Query gi|255764496|ref|YP_003065012.2| excinuclease ABC subunit C [Candidatus Liberibacter asiaticus str. psy62] Match_columns 616 No_of_seqs 192 out of 2410 Neff 6.8 Searched_HMMs 23785 Date Tue May 31 18:53:01 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 255764496.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3c65_A Uvrabc system protein C 100.0 0 0 561.9 14.9 224 366-609 2-226 (226) 2 2nrt_A Uvrabc system protein C 100.0 0 0 533.2 19.5 214 362-607 5-219 (220) 3 2nrr_A Uvrabc system protein C 100.0 0 0 406.1 14.8 156 365-551 3-158 (159) 4 1yd6_A UVRC; DNA binding prote 100.0 6.1E-29 2.6E-33 226.7 9.7 91 3-94 9-99 (99) 5 1yd0_A Uvrabc system protein C 100.0 3.2E-28 1.3E-32 221.5 9.9 87 3-92 9-95 (96) 6 2wsh_A Endonuclease II; GIY-YI 99.9 3.2E-26 1.3E-30 207.1 4.2 89 2-90 32-142 (143) 7 1kft_A UVRC, excinuclease ABC 99.6 3.8E-15 1.6E-19 127.2 5.9 68 542-609 10-78 (78) 8 2a1j_A DNA repair endonuclease 99.3 3.6E-12 1.5E-16 105.7 5.9 60 553-613 2-61 (63) 9 1z00_B DNA repair endonuclease 99.3 2.8E-12 1.2E-16 106.5 4.3 61 552-613 15-75 (84) 10 1x2i_A HEF helicase/nuclease; 99.1 8.2E-11 3.5E-15 95.9 7.0 60 554-613 13-72 (75) 11 2a1j_B DNA excision repair pro 99.1 1.2E-10 5.2E-15 94.7 7.2 58 553-610 30-87 (91) 12 1z00_A DNA excision repair pro 99.1 1.9E-10 7.8E-15 93.4 7.6 61 553-613 17-77 (89) 13 2bgw_A XPF endonuclease; hydro 98.9 2.5E-09 1E-13 85.3 6.4 56 555-610 162-217 (219) 14 1mk0_A Intron-associated endon 98.7 8E-08 3.4E-12 74.4 8.1 80 8-87 1-89 (97) 15 2zj8_A DNA helicase, putative 98.4 7.6E-07 3.2E-11 67.3 6.6 84 529-612 599-704 (720) 16 2owo_A DNA ligase; protein/DNA 98.2 3.4E-06 1.4E-10 62.6 7.2 54 557-610 514-567 (671) 17 1e52_A Excinuclease ABC subuni 98.2 1.1E-06 4.7E-11 66.1 4.5 49 186-234 12-61 (63) 18 1vq8_Y 50S ribosomal protein L 98.2 1.8E-07 7.6E-12 71.9 0.0 63 549-611 9-72 (241) 19 1dgs_A DNA ligase; AMP complex 98.2 3.3E-06 1.4E-10 62.8 6.2 52 558-609 510-561 (667) 20 3c1y_A DNA integrity scanning 98.1 6E-06 2.5E-10 60.9 6.2 85 525-609 271-369 (377) 21 1ixr_A Holliday junction DNA h 97.7 8.3E-05 3.5E-09 52.7 6.6 65 548-612 65-132 (191) 22 2ztd_A Holliday junction ATP-d 97.6 0.00011 4.5E-09 51.9 6.0 63 549-611 82-147 (212) 23 1cuk_A RUVA protein; DNA repai 97.5 0.00012 4.9E-09 51.6 5.4 60 550-609 68-130 (203) 24 2w36_A Endonuclease V; hypoxan 97.5 0.00064 2.7E-08 46.3 8.7 111 368-501 22-141 (225) 25 2ziu_A MUS81 protein; helix-ha 97.3 0.00019 7.9E-09 50.1 4.6 58 555-612 237-309 (311) 26 1c4o_A DNA nucleotide excision 97.0 7.6E-05 3.2E-09 52.9 0.0 39 44-83 38-79 (664) 27 3ga2_A Endonuclease V; alpha-b 96.8 0.00093 3.9E-08 45.1 4.2 114 367-501 22-147 (246) 28 3bz1_U Photosystem II 12 kDa e 96.8 0.00085 3.6E-08 45.4 4.0 56 554-615 32-87 (104) 29 1s5l_U Photosystem II 12 kDa e 96.8 0.0012 4.9E-08 44.4 4.6 57 553-615 61-117 (134) 30 1b22_A DNA repair protein RAD5 96.8 0.00031 1.3E-08 48.5 1.5 52 559-610 29-81 (114) 31 3ho1_A Argonaute; argonaute, p 96.7 0.02 8.5E-07 35.4 10.3 112 376-515 468-586 (685) 32 1jms_A Terminal deoxynucleotid 96.4 0.017 7.3E-07 35.9 8.3 20 213-233 55-74 (381) 33 3goc_A Endonuclease V; alpha-b 96.4 0.0013 5.3E-08 44.1 2.5 100 380-500 40-144 (237) 34 3oqg_A HPY188I; endonuclease-D 96.4 0.0028 1.2E-07 41.6 4.0 33 9-42 69-102 (180) 35 2p6r_A Afuhel308 helicase; pro 96.3 0.013 5.3E-07 36.9 7.2 76 529-607 589-682 (702) 36 2zix_A Crossover junction endo 96.2 0.00075 3.1E-08 45.8 0.3 59 555-613 233-306 (307) 37 1u04_A Argonaute, hypothetical 96.1 0.062 2.6E-06 31.9 9.9 119 364-502 530-661 (771) 38 2ihm_A POL MU, DNA polymerase 96.1 0.015 6.2E-07 36.4 6.7 40 193-232 15-54 (360) 39 2w9m_A Polymerase X; SAXS, DNA 95.8 0.01 4.3E-07 37.6 4.8 13 476-488 472-484 (578) 40 2duy_A Competence protein come 95.7 0.0063 2.6E-07 39.1 3.2 49 555-609 27-75 (75) 41 2fmp_A DNA polymerase beta; nu 95.6 0.023 9.6E-07 35.1 5.9 20 213-232 31-50 (335) 42 2edu_A Kinesin-like protein KI 95.6 0.015 6.4E-07 36.3 5.0 49 553-606 38-89 (98) 43 3mr3_A DNA polymerase ETA; POL 95.4 0.016 6.9E-07 36.1 4.6 55 556-612 254-310 (435) 44 1exn_A 5'-exonuclease, 5'-nucl 95.3 0.0093 3.9E-07 37.9 3.1 30 556-585 204-233 (290) 45 3maj_A DNA processing chain A; 95.3 0.026 1.1E-06 34.7 5.3 33 568-604 330-362 (382) 46 2va8_A SSO2462, SKI2-type heli 95.3 0.014 6E-07 36.5 4.0 78 529-609 610-709 (715) 47 2bcq_A DNA polymerase lambda; 95.3 0.024 9.9E-07 34.9 5.1 19 213-232 32-50 (335) 48 2qh9_A UPF0215 protein AF_1433 95.0 0.003 1.3E-07 41.4 -0.2 92 380-501 7-101 (184) 49 2izo_A FEN1, flap structure-sp 94.8 0.01 4.3E-07 37.6 2.1 49 555-604 233-282 (346) 50 1dgs_A DNA ligase; AMP complex 94.6 0.015 6.3E-07 36.4 2.5 56 556-611 442-499 (667) 51 3gqc_A DNA repair protein REV1 94.5 0.079 3.3E-06 31.1 5.9 56 555-613 315-372 (504) 52 3osn_A DNA polymerase IOTA; ho 94.4 0.097 4.1E-06 30.5 6.2 11 217-227 179-189 (420) 53 2owo_A DNA ligase; protein/DNA 94.2 0.056 2.4E-06 32.2 4.7 54 557-610 448-503 (671) 54 3mx1_A ECO29KIR; type II restr 94.1 0.0068 2.9E-07 38.8 -0.1 73 9-86 66-176 (235) 55 1zg2_A Hypothetical UPF0213 pr 93.9 0.018 7.7E-07 35.8 1.8 66 7-76 5-71 (107) 56 1ul1_X Flap endonuclease-1; pr 93.9 0.043 1.8E-06 33.1 3.6 31 555-585 232-262 (379) 57 3lda_A DNA repair protein RAD5 93.9 0.18 7.4E-06 28.6 6.7 12 213-224 142-153 (400) 58 2d7d_A Uvrabc system protein B 93.5 0.056 2.4E-06 32.2 3.6 41 45-86 46-86 (661) 59 2edu_A Kinesin-like protein KI 93.5 0.079 3.3E-06 31.2 4.4 31 578-608 31-61 (98) 60 3bq0_A POL IV, DBH, DNA polyme 93.4 0.071 3E-06 31.5 4.1 10 218-227 126-135 (354) 61 1rxw_A Flap structure-specific 93.3 0.049 2E-06 32.7 3.1 30 555-584 235-264 (336) 62 2ziu_B Crossover junction endo 93.0 0.3 1.2E-05 27.0 6.7 60 555-614 255-335 (341) 63 2aq4_A DNA repair protein REV1 92.6 0.14 5.8E-06 29.4 4.6 54 556-611 242-299 (434) 64 1b43_A Protein (FEN-1); nuclea 92.5 0.099 4.2E-06 30.5 3.8 41 557-604 239-279 (340) 65 1wcn_A Transcription elongatio 92.2 0.27 1.1E-05 27.3 5.7 51 556-606 8-59 (70) 66 1a76_A Flap endonuclease-1 pro 92.1 0.084 3.5E-06 31.0 3.0 27 557-583 227-253 (326) 67 2duy_A Competence protein come 92.1 0.052 2.2E-06 32.5 1.9 27 580-606 20-46 (75) 68 3mfi_A DNA polymerase ETA; DNA 92.0 0.066 2.8E-06 31.7 2.3 18 556-573 308-325 (520) 69 3im1_A Protein SNU246, PRE-mRN 91.1 0.66 2.8E-05 24.5 6.7 10 466-475 266-275 (328) 70 1t94_A Polymerase (DNA directe 90.8 0.67 2.8E-05 24.5 6.5 108 477-614 229-339 (459) 71 2q0z_X Protein Pro2281; SEC63, 90.5 0.72 3E-05 24.2 6.4 10 466-475 269-278 (339) 72 1s5l_U Photosystem II 12 kDa e 90.4 0.082 3.4E-06 31.1 1.5 21 556-576 90-110 (134) 73 1jms_A Terminal deoxynucleotid 90.3 0.42 1.8E-05 25.9 5.1 22 521-542 310-331 (381) 74 2ihm_A POL MU, DNA polymerase 90.3 0.061 2.6E-06 32.0 0.8 24 520-543 288-311 (360) 75 2i5h_A Hypothetical protein AF 90.1 0.52 2.2E-05 25.3 5.4 79 525-610 101-188 (205) 76 3bz1_U Photosystem II 12 kDa e 90.1 0.079 3.3E-06 31.1 1.2 26 580-605 26-51 (104) 77 1yvu_A Hypothetical protein AQ 89.9 0.96 4.1E-05 23.3 11.8 101 378-502 494-603 (706) 78 2bcq_A DNA polymerase lambda; 89.3 0.33 1.4E-05 26.7 3.9 13 476-488 204-216 (335) 79 1pu6_A 3-methyladenine DNA gly 88.3 1 4.3E-05 23.1 5.9 15 127-141 44-58 (218) 80 1ywl_A Hypothetical UPF0213 pr 88.2 0.13 5.5E-06 29.6 1.2 65 10-76 7-72 (96) 81 1bgx_T TAQ DNA polymerase; DNA 87.9 0.012 4.9E-07 37.2 -4.3 97 508-609 596-698 (832) 82 2csb_A Topoisomerase V, TOP61; 87.1 1.4 6.1E-05 22.0 6.5 41 556-597 469-509 (519) 83 2w42_A PIWI, putative uncharac 86.7 1.5 6.3E-05 21.9 15.3 106 379-502 179-297 (427) 84 1im4_A DBH; DNA polymerase PAL 85.9 0.29 1.2E-05 27.1 1.9 36 555-591 184-221 (221) 85 2abk_A Endonuclease III; DNA-r 84.8 0.8 3.4E-05 23.9 3.8 14 131-144 6-19 (211) 86 1u9l_A Transcription elongatio 82.3 1.6 6.5E-05 21.8 4.4 45 562-606 13-58 (70) 87 3fsp_A A/G-specific adenine gl 80.7 2 8.6E-05 21.0 4.6 27 461-488 269-295 (369) 88 1kea_A Possible G-T mismatches 80.5 1.3 5.5E-05 22.4 3.5 12 368-379 191-202 (221) 89 1orn_A Endonuclease III; DNA r 80.2 1.7 7.2E-05 21.5 4.0 16 128-143 7-22 (226) 90 2kp7_A Crossover junction endo 79.8 1 4.3E-05 23.1 2.8 32 516-547 8-43 (87) 91 1z3e_B DNA-directed RNA polyme 79.6 2.8 0.00012 20.0 5.3 56 554-610 8-64 (73) 92 1kg2_A A/G-specific adenine gl 78.9 2.1 8.9E-05 20.9 4.1 17 364-380 182-198 (225) 93 3lti_A DNA-directed RNA polyme 77.0 0.7 2.9E-05 24.3 1.2 21 6-27 2-28 (296) 94 3bzc_A TEX; helix-turn-helix, 75.8 1.3 5.7E-05 22.3 2.4 55 555-611 508-562 (785) 95 3ofo_B 30S ribosomal protein S 75.8 3.6 0.00015 19.2 5.9 56 434-502 128-183 (218) 96 3gfk_B DNA-directed RNA polyme 74.2 3.5 0.00015 19.3 4.2 56 554-610 15-71 (79) 97 1gm5_A RECG; helicase, replica 70.1 3.6 0.00015 19.2 3.5 17 173-189 262-278 (780) 98 3k4g_A DNA-directed RNA polyme 69.6 4.9 0.00021 18.2 6.1 56 553-610 10-67 (86) 99 3bbn_B Ribosomal protein S2; s 67.0 5.5 0.00023 17.9 7.2 54 435-501 137-190 (231) 100 1mpg_A ALKA, 3-methyladenine D 66.2 4.8 0.0002 18.3 3.5 54 555-608 207-261 (282) 101 3ecd_A Serine hydroxymethyltra 65.0 6 0.00025 17.6 5.5 26 464-489 320-347 (425) 102 2vqe_B 30S ribosomal protein S 63.9 6.3 0.00026 17.5 4.3 38 460-502 155-192 (256) 103 1rv3_A Serine hydroxymethyltra 63.7 6.3 0.00027 17.4 4.5 24 464-489 355-382 (483) 104 2gkg_A Response regulator homo 63.0 6.5 0.00027 17.4 3.7 39 462-501 48-90 (127) 105 2jba_A Phosphate regulon trans 57.8 7.9 0.00033 16.7 3.7 77 425-501 8-86 (127) 106 2qr3_A Two-component system re 57.0 8.1 0.00034 16.6 3.4 73 426-501 10-90 (140) 107 2jhn_A ALKA, 3-methyladenine D 56.8 8.2 0.00034 16.6 4.4 17 556-572 211-227 (295) 108 3gl9_A Response regulator; bet 54.2 8.9 0.00037 16.4 3.1 76 426-501 9-86 (122) 109 3c3m_A Response regulator rece 54.1 8.1 0.00034 16.7 2.9 75 426-501 10-87 (138) 110 1vdd_A Recombination protein R 54.0 6.6 0.00028 17.3 2.5 97 239-349 86-190 (228) 111 3kbq_A Protein TA0487; structu 53.6 9.2 0.00039 16.3 3.1 14 376-389 119-132 (172) 112 3i42_A Response regulator rece 53.3 8 0.00033 16.7 2.8 76 426-501 10-87 (127) 113 1ngn_A Methyl-CPG binding prot 52.6 9.5 0.0004 16.2 4.5 81 527-610 38-127 (155) 114 3lua_A Response regulator rece 52.3 9.6 0.0004 16.1 5.6 77 425-502 10-92 (140) 115 2etv_A Iron(III) ABC transport 50.1 7.9 0.00033 16.8 2.3 20 464-483 232-251 (346) 116 3cvo_A Methyltransferase-like 48.7 5.6 0.00024 17.8 1.4 24 463-487 122-145 (202) 117 1coo_A RNA polymerase alpha su 47.6 11 0.00047 15.6 3.8 55 555-610 24-79 (98) 118 3eod_A Protein HNR; response r 46.1 12 0.0005 15.5 5.5 76 425-502 13-90 (130) 119 3cg4_A Response regulator rece 45.6 12 0.00051 15.4 2.7 75 426-501 14-91 (142) 120 2qvg_A Two component response 45.5 12 0.00051 15.4 2.9 75 425-500 13-98 (143) 121 1mb3_A Cell division response 44.7 9.1 0.00038 16.3 2.0 39 463-501 45-85 (124) 122 2zay_A Response regulator rece 43.5 7.1 0.0003 17.1 1.3 38 463-500 52-91 (147) 123 3n0l_A Serine hydroxymethyltra 41.4 14 0.00058 15.0 5.4 24 465-488 313-338 (417) 124 1srr_A SPO0F, sporulation resp 39.9 11 0.00048 15.6 1.9 74 425-500 9-84 (124) 125 1zgz_A Torcad operon transcrip 38.5 12 0.00052 15.4 1.9 38 463-501 46-83 (122) 126 1d8b_A SGS1 RECQ helicase; fiv 38.5 14 0.0006 14.9 2.2 16 556-571 49-64 (81) 127 1gp8_A Protein (scaffolding pr 38.3 14 0.00057 15.1 2.0 30 198-227 9-38 (40) 128 3n5n_X A/G-specific adenine DN 37.6 16 0.00066 14.6 5.6 20 124-143 8-27 (287) 129 2h31_A Multifunctional protein 37.0 13 0.00054 15.2 1.8 29 464-498 322-351 (425) 130 1g8l_A Molybdopterin biosynthe 36.9 16 0.00068 14.5 2.7 100 398-525 199-302 (411) 131 2j48_A Two-component sensor ki 35.9 17 0.0007 14.4 2.5 40 463-503 45-87 (119) 132 1vi6_A 30S ribosomal protein S 33.6 18 0.00076 14.1 6.1 36 462-502 114-149 (208) 133 3h7f_A Serine hydroxymethyltra 32.4 19 0.0008 14.0 3.8 24 464-489 337-364 (447) 134 3e1s_A Exodeoxyribonuclease V, 32.2 6.8 0.00028 17.2 -0.3 30 513-550 473-502 (574) 135 3gbx_A Serine hydroxymethyltra 31.4 20 0.00083 13.9 3.3 26 464-489 319-346 (420) 136 3kht_A Response regulator; PSI 30.9 20 0.00084 13.8 4.5 79 462-541 50-130 (144) 137 1zh2_A KDP operon transcriptio 30.8 11 0.00048 15.6 0.6 36 463-502 45-83 (121) 138 3bqs_A Uncharacterized protein 30.4 20 0.00085 13.8 2.9 31 554-585 3-35 (93) 139 1jlj_A Gephyrin; globular alph 29.9 21 0.00087 13.7 3.2 30 425-474 60-89 (189) 140 3m6m_D Sensory/regulatory prot 29.1 21 0.0009 13.6 2.2 76 425-501 20-100 (143) 141 1uz5_A MOEA