssp TTCCHHHHTTSTTCHHHHHHHHHHHHHH T ss_pred HHCCHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 8789999985789867369999999998 No 131 >>1wr1_B Ubiquitin-like protein DSK2; UBA domain, UBA-ubiquitin complex, signaling protein; NMR {Saccharomyces cerevisiae} (B:) Probab=39.73 E-value=26 Score=15.69 Aligned_cols=27 Identities=15% Similarity=0.171 Sum_probs=20.8 Q ss_pred CHHHHHHHHHHHCCCC-HHHHHHHHHHH Q ss_conf 1589999999967999-89999999999 Q gi|254780553|r 158 SFAINAISALVNLGYG-QDQATTAVVSV 184 (207) Q Consensus 158 ~~~~d~~~AL~~LGy~-~~ea~~ai~~i 184 (207) ....+.++-|..+||. +..+.+|+... T Consensus 15 ~~~~~~l~~L~~MGF~d~~~~~~AL~~t 42 (58) T 1wr1_B 15 ERYEHQLRQLNDMGFFDFDRNVAALRRS 42 (58) T ss_dssp HHTHHHHHHHHHHTCCCHHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHC T ss_conf 9889999999994999789999999991 No 132 >>3fia_A Intersectin-1; EH 1 domain, NESG, structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 1.45A {Homo sapiens} PDB: 2khn_A (A:) Probab=39.02 E-value=26 Score=15.62 Aligned_cols=39 Identities=10% Similarity=-0.015 Sum_probs=31.8 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHH Q ss_conf 899999999679998999999999985168888989999 Q gi|254780553|r 160 AINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQII 198 (207) Q Consensus 160 ~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelI 198 (207) ..|+..+|.++|+++.++...+..+..+.....+.+|-+ T Consensus 51 ~~el~~~l~~~gl~~~el~~i~~~~D~d~~G~l~~~EF~ 89 (121) T 3fia_A 51 GDQARNFFFQSGLPQPVLAQIWALADXNNDGRXDQVEFS 89 (121) T ss_dssp HHHHHHHHGGGCCCHHHHHHHHHHHCTTCSSEECHHHHH T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCHHHHH T ss_conf 999999999929999999999998478999918699999 No 133 >>2j8s_A ACRB, acriflavine resistance protein B; membrane protein/complex, designed ankyrin repeat protein, multidrug resistance protein; HET: LMT LMU; 2.54A {Escherichia coli} PDB: 2dhh_A 1iwg_A 2dr6_A* 2drd_A* 2hqf_A 2hqg_A 2hqd_A 2hqc_A 2i6w_A 1oy6_A* 1oy9_A* 1oyd_A* 1oy8_A* 1oye_A 2rdd_A* 2w1b_A* 3d9b_A 1t9x_A* 1t9t_A* 1t9v_A* ... (A:135-181,A:275-329,A:568-673) Probab=36.18 E-value=24 Score=15.91 Aligned_cols=24 Identities=8% Similarity=0.209 Sum_probs=11.9 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHCC Q ss_conf 457116799999999742221101 Q gi|254780553|r 113 IPGISMKIASRIMTELKGKAISLS 136 (207) Q Consensus 113 vpGIGkKtA~rIi~ELk~K~~~~~ 136 (207) -||..-...++++-++.+.+.+.. T Consensus 114 P~Gtsle~T~~~~~~ie~~l~~~~ 137 (208) T 2j8s_A 114 PAGATQERTQKVLNEVTHYYLTKE 137 (208) T ss_dssp CTTCCHHHHHHHHHHHHHHHHHTT T ss_pred HHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 330139999999999999874026 No 134 >>3gi1_A LBP, laminin-binding protein of group A streptococci; zinc-binding receptor, metal-binding, helical backbone, alpha/beta domains; 2.45A {Streptococcus pyogenes} PDB: 3hjt_A (A:178-286) Probab=35.61 E-value=19 Score=16.58 Aligned_cols=46 Identities=24% Similarity=0.190 Sum_probs=38.8 Q ss_pred CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 8999999985156687510457116799999999742221101133 Q gi|254780553|r 94 TATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVV 139 (207) Q Consensus 94 ~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~ 139 (207) ...++++.|.+.+++.+-.-|..+.|++++|.-++..+...+.... T Consensus 39 ~i~~l~~~ik~~~i~~i~~e~~~~~~~~~~ia~~~~~~~~~l~~l~ 84 (109) T 3gi1_A 39 QLKEIQDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLE 84 (109) T ss_dssp HHHHHHHHHHHTTCCEEEECTTSCTHHHHHHHHTTTCEEEECCCSC T ss_pred HHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHCCCEEEECCCC T ss_conf 9999999999759988999588993999999998299878747776 No 135 >>3fe3_A MAP/microtubule affinity-regulating kinase 3; serine/threonine protein kinase, MARK;PAR-1, UBA domain;C-TAK1;P78;MARK3, alternative splicing; 1.90A {Homo sapiens} PDB: 2qnj_A 1y8g_A* 1zmw_A 1zmu_A 1zmv_A 2r0i_A 2hak_A 3iec_A (A:1-95,A:269-328) Probab=34.95 E-value=30 Score=15.21 Aligned_cols=22 Identities=23% Similarity=0.551 Sum_probs=18.6 Q ss_pred HHHHHHHHCCCCHHHHHHHHHH Q ss_conf 9999999679998999999999 Q gi|254780553|r 162 NAISALVNLGYGQDQATTAVVS 183 (207) Q Consensus 162 d~~~AL~~LGy~~~ea~~ai~~ 183 (207) .