protein, 402AA lon 29.0 21 0.0009 13.6 4.3 99 399-525 203-305 (402) 142 2a7v_A Serine hydroxymethyltra 27.9 22 0.00094 13.5 4.2 26 464-489 365-392 (490) 143 3lu0_A DNA-directed RNA polyme 27.2 11 0.00045 15.8 0.0 22 120-142 26-47 (329) 144 2q6t_A DNAB replication FORK h 27.1 23 0.00097 13.4 3.8 36 464-499 311-361 (444) 145 3f6p_A Transcriptional regulat 27.1 23 0.00097 13.4 3.5 75 425-500 8-82 (120) 146 3er9_B Poly(A) polymerase cata 26.8 20 0.00084 13.8 1.3 30 26-55 69-98 (479) 147 3nhm_A Response regulator; pro 26.7 23 0.00099 13.3 2.4 37 462-499 46-85 (133) 148 2pl1_A Transcriptional regulat 26.6 24 0.00099 13.3 2.6 74 426-502 7-83 (121) 149 3hdv_A Response regulator; PSI 26.5 24 0.00099 13.3 2.2 75 425-500 13-90 (136) 150 2db7_A Hairy/enhancer-OF-split 26.5 18 0.00075 14.2 1.0 44 536-579 11-59 (64) 151 3n2l_A OPRT, oprtase, orotate 26.2 22 0.00094 13.5 1.5 32 466-501 176-210 (238) 152 3cnb_A DNA-binding response re 25.7 24 0.001 13.2 4.1 74 426-500 15-93 (143) 153 2qzj_A Two-component response 25.2 20 0.00085 13.8 1.1 35 462-501 47-85 (136) 154 1xl7_A COT, peroxisomal carnit 23.6 27 0.0011 12.9 2.0 34 196-229 215-259 (612) 155 1i3c_A Response regulator RCP1 23.6 27 0.0011 12.9 5.0 40 461-501 59-101 (149) 156 1qkk_A DCTD, C4-dicarboxylate 23.3 27 0.0011 12.9 3.5 73 426-501 10-85 (155) 157 2is8_A Molybdopterin biosynthe 23.2 27 0.0011 12.9 3.2 42 425-486 44-87 (164) 158 3h5i_A Response regulator/sens 22.9 20 0.00086 13.8 0.8 73 425-501 11-88 (140) 159 2rjn_A Response regulator rece 22.8 28 0.0012 12.8 1.8 74 425-500 13-88 (154) 160 2a9o_A Response regulator; ess 22.7 16 0.00068 14.5 0.2 36 463-502 45-83 (120) 161 3opy_B 6-phosphofructo-1-kinas 22.3 28 0.0012 12.8 3.5 37 464-500 663-701 (941) 162 2a6h_A DNA-directed RNA polyme 22.3 15 0.00063 14.7 0.0 39 103-142 6-44 (315) 163 2ixs_A SDAI restriction endonu 22.0 28 0.0012 12.7 2.1 18 400-417 275-292 (323) 164 1m3q_A 8-oxoguanine DNA glycos 21.5 29 0.0012 12.7 5.4 16 555-570 230-245 (317) 165 2rhf_A DNA helicase RECQ; HRDC 21.4 29 0.0012 12.6 3.3 47 524-570 5-62 (77) 166 2x8r_A Glycosyl hydrolase; pep 21.3 29 0.0012 12.6 1.6 14 465-478 193-206 (210) 167 1wud_A ATP-dependent DNA helic 21.1 30 0.0012 12.6 3.4 14 556-569 56-69 (89) 168 3heb_A Response regulator rece 20.9 30 0.0013 12.6 4.4 40 461-501 57-99 (152) 169 2i2c_A Probable inorganic poly 20.7 30 0.0013 12.5 5.4 12 216-227 11-22 (272) 170 3gt7_A Sensor protein; structu 20.3 31 0.0013 12.5 4.9 75 425-500 13-90 (154) 171 1k68_A Phytochrome response re 20.1 31 0.0013 12.5 4.7 75 426-501 9-95 (140) No 1 >3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Probab=100.00 E-value=0 Score=561.92 Aligned_cols=224 Identities=35% Similarity=0.609 Sum_probs=207.9 Q ss_pred HHHHHHHHCCCCCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 99998751566435169997074437754048888851687280323211024444554116899899999999775313 Q gi|255764496|r 366 LKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKN 445 (616) Q Consensus 366 l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~ 445 (616) +.+|++.|+|+. |+|||||||||++|+++|||||||++|+|.|+.||+|||++ +.++|||+||+||++|||+++.++ T Consensus 2 ~~~L~~~L~l~~-p~rIE~fDiSh~~G~~~V~s~Vvf~~g~~~K~~YR~f~ik~--~~~~DDy~~m~Evl~Rr~~r~~~~ 78 (226) T 3c65_A 2 SHMLGERLGIPA-PRRIEAFDNSNIYGADPVSALVVFLDGKPAKKEYRKYKVKT--VAGPNDYETMREVVRRRYTRVLKE 78 (226) T ss_dssp HHHHHHHHTSCC-CSEEEEEEEEESSSSSCEEEEEEEETTEECGGGCEEEECCC--CCTTCHHHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHCCCC-CCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHCCCCCCCC--CCCCCHHHHHHHHHHHHHHHHHHC T ss_conf 789999858499-88799997876589885599999978953867660226567--889974999999999987776631 Q ss_pred CCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCH Q ss_conf 11123333333345457984899809858999999999975887787189997187767663489817983488579989 Q gi|255764496|r 446 EENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDP 525 (616) Q Consensus 446 ~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~ 525 (616) +. ++|||||||||+||||+|.++|++.+.. .|||+||||+++|++. +.+++..++++.|+++++ T Consensus 79 ~~--------------~~PDLilIDGGkgQl~~a~~~l~~~~~~-~i~ii~iaK~~~~~~~-~~~~~~~~~~i~l~~~s~ 142 (226) T 3c65_A 79 GL--------------PLPDLIIIDGGKGHLSAVRDVLENELGL-DVPLAGLAKDEKHRTS-ELLAGDPPDVVPLDRQSQ 142 (226) T ss_dssp TC--------------CCCSEEEESSCHHHHHHHHHHHHHTSCC-CCCEEEC--------C-CCEETTTTEECCCCTTSH T ss_pred CC--------------CCCCEEEECCCHHHHHHHHHHHHHHCCC-CCCEEEECCCCCCCCC-CCCCCCCCCCEECCCCCH T ss_conf 89--------------9999899789889999999999974788-8544430245211343-220158754230687888 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHH Q ss_conf 999999887877887889899864321-4771004888798999999998088898993898888627899989999999 Q gi|255764496|r 526 ILYFIQRLRDEAHRFAITTHRKRRKKA-AYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIY 604 (616) Q Consensus 526 ~l~~Lq~iRDEaHRFAi~~hRk~r~k~-~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~ 604 (616) +|+|||+||||||||||+|||++|+|. +.|.||+||||||+|+++||+||||+++|++||.|||++| |||+++|++|| T Consensus 143 ~l~lLq~iRDEaHRFAi~~hRk~r~k~~~~S~Ld~I~GIG~~~~~~Ll~~Fgs~~~i~~As~eeL~~v-gI~~~~A~~I~ 221 (226) T 3c65_A 143 EFYLLQRIQDEVHRFAVMFHRKTRQKTMFHSVLDDIPGVGEKRKKALLNYFGSVKKMKEATVEELQRA-NIPRAVAEKIY 221 (226) T ss_dssp HHHHHHHHHHHHHHHTTC-------------------------------------------------------------- T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHC-CCCHHHHHHHH T ss_conf 99999999999999999999998740320371102688699999999998189999973899999876-99999999999 Q ss_pred HHHCC Q ss_conf 98547 Q gi|255764496|r 605 NHFHK 609 (616) Q Consensus 605 ~~l~~ 609 (616) ++||+ T Consensus 222 ~~l~e 226 (226) T 3c65_A 222 EKLHE 226 (226) T ss_dssp ----- T ss_pred HHHCC T ss_conf 99629 No 2 >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 Probab=100.00 E-value=0 Score=533.17 Aligned_cols=214 Identities=33% Similarity=0.583 Sum_probs=198.3 Q ss_pred HHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 89999999875156643516999707443775404888885168728032321102444455411689989999999977 Q gi|255764496|r 362 HQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQ 441 (616) Q Consensus 362 ~~~~l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r 441 (616) ++.+|++|++.|+|+++|+|||||||||++|+++|||||||.+|+|.|+.||+|+|+. .++|||+||+||++|||++ T Consensus 5 ~~~~l~~L~~~l~l~~~p~rIE~fDiSh~~G~~~V~s~Vvf~~g~~~k~~YR~y~ik~---~~~dDy~~m~evl~Rr~~~ 81 (220) T 2nrt_A 5 RKEALEELMKLLNMKDFPYRIEGIDISHLQGKYTVASLVVFEDGFPKKGDYRRYKIEQ---DHPDDYESIRTVVKRRYSK 81 (220) T ss_dssp CHHHHHHHHHHTTCSSCCCEEEEEEEEEETTTEEEEEEEEEETTEECGGGCEEEEEEC---SSCCHHHHHHHHHHHHHTT T ss_pred HHHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCEEEEEEECCCCCCHHHHHHHCCCC---CCCHHHHHHHHHHHHHCCC T ss_conf 9999999999819999988599998975589874599999807987666656625788---8970799999999983045 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEEC Q ss_conf 53131112333333334545798489980985899999999997588778718999718776766348981798348857 Q gi|255764496|r 442 LIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLN 521 (616) Q Consensus 442 ~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~ 521 (616) .++|||||||||+||||+|.++|++++++ ++++|++|.++ ++..++.++.|+ T Consensus 82 -------------------~~~PDLilIDGGkgQL~~a~~~l~~~~~~--i~~~~~~k~~~-------~~~~~~~~i~l~ 133 (220) T 2nrt_A 82 -------------------HPLPNLLFVDGGIGQVNAAIEALKEIGKD--CPVVGLAKKEE-------TVVFENREIHLP 133 (220) T ss_dssp -------------------SCCCSEEEESSSHHHHHHHHHHHHHTTCC--CCEEEECTTTC-------CEEETTEEECCC T ss_pred -------------------CCCCEEEEEECCHHHHHHHHHHHHHCCCC--CHHHCCCCCCE-------EECCCCCEEECC T ss_conf -------------------89985899819999999999998740776--21220356542-------661799435569 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHH Q ss_conf 9989999999887877887889899864321-477100488879899999999808889899389888862789998999 Q gi|255764496|r 522 MRDPILYFIQRLRDEAHRFAITTHRKRRKKA-AYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIA 600 (616) Q Consensus 522 ~~~~~l~~Lq~iRDEaHRFAi~~hRk~r~k~-~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A 600 (616) .++++|+|||+||||||||||+|||++|+|. +.|.||+||||||+|+++||+||||+++|++||++||++|+|+ +++| T Consensus 134 ~~~~~~~~Lq~iRDEaHRFAi~~hRk~r~k~~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~I~~As~eeL~~v~g~-~k~A 212 (220) T 2nrt_A 134 HDHPVLRLLVQIRDETHRFAVSYHRKRREKESLRSVLDNVPGIGPIRKKKLIEHFGSLENIRSASLEEIARVIGS-TEIA 212 (220) T ss_dssp TTCHHHHHHHHHHHHHHHHHHGGGHHHHHHHHHHHHHTTSTTCCHHHHHHHHHHHCSHHHHHTSCHHHHHHHHTC-HHHH T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHCCCC-HHHH T ss_conf 999899999999999989879879999752103464100379699999999998189999971899999868695-9999 Q ss_pred HHHHHHH Q ss_conf 9999985 Q gi|255764496|r 601 CKIYNHF 607 (616) Q Consensus 601 ~~I~~~l 607 (616) ++||++| T Consensus 213 ~~I~~~l 219 (220) T 2nrt_A 213 RRVLDIL 219 (220) T ss_dssp HHHHHHC T ss_pred HHHHHHH T ss_conf 9999971 No 3 >2nrr_A Uvrabc system protein C; UVRC, endonuclase, NER, hydrolase; 1.20A {Thermotoga maritima} Probab=100.00 E-value=0 Score=406.11 Aligned_cols=156 Identities=33% Similarity=0.589 Sum_probs=143.6 Q ss_pred HHHHHHHHHCCCCCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC Q ss_conf 99999875156643516999707443775404888885168728032321102444455411689989999999977531 Q gi|255764496|r 365 ILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIK 444 (616) Q Consensus 365 ~l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~ 444 (616) +|++|++.|+|++.|+|||||||||++|+++|||||||.+|+|.|+.||+|||++ .++|||+||+||++|||++ T Consensus 3 al~~L~~~l~l~~~p~rIE~fDiSh~~G~~~Vgs~Vvf~~g~~~k~~YR~f~i~~---~~~dDy~~m~evl~RR~~~--- 76 (159) T 2nrr_A 3 ALEELMKLLNMKDFPYRIEGIDISHLQGKYTVASLVVFEDGFPKKGDYRRYKIEQ---DHPDDYESIRTVVKRRYSK--- 76 (159) T ss_dssp HHHHHHHHTTCSSCCCEEEEEEEECC---CCEEEEEEEETTEECGGGCEEEEC--------CHHHHHHHHHHHHHTT--- T ss_pred HHHHHHHHCCCCCCCCEEEEEECCCCCCCCCEEEEEEECCCCCCHHHHHHHCCCC---CCCHHHHHHHHHHHHHHCC--- T ss_conf 9999999819899988499998975589776699999828985646788853377---7861999999999998567--- Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCC Q ss_conf 31112333333334545798489980985899999999997588778718999718776766348981798348857998 Q gi|255764496|r 445 NEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRD 524 (616) Q Consensus 445 ~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~ 524 (616) .++|||||||||+||||+|.++|++++++ ||++|+||+++ .++. .++++.++.++ T Consensus 77 ----------------~~lPDLilIDGGkgQL~~a~~~l~~~~~~--i~~i~laK~~~------~~~~-~~~~~~l~~~~ 131 (159) T 2nrr_A 77 ----------------HPLPNLLFVDGGIGQVNAAIEALKEIGKD--CPVVGLAKKEE------TVVF-ENREIHLPHDH 131 (159) T ss_dssp ----------------SCCCSEEEESSCHHHHHHHHHHHHHTTCC--CCEEEEC----------CEEE-TTEEECCCTTC T ss_pred ----------------CCCCCEEEECCCHHHHHHHHHHHHHCCCC--CCCCCCCCCCH------HHCC-CCCEECCCCCC T ss_conf ----------------99985899809989999999999984996--63123345211------0023-68612379999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999988787788788989986432 Q gi|255764496|r 525 PILYFIQRLRDEAHRFAITTHRKRRKK 551 (616) Q Consensus 525 ~~l~~Lq~iRDEaHRFAi~~hRk~r~k 551 (616) ++|+|||+||||||||||+|||++|+| T Consensus 132 ~~l~lLq~iRDEaHRFAi~~hR~~r~K 158 (159) T 2nrr_A 132 PVLRLLVQIRDETHRFAVSYHRKRREK 158 (159) T ss_dssp HHHHHHHHHHHHHHHHHHTC------- T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 899999999999999999999988765 No 4 >1yd6_A UVRC; DNA binding protein; 2.00A {Bacillus caldotenax} Probab=99.96 E-value=6.1e-29 Score=226.69 Aligned_cols=91 Identities=41% Similarity=0.800 Sum_probs=86.9 Q ss_pred HHHCCCCCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHCC Q ss_conf 12586788625888699888899601258788876137887787999999734442999828719999999988776187 Q gi|255764496|r 3 SEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKP 82 (616) Q Consensus 3 ~~~lP~~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~~~P 82 (616) .++||++||||+|+|++|+|||||||+|||+||+|||++. .+.++.+|+.++.+|+|++|.||.+|++||+.||++|+| T Consensus 9 l~~lP~~pGVY~f~d~~g~vlYVGKaknLr~Rv~shf~~~-~~~~~~~l~~~~~~i~~~~t~~e~~A~llE~~lIk~~~P 87 (99) T 1yd6_A 9 LAVLPEQPGCYLMKDKHGTVIYVGKAKSLKERVRSYFTGT-HDGKTQRLVEEIADFEYIVTSSNAEALILEMNLIKKHDP 87 (99) T ss_dssp HHTCCSSCEEEEEECSSCCEEEEEEESCHHHHHHGGGSSC-CCHHHHHHHHHCSEEEEEECSSHHHHHHHHHHHHHHHCC T ss_pred HHHCCCCCEEEEEECCCCCEEEEECCHHHHHHHHHHHHHC-CHHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHHHCC T ss_conf 9868999868999899998999767375889999996213-227899999873372089849788889999999998299 Q ss_pred CCEECCCCCCCC Q ss_conf 200336468977 Q gi|255764496|r 83 RFNILLRDDKSF 94 (616) Q Consensus 83 ~yNi~LkDdk~y 94 (616) +||++|||||+| T Consensus 88 ~yN~~~k~~k~y 99 (99) T 1yd6_A 88 KYNVMLKDDKSY 99 (99) T ss_dssp HHHHHTCC---- T ss_pred CCHHCCCCCCCC T ss_conf 740102589999 No 5 >1yd0_A Uvrabc system protein C; DNA binding protein; 1.50A {Thermotoga maritima} PDB: 1ycz_A 1yd1_A 1yd4_A 1yd3_A 1yd2_A 1yd5_A Probab=99.95 E-value=3.2e-28 Score=221.49 Aligned_cols=87 Identities=34% Similarity=0.652 Sum_probs=82.7 Q ss_pred HHHCCCCCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHCC Q ss_conf 12586788625888699888899601258788876137887787999999734442999828719999999988776187 Q gi|255764496|r 3 SEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKP 82 (616) Q Consensus 3 ~~~lP~~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~~~P 82 (616) .+.+|++||||+|.| +|+|||||||+|||+||+|||++ .+.|+..|+.++.+|||++|+||.|||+||++||++|+| T Consensus 9 l~~lP~~pGVY~f~d-~~~vLYVGKAknLr~Rv~syf~~--~~~k~~~l~~~~~~i~~~~t~se~eAlllE~~lIk~~kP 85 (96) T 1yd0_A 9 ILLAPEEPGVYIFKN-KGVPIYIGKAKRLSNRLRSYLNP--QTEKVFRIGEEADELETIVVMNEREAFILEANLIKKYRP 85 (96) T ss_dssp HHHCCSSCEEEEEEE-TTEEEEEEEESSHHHHHHGGGSC--SSHHHHHHHHHCSEEEEEECSSHHHHHHHHHHHHHHHCC T ss_pred HHHCCCCCEEEEECC-CCCEEEEECCHHHHHHHHHHHCC--CHHHHHHHHHHHHEEEEEEECCHHHHHHHHHHHHHHHCC T ss_conf 985899986899879-99478972608899999988501--118888888762204568418999999999999998589 Q ss_pred CCEECCCCCC Q ss_conf 2003364689 Q gi|255764496|r 83 RFNILLRDDK 92 (616) Q Consensus 83 ~yNi~LkDdk 92 (616) +||++||||| T Consensus 86 ~yN~~lkd~k 95 (96) T 1yd0_A 86 KYNVRLKDTD 95 (96) T ss_dssp TTCC------ T ss_pred CCHHHCCCCC T ss_conf 5176605789 No 6 >2wsh_A Endonuclease II; GIY-YIG, hydrolase; 1.90A {Enterobacteria phage T4} Probab=99.92 E-value=3.2e-26 Score=207.07 Aligned_cols=89 Identities=26% Similarity=0.360 Sum_probs=81.2 Q ss_pred CHHHCCCCCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCC---------CCHHHHHHHHHCCCEEEEE---------- Q ss_conf 912586788625888699888899601258788876137887---------7879999997344429998---------- Q gi|255764496|r 2 SSEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNN---------HTHRITHMISQINNIRFTV---------- 62 (616) Q Consensus 2 ~~~~lP~~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~---------~~~k~~~l~~~~~~ie~~~---------- 62 (616) +...+|++||||+|++.+|+|||||||+|||+||+|||++.. .+.|+..|++++.+|||++ T Consensus 32 ~~~~lP~~~GVyy~~~~~~~IlYVGKAknLrkRv~SYf~~~~~~~~~s~~~~~~ki~~~v~~~~~ve~~v~~~~~~~~~~ 111 (143) T 2wsh_A 32 KQLSIPNKYNVIYAIAINDELVYIGKTKNLRKRINYYRTAINRKDKTSDSTKSALIHSALKEGSKVEFYARQCFNLSMTN 111 (143) T ss_dssp CCCCCCCCCSEEEEEEETTEEEEEEEESCHHHHHHHHHHHHHTTCCSSCCHHHHHHHHHHHTTCCEEEEEEECCEEEEEE T ss_pred EECCCCCCCCEEEEEECCCEEEEEECCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCC T ss_conf 26558999988999947993999975303778899980778865544202453899999862666999997034200024 Q ss_pred ---CCCHHHHHHHHHHHHHHHCCCCEECCCC Q ss_conf ---2871999999998877618720033646 Q gi|255764496|r 63 ---TCTEVEALLLEANMIKRLKPRFNILLRD 90 (616) Q Consensus 63 ---t~~e~eAlilE~~lIk~~~P~yNi~LkD 90 (616) |.||.|||+||++|||+|+|+||+.||. T Consensus 112 ~~~T~se~eAlllE~~LIkk~~P~yN~~~K~ 142 (143) T 2wsh_A 112 ELGTMTIATIDLEAPLFIKLFNPPWNIQHKK 142 (143) T ss_dssp TTEEEEEETHHHHHHHHHHHHCCTTCCC--- T ss_pred CCCCCCHHHHHHHHHHHHHHHCCHHHHHCCC T ss_conf 6678889999999999998839837864367 No 7 >1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Probab=99.55 E-value=3.8e-15 Score=127.20 Aligned_cols=68 Identities=29% Similarity=0.493 Sum_probs=62.9 Q ss_pred HHHHHHHHHHH-CCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC Q ss_conf 89899864321-477100488879899999999808889899389888862789998999999998547 Q gi|255764496|r 542 ITTHRKRRKKA-AYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616) Q Consensus 542 i~~hRk~r~k~-~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616) .+.|+.+|+|. ..|.||+||||||+|+++|+++|||+++|++||+|||.+|+|||+++|++||++||. T Consensus 10 ~~~~~~~R~K~~~~S~L~~IpGIG~k~ak~Ll~~F~si~~i~~As~eeL~~v~GIg~~~A~~I~~~l~n 78 (78) T 1kft_A 10 HSSGLVPRGSHMNTSSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLKH 78 (78) T ss_dssp -------------CCGGGGCTTCSSSHHHHHHHHHSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHTC T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHCHHHHHCCCCCCHHHHHHHHHHHCC T ss_conf 344656675442338265699932999999999929949998837999980799899999999999668 No 8 >2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A* Probab=99.28 E-value=3.6e-12 Score=105.74 Aligned_cols=60 Identities=20% Similarity=0.298 Sum_probs=56.5 Q ss_pred CCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCC Q ss_conf 4771004888798999999998088898993898888627899989999999985478678 Q gi|255764496|r 553 AYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSH 613 (616) Q Consensus 553 ~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~ 613 (616) ..+.|++|||||+++.+.|++||||+++|.+||.+||.+|+| |++.|+.||++||...++ T Consensus 2 ~~d~L~~IPGIg~~~~~~Ll~~fgSi~~l~~as~eeL~~v~G-~~~~A~~i~~~l~~~~~~ 61 (63) T 2a1j_A 2 PQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG-NAANAKQLYDFIHTSFAE 61 (63) T ss_dssp CCHHHHTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHHHS-CHHHHHHHHHHHHCCCCC T ss_pred CHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHCCC-CHHHHHHHHHHHCCCCCC T ss_conf 588885299988999999999867999998799999987869-899999999998021001 No 9 >1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Probab=99.26 E-value=2.8e-12 Score=106.55 Aligned_cols=61 Identities=20% Similarity=0.296 Sum_probs=56.7 Q ss_pred HCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCC Q ss_conf 14771004888798999999998088898993898888627899989999999985478678 Q gi|255764496|r 552 AAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSH 613 (616) Q Consensus 552 ~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~ 613 (616) ...+.|+.|||||+++.+.||+||||+++|++||++||++|+| +++.|++||++||..-.+ T Consensus 15 ~~~~~L~~iPGIg~k~~~~Ll~~f~sl~~i~~AS~eeL~~v~G-~~~~Ak~i~~~lh~~~~~ 75 (84) T 1z00_B 15 GPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG-NAANAKQLYDFIHTSFAE 75 (84) T ss_dssp HHHHHHHTCSSCCHHHHHHHHHHSSCHHHHHHSCHHHHHHHHS-CHHHHHHHHHHHTSBHHH T ss_pred HHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHCCC-CHHHHHHHHHHHCCCCCC T ss_conf 1999998389999999999999966999998599999988759-799999999998553555 No 10 >1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Probab=99.14 E-value=8.2e-11 Score=95.93 Aligned_cols=60 Identities=25% Similarity=0.311 Sum_probs=56.3 Q ss_pred CCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCC Q ss_conf 771004888798999999998088898993898888627899989999999985478678 Q gi|255764496|r 554 YSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSH 613 (616) Q Consensus 554 ~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~ 613 (616) .+.|+.|||||+++.++|++||||+++|.+||.+||..|+|||+++|+.|+++||..-.. T Consensus 13 ~~~L~~IpgIG~~~a~~L~~~F~s~~~i~~As~eeL~~v~GIG~~~a~~i~~~~~~~~~~ 72 (75) T 1x2i_A 13 RLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYIE 72 (75) T ss_dssp HHHHTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSCCCC T ss_pred HHHHCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCHHHC T ss_conf 999848999429999999999688898999789999855897999999999998576320 No 11 >2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Probab=99.12 E-value=1.2e-10 Score=94.65 Aligned_cols=58 Identities=21% Similarity=0.396 Sum_probs=55.2 Q ss_pred CCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC Q ss_conf 4771004888798999999998088898993898888627899989999999985478 Q gi|255764496|r 553 AYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616) Q Consensus 553 ~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616) +.+.|+.|+|||+++.+.|+++|||+++|.+||.+||.+++|||+++|+.|+++||+. T Consensus 30 ~~~~L~~I~gIGk~~A~~L~~~F~Si~~l~~As~eeL~~i~GIG~~~A~~I~~~f~~p 87 (91) T 2a1j_B 30 VTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEP 87 (91) T ss_dssp HHHHHTTSTTCCHHHHHHHHHHHSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHSC T ss_pred HHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCC T ss_conf 9998646888599999999999588298999899975577996999999999998481 No 12 >1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Probab=99.10 E-value=1.9e-10 Score=93.39 Aligned_cols=61 Identities=20% Similarity=0.356 Sum_probs=56.3 Q ss_pred CCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCC Q ss_conf 4771004888798999999998088898993898888627899989999999985478678 Q gi|255764496|r 553 AYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSH 613 (616) Q Consensus 553 ~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~ 613 (616) +.+.|+.|||||+++.+.|+++|||+++|.+||.+||.+|+|||+++|+.|+++|+..-.- T Consensus 17 ~~~~L~~I~gIG~~~a~~L~~~Fgsl~~i~~As~eeL~~i~GiG~~~A~~I~~~f~~pf~~ 77 (89) T 1z00_A 17 VTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLK 77 (89) T ss_dssp HHHHHTTSSSCCHHHHHHHHHHTCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSCSSS T ss_pred HHHHHCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCHHCC T ss_conf 9998758997599999999999488899999878777268996999999999998084204 No 13 >2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Probab=98.89 E-value=2.5e-09 Score=85.28 Aligned_cols=56 Identities=25% Similarity=0.373 Sum_probs=53.5 Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC Q ss_conf 71004888798999999998088898993898888627899989999999985478 Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616) ..|..|||||+++.+.|++||||++++.+||.+||.+|+|||++.|+.|+++||.. T Consensus 162 ~~L~~Ipgi~~~~A~~Ll~~f~Sl~~l~~as~~eL~~v~giG~~~A~~I~~~l~~p 217 (219) T 2bgw_A 162 YILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTP 217 (219) T ss_dssp HHHHTSTTCCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHSC T ss_pred HHHHCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHCCC T ss_conf 99840799899999999998699999986889999608997999999999996385 No 14 >1mk0_A Intron-associated endonuclease 1; alpha/beta fold, catalytic domain, DNA-binding surface, hydrolase; HET: CIT; 1.60A {Enterobacteria phage T4} SCOP: d.226.1.1 PDB: 1ln0_A Probab=98.66 E-value=8e-08 Score=74.40 Aligned_cols=80 Identities=19% Similarity=0.266 Sum_probs=59.4 Q ss_pred CCCCEEEEECCCCCEEEEEECHHHHHHHHHHCCC----CCCCHHHHHHHHH-CCCEEEEE----CCCHHHHHHHHHHHHH Q ss_conf 7886258886998888996012587888761378----8778799999973-44429998----2871999999998877 Q gi|255764496|r 8 ECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHS----NNHTHRITHMISQ-INNIRFTV----TCTEVEALLLEANMIK 78 (616) Q Consensus 8 ~~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~----~~~~~k~~~l~~~-~~~ie~~~----t~~e~eAlilE~~lIk 78 (616) .++|||.+.|..+..+|||.|+||++|..+|+.. .....+.+.-+.. -.+++|.+ +.++.+++.+|..+|+ T Consensus 1 mk~GIY~i~n~~~gk~YIG~t~nl~~R~~~h~~~~~~~~~~~~~L~~~~~k~g~~F~~~ile~~~~~~~~l~~~E~~~I~ 80 (97) T 1mk0_A 1 MKSGIYQIKNTLNNKVYVGSAKDFEKRWKRHFKDLEKGCHSSIKLQRSFNKHGNVFECSILEEIPYEKDLIIERANFWIK 80 (97) T ss_dssp CCCEEEEEEETTTCCEEEEEESSHHHHHHHHHHHHHHTCCSCHHHHHHHHHHSSCEEEEEEEECCCCHHHHHHHHHHHHH T ss_pred CCCEEEEEEECCCCEEEEEEECCHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCEEEEEEEEECCCHHHHHHHHHHHHH T ss_conf 94789999979999799988688889999998775226997699999999633365999999969999999999999999 Q ss_pred HHCCCCEEC Q ss_conf 618720033 Q gi|255764496|r 79 RLKPRFNIL 87 (616) Q Consensus 79 ~~~P~yNi~ 87 (616) ++.|+||.. T Consensus 81 ~~~~~~ngy 89 (97) T 1mk0_A 81 ELNSKINGY 89 (97) T ss_dssp HTTTTTSSS T ss_pred HHCCCCCCE T ss_conf 868976720 No 15 >2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Probab=98.36 E-value=7.6e-07 Score=67.34 Aligned_cols=84 Identities=31% Similarity=0.432 Sum_probs=64.4 Q ss_pred HHHHHHHHHHHHHHHHHH-----------------HHHHH-HC---CCCHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCH Q ss_conf 999887877887889899-----------------86432-14---771004888798999999998-088898993898 Q gi|255764496|r 529 FIQRLRDEAHRFAITTHR-----------------KRRKK-AA---YSPLDEINGIGPLRKRLLLQS-FGTVKMISRSSP 586 (616) Q Consensus 529 ~Lq~iRDEaHRFAi~~hR-----------------k~r~k-~~---~S~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~ 586 (616) .+|.+.+.|.+|+-.-.+ ..|-. .. .++|-+|||||+++.++|+++ |+|+++|.