-++++.++||++.+++..+.+ T Consensus 118 ~~~~~~~~mg~~~~~~~~sl~~ 139 (155) T 3fe3_A 118 KRIDIMVGMGYSQEEIQESLSK 139 (155) T ss_dssp HHHHHHHHTTCCHHHHHHHHHT T ss_pred HHHHHHHHCCCCHHHHHHHHHH T ss_conf 9999998769999999999986 No 136 >>1nkw_E 50S ribosomal protein L6; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} (E:110-212) Probab=33.42 E-value=21 Score=16.21 Aligned_cols=62 Identities=16% Similarity=0.151 Sum_probs=34.2 Q ss_pred EEEEEECCEEEEEECCHHHHHHCCCCC--CEEEEEEEEE-----ECCCCEEEEEEECHHHHHHHHHHHHHH Q ss_conf 799985883238970868898502479--8499999999-----738841899970677999999985010 Q gi|254780553|r 16 YVLIDVQGVCYIIYCPIRTLSCLGKIG--DFCTLFVETH-----MRQDQIRLFGFLSDLDRQWFMLLQSVQ 79 (207) Q Consensus 16 ~ivi~v~GvGY~i~vs~~~~~~l~~~g--~~v~l~~~~~-----vrEd~~~LyGF~~~~Er~~F~~Li~V~ 79 (207) ...|+..||||.+.+..+.+.- ..| ..+.+.+-.. -..+.+.++|..-..=-++-..+.+.. T Consensus 2 ~k~LelvGVGYra~~~~~~L~l--~LG~SH~i~~~iP~~I~v~~~~~t~i~i~G~dKq~vg~faa~Ir~~r 70 (103) T 1nkw_E 2 TINLELRGVGFRAKLTGKALEM--NIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQLVGQVAANVRKVR 70 (103) T ss_pred EEEEEEEEEEEEEEECCCCCEE--EECCCCCEEEECCCCCEEEECCCCEEEEEECCHHHHHHHHHHHHHCC T ss_conf 8999997657745861664236--63123543576897767985489899999789999999999985148 No 137 >>2kgr_A Intersectin-1; structure, alternative splicing, calcium, cell junction, cell projection, coiled coil, endocytosis, membrane, phosphoprotein; NMR {Homo sapiens} (A:) Probab=33.19 E-value=32 Score=15.02 Aligned_cols=43 Identities=12% Similarity=-0.047 Sum_probs=33.3 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHH Q ss_conf 5899999999679998999999999985168888989999999 Q gi|254780553|r 159 FAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLA 201 (207) Q Consensus 159 ~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~a 201 (207) ...|...+|.++|+++.++...+..+..+.....+.+|.++.. T Consensus 32 ~~~El~~~l~~~g~~~~~i~~~~~~~D~d~dG~I~~~EF~~~~ 74 (111) T 2kgr_A 32 TGPQARTILMQSSLPQAQLASIWNLSDIDQDGKLTAEEFILAM 74 (111) T ss_dssp EHHHHHHHHHTTCCCHHHHHHHHHHHCSSCCSEEEHHHHHHHH T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCEECHHHHHHHH T ss_conf 2999999999839899999999988636999839699999999 No 138 >>2v50_A Multidrug resistance protein MEXB; DDM, RND, membrane, detergent, transport, cell membrane, transmembrane, membrane protein; HET: LMT; 3.00A {Pseudomonas aeruginosa PA01} (A:135-180,A:275-329,A:567-673) Probab=31.54 E-value=34 Score=14.84 Aligned_cols=27 Identities=15% Similarity=0.274 Sum_probs=17.4 Q ss_pred CCCHHHHHHHHHCCCHHHHHHCCCCCH Q ss_conf 578999999985156687510457116 Q gi|254780553|r 92 RITATELVESIILQNSKVIAQIPGISM 118 (207) Q Consensus 92 ~l~~~~l~~aI~~~D~~~L~~vpGIGk 118 (207) +++...|.+.+..+=...|+++||||. T Consensus 14 ~~~~~~l~~y~~~~~~~~l~r~~gvg~ 40 (208) T 2v50_A 14 SMTKEDLSNYIVSNIQDPLSRTKGVGD 40 (208) T ss_dssp TSCHHHHHHHHHHHTHHHHHTSTTEEE T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCEEE T ss_conf 979999999999999999846999489 No 139 >>1qjt_A EH1, epidermal growth factor receptor substrate substrate 15, EPS15; EH domain, EF-hand, solution structure, S100 protein; NMR {Mus musculus} (A:) Probab=30.61 E-value=35 Score=14.74 Aligned_cols=41 Identities=10% Similarity=-0.016 Sum_probs=32.1 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHH Q ss_conf 99999999679998999999999985168888989999999 Q gi|254780553|r 161 INAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLA 201 (207) Q Consensus 161 ~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~a 201 (207) .|...+|.++|+++.++...+..+..+.....+.++.+... T Consensus 31 ~El~~~l~~~~~~~~~~~~~~~~~D~~~dg~I~~~eF~~~~ 71 (99) T 1qjt_A 31 LDAAAFLKKSGLPDLILGKIWDLADTDGKGVLSKQEFFVAL 71 (99) T ss_dssp HHHHHHHHTSSSCHHHHHHHHHHHCCSSSSSCCSHHHHHHH T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHH T ss_conf 99999999818759999999997278999918899999999 No 140 >>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A (A:1-96,A:300-320) Probab=29.37 E-value=34 Score=14.86 Aligned_cols=31 Identities=19% Similarity=0.327 Sum_probs=23.6 Q ss_pred HHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 9999999851566875104571167999999997422211 Q gi|254780553|r 95 ATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAIS 134 (207) Q Consensus 95 ~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~ 134 (207) +++|=......