+|+. T Consensus 599 ~i~~l~~~a~~~~~~~~~~~~~~~~~~~~~~l~~l~~r~~~g~~~e~~~L~~i~~ig~~~ar~L~~~G~~s~~~i~~~~~ 678 (720) T 2zj8_A 599 DIYRIVETAEWLVYSLKEIAKVLGAYEIVDYLETLRVRVKYGIREELIPLMQLPLVGRRRARALYNSGFRSIEDISQARP 678 (720) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTCGGGHHHHHHHHHHHHHTCCGGGGGGTTSTTCCHHHHHHHHTTTCCSHHHHHTCCH T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHCCCH T ss_conf 99999999999999999999986988999999999999985898110562278999999999999879999999974998 Q ss_pred HHHHHCCCCCHHHHHHHHHHHCCCCC Q ss_conf 88862789998999999998547867 Q gi|255764496|r 587 ETLASIEGISKKIACKIYNHFHKNTS 612 (616) Q Consensus 587 eeL~~v~gi~~~~A~~I~~~l~~~~~ 612 (616) ++|.+++|+|+++|+.|.++...+.. T Consensus 679 ~~l~~v~g~g~k~a~~i~~~~~~~~~ 704 (720) T 2zj8_A 679 EELLKIEGIGVKTVEAIFKFLGKNVK 704 (720) T ss_dssp HHHHTSTTCCHHHHHHHHHHHC---- T ss_pred HHHHHCCCCCHHHHHHHHHHHCHHCC T ss_conf 89852769489999999974450058 No 16 >2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Probab=98.21 E-value=3.4e-06 Score=62.64 Aligned_cols=54 Identities=22% Similarity=0.316 Sum_probs=51.4 Q ss_pred HHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC Q ss_conf 004888798999999998088898993898888627899989999999985478 Q gi|255764496|r 557 LDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616) Q Consensus 557 Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616) =..|++||..+.+.|..+|++++.+.+||.++|.+++||++.+|+.|.+||+.. T Consensus 514 ALGI~~vG~~~ak~La~~f~~l~~l~~as~eeL~~I~gIG~~~A~si~~ff~~~ 567 (671) T 2owo_A 514 ALGIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAEE 567 (671) T ss_dssp HTTCTTCCHHHHHHHHHHHCSHHHHHTCCHHHHTTSTTCCHHHHHHHHHHHTCH T ss_pred HCCCCCCCHHHHHHHHHHCCCHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHCCH T ss_conf 643777547789999886299999873899999644981699999999997498 No 17 >1e52_A Excinuclease ABC subunit; DNA excision repair, UVRB, DNA repair, UVRC binding domain; NMR {Escherichia coli} SCOP: a.2.9.1 PDB: 1qoj_A Probab=98.20 E-value=1.1e-06 Score=66.12 Aligned_cols=49 Identities=18% Similarity=0.134 Sum_probs=40.4 Q ss_pred HHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2345503871-589999999999998633388888899999999862211 Q gi|255764496|r 186 EAKKFLSGGN-HNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNH 234 (616) Q Consensus 186 ~~~~fL~G~~-~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~i~~~ 234 (616) .+...|+++. .+.++.|+++|..||++++||+||.+||+|.+|+..... T Consensus 12 ~~~~~ls~~el~k~I~~Le~~M~~aA~~ldFE~AA~~RD~I~~L~~~L~~ 61 (63) T 1e52_A 12 NVPMDMSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIA 61 (63) T ss_dssp TSSCCSCCSHHHHHHHHHHHHHHHHHHTTCHHHHTTHHHHHHHHHHHHHH T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH T ss_conf 54213899999999999999999999968899999999999999999876 No 18 >1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Probab=98.17 E-value=1.8e-07 Score=71.85 Aligned_cols=63 Identities=24% Similarity=0.469 Sum_probs=56.2 Q ss_pred HHHHCCCCHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCC Q ss_conf 43214771004888798999999998-0888989938988886278999899999999854786 Q gi|255764496|r 549 RKKAAYSPLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNT 611 (616) Q Consensus 549 r~k~~~S~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~ 611 (616) ..+..+..|.+|+|||+++.++|+.+ |.+++.|..++.++|.+++||+++.|++|++.++.-. T Consensus 9 ~~~~~~~~l~~i~gvG~~~~~~l~~~g~~~~~~i~~~~~~~L~~~~g~g~k~a~~i~~~i~~~~ 72 (241) T 1vq8_Y 9 EAEEEYTELTDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARIKADVGGLE 72 (241) T ss_dssp ---------------------------------------------------------------- T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCC T ss_conf 8688674325889989999999997689999999869999997468957999999999986500 No 19 >1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Probab=98.16 E-value=3.3e-06 Score=62.78 Aligned_cols=52 Identities=25% Similarity=0.378 Sum_probs=50.4 Q ss_pred HCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC Q ss_conf 0488879899999999808889899389888862789998999999998547 Q gi|255764496|r 558 DEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616) Q Consensus 558 d~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616) ..|||||..+.+.|..+|++++.+.+||.++|.+++|||+.+|++|.++|+. T Consensus 510 LGIp~vG~~~ak~L~~~f~~l~~l~~as~e~L~~I~GIG~~~A~si~~~f~~ 561 (667) T 1dgs_A 510 LGLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILETLKD 561 (667) T ss_dssp TTCSSCCHHHHHHHHHTTSBHHHHTTCCHHHHHTSTTCCHHHHHHHHHHHHC T ss_pred CCCCCCCHHHHHHHHHHCCCHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHCC T ss_conf 0678744899999988759999986079999857799489999999999759 No 20 >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* Probab=98.08 E-value=6e-06 Score=60.88 Aligned_cols=85 Identities=22% Similarity=0.196 Sum_probs=65.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-----HC----CC-----CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHH Q ss_conf 999999988787788788989986432-----14----77-----10048887989999999980888989938988886 Q gi|255764496|r 525 PILYFIQRLRDEAHRFAITTHRKRRKK-----AA----YS-----PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLA 590 (616) Q Consensus 525 ~~l~~Lq~iRDEaHRFAi~~hRk~r~k-----~~----~S-----~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~ 590 (616) .+...|+.+.++...-.....|-+--. .. .| .|..||.+-....+.|.+||||+++|.+||.|||. T Consensus 271 ~a~~~L~~L~~~elldl~~ia~~LGy~~~g~~~llD~~v~pRGyRiLskiprlp~~vienLV~~FgsLq~Ll~AS~EeL~ 350 (377) T 3c1y_A 271 TAQNILQDFITRREPSPISISRVLGYDVQQAAQLDDVLVSARGYRLLKTVARIPLSIGYNVVRMFKTLDQISKASVEDLK 350 (377) T ss_dssp HHHHHHHHHHTTSCCCHHHHHHHTTCCCSCGGGGGGCBCCCCSHHHHHHTSCCCHHHHHHHHHHHCSHHHHTTCCHHHHT T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHH T ss_conf 89999986222244676899998299987866644456574178887238999788999999984689999858998896 Q ss_pred HCCCCCHHHHHHHHHHHCC Q ss_conf 2789998999999998547 Q gi|255764496|r 591 SIEGISKKIACKIYNHFHK 609 (616) Q Consensus 591 ~v~gi~~~~A~~I~~~l~~ 609 (616) +|.|||+..|+.|.+.|.. T Consensus 351 eVeGIGe~RAr~IreGL~R 369 (377) T 3c1y_A 351 KVEGIGEKRARAISESISS 369 (377) T ss_dssp TSTTCCHHHHHHHHHHHHH T ss_pred HCCCCCHHHHHHHHHHHHH T ss_conf 4588589999999999999 No 21 >1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2 Probab=97.70 E-value=8.3e-05 Score=52.65 Aligned_cols=65 Identities=18% Similarity=0.331 Sum_probs=55.0 Q ss_pred HHHHHCCCCHHCCCCCCHHHHHHHHHHHC---CHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCC Q ss_conf 64321477100488879899999999808---889899389888862789998999999998547867 Q gi|255764496|r 548 RRKKAAYSPLDEINGIGPLRKRLLLQSFG---TVKMISRSSPETLASIEGISKKIACKIYNHFHKNTS 612 (616) Q Consensus 548 ~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fg---s~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~ 612 (616) +..+.++..|-.|+|||||..-.+|..+. =+..|.+-+..-|+++||||+++|++|.-.|+..-. T Consensus 65 ~~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~K~~ 132 (191) T 1ixr_A 65 EENLALFELLLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELKGKVP 132 (191) T ss_dssp HHHHHHHHHHHSSSCCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHTTTSC T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHHHCC T ss_conf 89999999985768837788988872599999999998399999501888468899999999986434 No 22 >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 Probab=97.60 E-value=0.00011 Score=51.87 Aligned_cols=63 Identities=16% Similarity=0.290 Sum_probs=53.2 Q ss_pred HHHHCCCCHHCCCCCCHHHHHHHHHHHC---CHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCC Q ss_conf 4321477100488879899999999808---88989938988886278999899999999854786 Q gi|255764496|r 549 RKKAAYSPLDEINGIGPLRKRLLLQSFG---TVKMISRSSPETLASIEGISKKIACKIYNHFHKNT 611 (616) Q Consensus 549 r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fg---s~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~ 611 (616) ..+.++-.|-.|.|||||+.-.+|..+. =+..|.+-...-|++|||||+++|++|.-.|+.-- T Consensus 82 ~Er~lF~~Li~VsGIGPK~AL~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdKl 147 (212) T 2ztd_A 82 ETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKV 147 (212) T ss_dssp HHHHHHHHHHTSTTCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHTTTC T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHH T ss_conf 999999999834897746787888549999999999808999985177824888999999997543 No 23 >1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A Probab=97.53 E-value=0.00012 Score=51.57 Aligned_cols=60 Identities=23% Similarity=0.412 Sum_probs=50.6 Q ss_pred HHHCCCCHHCCCCCCHHHHHHHHHHHC---CHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC Q ss_conf 321477100488879899999999808---889899389888862789998999999998547 Q gi|255764496|r 550 KKAAYSPLDEINGIGPLRKRLLLQSFG---TVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616) Q Consensus 550 ~k~~~S~Ld~I~GIG~k~~~~Ll~~Fg---s~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616) .+.++..|-.|+|||||..-.+|..+. =+..|.+-...-|.++||||+++|++|.-.|+. T Consensus 68 Er~lF~~Li~VsGIGPK~AL~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIilELkd 130 (203) T 1cuk_A 68 ERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKD 130 (203) T ss_dssp HHHHHHHHHHSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHH T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 999999985768857566888861279899999987189988606998779999999999999 No 24 >2w36_A Endonuclease V; hypoxanthine, endonuclease, endonucleasev, hydrolase, inosine, DNA damage, DNA repair; HET: BRU; 2.10A {Thermotoga maritima} PDB: 2w35_A 3hd0_A Probab=97.48 E-value=0.00064 Score=46.26 Aligned_cols=111 Identities=20% Similarity=0.158 Sum_probs=61.4 Q ss_pred HHHHHHCCC---CCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHH--HHHHHHHH Q ss_conf 998751566---4351699970744377540488888516872803232110244445541168998999--99999775 Q gi|255764496|r 368 DFTKKFALP---HIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMV--LERRFSQL 442 (616) Q Consensus 368 ~Lk~~L~L~---~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Ev--i~RR~~r~ 442 (616) +|++.+.+. ..++.|-|+|+|...+...+|+.||++-.... --+..+-....+.-..--|-+.||+ +..-+.++ T Consensus 22 ~L~~~v~~~~~~~~~~~VaGvDvsy~~~~~~~A~~Vv~~~~~~~-~v~~~~~~~~~~~PYIPG~LafRE~P~ll~al~~L 100 (225) T 2w36_A 22 ELRKKIKLTPYEGEPEYVAGVALSFPGKEEGLAVIVVLEYPSFK-ILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKL 100 (225) T ss_dssp HHGGGCCCCCCCSCCSEEEEEEEEEEETTEEEEEEEEEETTTTE-EEEEEEEEEECCSCCCTTCTHHHHHHHHHHHHTTC T ss_pred HHHHCEECCCCCCCCCEEEEEEEEECCCCCEEEEEEEEECCCCE-EEEEEEEEEECCCCCCCCCEECCHHHHHHHHHHHC T ss_conf 99850254788998588999985875899359999999779955-99999999632577566411201048999999965 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCEEEEECC-HHH---HHHHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 313111233333333454579848998098-589---99999999975887787189997187 Q gi|255764496|r 443 IKNEENLNFHPKKQEYSFPSWPDVVILDGG-KGQ---LSAAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 443 ~~~~~~l~~~~~~~~~~~~~~PDLilIDGG-kgQ---ln~a~~vl~~l~i~~~i~viglaK~~ 501 (616) . ..||+|||||= .-| +..|-.+ |+..++|.||+||.. T Consensus 101 ~------------------~~PdvilvDG~G~~HPR~~GlA~Hl----Gv~l~~PtIGVAK~~ 141 (225) T 2w36_A 101 R------------------TKPDVVVFDGQGLAHPRKLGIASHM----GLFIEIPTIGVAKSR 141 (225) T ss_dssp C------------------SCCSEEEEESCSSSSTTSCCHHHHH----HHHHTSCEEEEESSC T ss_pred C------------------CCCCEEEECCCEEECCCCCCHHHEE----EEECCCCEEEEECCE T ss_conf 7------------------8999999848533368766442200----342298876333343 No 25 >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 Probab=97.34 E-value=0.00019 Score=50.06 Aligned_cols=58 Identities=19% Similarity=0.372 Sum_probs=47.9 Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHC-----CHHH----HHHCC------CCCHHHHHHHHHHHCCCCC Q ss_conf 710048887989999999980888989938-----9888----86278------9998999999998547867 Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRS-----SPET----LASIE------GISKKIACKIYNHFHKNTS 612 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~A-----s~ee----L~~v~------gi~~~~A~~I~~~l~~~~~ 612 (616) ..|.+|||||+.....|+++|+|+..+.+| +..| |+.++ .||+++|++||++|....+ T Consensus 237 ~~L~qIpGIs~~~A~~I~~~y~T~~~L~~a~~~~~~~~e~~~ll~~~~~~~~~RkiG~~~S~~Iy~~~~~~~~ 309 (311) T 2ziu_A 237 RQLMQISGVSGDKAAAVLEHYSTVSSLLQAYDKCSSETEKEKLLSSVKYGKLKRNLGPALSRTIYQLYCTRGP 309 (311) T ss_dssp HHHTTBTTCCHHHHHHHHHHCSSHHHHHHHHHHCSSHHHHTTTTTTCEETTTTEECHHHHHHHHHHHHHCSSC T ss_pred HHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCC T ss_conf 9998279999999999999769999999999856988889998764435655577389999999999677899 No 26 >1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hyperthermostable protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus HB8} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A* Probab=97.04 E-value=7.6e-05 Score=52.91 Aligned_cols=39 Identities=18% Similarity=0.243 Sum_probs=25.2 Q ss_pred CCHHH---HHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHCCC Q ss_conf 78799---99997344429998287199999999887761872 Q gi|255764496|r 44 HTHRI---THMISQINNIRFTVTCTEVEALLLEANMIKRLKPR 83 (616) Q Consensus 44 ~~~k~---~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~~~P~ 83 (616) -|.|+ ..++.+...=-.++|.|+.+|--|-..|-. +-|. T Consensus 38 GS~kt~~iA~~~~~~~rp~LVvt~n~~~A~qL~~el~~-~~p~ 79 (664) T 1c4o_A 38 GTGKTVTMAKVIEALGRPALVLAPNKILAAQLAAEFRE-LFPE 79 (664) T ss_dssp TSCHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHH-HCTT T ss_pred CCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHH-HCCC T ss_conf 75899999999998689989991899999999999998-6688 No 27 >3ga2_A Endonuclease V; alpha-beta protein, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Bacillus subtilis} Probab=96.85 E-value=0.00093 Score=45.07 Aligned_cols=114 Identities=17% Similarity=0.105 Sum_probs=59.4 Q ss_pred HHHHHHHCCCC-----CCCEEEEEECCCCCCC---CCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHH Q ss_conf 99987515664-----3516999707443775---404888885168728032321102444455411689989999999 Q gi|255764496|r 367 KDFTKKFALPH-----IPKRIEIYDNSHIMGC---SAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERR 438 (616) Q Consensus 367 ~~Lk~~L~L~~-----~p~rIE~fDiSh~~G~---~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR 438 (616) .+|++.+.+.. ..+.|-|+|+|....+ .++|+.||+.-... +--|+.+-+..-+.-..--|-|.||+-- T Consensus 22 ~~L~~~v~~~~~~~~~~v~~VaGvDvsy~~~~~~~~~~a~~Vvl~~~~~-~~v~~~~~~~~~~~PYIPG~LaFRE~p~-- 98 (246) T 3ga2_A 22 FNLKNRINLSPTIHPDSINTTAGVDLAYWEQDGEPYGVCCIIVIDADTK-EVIEKVHSMGRISVPYVSGFLAFRELPL-- 98 (246) T ss_dssp HHHHTTCCCCCCCCGGGCSEEEEEEEEEEEETTEEEEEEEEEEEETTTC-CEEEEEEEEEECCCCSSSSCGGGGTHHH-- T ss_pred HHHHHHEEECCCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEECCCC-CEEEEEEEEEECCCCCCCCHHHHHHHHH-- T ss_conf 9998514746788987676899998666548886489999999977987-1899999996236883652365621799-- Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECC-HHHH---HHHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 9775313111233333333454579848998098-5899---9999999975887787189997187 Q gi|255764496|r 439 FSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGG-KGQL---SAAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 439 ~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGG-kgQl---n~a~~vl~~l~i~~~i~viglaK~~ 501 (616) +..+.+. | ...||||+|||- .-|= ..|-. +|+..++|.||+||.. T Consensus 99 ll~al~~---L-----------~~~PDvllvDG~Gi~HPR~~GlA~H----lGv~l~~PtIGVAK~~ 147 (246) T 3ga2_A 99 IIEAAKK---L-----------ETEPDVFLFDGNGYLHYNHMGVATH----AAFFLGKPTIGIAKTY 147 (246) T ss_dssp HHHHHHH---C-----------SSCCSCEEEEBCSSSSTTSCCHHHH----HHHHHTSCEEEEESSC T ss_pred HHHHHHH---C-----------CCCCCEEEECCCCCCCCCCCCHHHH----EEEECCCCEEEEECCE T ss_conf 9999985---6-----------7899999992862106877645331----0000398876441333 No 28 >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* 3kzi_U* 3a0b_U* 3a0h_U* Probab=96.84 E-value=0.00085 Score=45.36 Aligned_cols=56 Identities=14% Similarity=0.252 Sum_probs=47.5 Q ss_pred CCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCCCC Q ss_conf 77100488879899999999808889899389888862789998999999998547867898 Q gi|255764496|r 554 YSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSHTP 615 (616) Q Consensus 554 ~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~~~ 615 (616) ...|..+||||+...+++.+| |.+ -|++||.+|+||+++..+.|..+++.-.-.+| T Consensus 32 ~~eL~~lpGig~~~A~~Iv~~-gpf-----~s~~dL~~V~Gig~~~~e~ik~yl~~~~~~~p 87 (104) T 3bz1_U 32 IAAFIQYRGLYPTLAKLIVKN-APY-----ESVEDVLNIPGLTERQKQILRENLEHFTVTEV 87 (104) T ss_dssp GGGGGGSTTTTHHHHHHHHHS-CCC-----SSGGGGGGCTTCCHHHHHHHHHHGGGEECCCC T ss_pred HHHHHHCCCCCHHHHHHHHHC-CCC-----CCHHHHHCCCCCCHHHHHHHHHHHCCCEECCC T ss_conf 999965899799999999974-997-----98999963899899999999986545544487 No 29 >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} Probab=96.83 E-value=0.0012 Score=44.39 Aligned_cols=57 Identities=14% Similarity=0.246 Sum_probs=48.0 Q ss_pred CCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCCCC Q ss_conf 477100488879899999999808889899389888862789998999999998547867898 Q gi|255764496|r 553 AYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSHTP 615 (616) Q Consensus 553 ~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~~~ 615 (616) ..+.|..+|||||++.+++.+| |.+ .|+|||.+|+||+++.-+.|..++..-+-.+| T Consensus 61 ~~~eL~~lpGig~~~A~~Iv~~-gpf-----~svedl~~v~Gig~~~~e~l~~~l~~ftv~~p 117 (134) T 1s5l_U 61 NIAAFIQYRGLYPTLAKLIVKN-APY-----ESVEDVLNIPGLTERQKQILRENLEHFTVTEV 117 (134) T ss_dssp CGGGGGGSTTCTHHHHHHHHHT-CCC-----SSGGGGGGCTTCCHHHHHHHHHHHTTEECCCC T ss_pred CHHHHHHHHHHHHHHHHHHHHC-CCC-----CCHHHHHCCCCCCHHHHHHHHHHHCCCEECCC T ss_conf 8999977103469999999982-784-----87999961775799999999986535312688 No 30 >1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1 Probab=96.79 E-value=0.00031 Score=48.51 Aligned_cols=52 Identities=31% Similarity=0.332 Sum_probs=46.9 Q ss_pred CCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC Q ss_conf 4888798999999998-088898993898888627899989999999985478 Q gi|255764496|r 559 EINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616) Q Consensus 559 ~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616) +++||||.+.++|... |.|++.|..|+.++|..++||+++.|++|.+..++- T Consensus 29 ~~~Gvg~~~i~KL~~aG~~Tv~~Ia~~t~~eL~~i~Gi~e~~A~KIi~aark~ 81 (114) T 1b22_A 29 EQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKL 81 (114) T ss_dssp HHTTCSHHHHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHHHH T ss_pred HHCCCCHHHHHHHHHCCCCHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 76899999999999969744999984899999766698899999999999987 No 31 >3ho1_A Argonaute; argonaute, protein-DNA-RNA complex, plasmid; 2.60A {Thermus thermophilus HB27} PDB: 3dlb_A* 3dlh_A* 3f73_A* 3hm9_A 3hvr_A 3hxm_A* 3hk2_A 3hjf_A Probab=96.72 E-value=0.02 Score=35.44 Aligned_cols=112 Identities=12% Similarity=0.084 Sum_probs=63.7 Q ss_pred CCCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHH--HCCCCCCCCCHHH-HHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 6435169997074437754048888851687280323211--0244445541168-998999999997753131112333 Q gi|255764496|r 376 PHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKF--NLHPNDVKTQDDC-AMMRMVLERRFSQLIKNEENLNFH 452 (616) Q Consensus 376 ~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f--~Ik~~~v~~~DD~-~~m~Evi~RR~~r~~~~~~~l~~~ 452 (616) +..|.-|-|+|++|=.+ ..++|+|.--+.... .|+.. ..........+|. .+|.+.|...+.. T Consensus 468 ~~~~~miiG~DV~h~~~-~s~~~~vas~~~~~~--~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~----------- 533 (685) T 3ho1_A 468 AYPAELAVGFDAGGRES-FRFGGAACAVGGDGG--HLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRK----------- 533 (685) T ss_dssp CCSCSEEEEEEEEETTE-EEEEEEEEEECC--C--CCEEECCCCCCSCCCHHHHHHHHHHHHHHHHHHH----------- T ss_pred CCCCCEEEEEEEECCCC-CCEEEEEEEECCCCC--EEEEEEEEECCCCEEHHHHHHHHHHHHHHHHHHH----------- T ss_conf 99982899999836999-965899999818998--8889899714883763989999999999999998----------- Q ss_pred CCCCCCCCCCCCCEEEE--EC--CHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCC Q ss_conf 33333454579848998--09--85899999999997588778718999718776766348981798 Q gi|255764496|r 453 PKKQEYSFPSWPDVVIL--DG--GKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKG 515 (616) Q Consensus 453 ~~~~~~~~~~~PDLilI--DG--GkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~ 515 (616) .+.+|+-|+| || ..+++.++++++++++. ++.+|.+.|... -++++.++ T Consensus 534 -------~~~~P~~IiiyRDG~v~~~E~~~i~~~~~~~~~--~~~~i~V~k~~~-----~R~f~~~~ 586 (685) T 3ho1_A 534 -------AGRLPSRVLLLRNGRVPQDEFALALEALAREGI--AYDLVSVRKSGG-----GRVYPVQG 586 (685) T ss_dssp -------HSSCCSEEEEEECSSSCSGGGHHHHHHHHHTTC--EEEEEEEESSCC-----CCEEESSS T ss_pred -------HCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCC--CEEEEEEECCCC-----CEEECCCC T ss_conf -------489975699961687668999999999875199--589999983687-----20316899 No 32 >1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A* Probab=96.42 E-value=0.017 Score=35.90 Aligned_cols=20 Identities=10% Similarity=0.071 Sum_probs=14.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 338888889999999986221 Q gi|255764496|r 213 EDYESAIIHRDRLAALSHIQN 233 (616) Q Consensus 213 l~FE~Aa~~RD~I~aL~~i~~ 233 (616) ..| ++.-||--+.+|+.+.. T Consensus 55 d~f-r~~AY~rAa~~i~~l~~ 74 (381) T 1jms_A 55 NEG-SCLAFMRASSVLKSLPF 74 (381) T ss_dssp CHH-HHHHHHHHHHHHHTCSS T ss_pred CCH-HHHHHHHHHHHHHHCCC T ss_conf 808-79999999999985897 No 33 >3goc_A Endonuclease V; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; HET: YES; 1.60A {Streptomyces avermitilis ma-4680} Probab=96.41 E-value=0.0013 Score=44.11 Aligned_cols=100 Identities=15% Similarity=0.119 Sum_probs=54.0 Q ss_pred CEEEEEECCCCCCC-CCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC Q ss_conf 16999707443775-40488888516872803232110244445541168998999999997753131112333333334 Q gi|255764496|r 380 KRIEIYDNSHIMGC-SAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEY 458 (616) Q Consensus 380 ~rIE~fDiSh~~G~-~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~ 458 (616) ++|-|+|+|.-.+. .++|++||++-.... --+..+-......-..--|-+.||+-- +..+.+. T Consensus 40 ~~VaGvDvsy~~~~~~~~a~~Vvl~~~~~~-~v~~~~~~~~~~~PYIPG~LaFRE~p~--~l~al~~------------- 103 (237) T 3goc_A 40 GRVTGVDVAYDDERDVVVAAAVVLDAATLD-VVAEATAVGEVSFPYVPGLLAFREIPT--VLAALDA------------- 103 (237) T ss_dssp SEEEEEEEEECSSSSEEEEEEEEEETTTCC-EEEEEEEEEECCSCCCTTCGGGGTHHH--HHHHHHT------------- T ss_pred CEEEEEEEEEECCCCEEEEEEEEEECCCCE-EEEEEEEEEECCCCCCCCHHHHHHHHH--HHHHHHH------------- T ss_conf 789999866856998699999999889854-999999994047875653254520189--9999985------------- Q ss_pred CCCCCCCEEEEECC-HHH---HHHHHHHHHHCCCCCCCCEEEEECC Q ss_conf 54579848998098-589---9999999997588778718999718 Q gi|255764496|r 459 SFPSWPDVVILDGG-KGQ---LSAAQGVLKKLNVENRITIISIAKG 500 (616) Q Consensus 459 ~~~~~PDLilIDGG-kgQ---ln~a~~vl~~l~i~~~i~viglaK~ 500 (616) ....||||||||= ..| +..|-.+ |+..++|.||+||. T Consensus 104 -l~~~PdlllvDG~Gi~HPR~~GlAsHl----Gv~l~~PtIGVAK~ 144 (237) T 3goc_A 104 -LPCPPGLIVCDGYGVAHPRRFGLASHL----GVLTGLPTIGVAKN 144 (237) T ss_dssp -SSSCCSEEEEESCSSCSTTSCCHHHHH----HHHHCSCEEEEESS T ss_pred -CCCCCCEEEECCCEEECCCCCCHHHEE----EECCCCCEEEEECC T ss_conf -678999999828602278766642203----21059886754144 No 34 >3oqg_A HPY188I; endonuclease-DNA complex, restriction enzyme, HPY188I, inter GIY-YIG nuclease, catalytic mechanism; HET: DNA; 1.75A {Helicobacter pylori} PDB: 3or3_A Probab=96.36 E-value=0.0028 Score=41.63 Aligned_cols=33 Identities=27% Similarity=0.536 Sum_probs=27.2 Q ss_pred CCCEEEEECCCCCEEEEEECH-HHHHHHHHHCCCC Q ss_conf 886258886998888996012-5878887613788 Q gi|255764496|r 9 CPGVYQMLDIAGRVLYVGKAY-NLQKRIKSYMHSN 42 (616) Q Consensus 9 ~pGvY~~~~~~~~iiYvGKak-nL~~Rv~syf~~~ 42 (616) .-=||.|- -+|+|.|||+++ +|++|+.||-.+. T Consensus 69 ~g~vY~~v-vdg~I~kIG~T~~gLkkR~~sY~~G~ 102 (180) T 3oqg_A 69 EGLVYVFV-IQGKIFKIGHSITPITKRVQSYNCGK 102 (180) T ss_dssp CCEEEEEE-ETTEEEEEEEESSCHHHHHHHHTTCC T ss_pred CCEEEEEE-ECCEEEEECCCCCCHHHHHHHHHCCC T ss_conf 75799999-99999994287632667688871735 No 35 >2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A Probab=96.32 E-value=0.013 Score=36.89 Aligned_cols=76 Identities=24% Similarity=0.329 Sum_probs=57.4 Q ss_pred HHHHHHHHHHHHHHHHHH--H---------HHHHH---CC---CCHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHH Q ss_conf 999887877887889899--8---------64321---47---71004888798999999998-0888989938988886 Q gi|255764496|r 529 FIQRLRDEAHRFAITTHR--K---------RRKKA---AY---SPLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLA 590 (616) Q Consensus 529 ~Lq~iRDEaHRFAi~~hR--k---------~r~k~---~~---S~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~ 590 (616) .||.+++.|.+||-.-.+ + .+.+. .. .+|-+|||||.+|.++|++. |.|++.|..|+ +.