| ||..||++|+-+|+.++.+ T Consensus 37 lEeLEe~LI~aD---------vGv~tt~~Ii~~lr~r~kk 67 (117) T 1zu4_A 37 FEELEDVLIQTD---------MGMKMVLKVSNLVRKKTKR 67 (117) T ss_dssp HHHHHHHHHHTT---------CCHHHHHHHHHHHHHHCCT T ss_pred HHHHHHHHHHCC---------CCHHHHHHHHHHHHHHHCC T ss_conf 999999999828---------9899999999999999714 No 141 >>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} (B:) Probab=29.15 E-value=37 Score=14.58 Aligned_cols=50 Identities=12% Similarity=0.157 Sum_probs=28.1 Q ss_pred HCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 0051011244315789999999851566875104571167999999997422 Q gi|254780553|r 80 GVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGK 131 (207) Q Consensus 80 GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K 131 (207) +..+++. ..|.......+-+- .+-...-|.++||+|+|+.+.|.--|+.. T Consensus 15 ~Ls~R~~-N~L~~~gI~ti~dL-~~~s~~dLl~i~n~G~kSl~EI~~~L~~~ 64 (73) T 1z3e_B 15 DLSVRSY-NCLKRAGINTVQEL-ANKTEEDMMKVRNLGRKSLEEVKAKLEEL 64 (73) T ss_dssp CCBHHHH-HHHHHTTCCBHHHH-HTSCHHHHHTSTTCCHHHHHHHHHHHHHT T ss_pred CCCHHHH-HHHHHCCCCCHHHH-HHCCHHHHHHCCCCCHHHHHHHHHHHHHC T ss_conf 5889999-99988389479999-87799999758897660599999999985 No 142 >>1pq4_A Periplasmic binding protein component of AN ABC type zinc uptake transporter; ZNUA, loop, metal-binding, metal binding protein; 1.90A {Synechocystis SP} (A:189-270) Probab=28.91 E-value=27 Score=15.48 Aligned_cols=42 Identities=17% Similarity=0.158 Sum_probs=35.0 Q ss_pred HHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCC Q ss_conf 999999985156687510457116799999999742221101 Q gi|254780553|r 95 ATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLS 136 (207) Q Consensus 95 ~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~ 136 (207) ..++++.|.+.+++.+-.-|...+|+|+.|.-|+.-|+.-++ T Consensus 38 i~~l~~~ik~~~i~~if~e~~~~~k~~~~ia~etg~~~~~ld 79 (82) T 1pq4_A 38 LKQLIDTAKENNLTMVFGETQFSTKSSEAIAAEIGAGVELLD 79 (82) T ss_dssp HHHHHHHHHTTTCCEEEEETTSCCHHHHHHHHHHTCEEEEEC T ss_pred HHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHCCCEEEEC T ss_conf 999999999749988997289991999999998099879878 No 143 >>1h9m_A MODG, molybdenum-binding-protein; molybdate homeostasis; 1.65A {Azotobacter vinelandii} (A:66-137) Probab=28.67 E-value=38 Score=14.53 Aligned_cols=47 Identities=15% Similarity=0.230 Sum_probs=37.3 Q ss_pred CEEEEEEEEEECC----EEEEEE-CCEEEEEECCHHHHHHCC-CCCCEEEEEE Q ss_conf 2589999996099----799985-883238970868898502-4798499999 Q gi|254780553|r 3 GKIKGNIEGLYED----YVLIDV-QGVCYIIYCPIRTLSCLG-KIGDFCTLFV 49 (207) Q Consensus 3 ~~i~G~i~~~~~~----~ivi~v-~GvGY~i~vs~~~~~~l~-~~g~~v~l~~ 49 (207) ..+.|+|..+.++ .+.+++ +|.-....++......|. +.|+++...+ T Consensus 17 N~l~g~V~~i~~~~~~~~V~l~~~~g~~l~A~IT~~s~~~L~L~~G~~V~a~i 69 (72) T 1h9m_A 17 NILTGTVKTIETGAVNAEVTLALQGGTEITSMVTKEAVAELGLKPGASASAVI 69 (72) T ss_dssp EEEEEEEEEEEECSSEEEEEEEETTSCEEEEEEEHHHHHHTTCCTTCEEEEEE T ss_pred EEEEEEEEEEEECCCCEEEEEEECCCCEEEEEECHHHHHHCCCCCCCEEEEEE T ss_conf 07779999999899848999994999799999889999777999999999999 No 144 >>2o1e_A YCDH; alpha-beta protein, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.60A {Bacillus subtilis} (A:190-271) Probab=28.07 E-value=23 Score=16.05 Aligned_cols=42 Identities=26% Similarity=0.171 Sum_probs=35.3 Q ss_pred CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHC Q ss_conf 899999998515668751045711679999999974222110 Q gi|254780553|r 94 TATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISL 135 (207) Q Consensus 94 ~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~ 135 (207) +..++++.|..++++.+-.-|....|+|+.|.-++.-|+..