+. T Consensus 589 ~l~~l~~~a~~~~~~~~~~~~~~~~~~l~~l~~rl~~gv~~e~~~L~~i~~v~~~~ar~L~~~g~~s~~~i~~~~-~~~~ 667 (702) T 2p6r_A 589 DLRRIVETAEWLSNAMNRIAEEVGNTSVSGLTERIKHGVKEELLELVRIRHIGRVRARKLYNAGIRNAEDIVRHR-EKVA 667 (702) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTCCSSTTHHHHHHHTCCGGGHHHHTSTTCCHHHHHHHHTTTCCSHHHHHHTH-HHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHCCCCCCCHHHHHHHHHCCCCCHHHHHHCC-HHHH T ss_conf 999999999999999999999738898999999998499841696708899999999999987999999997097-7889 Q ss_pred HCCCCCHHHHHHHHHHH Q ss_conf 27899989999999985 Q gi|255764496|r 591 SIEGISKKIACKIYNHF 607 (616) Q Consensus 591 ~v~gi~~~~A~~I~~~l 607 (616) .+ +++++|++|.+.+ T Consensus 668 ~~--~~~~~~~~~~~~~ 682 (702) T 2p6r_A 668 SL--IGRGIAERVVEGI 682 (702) T ss_dssp HH--HCHHHHHHHHHHH T ss_pred HH--HCCCHHHHHHHHH T ss_conf 77--4705499999874 No 36 >2zix_A Crossover junction endonuclease MUS81; helix-hairpin-helix, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium, metal-binding, nucleus; 3.50A {Homo sapiens} Probab=96.20 E-value=0.00075 Score=45.76 Aligned_cols=59 Identities=12% Similarity=0.284 Sum_probs=47.0 Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHC-----CHHH----HHHCC------CCCHHHHHHHHHHHCCCCCC Q ss_conf 710048887989999999980888989938-----9888----86278------99989999999985478678 Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRS-----SPET----LASIE------GISKKIACKIYNHFHKNTSH 613 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~A-----s~ee----L~~v~------gi~~~~A~~I~~~l~~~~~~ 613 (616) ..|.+|||||+...+.|+++|+|+..+..| +.++ |..+. .||++++++||++|...++- T Consensus 233 ~mL~qIpGIs~~~A~~I~~~ypT~~~L~~ay~~~~~~~e~~~ll~~~~~~~~~RkiG~~~Sk~I~~~~~~~~~~ 306 (307) T 2zix_A 233 RQLMQVRGVSGEKAAALVDRYSTPASLLAAYDACATPKEQETLLSTIKCGRLQRNLGPALSRTLSQLYCSYGPL 306 (307) T ss_dssp HTTTCSTTCCSTTTTTSSSSSCSHHHHHHHHHCCSSGGGTTTTTSCCCCTTTTCCCCHHHHHHHHHHHTCSSCC T ss_pred HHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCC T ss_conf 99962789999999999997799999999998589888999998743356566742999999999997157999 No 37 >1u04_A Argonaute, hypothetical protein PF0537; RNAI, silencing, PIWI, PAZ, RISC, slicer, RNAse H, hydrolase/gene regulation complex; 2.25A {Pyrococcus furiosus dsm 3638} SCOP: b.34.14.1 c.55.3.10 PDB: 1z25_A 1z26_A Probab=96.14 E-value=0.062 Score=31.93 Aligned_cols=119 Identities=10% Similarity=0.115 Sum_probs=74.2 Q ss_pred HHHHHHHHHHC-------CCCCCCEEEEEECCCC--CCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHH Q ss_conf 99999987515-------6643516999707443--77540488888516872803232110244445541168998999 Q gi|255764496|r 364 MILKDFTKKFA-------LPHIPKRIEIYDNSHI--MGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMV 434 (616) Q Consensus 364 ~~l~~Lk~~L~-------L~~~p~rIE~fDiSh~--~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Ev 434 (616) ..+-++.-+|| .+-.+--|.|+|++|- .+...+|++|+..+.+..+..+ ...+....-+..|...+|.+. T Consensus 530 nIaLQiN~KLGG~~w~l~ipl~~~MiVG~DV~H~~~~~~~s~~~~vas~~~~~~~~~s-~~~~q~~~~E~i~~~~~~~~~ 608 (771) T 1u04_A 530 NLLFQVLSKLGVKYYVLDYRFNYDYIIGIDVAPMKRSEGYIGGSAVMFDSQGYIRKIV-PIKIGEQRGESVDMNEFFKEM 608 (771) T ss_dssp HHHHHHHHHTTCBCCEESCCCSSSEEEEEEEEEECCTTTCEEEEEEEEETTSCEEEEE-EEECCCCSSSSCCHHHHHHHH T ss_pred HHHHHHHHHHCCEEEEECCCCCCCEEEEEEEEECCCCCCCEEEEEEEEECCCCCEEEE-EEEECCCCEEHHHHHHHHHHH T ss_conf 9998777862885588515888837998777704777871699999997787765999-999337860125079999999 Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEE--EC-CHH-HHHHHHHHHHHCCCCCCCCEEEEECCCC Q ss_conf 99999775313111233333333454579848998--09-858-9999999999758877871899971877 Q gi|255764496|r 435 LERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVIL--DG-GKG-QLSAAQGVLKKLNVENRITIISIAKGPK 502 (616) Q Consensus 435 i~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilI--DG-Gkg-Qln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616) +.+.+... ...+|+-||| || ..+ -|.+.++++++.+. ++.+|-+.|+.+ T Consensus 609 l~~~~~~n-----------------~~~~P~~IIiYRDGvV~~~El~~ik~a~~~y~p--kit~IvV~KR~~ 661 (771) T 1u04_A 609 VDKFKEFN-----------------IKLDNKKILLLRDGRITNNEEEGLKYISEMFDI--EVVTMDVIKNHP 661 (771) T ss_dssp HHHHHHTT-----------------CCCTTCEEEEECSBCCCHHHHHHHHHHHHHHTC--EEEEEEEESCCC T ss_pred HHHHHHHH-----------------CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCC--CEEEEEEEECCC T ss_conf 99999995-----------------899998699987888557999999999997199--689999994478 No 38 >2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Probab=96.14 E-value=0.015 Score=36.43 Aligned_cols=40 Identities=13% Similarity=0.108 Sum_probs=21.0 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8715899999999999986333888888999999998622 Q gi|255764496|r 193 GGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQ 232 (616) Q Consensus 193 G~~~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~i~ 232 (616) ..+..+++.|++-.+..--+-+-=++.-|+--+.+|+.+. T Consensus 15 ~~N~~i~~~l~~la~~~~~~g~~fr~~aY~~Aa~~i~~l~ 54 (360) T 2ihm_A 15 HHNTLLSEALETLAEAAGFEANEGRLLSFSRAASVLKSLP 54 (360) T ss_dssp CSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCS T ss_pred CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCC T ss_conf 9659999999999999997599487999999999998599 No 39 >2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Probab=95.82 E-value=0.01 Score=37.56 Aligned_cols=13 Identities=23% Similarity=0.227 Sum_probs=6.0 Q ss_pred HHHHHHHHHHCCC Q ss_conf 9999999997588 Q gi|255764496|r 476 LSAAQGVLKKLNV 488 (616) Q Consensus 476 ln~a~~vl~~l~i 488 (616) +..+.+++.+.|+ T Consensus 472 ~e~v~~~~~~~g~ 484 (578) T 2w9m_A 472 LDAVLGACEANGT 484 (578) T ss_dssp HHHHHHHHHHHTC T ss_pred HHHHHHHHHHHCC T ss_conf 9999999998199 No 40 >2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} SCOP: a.60.2.7 Probab=95.68 E-value=0.0063 Score=39.09 Aligned_cols=49 Identities=20% Similarity=0.347 Sum_probs=42.2 Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC Q ss_conf 7100488879899999999808889899389888862789998999999998547 Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616) ..|..+||||++..++++.+ .- =-|++||..|+||+++..++|..++++ T Consensus 27 ~eL~~lpGig~~~A~~Iv~~-R~-----f~s~~dL~~v~gi~~~~~~~i~~~lr~ 75 (75) T 2duy_A 27 EELMALPGIGPVLARRIVEG-RP-----YARVEDLLKVKGIGPATLERLRPYLRP 75 (75) T ss_dssp HHHTTSTTCCHHHHHHHHHT-CC-----CSSGGGGGGSTTCCHHHHHHHGGGEEC T ss_pred HHHHHCCCCCHHHHHHHHHC-CC-----CCCHHHHHHCCCCCHHHHHHHHHHCCC T ss_conf 99977789899999999985-89-----898999975789899999999977288 No 41 >2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ... Probab=95.62 E-value=0.023 Score=35.06 Aligned_cols=20 Identities=5% Similarity=0.026 Sum_probs=12.6 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 33888888999999998622 Q gi|255764496|r 213 EDYESAIIHRDRLAALSHIQ 232 (616) Q Consensus 213 l~FE~Aa~~RD~I~aL~~i~ 232 (616) .+.=++.-|+.-+.+|+.+. T Consensus 31 e~~fk~~AY~rAa~~i~~l~ 50 (335) T 2fmp_A 31 QAIHKYNAYRKAASVIAKYP 50 (335) T ss_dssp CCHHHHHHHHHHHHHHHHCS T ss_pred CCCHHHHHHHHHHHHHHHCC T ss_conf 98278999999999998599 No 42 >2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7 Probab=95.60 E-value=0.015 Score=36.30 Aligned_cols=49 Identities=27% Similarity=0.407 Sum_probs=40.6 Q ss_pred CCCCHHCCCCCCHHHHHHHHHH---HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH Q ss_conf 4771004888798999999998---08889899389888862789998999999998 Q gi|255764496|r 553 AYSPLDEINGIGPLRKRLLLQS---FGTVKMISRSSPETLASIEGISKKIACKIYNH 606 (616) Q Consensus 553 ~~S~Ld~I~GIG~k~~~~Ll~~---Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616) ....|..+||||+++.++++.+ .|.+ -|++||..|+||+++..++|.+. T Consensus 38 s~~eL~~lpgIg~~~A~~Iv~~R~~~G~f-----~sledL~~v~Gi~~k~~eki~k~ 89 (98) T 2edu_A 38 SARDLRSLQRIGPKKAQLIVGWRELHGPF-----SQVEDLERVEGITGKQMESFLKA 89 (98) T ss_dssp CHHHHHHSTTCCHHHHHHHHHHHHHHCCC-----SSGGGGGGSTTCCHHHHHHHHHH T ss_pred CHHHHHHCCCCCHHHHHHHHHHHHHCCCC-----CCHHHHHCCCCCCHHHHHHHHHC T ss_conf 99999647998999999999999985992-----88999844899899999999983 No 43 >3mr3_A DNA polymerase ETA; POL ETA, polymerase, thymine dimer, CPD, XPV, xeroderma PIGM variant, DNA damage; HET: DNA TTD DZ4; 1.75A {Homo sapiens} PDB: 3mr2_A* 3mr5_A* 3mr6_A* Probab=95.44 E-value=0.016 Score=36.10 Aligned_cols=55 Identities=15% Similarity=0.203 Sum_probs=25.6 Q ss_pred CHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCC Q ss_conf 100488879899999999808--889899389888862789998999999998547867 Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLASIEGISKKIACKIYNHFHKNTS 612 (616) Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~ 612 (616) ++.+++|||++...++|..+| ++..+.+++.++|.+.. +.+.+..+++..+..+. T Consensus 254 pi~~l~GiG~k~~~~~L~~~gi~ti~dl~~~~~~~L~~~~--G~~~g~~l~~~a~G~d~ 310 (435) T 3mr3_A 254 PIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHF--GEKNGSWLYAMCRGIEH 310 (435) T ss_dssp BGGGSTTCSSHHHHHHHHHHTCCBGGGGGGSCHHHHHHHH--CHHHHHHHHHHTTTCCC T ss_pred CCCEECCCCHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHH--CHHHHHHHHHHHCCCCC T ss_conf 6776077675789999999589478998739998999997--86889999999669989 No 44 >1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A Probab=95.34 E-value=0.0093 Score=37.86 Aligned_cols=30 Identities=27% Similarity=0.431 Sum_probs=25.8 Q ss_pred CHHCCCCCCHHHHHHHHHHHCCHHHHHHCC Q ss_conf 100488879899999999808889899389 Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFGTVKMISRSS 585 (616) Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As 585 (616) -+-.|||||+||..+||+.|||+++|.++- T Consensus 204 NIpGV~GiG~KtA~kLl~~ygsle~i~~~~ 233 (290) T 1exn_A 204 NIRGVEGIGAKRGYNIIREFGNVLDIIDQL 233 (290) T ss_dssp TBCCCTTCCHHHHHHHHHHHCSHHHHHHHC T ss_pred CCCCCCCCCHHHHHHHHHHHCCHHHHHHHH T ss_conf 799999858999999998738999999877 No 45 >3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein structure initiati midwest center for structural genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris} Probab=95.33 E-value=0.026 Score=34.67 Aligned_cols=33 Identities=21% Similarity=0.345 Sum_probs=20.6 Q ss_pred HHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHH Q ss_conf 9999998088898993898888627899989999999 Q gi|255764496|r 568 KRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIY 604 (616) Q Consensus 568 ~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~ 604 (616) .+.+|..++.- ..++++|....|++..-.-.+. T Consensus 330 ~~~il~~l~~~----~~~~d~l~~~~gl~~~~~~~~L 362 (382) T 3maj_A 330 RTRILALLGPS----PVGIDDLIRLSGISPAVVRTIL 362 (382) T ss_dssp HHHHHHHCCSS----CEEHHHHHHHHCCCHHHHHHHH T ss_pred HHHHHHHCCCC----CCCHHHHHHHHCCCHHHHHHHH T ss_conf 99999866999----9889999999890999999999 No 46 >2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-binding, nucleotide-binding; 2.30A {Sulfolobus solfataricus} Probab=95.32 E-value=0.014 Score=36.50 Aligned_cols=78 Identities=14% Similarity=0.275 Sum_probs=56.2 Q ss_pred HHHHHHHHHHHHHHHHHH---------------HHHHH---HCC---CCHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCH Q ss_conf 999887877887889899---------------86432---147---71004888798999999998-088898993898 Q gi|255764496|r 529 FIQRLRDEAHRFAITTHR---------------KRRKK---AAY---SPLDEINGIGPLRKRLLLQS-FGTVKMISRSSP 586 (616) Q Consensus 529 ~Lq~iRDEaHRFAi~~hR---------------k~r~k---~~~---S~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~ 586 (616) -+|.+.+.|.+||-...+ ..+.+ ... .+|-+|||||..+.++|++. |.|++.|. ++. T Consensus 610 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~rl~~g~~~e~~~L~~i~~v~~~~ar~L~~~g~~s~~~i~-~~~ 688 (715) T 2va8_A 610 DLRNMVETMDWLTYSAYHLSRELKLNEHADKLRILNLRVRDGIKEELLELVQISGVGRKRARLLYNNGIKELGDVV-MNP 688 (715) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCCGGGHHHHTSTTCCHHHHHHHHHTTCCSHHHHH-HCH T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHCCCCCCCHHHHHHHHHCCCCCHHHHH-CCH T ss_conf 9999999999999999999998598799999999999998599777797738899999999999987999999996-699 Q ss_pred HHHHHCCCCCHHHHHHHHHHHCC Q ss_conf 88862789998999999998547 Q gi|255764496|r 587 ETLASIEGISKKIACKIYNHFHK 609 (616) Q Consensus 587 eeL~~v~gi~~~~A~~I~~~l~~ 609 (616) +++..+ +++++|.+|.+..++ T Consensus 689 ~~~~~~--~~~~~~~~i~~~~~~ 709 (715) T 2va8_A 689 DKVKNL--LGQKLGEKVVQEAAR 709 (715) T ss_dssp HHHHHH--HCHHHHHHHHHHHHH T ss_pred HHHHHH--HCHHHHHHHHHHHHH T ss_conf 999988--687899999999999 No 47 >2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ... Probab=95.30 E-value=0.024 Score=34.94 Aligned_cols=19 Identities=16% Similarity=0.280 Sum_probs=11.4 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 33888888999999998622 Q gi|255764496|r 213 EDYESAIIHRDRLAALSHIQ 232 (616) Q Consensus 213 l~FE~Aa~~RD~I~aL~~i~ 232 (616) ..| ++.-|+.-+.+|+.+. T Consensus 32 d~f-r~~AY~rAa~~l~~l~ 50 (335) T 2bcq_A 32 DKW-RALGYAKAINALKSFH 50 (335) T ss_dssp CHH-HHHHHHHHHHHHHSCC T ss_pred CCH-HHHHHHHHHHHHHHCC T ss_conf 947-7999999999998599 No 48 >2qh9_A UPF0215 protein AF_1433; structural genomics, PSI-2, MCSG, protein structure initiative, midwest center for structural genomics; 1.80A {Archaeoglobus fulgidus} Probab=95.03 E-value=0.003 Score=41.43 Aligned_cols=92 Identities=15% Similarity=0.162 Sum_probs=57.7 Q ss_pred CEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 16999707443775404888885168728032321102444455411689989999999977531311123333333345 Q gi|255764496|r 380 KRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYS 459 (616) Q Consensus 380 ~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~ 459 (616) .|+-++|.|.. +..++++.||+.++-++.-.+.. -.+.|.|.+..+-.++.++ + T Consensus 7 ~Rv~GvD~s~~-~~~~~~~gvv~~~~~~dgv~~~~-----i~vdG~dat~~i~~l~~~~--~------------------ 60 (184) T 2qh9_A 7 WRFLGIDDSFD-DRKCCVVGCVTCGGYVEGFLYTE-----IDIDGLDATDKLISMVRRS--K------------------ 60 (184) T ss_dssp SEEEEEEEEEC-SSCEEEEEEEEETTEEEEEEEEE-----ECTTCSCHHHHHHHHHTTC--T------------------ T ss_pred EEEEEEEECCC-CCCCEEEEEEEECCEEEEEEEEE-----EEECCCHHHHHHHHHHHHC--C------------------ T ss_conf 48999983667-89848999999899870289999-----9878841299999999971--4------------------ Q ss_pred CCCCCCEEEEEC-CHHHHHHHH--HHHHHCCCCCCCCEEEEECCC Q ss_conf 457984899809-858999999--999975887787189997187 Q gi|255764496|r 460 FPSWPDVVILDG-GKGQLSAAQ--GVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 460 ~~~~PDLilIDG-GkgQln~a~--~vl~~l~i~~~i~viglaK~~ 501 (616) +.+-||+|++|| |.++-|.+= ..-..+ .+|+||++|.. T Consensus 61 ~r~~~~vv~ldG~~~a~fn~~di~~l~~~~----~~PvIgVak~~ 101 (184) T 2qh9_A 61 FREQIKCIFLPGITLGGFNLVDIQRVYRET----KIPVVVVMRRK 101 (184) T ss_dssp TTTTEEEEEESSSEETTTEECCHHHHHHHH----CCCEEEEESSC T ss_pred CCCCCCEEEECCEEECCCCEECHHHHHHHH----CCCEEEEEECC T ss_conf 578985999988834158368899999886----99989999767 No 49 >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} Probab=94.82 E-value=0.01 Score=37.55 Aligned_cols=49 Identities=18% Similarity=0.272 Sum_probs=33.7 Q ss_pred CC-HHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHH Q ss_conf 71-004888798999999998088898993898888627899989999999 Q gi|255764496|r 555 SP-LDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIY 604 (616) Q Consensus 555 S~-Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~ 604 (616) |- +..|||||+||..+|++.|||+++|.+.. +.+....+.+-+-+..+| T Consensus 233 dyn~~gv~giG~ktA~kli~~~~sle~i~~~~-~~~~~~~~~~~~~~~~~f 282 (346) T 2izo_A 233 DYNPDGIRGIGPERALKIIKKYGKIEKAMEYG-EISKKDINFNIDEIRGLF 282 (346) T ss_dssp SSSTTCSTTCCHHHHHHHHHHSSCC------------------CTTHHHHH T ss_pred CCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHH-HHHCCCCCCCHHHHHHHH T ss_conf 56866689837999999999939999999989-985677786889999997 No 50 >1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Probab=94.60 E-value=0.015 Score=36.38 Aligned_cols=56 Identities=20% Similarity=0.264 Sum_probs=49.5 Q ss_pred CHHCCCCCCHHHHHHHHHH--HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCC Q ss_conf 1004888798999999998--0888989938988886278999899999999854786 Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQS--FGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNT 611 (616) Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~--Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~ 611 (616) .-.+|.|+|+++.++|+.. ..++..|...+.++|.+++|++++.|++|++.+.+.. T Consensus 442 ~~l~I~GlG~~~i~~L~e~g~I~~i~Diy~L~~~~l~~l~gfg~ksa~nll~sIe~sk 499 (667) T 1dgs_A 442 KAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEESK 499 (667) T ss_dssp TSSCCTTCCHHHHHHHHHTTSCSSGGGGGGGCCHHHHTTSSCCSTTHHHHHHHHHHGG T ss_pred CCCCCCCCCHHHHHHHHHCCCCCCHHHHHCCCHHHHHCCCCCCCHHHHHHHHHHHHHC T ss_conf 4427576089999999867872767884137887763577634023789999987641 No 51 >3gqc_A DNA repair protein REV1; protein-DNA complex, alternative splicing, DNA damage, DNA repair, DNA synthesis; HET: DNA DOC DCP; 2.50A {Homo sapiens} Probab=94.46 E-value=0.079 Score=31.15 Aligned_cols=56 Identities=16% Similarity=0.173 Sum_probs=47.3 Q ss_pred CCHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCC Q ss_conf 7100488879899999999808--8898993898888627899989999999985478678 Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSH 613 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~ 613 (616) -++.++||||+++.++ |..+| ++..+.+.+.++|.+.. |++.++.+++..+..+.. T Consensus 315 lpv~~lpGIG~~~~~k-L~~lGI~Ti~DL~~l~~~~L~~~f--G~k~g~~L~~~a~Gid~~ 372 (504) T 3gqc_A 315 QLVTNLPGVGHSMESK-LASLGIKTCGDLQYMTMAKLQKEF--GPKTGQMLYRFCRGLDDR 372 (504) T ss_dssp SBGGGSTTCCHHHHHH-HHHTTCCBHHHHTTSCHHHHHHHH--CHHHHHHHHHHTTTCCCC T ss_pred HCCCCCCCCCHHHHHH-HHHHCCCCHHHHHCCCHHHHHHHH--CCHHHHHHHHHCCCCCCC T ss_conf 1333447878789999-986168509998559999999884--717899999960798742 No 52 >3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex, Y-family DNA polym translesion synthesis, nucleoside triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens} PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A* 2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A* 3gv5_B* 3h4d_A* 3h4b_A* 2alz_A* 3h40_A* 1t3n_A* 1zet_A* Probab=94.39 E-value=0.097 Score=30.53 Aligned_cols=11 Identities=18% Similarity=0.090 Sum_probs=4.7 Q ss_pred HHHHHHHHHHH Q ss_conf 88889999999 Q gi|255764496|r 217 SAIIHRDRLAA 227 (616) Q Consensus 217 ~Aa~~RD~I~a 227 (616) -|+.+|++|.. T Consensus 179 la~~ir~~I~~ 189 (420) T 3osn_A 179 IAAEMREAMYN 189 (420) T ss_dssp HHHHHHHHHHH T ss_pred HHHHHHHHHHH T ss_conf 99999999998 No 53 >2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Probab=94.21 E-value=0.056 Score=32.23 Aligned_cols=54 Identities=19% Similarity=0.229 Sum_probs=44.3 Q ss_pred HHCCCCCCHHHHHHHHHHH--CCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC Q ss_conf 0048887989999999980--88898993898888627899989999999985478 Q gi|255764496|r 557 LDEINGIGPLRKRLLLQSF--GTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616) Q Consensus 557 Ld~I~GIG~k~~~~Ll~~F--gs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616) =.+|.|+|+++.++|+..= .++..|...+.++|.+++|.+++.|+++++.+.+. T Consensus 448 ~mdI~GlG~~~i~~L~~~G~i~~~~Di~~L~~~~l~~l~gfg~Ksa~nL~~sIe~s 503 (671) T 2owo_A 448 AMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAGKLTGLERMGPKSAQNVVNALEKA 503 (671) T ss_dssp TTCCTTCCHHHHHHHHHTTCCSSGGGGGTCCHHHHHTSTTCCHHHHHHHHHHHHHH T ss_pred CCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 13777724899998736578688899965017777665411426789999999875 No 54 >3mx1_A ECO29KIR; type II restriction endonuclease, GIY-YIG endonuclease, HYDR; 2.30A {Escherichia coli} PDB: 3mx4_A* 3nic_A* Probab=94.13 E-value=0.0068 Score=38.84 Aligned_cols=73 Identities=27% Similarity=0.388 Sum_probs=42.6 Q ss_pred CCCEEEEE----------------CCCCCEEEEEEC------------------HHHHHHHHHHCCCCCCCHHHHHHHHH Q ss_conf 88625888----------------699888899601------------------25878887613788778799999973 Q gi|255764496|r 9 CPGVYQML----------------DIAGRVLYVGKA------------------YNLQKRIKSYMHSNNHTHRITHMISQ 54 (616) Q Consensus 9 ~pGvY~~~----------------~~~~~iiYvGKa------------------knL~~Rv~syf~~~~~~~k~~~l~~~ 54 (616) -.|||-.+ +....+|||||| .-|.+|++-|+.+-....- -. T Consensus 66 GaGVYALYY~G~~~~Y~~la~~Nr~~~~~PIYVGKAvp~g~Rkg~~~~~~~~~g~~L~~RL~eH~rSI~~~~n-----Ld 140 (235) T 3mx1_A 66 GAGVYALYYTGHYSLYDEYSRINRLAYNLPIYVGKAVPAGWRQSRISDHETRAGSELSNRIREHGRNIAKTSN-----LD 140 (235) T ss_dssp CCEEEEEEECSCCGGGTTHHHHTSSSCCCCSEEEEECCTTTSCSSCSSCSSCCCSHHHHHHHHHHHHHHTCSS-----CC T ss_pred CCEEEEEEEECCCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCC-----CC T ss_conf 8658999971785376899986335765562750346654423677766665329999999999987740259-----98 Q ss_pred CCCEE--EEEC-CCHHH-HHHHHHHHHHHHCCCCEE Q ss_conf 44429--9982-87199-999999887761872003 Q gi|255764496|r 55 INNIR--FTVT-CTEVE-ALLLEANMIKRLKPRFNI 86 (616) Q Consensus 55 ~~~ie--~~~t-~~e~e-AlilE~~lIk~~~P~yNi 86 (616) +.|+. |.|+ +.+.+ .-+-|+-||+.|+|-.|. T Consensus 141 ~~DF~cR~lV~~~~~s~wIpl~Es~LIr~~~P~WN~ 176 (235) T 3mx1_A 141 LCDFSCRFVIFEATGSDMISTVQAALIKIYKPLWNT 176 (235) T ss_dssp GGGEEEEEEECCSGGGGGHHHHHHHHHHHHCCHHHH T ss_pred HHHEEEEEEEEECCCCCHHHHHHHHHHHHCCCCHHC T ss_conf 667489999982575413568999999860730330 No 55 >1zg2_A Hypothetical UPF0213 protein BH0048; BHR2, structure, autostructure, northeast structural genomics consortium, PSI; NMR {Bacillus halodurans} Probab=93.93 E-value=0.018 Score=35.75 Aligned_cols=66 Identities=20% Similarity=0.182 Sum_probs=44.7 Q ss_pred CCCCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCC-CCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHH Q ss_conf 678862588869988889960125878887613788-7787999999734442999828719999999988 Q gi|255764496|r 7 PECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSN-NHTHRITHMISQINNIRFTVTCTEVEALLLEANM 76 (616) Q Consensus 7 P~~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~-~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~l 76 (616) |..-=||+....+|. +|||-+.||.+|+.+|-++. ...-+-. .-..-+-+....+..+|+-.|..+ T Consensus 5 ~M~~yVYIL~~~~~~-~Y~G~T~dl~rRl~qHn~g~gak~T~~~---~p~~lvy~e~f~~~~~A~~~E~~l 71 (107) T 1zg2_A 5 PMNHYVYILECKDGS-WYTGYTTDVDRRIKKHASGKGAKYTRGR---GPFRLVATWAFPSKEEAMRWEYEV 71 (107) T ss_dssp -CCEEEEEEECTTSC-EEEEEECCHHHHHHHHHHHTTCCSCCCC---SSCEEEEEEEESCHHHHHHHHHHH T ss_pred CCCEEEEEEEECCCC-EEEEECCCHHHHHHHHHCCCCCCCCCCC---CCEEEEEEEECCCHHHHHHHHHHH T ss_conf 961899999938899-9999859999999998381788833678---970578888479999999999998 No 56 >1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2 Probab=93.89 E-value=0.043 Score=33.07 Aligned_cols=31 Identities=32% Similarity=0.449 Sum_probs=27.3 Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCC Q ss_conf 7100488879899999999808889899389 Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSS 585 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As 585 (616) .-...|||||+||.-+|++.|||+++|.+.- T Consensus 232 Dy~~gv~giG~ktA~kli~~~~sle~i~~~~ 262 (379) T 1ul1_X 232 DYCESIRGIGPKRAVDLIQKHKSIEEIVRRL 262 (379) T ss_dssp SSSCCCTTCCHHHHHHHHHHSSSHHHHHTTC T ss_pred CCCCCCCCCCHHHHHHHHHHCCCHHHHHHHH T ss_conf 6677678866899999999819999999999 No 57 >3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A* Probab=93.86 E-value=0.18 Score=28.63 Aligned_cols=12 Identities=17% Similarity=0.080 Sum_probs=6.0 Q ss_pred HHHHHHHHHHHH Q ss_conf 338888889999 Q gi|255764496|r 213 EDYESAIIHRDR 224 (616) Q Consensus 213 l~FE~Aa~~RD~ 224 (616) ..|..|..+..+ T Consensus 142 ~~f~ta~~~~~~ 153 (400) T 3lda_A 142 MGFVTAADFHMR 153 (400) T ss_dssp CSCCCHHHHHHH T ss_pred CCCCCHHHHHHH T ss_conf 899559999974 No 58 >2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B* Probab=93.47 E-value=0.056 Score=32.22 Aligned_cols=41 Identities=15% Similarity=0.216 Sum_probs=27.1 Q ss_pred CHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHCCCCEE Q ss_conf 879999997344429998287199999999887761872003 Q gi|255764496|r 45 THRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKPRFNI 86 (616) Q Consensus 45 ~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~~~P~yNi 86 (616) ..=+..+..+...==.+||.++.+|--|.+.|.-- -|.=.| T Consensus 46 a~~~a~l~~~~~~p~lvVt~~~~~A~~l~~dL~~~-~~~~~V 86 (661) T 2d7d_A 46 TFTVSNLIKEVNKPTLVIAHNKTLAGQLYSEFKEF-FPNNAV 86 (661) T ss_dssp HHHHHHHHHHHCCCEEEECSSHHHHHHHHHHHHHH-CTTSEE T ss_pred HHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHHH-CCCCCE T ss_conf 99999999973999999908999999999999976-698728 No 59 >2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7 Probab=93.46 E-value=0.079 Score=31.17 Aligned_cols=31 Identities=23% Similarity=0.261 Sum_probs=27.0 Q ss_pred HHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC Q ss_conf 8989938988886278999899999999854 Q gi|255764496|r 578 VKMISRSSPETLASIEGISKKIACKIYNHFH 608 (616) Q Consensus 578 ~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~ 608 (616) +..|-.||.+||.++|||++++|+.|.++=. T Consensus 31 L~~iNtAs~~eL~~lpgIg~~~A~~Iv~~R~ 61 (98) T 2edu_A 31 LDLLNEGSARDLRSLQRIGPKKAQLIVGWRE 61 (98) T ss_dssp HHHHHHSCHHHHHHSTTCCHHHHHHHHHHHH T ss_pred CCCCCCCCHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 1004378999996479989999999999999 No 60 >3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} SCOP: d.240.1.1 e.8.1.7 PDB: 3bq1_A* 3bq2_A* 1k1q_A 1k1s_A Probab=93.44 E-value=0.071 Score=31.51 Aligned_cols=10 Identities=10% Similarity=0.046 Sum_probs=4.5 Q ss_pred HHHHHHHHHH Q ss_conf 8889999999 Q gi|255764496|r 218 AIIHRDRLAA 227 (616) Q Consensus 218 Aa~~RD~I~a 227 (616) |..