+ T Consensus 38 ~i~~l~~~ik~~~i~~if~e~~~~~k~~~~ia~~~g~~v~~l 79 (82) T 2o1e_A 38 SLAKLKTYAKEHNVKVIYFEEIASSKVADTLASEIGAKTEVL 79 (82) T ss_dssp HHHHHHHHTTSSCCCEEECSSCCCHHHHHHHHHHTCCEEECC T ss_pred HHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHCCCEEEE T ss_conf 799999876525886899948889499999999719976554 No 145 >>2awn_A Maltose/maltodextrin import ATP-binding protein MALK; ATP-binding cassette, transport protein; HET: ADP; 2.30A {Escherichia coli K12} (A:237-288,A:350-381) Probab=28.05 E-value=39 Score=14.45 Aligned_cols=54 Identities=13% Similarity=0.180 Sum_probs=40.4 Q ss_pred CEEEEEEEEEECCEEEEEE-CCEEEEEECCHHHHHHCCCCCCEEEEEEE-----EEECCCCE Q ss_conf 2589999996099799985-88323897086889850247984999999-----99738841 Q gi|254780553|r 3 GKIKGNIEGLYEDYVLIDV-QGVCYIIYCPIRTLSCLGKIGDFCTLFVE-----THMRQDQI 58 (207) Q Consensus 3 ~~i~G~i~~~~~~~ivi~v-~GvGY~i~vs~~~~~~l~~~g~~v~l~~~-----~~vrEd~~ 58 (207) .+|.|+|.....+.+.|+. +|-+..+..+..... ...|+.|+|=|- +..|||.. T Consensus 4 NFLpgtV~~~~g~~v~V~L~~g~~~~i~lp~~~~~--~~~G~~VtLGIRPE~~~~~~~~~~~ 63 (84) T 2awn_A 4 NFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRD--VQVGANMSLGIRPEERCHLFREDGT 63 (84) T ss_dssp EEEEEEEEECCTTCEEEECSSTTCCEEEECBCCTT--CCTTCEEEEEECGGGGCEEECTTSB T ss_pred HEEEEEEECCCCCEEEEEEECCCCCEEEECCCCCC--CCCCCEEEEEECHHHHEEEECCCCC T ss_conf 16999998122440479984488844651033355--6899879999972144899799984 No 146 >>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:1-64) Probab=27.23 E-value=40 Score=14.36 Aligned_cols=49 Identities=20% Similarity=0.238 Sum_probs=40.2 Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCC Q ss_conf 58999999609979998588323897086889850247984999999997388 Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQD 56 (207) Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd 56 (207) -+.|+|++-++.+.-+...|+-|++-=+.. -.++|+.|+=|+|...... T Consensus 9 vi~g~V~DENd~~yFvQ~dG~Tf~L~K~E~----~~~iGd~V~GF~Yen~~~~ 57 (64) T 3go5_A 9 FIVGLIIDENDRFYFVQKDGQTYALAKEEG----QHTVGDTVKGFAYTDXKQK 57 (64) T ss_dssp EEEEEEEEECSSEEEEEETTEEEEEEGGGC----CCCTTSEEEEEEEECTTSC T ss_pred EEEEEEEEEECCEEEEECCCEEEEEECCCC----CCCCCCEEEEEEEECCCCC T ss_conf 899999997087399942998999502006----6779989999999988888 No 147 >>2qpt_A EH domain-containing protein-2; protein-nucleotide complex, membrane protein, endocytosis; HET: ANP; 3.10A {Mus musculus} (A:433-550) Probab=27.04 E-value=41 Score=14.34 Aligned_cols=41 Identities=10% Similarity=-0.052 Sum_probs=31.4 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHH Q ss_conf 58999999996799989999999999851688889899999 Q gi|254780553|r 159 FAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIR 199 (207) Q Consensus 159 ~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk 199 (207) ..+|+..+|..+|+++.++...+..+..+.....+.+|.+. T Consensus 43 s~~el~~~l~~~~l~~~~~~~i~~~~D~d~dG~I~~~EF~~ 83 (118) T 2qpt_A 43 SGSKAKTWMVGTKLPNSVLGRIWKLSDVDRDGMLDDEEFAL 83 (118) T ss_dssp CHHHHHHHHHHTTCCHHHHHHHHHHHCSSCSSSEEHHHHHH T ss_pred CHHHHHHHHHHCCCCHHHHHHHCHHHHCCCCCCCCHHHHHH T ss_conf 38999999997499878997633186569989968999999 No 148 >>2pmy_A RAS and EF-hand domain-containing protein; rasef, calcium-binding domain, structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens} (A:1-81) Probab=26.85 E-value=41 Score=14.32 Aligned_cols=29 Identities=7% Similarity=-0.075 Sum_probs=24.0 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHC Q ss_conf 89999999967999899999999998516 Q gi|254780553|r 160 AINAISALVNLGYGQDQATTAVVSVLKKE 188 (207) Q Consensus 160 ~~d~~~AL~~LGy~~~ea~~ai~~i~~~~ 188 (207) ..|...+|.++|+++.++...+..+..+. T Consensus 46 ~~el~~~l~~~~~~~~e~~~i~~~~D~d~ 74 (81) T 2pmy_A 46 REEFRALCTELRVRPADAEAVFQRLDADR 74 (81) T ss_dssp HHHHHHHHHHTTCCHHHHHHHHHHHCTTC T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 57899998872113489999999837889 No 149 >>3hh8_A Metal ABC transporter substrate-binding lipoprotein; metal binding, cell membrane, copper, copper transport, ION transport; 1.87A {Streptococcus pyogenes serotype M1} PDB: 1psz_A (A:180-294) Probab=26.25 E-value=42 Score=14.25 Aligned_cols=45 Identities=7% Similarity=0.014 Sum_probs=38.4 Q ss_pred CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCC Q ss_conf 899999998515668751045711679999999974222110113 Q gi|254780553|r 94 TATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSV 138 (207) Q Consensus 94 ~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~ 138 (207) ...++++.|...+++.+-.-|..+.|+|++|.-++.-++..+... T Consensus 41 ~i~~l~~~ik~~~i~~if~e~~~~~~~~~~ia~~~~~~~~~l~pl 85 (115) T 3hh8_A 41 QISSLIEKLKVIKPSALFVESSVDRRPMETVSKDSGIPIYSEIFT 85 (115) T ss_dssp HHHHHHHHHHHSCCSCEEEETTSCSHHHHHHHHHHCCCEEEEECS T ss_pred HHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHCCCEECCCCC T ss_conf 999999997605875899738899399999999809976411465 No 150 >>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi} (A:1-202) Probab=26.22 E-value=42 Score=14.24 Aligned_cols=33 Identities=15% Similarity=0.095 Sum_probs=27.6 Q ss_pred HHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHH Q ss_conf 999999985156687510457116799999999 Q gi|254780553|r 95 ATELVESIILQNSKVIAQIPGISMKIASRIMTE 127 (207) Q Consensus 95 ~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~E 127 (207) .+.+.+++.++..-.+..-||+||-+--+-+.+ T Consensus 21 l~~l~~~l~~~~~v~i~G~~G~GKTsL~~~~~~ 53 (202) T 2qen_A 21 SRKLEESLENYPLTLLLGIRRVGKSSLLRAFLN 53 (202) T ss_dssp HHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHH T ss_pred HHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHH T ss_conf 999999985399799981999989999999999 No 151 >>1vej_A Riken cDNA 4931431F19; UBA domain, three helix bundle, ubiquitin associated domain, structural genomics; NMR {Mus musculus} (A:) Probab=26.18 E-value=42 Score=14.24 Aligned_cols=26 Identities=23% Similarity=0.362 Sum_probs=18.8 Q ss_pred CHHHHHHHHHHHCCCC-HHHHHHHHHH Q ss_conf 1589999999967999-8999999999 Q gi|254780553|r 158 SFAINAISALVNLGYG-QDQATTAVVS 183 (207) Q Consensus 158 ~~~~d~~~AL~~LGy~-~~ea~~ai~~ 183 (207) ....+.++.|+.+||. +...++|+.. T Consensus 27 ~~~~~~l~~L~~MGF~d~~~~~~AL~~ 53 (74) T 1vej_A 27 GRYQQELEELKALGFANRDANLQALVA 53 (74) T ss_dssp TTSHHHHHHHHHHTCCCHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHH T ss_conf 899999999999489978999999999 No 152 >>3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} (A:185-235) Probab=25.99 E-value=31 Score=15.15 Aligned_cols=11 Identities=45% Similarity=0.848 Sum_probs=9.5 Q ss_pred CCCCHHHHHHH Q ss_conf 57116799999 Q gi|254780553|r 114 PGISMKIASRI 124 (207) Q Consensus 114 pGIGkKtA~rI 124 (207) ||||+=+++|+ T Consensus 1 PGiG~i~~~kL 11 (51) T 3bq0_A 1 PGIGSVLARRL 11 (51) T ss_dssp TTCCHHHHHHH T ss_pred CCCCHHHHHHH T ss_conf 29633334554 No 153 >>2kld_A Polycystin-2; PC2, PKD2, calcium binding domain, EF hand, cytosolic, calcium, coiled coil, disease mutation, glycoprotein, ION transport; NMR {Homo sapiens} PDB: 2kle_A (A:) Probab=25.94 E-value=43 Score=14.21 Aligned_cols=62 Identities=10% Similarity=-0.040 Sum_probs=37.1 Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 11679999999974222110113344323333344555565315899999999679998999999999985 Q gi|254780553|r 116 ISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTAVVSVLK 186 (207) Q Consensus 116 IGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL~~LGy~~~ea~~ai~~i~~ 186 (207) +=||...+++.-|+=|-......... .......-..+|..+||...||+..++..+...-.. T Consensus 30 ~iKkgy~k~l~KLklKK~~v~diqk~---------l~~~~~~~~~ee~r~aLk~~g~~d~ei~~~Fskyd~ 91 (123) T 2kld_A 30 LIRKGYHKALVKLKLKKNTVDDISES---------LRQGGGKLNFDELRQDLKGKGHTDAEIEAIFTKYDQ 91 (123) T ss_dssp ---------------------CCSCS---------STTTTTCEEHHHHHHHTTTCCSSHHHHHHHHHHHSS T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHH---------HHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCC T ss_conf 99999999999986123554079999---------757544589799999999855438999999988703 No 154 >>1d8b_A SGS1 RECQ helicase; five helices, three-helical bundle flanked by two helices, DNA binding protein; NMR {Saccharomyces cerevisiae} (A:) Probab=25.06 E-value=44 Score=14.10 Aligned_cols=21 Identities=19% Similarity=0.227 Sum_probs=18.1 Q ss_pred HCCCHHHHHHCCCCCHHHHHH Q ss_conf 515668751045711679999 Q gi|254780553|r 103 ILQNSKVIAQIPGISMKIASR 123 (207) Q Consensus 103 ~~~D~~~L~~vpGIGkKtA~r 123 (207) .-.+...|.+++|+|++.++| T Consensus 43 ~P~t~~eL~~i~G~~~~k~~~ 63 (81) T 1d8b_A 43 LPMNDSAFATLGTVEDKYRRR 63 (81) T ss_dssp CCCSHHHHGGGSCCCHHHHHH T ss_pred CCCCHHHHHCCCCCCHHHHHH T ss_conf 899999981799999999999 No 155 >>3cx3_A Lipoprotein; zinc-binding, transport, lipid binding protein, metal binding protein; 2.40A {Streptococcus pneumoniae} (A:177-261) Probab=24.49 E-value=19 Score=16.55 Aligned_cols=44 Identities=20% Similarity=0.138 Sum_probs=36.7 Q ss_pred CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCC Q ss_conf 89999999851566875104571167999999997422211011 Q gi|254780553|r 94 TATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSS 137 (207) Q Consensus 94 ~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~ 137 (207) ...++++.|...+++.+-.-|...+|+|++|.-|+.-|+..++. T Consensus 38 ~i~~~~~~ik~~~i~~If~e~~~~~k~~~~ia~e~g~~~~~ldp 81 (85) T 3cx3_A 38 QLTEIQEFVKTYKVKTIFTESNASSKVAETLVKSTGVGLKTLNP 81 (85) T ss_dssp HHHHHHHHHHHTTCCCEEECSSSCCHHHHHHHSSSSCCEEECCC T ss_pred HHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHCCCCEEEECC T ss_conf 89999987524675599984889919999999980998688577 No 156 >>3i1n_R 50S ribosomal protein L21; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_R 2aw4_R 2awb_R 1vs6_R 2i2v_R 2j28_R 2i2t_R* 2qao_R* 2qba_R* 2qbc_R* 2qbe_R 2qbg_R 2qbi_R* 2qbk_R* 2qov_R 2qox_R 2qoz_R* 2qp1_R* 2rdo_R 2vhm_R ... (R:) Probab=24.06 E-value=30 Score=15.20 Aligned_cols=50 Identities=10% Similarity=0.008 Sum_probs=37.2 Q ss_pred EEEEEECCEEEEEECCHHHH-HHCC-CCCCEEEEEEEEEECCCCEEEEEEEC Q ss_conf 79998588323897086889-8502-47984999999997388418999706 Q gi|254780553|r 16 YVLIDVQGVCYIIYCPIRTL-SCLG-KIGDFCTLFVETHMRQDQIRLFGFLS 65 (207) Q Consensus 16 ~ivi~v~GvGY~i~vs~~~~-~~l~-~~g~~v~l~~~~~vrEd~~~LyGF~~ 65 (207) |+|++++|-=|.|..-.-.. ..++ +.|+.+.|..-+.+..++.++.|-+. T Consensus 2 yAIi~~ggkQykV~~Gd~i~v~~l~~~~Gd~i~l~~Vl~v~~~~~~~iG~P~ 53 (103) T 3i1n_R 2 YAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPF 53 (103) T ss_dssp EEEECCSSSCCEEETTCCEEESCCCSCTTCEEEECCEEEEESSSCEECSSSS T ss_pred EEEEEECCEEEEECCCCEEEEECCCCCCCCCEEHHHEEEECCCCCEEECCCC T ss_conf 8999979999999389999996467788870882550480279817855975 No 157 >>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} (A:1-177) Probab=23.59 E-value=47 Score=13.92 Aligned_cols=34 Identities=15% Similarity=0.232 Sum_probs=25.9 Q ss_pred HHHHHHHHHCCCH---HHHHHCCCCCHHHHHHHHHHH Q ss_conf 9999999851566---875104571167999999997 Q gi|254780553|r 95 ATELVESIILQNS---KVIAQIPGISMKIASRIMTEL 128 (207) Q Consensus 95 ~~~l~~aI~~~D~---~~L~~vpGIGkKtA~rIi~EL 128 (207) .+++.+++..+.. -.|..-||+||.+.-|.+... T Consensus 25 ~~~l~~~i~~~~~~~~~Ll~GppG~GKT~~A~~la~~ 61 (177) T 1jr3_A 25 LTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKG 61 (177) T ss_dssp HHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHH T ss_pred HHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHH T ss_conf 9999999986997723765799998799999999999 No 158 >>1gnt_A HCP, hybrid cluster protein; oxidoreductase, aerobic desulfovibrio vulgaris; HET: FSO; 1.25A {Desulfovibrio vulgaris} (A:1-222) Probab=23.54 E-value=47 Score=13.92 Aligned_cols=36 Identities=11% Similarity=0.281 Sum_probs=32.4 Q ss_pred HHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH Q ss_conf 967999899999999998516888898999999999 Q gi|254780553|r 168 VNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALR 203 (207) Q Consensus 168 ~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk 203 (207) ..|||...++.+.+.+.+.......+.+++|..+|+ T Consensus 166 ~~lg~~d~ei~~f~~~aL~~~~~~~~~~~~~~l~l~ 201 (222) T 1gnt_A 166 AVLGFRKTEIDEFMLEALASTTKDLSVDEMVALVMK 201 (222) T ss_dssp HHTTCCCHHHHHHHHHHHHHTTSCCCHHHHHHHHHH T ss_pred HHHCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHH T ss_conf 874654105899999999971898657899999998 No 159 >>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} (A:1-168) Probab=23.36 E-value=48 Score=13.89 Aligned_cols=37 Identities=14% Similarity=0.073 Sum_probs=26.4 Q ss_pred CHHHHHHHHHCC--CHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 899999998515--6687510457116799999999742 Q gi|254780553|r 94 TATELVESIILQ--NSKVIAQIPGISMKIASRIMTELKG 130 (207) Q Consensus 94 ~~~~l~~aI~~~--D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207) ..+.|.++|.++ ..-.|..-||+||.+.-+.+..--+ T Consensus 33 ~~~~l~~~i~~~~~~~~Ll~GppG~GKT~~a~~ia~~~~ 71 (168) T 1iqp_A 33 IVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELF 71 (168) T ss_dssp HHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHH T ss_pred HHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHH T ss_conf 999999999779998798889799999999999999976 No 160 >>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} (A:1-28,A:102-142) Probab=23.32 E-value=25 Score=15.76 Aligned_cols=11 Identities=45% Similarity=0.588 Sum_probs=3.6 Q ss_pred HHCCCCCHHHH Q ss_conf 10457116799 Q gi|254780553|r 111 AQIPGISMKIA 121 (207) Q Consensus 111 ~~vpGIGkKtA 121 (207) ..+.|+|-|-| T Consensus 47 vniKGiGyKEA 57 (69) T 3fhg_A 47 LNIKGIGMQEA 57 (69) T ss_dssp TTSTTCCHHHH T ss_pred HHCCCCHHHHH T ss_conf 96758539999 No 161 >>1eh2_A EPS15; calcium binding, signaling domain, NPF binding, EF-hand, EH domain; NMR {Homo sapiens} (A:) Probab=23.11 E-value=48 Score=13.86 Aligned_cols=42 Identities=10% Similarity=-0.077 Sum_probs=32.4 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHH Q ss_conf 589999999967999899999999998516888898999999 Q gi|254780553|r 159 FAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRL 200 (207) Q Consensus 159 ~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~ 200 (207) ...+...+|..||+++.+.+..+..+..+.....+.+|.+.. T Consensus 32 ~~~el~~~l~~lg~~~~~~~~i~~~~D~d~~G~I~f~EF~~~ 73 (106) T 1eh2_A 32 SGDKVKPVLLNSKLPVDILGRVWELSDIDHDGMLDRDEFAVA 73 (106) T ss_dssp BHHHHHHHHHTTTCCHHHHHHHHHHHCSSCSSBCCHHHHHHH T ss_pred EHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCEECHHHHHHH T ss_conf 199999999864898999999999838999981839999999 No 162 >>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana} (A:1-92,A:293-302) Probab=22.33 E-value=50 Score=13.76 Aligned_cols=30 Identities=27% Similarity=0.484 Sum_probs=21.0 Q ss_pred HHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHH Q ss_conf 999999985156687510457116799999999742221 Q gi|254780553|r 95 ATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAI 133 (207) Q Consensus 95 ~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~ 133 (207) +++|=......| ||..||++|+-+|+.++. T Consensus 33 leeLEe~LI~aD---------vGv~tt~~Ii~~lk~~~~ 62 (102) T 3b9q_A 33 LDELEEALLVSD---------FGPKITVRIVERLREDIM 62 (102) T ss_dssp HHHHHHHHHHTT---------CCHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHCC---------CCHHHHHHHHHHHHHHHH T ss_conf 999999999758---------987999999999998875 No 163 >>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli} (A:1-166) Probab=21.80 E-value=51 Score=13.69 Aligned_cols=35 Identities=17% Similarity=0.204 Sum_probs=27.0 Q ss_pred HHHHHHHHHCCCH---HHHHHCCCCCHHHHHHHHHHHH Q ss_conf 9999999851566---8751045711679999999974 Q gi|254780553|r 95 ATELVESIILQNS---KVIAQIPGISMKIASRIMTELK 129 (207) Q Consensus 95 ~~~l~~aI~~~D~---~~L~~vpGIGkKtA~rIi~ELk 129 (207) .+.|.+++.++.. =.|..-||.||.+..|.+..-- T Consensus 11 ~~~L~~~~~~~~~~~~iLl~GppGtGKt~lA~~lA~~l 48 (166) T 1a5t_A 11 FEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYL 48 (166) T ss_dssp HHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHH T ss_pred HHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHH T ss_conf 99999999859967258468999977999999999997 No 164 >>1ci4_A Protein (barrier-TO-autointegration factor (BAF) ); DNA binding protein, retroviral integration, preintegration complex; 1.90A {Homo sapiens} (A:) Probab=21.76 E-value=38 Score=14.52 Aligned_cols=19 Identities=16% Similarity=0.394 Sum_probs=14.2 Q ss_pred HHHHHCCCCCHHHHHHHHH Q ss_conf 8751045711679999999 Q gi|254780553|r 108 KVIAQIPGISMKIASRIMT 126 (207) Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ 126 (207) +..+.+||||+..+.|+.- T Consensus 18 K~V~~l~GIg~~lg~~L~~ 36 (89) T 1ci4_A 18 KPVGSLAGIGEVLGKKLEE 36 (89) T ss_dssp CCGGGSTTCCHHHHHHHHH T ss_pred CCCCCCCCCCHHHHHHHHH T ss_conf 9645168863899889998 No 165 >>1ju2_A HydroxynitrIle lyase; flavin, GMC oxidoreductase, almond, cyanogenesis; HET: NAG NDG FUC BMA MAN FAD; 1.47A {Prunus dulcis} (A:258-298,A:366-472) Probab=21.56 E-value=32 Score=15.00 Aligned_cols=31 Identities=23% Similarity=0.277 Sum_probs=23.8 Q ss_pred HHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHH Q ss_conf 9850100051011244315789999999851566875104571167 Q gi|254780553|r 74 LLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMK 119 (207) Q Consensus 74 ~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkK 119 (207) +|+-.|||||+.-|+-++ +..+.-.||||+. T Consensus 7 ~lL~~SGIGp~~~L~~~g---------------I~~~~~lp~VG~n 37 (148) T 1ju2_A 7 QLLLLSGVGPESYLSSLN---------------IPVVLSHPYVGQF 37 (148) T ss_dssp HHHHHTTEECHHHHHHTT---------------CCCSEECTTTTEE T ss_pred HHHHHCCCCCCHHHHHCC---------------CCEEECCCCCCCC T ss_conf 899864788826777449---------------9648437774665 No 166 >>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} (A:1-160) Probab=20.89 E-value=53 Score=13.57 Aligned_cols=38 Identities=13% Similarity=0.126 Sum_probs=26.8 Q ss_pred HHHHHHHHCCC--HHHHHHCCCCCHHHHHHHHHHH-HHHHH Q ss_conf 99999985156--6875104571167999999997-42221 Q gi|254780553|r 96 TELVESIILQN--SKVIAQIPGISMKIASRIMTEL-KGKAI 133 (207) Q Consensus 96 ~~l~~aI~~~D--~~~L~~vpGIGkKtA~rIi~EL-k~K~~ 133 (207) +.|.+++.++- .-.|..-||.||.+.-|++..- ..... T Consensus 27 ~~l~~~i~~~~~~~~Ll~GppGtGKT~~a~~la~~l~~~~~ 67 (160) T 2chg_A 27 QRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENW 67 (160) T ss_dssp HHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGGGG T ss_pred HHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCC T ss_conf 99999997699885998889998677899988888752566 No 167 >>2w1o_A 60S acidic ribosomal protein P2; ribonucleoprotein, ribosome, translation, dimerization, phosphoprotein; NMR {Homo sapiens} (A:) Probab=20.53 E-value=54 Score=13.52 Aligned_cols=44 Identities=14% Similarity=0.182 Sum_probs=28.8 Q ss_pred HHHHHHHHHHHCCCCHH--HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCC Q ss_conf 58999999996799989--99999999985168888989999999997459 Q gi|254780553|r 159 FAINAISALVNLGYGQD--QATTAVVSVLKKEKNIADDSQIIRLALRAISC 207 (207) Q Consensus 159 ~~~d~~~AL~~LGy~~~--ea~~ai~~i~~~~~~~~~~eelIk~aLk~Ls~ 207 (207) ...|+..-|.+-|-.-. .+...+.++ +..+.+|+|.....+|+| T Consensus 20 s~~dvkkIL~svG~e~d~~~l~~lv~~l-----~gK~i~elI~~G~~Klas 65 (70) T 2w1o_A 20 SAKDIKKILDSVGIEADDDRLNKVISEL-----NGKNIEDVIAQGIGKLAS 65 (70) T ss_dssp CHHHHHHHHHHHTCCCCSHHHHHHHHHH-----HHSCHHHHHHHHSGGGSC T ss_pred CHHHHHHHHHHCCCCCCHHHHHHHHHHH-----CCCCHHHHHHHHHHHHCC T ss_conf 9999999999848863699999999995-----699899999964898704 No 168 >>2z1c_A Hydrogenase expression/formation protein HYPC; [NIFE] hydrogenase maturation, OB-fold, chaperone, metal binding protein; HET: PG4; 1.80A {Thermococcus kodakarensis} (A:) Probab=20.51 E-value=54 Score=13.52 Aligned_cols=47 Identities=15% Similarity=0.245 Sum_probs=36.9 Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEE Q ss_conf 58999999609979998588323897086889850247984999999997 Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHM 53 (207) Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~v 53 (207) .+-|+|.++.++...+|.+|+--+|.+.. .... +.|+.|.+|.=+.+ T Consensus 4 ~iP~kVv~i~~~~A~vd~~G~~r~v~l~l--v~e~-~vGD~VLvh~G~Ai 50 (75) T 2z1c_A 4 AVPGKVIEVNGPVAVVDFGGVKREVRLDL--MPDT-KPGDWVIVHTGFAI 50 (75) T ss_dssp SCCEEEEEEETTEEEEEETTEEEEEECTT--STTC-CTTCEEEEETTEEE T ss_pred CCCEEEEEECCCEEEEEECCEEEEEEEEE--ECCC-CCCCEEEEEECHHH T ss_conf 44469999879989998099499999986--0889-98989999407365 No 169 >>1kk8_A Myosin heavy chain, striated muscle; actin-detached, mechanics of motor, contractIle protein; HET: ADP; 2.30A {Argopecten irradians} (A:79-466,A:598-699) Probab=20.28 E-value=55 Score=13.49 Aligned_cols=29 Identities=17% Similarity=0.120 Sum_probs=19.7 Q ss_pred CCHHHHHHHHHHHCCCCHHH---HHHHHHHHH Q ss_conf 31589999999967999899---999999998 Q gi|254780553|r 157 PSFAINAISALVNLGYGQDQ---ATTAVVSVL 185 (207) Q Consensus 157 ~~~~~d~~~AL~~LGy~~~e---a~~ai~~i~ 185 (207) .....+...||..|||++.+ +.+.+..++ T Consensus 247 ~~~f~~l~~al~~lGis~~e~~~I~~iLAaIL 278 (490) T 1kk8_A 247 VEEFKLCDEAFDILGFTKEEKQSMFKCTASIL 278 (490) T ss_dssp HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 99999999999772999999999999888876 Done!