+|++|.. T Consensus 126 a~~ir~~I~~ 135 (354) T 3bq0_A 126 ARKIKQEILE 135 (354) T ss_dssp HHHHHHHHHH T ss_pred HHHHHHHHHH T ss_conf 9999999999 No 61 >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} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A Probab=93.33 E-value=0.049 Score=32.68 Aligned_cols=30 Identities=10% Similarity=0.293 Sum_probs=26.3 Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHC Q ss_conf 710048887989999999980888989938 Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRS 584 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~A 584 (616) .-...|||||++|..+|++.|||+++|.++ T Consensus 235 Dy~~gv~giG~ktA~kli~~~~~i~~i~~~ 264 (336) T 1rxw_A 235 DYNEGVKGVGVKKALNYIKTYGDIFRALKA 264 (336) T ss_dssp TTBCCCTTCCHHHHHHHHHHHSSHHHHHHH T ss_pred CCCCCCCCCCHHHHHHHHHHHCCHHHHHHH T ss_conf 768999996889999999992999999998 No 62 >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 Probab=92.98 E-value=0.3 Score=27.02 Aligned_cols=60 Identities=15% Similarity=0.327 Sum_probs=47.3 Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHC-----CHHH----HHHC------------CCCCHHHHHHHHHHHCCCCCC Q ss_conf 710048887989999999980888989938-----9888----8627------------899989999999985478678 Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRS-----SPET----LASI------------EGISKKIACKIYNHFHKNTSH 613 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~A-----s~ee----L~~v------------~gi~~~~A~~I~~~l~~~~~~ 613 (616) .-|-+|+||++.....+..+|.|...+..| |.+| |+.+ --||+.++++||..|-..+++ T Consensus 255 ~~L~qi~~vs~~~A~aI~~~Ypt~~~L~~ay~~~~~~~e~~~lL~~i~~~~~~~~~~~~rriG~~lSkriy~~~ts~dp~ 334 (341) T 2ziu_B 255 RQIQQLNRVSLEMASAVVNAYPSPQLLVQAYQQCFSDKERQNLLADIQVRRGEGVTSTSRRIGPELSRRIYLQMTTLQPH 334 (341) T ss_dssp HHHTTSTTCCHHHHHHHHHHSCSHHHHHHHHHTCSCHHHHTTTTTTCBTTTTC----CCCBCCHHHHHHHHHHHHCSCTT T ss_pred HHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHCEECCCCCCCCCCCCCCHHHHHHHHHHHHCCCCC T ss_conf 99987149999999999997899999999998368756788886432323478877566743799999999998469944 Q ss_pred C Q ss_conf 9 Q gi|255764496|r 614 T 614 (616) Q Consensus 614 ~ 614 (616) . T Consensus 335 ~ 335 (341) T 2ziu_B 335 L 335 (341) T ss_dssp C T ss_pred H T ss_conf 2 No 63 >2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A* Probab=92.62 E-value=0.14 Score=29.40 Aligned_cols=54 Identities=20% Similarity=0.334 Sum_probs=36.3 Q ss_pred CHHCCCCCCHHHHHHHHHHH---CCHHHHHH-CCHHHHHHCCCCCHHHHHHHHHHHCCCC Q ss_conf 10048887989999999980---88898993-8988886278999899999999854786 Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSF---GTVKMISR-SSPETLASIEGISKKIACKIYNHFHKNT 611 (616) Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~F---gs~~~i~~-As~eeL~~v~gi~~~~A~~I~~~l~~~~ 611 (616) ++.+|||||+++.++|-.-+ .++..+.+ .+.+.|....| .+.++.+++..+..+ T Consensus 242 pv~~LpGIG~~~~~kL~~~~~Gi~ti~DL~~~~~~~~L~~~fG--~~~g~~l~~~~rG~D 299 (434) T 2aq4_A 242 KLDDLPGVGHSTLSRLESTFDSPHSLNDLRKRYTLDALKASVG--SKLGMKIHLALQGQD 299 (434) T ss_dssp CGGGSTTCCHHHHHHHHHHTTCCCSHHHHHHHCCHHHHHHHHC--SSHHHHHHHHTTTCC T ss_pred CCCCCCCCCHHHHHHHHHHHCCCEEHHHHHHHCCHHHHHHHHC--CHHHHHHHHHHCCCC T ss_conf 7210668678999999987658807999763282989999967--489999999971887 No 64 >1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A Probab=92.55 E-value=0.099 Score=30.45 Aligned_cols=41 Identities=10% Similarity=0.057 Sum_probs=29.6 Q ss_pred HHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHH Q ss_conf 004888798999999998088898993898888627899989999999 Q gi|255764496|r 557 LDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIY 604 (616) Q Consensus 557 Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~ 604 (616) ...||||||||.-+|+++|||++++.. ....++...+..+| T Consensus 239 ~~gi~giG~ktA~~li~~~~~~~~~~~-------~~~~~~~~~~~~~~ 279 (340) T 1b43_A 239 PGGIKGIGLKKALEIVRHSKDPLAKFQ-------KQSDVDLYAIKEFF 279 (340) T ss_dssp TTCSTTCCHHHHHHHHHTCSSGGGGTG-------GGCSSCHHHHHHHH T ss_pred CCCCCCCCHHHHHHHHHHHCCHHHHHH-------HCCCCCHHHHHHHH T ss_conf 555798279999999999599999987-------50102689999982 No 65 >1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B Probab=92.20 E-value=0.27 Score=27.30 Aligned_cols=51 Identities=20% Similarity=0.218 Sum_probs=47.1 Q ss_pred CHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH Q ss_conf 1004888798999999998-08889899389888862789998999999998 Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKIYNH 606 (616) Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616) .|.+++|+++....+|-.+ +.|++.+...|++||..+.||+...|.+|--. T Consensus 8 dL~~leG~~~~~~~~L~e~gI~t~edLAdls~dEL~ei~~i~ee~A~~lIM~ 59 (70) T 1wcn_A 8 DLLNLEGVDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMA 59 (70) T ss_dssp HHHSSTTCCHHHHHHHHTTTCCSHHHHHTSCHHHHHTSSSCCHHHHHHHHHH T ss_pred HHHHCCCCCHHHHHHHHHCCCCCHHHHHHHCHHHHHHHCCCCHHHHHHHHHH T ss_conf 9971789899999999996997499998728999987616899999999999 No 66 >1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A Probab=92.14 E-value=0.084 Score=30.97 Aligned_cols=27 Identities=22% Similarity=0.242 Sum_probs=23.5 Q ss_pred HHCCCCCCHHHHHHHHHHHCCHHHHHH Q ss_conf 004888798999999998088898993 Q gi|255764496|r 557 LDEINGIGPLRKRLLLQSFGTVKMISR 583 (616) Q Consensus 557 Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~ 583 (616) ...|||||+++.-+|++.|||++.|.+ T Consensus 227 ~~gi~giG~k~A~~li~~~~s~e~i~~ 253 (326) T 1a76_A 227 PGGVKGIGFKRAYELVRSGVAKDVLKK 253 (326) T ss_dssp TTTTTTCCHHHHHHHHHHTCHHHHHHH T ss_pred CCCCCCCCHHHHHHHHHHCCCHHHHHH T ss_conf 889994249999999998499999988 No 67 >2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} SCOP: a.60.2.7 Probab=92.07 E-value=0.052 Score=32.47 Aligned_cols=27 Identities=26% Similarity=0.380 Sum_probs=23.8 Q ss_pred HHHHCCHHHHHHCCCCCHHHHHHHHHH Q ss_conf 899389888862789998999999998 Q gi|255764496|r 580 MISRSSPETLASIEGISKKIACKIYNH 606 (616) Q Consensus 580 ~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616) +|-.||.+||.++||||+.+|+.|.++ T Consensus 20 diN~As~~eL~~lpGig~~~A~~Iv~~ 46 (75) T 2duy_A 20 SLNEASLEELMALPGIGPVLARRIVEG 46 (75) T ss_dssp ETTTCCHHHHTTSTTCCHHHHHHHHHT T ss_pred ECCCCCHHHHHHCCCCCHHHHHHHHHC T ss_conf 071287999977789899999999985 No 68 >3mfi_A DNA polymerase ETA; DNA damage, DNA repair, DNA replication, DNA synthesis, NUCL binding, magnesium; HET: DNA DOC TTD DTP; 1.76A {Saccharomyces cerevisiae} PDB: 3mfh_A* 2r8j_A* 2r8k_A* 2wtf_A* 1jih_A* Probab=91.97 E-value=0.066 Score=31.74 Aligned_cols=18 Identities=11% Similarity=0.237 Sum_probs=7.7 Q ss_pred CHHCCCCCCHHHHHHHHH Q ss_conf 100488879899999999 Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQ 573 (616) Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~ 573 (616) ++.+|+|||+++.++|.. T Consensus 308 pI~~i~GIG~~~~~kL~~ 325 (520) T 3mfi_A 308 EITSFWTLGGVLGKELID 325 (520) T ss_dssp CGGGSTTCSSHHHHHHHH T ss_pred CCCEECCCCHHHHHHHHH T ss_conf 801006747899999999 No 69 >3im1_A Protein SNU246, PRE-mRNA-splicing helicase BRR2; ATPase, RNA helicase, rnpase, RNA unwindase, molecular modeling; 1.65A {Saccharomyces cerevisiae} PDB: 3im2_A* 3hib_A Probab=91.09 E-value=0.66 Score=24.52 Aligned_cols=10 Identities=20% Similarity=0.242 Sum_probs=5.1 Q ss_pred EEEEECCHHH Q ss_conf 8998098589 Q gi|255764496|r 466 VVILDGGKGQ 475 (616) Q Consensus 466 LilIDGGkgQ 475 (616) ++|.|.--++ T Consensus 266 ~~v~d~~~~~ 275 (328) T 3im1_A 266 LVLGEVSKKE 275 (328) T ss_dssp EEEEEGGGTE T ss_pred EEEEECCCCE T ss_conf 9999889998 No 70 >1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family DNA polymerase, translesion DNA synthesis, lesion bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7 PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A* Probab=90.82 E-value=0.67 Score=24.46 Aligned_cols=108 Identities=17% Similarity=0.199 Sum_probs=63.0 Q ss_pred HHHHHHHHHCCCCCCCCEEEEECCCC-CCCCCEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 99999999758877871899971877-67663489817983488579989999999887877887889899864321477 Q gi|255764496|r 477 SAAQGVLKKLNVENRITIISIAKGPK-RSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKAAYS 555 (616) Q Consensus 477 n~a~~vl~~l~i~~~i~viglaK~~~-r~~~~e~~~~~~~~~i~l~~~~~~l~~Lq~iRDEaHRFAi~~hRk~r~k~~~S 555 (616) ..-..+.+++|+. .-+|||.+.- -|-+.+ +-.++|..+.++....+..|| ..- T Consensus 229 ~ir~~I~~~~gl~---~SiGIa~nk~lAKlAs~-~~KP~G~~~~~~~~~~~~~~L----------------------~~l 282 (459) T 1t94_A 229 EIRFRIEQKTTLT---ASAGIAPNTMLAKVCSD-KNKPNGQYQILPNRQAVMDFI----------------------KDL 282 (459) T ss_dssp HHHHHHHHHHSCC---EEEEEESSHHHHHHHHH-HTTTTCEEECCSSHHHHHHHH----------------------TTC T ss_pred HHHHHHHHHHCCC---EEEEECCCHHHHHHHHH-HCCCCCCEEEECCHHHHHHHH----------------------HHC T ss_conf 9999999986996---25442476888898897-369987089914689999998----------------------629 Q ss_pred CHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCCC Q ss_conf 100488879899999999808--88989938988886278999899999999854786789 Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSHT 614 (616) Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~~ 614 (616) ++.+|+|||+++.++| ..+| ++..+.+.. +.|..+. ++..++.+++..+..+.++ T Consensus 283 pv~~l~GIG~~~~~~L-~~~gI~ti~dL~~~~-~~l~~~~--g~~~~~~~~~~~~Gid~~~ 339 (459) T 1t94_A 283 PIRKVSGIGKVTEKML-KALGIITCTELYQQR-ALLSLLF--SETSWHYFLHISLGLGSTH 339 (459) T ss_dssp BGGGCTTSCHHHHHHH-HHTTCCBHHHHHHTH-HHHHHHS--CHHHHHHHHHHHTTCCCSC T ss_pred CCCEECCCCCHHHHHH-HHHCCCCHHHHHHHH-HHHHHHH--CCHHHHHHHHHHCCCCCCC T ss_conf 8353368884137889-870784999999858-8899984--5136664687762867633 No 71 >2q0z_X Protein Pro2281; SEC63, SEC, NESG, HR1979, structural genomics, translocase, northeast structural genomics consortium, PSI-2; 2.00A {Homo sapiens} SCOP: a.289.1.1 b.1.18.22 Probab=90.55 E-value=0.72 Score=24.24 Aligned_cols=10 Identities=40% Similarity=0.375 Sum_probs=4.9 Q ss_pred EEEEECCHHH Q ss_conf 8998098589 Q gi|255764496|r 466 VVILDGGKGQ 475 (616) Q Consensus 466 LilIDGGkgQ 475 (616) ++|.|.--++ T Consensus 269 v~v~d~~~~~ 278 (339) T 2q0z_X 269 VVIGDAKSNS 278 (339) T ss_dssp EEEEETTTTE T ss_pred EEEEECCCCE T ss_conf 9999889998 No 72 >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} Probab=90.41 E-value=0.082 Score=31.06 Aligned_cols=21 Identities=19% Similarity=0.339 Sum_probs=13.1 Q ss_pred CHHCCCCCCHHHHHHHHHHHC Q ss_conf 100488879899999999808 Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFG 576 (616) Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fg 576 (616) .|.+|+|||+++.++|-.+.. T Consensus 90 dl~~v~Gig~~~~e~l~~~l~ 110 (134) T 1s5l_U 90 DVLNIPGLTERQKQILRENLE 110 (134) T ss_dssp GGGGCTTCCHHHHHHHHHHHT T ss_pred HHHCCCCCCHHHHHHHHHHHC T ss_conf 996177579999999998653 No 73 >1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A* Probab=90.33 E-value=0.42 Score=25.91 Aligned_cols=22 Identities=0% Similarity=-0.049 Sum_probs=8.6 Q ss_pred CCCCHHHHHHHHHHHHHHHHHH Q ss_conf 7998999999988787788788 Q gi|255764496|r 521 NMRDPILYFIQRLRDEAHRFAI 542 (616) Q Consensus 521 ~~~~~~l~~Lq~iRDEaHRFAi 542 (616) +.++-.+.+|----...|--++ T Consensus 310 ~~~~~~~aLlyfTGS~~fN~~l 331 (381) T 1jms_A 310 PYDRRAFALLGWTGSRQFERDL 331 (381) T ss_dssp CGGGHHHHHHHHHCCHHHHHHH T ss_pred CHHHHHHHHHHCCCCHHHHHHH T ss_conf 8998789886320879999999 No 74 >2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Probab=90.31 E-value=0.061 Score=31.98 Aligned_cols=24 Identities=0% Similarity=-0.136 Sum_probs=11.3 Q ss_pred ECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 579989999999887877887889 Q gi|255764496|r 520 LNMRDPILYFIQRLRDEAHRFAIT 543 (616) Q Consensus 520 l~~~~~~l~~Lq~iRDEaHRFAi~ 543 (616) .+.++-.+.+|----...|--++. T Consensus 288 v~~~~~~~aLlyfTGS~~fN~~lR 311 (360) T 2ihm_A 288 TPSSQFPFALLGWTGSQFFERELR 311 (360) T ss_dssp CCTTSHHHHHHHHHSCHHHHHHHH T ss_pred CCHHHHHHHHHHHHCCHHHHHHHH T ss_conf 588998999998027699999999 No 75 >2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} SCOP: e.71.1.1 Probab=90.12 E-value=0.52 Score=25.28 Aligned_cols=79 Identities=13% Similarity=0.315 Sum_probs=52.4 Q ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHCCCCHHCCCCCCHHHHHHHHHH-----HCCHHHHHHCCHHHHHHCCC-CCH Q ss_conf 999999988-78778878898998643214771004888798999999998-----08889899389888862789-998 Q gi|255764496|r 525 PILYFIQRL-RDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQS-----FGTVKMISRSSPETLASIEG-ISK 597 (616) Q Consensus 525 ~~l~~Lq~i-RDEaHRFAi~~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~-----Fgs~~~i~~As~eeL~~v~g-i~~ 597 (616) .+-..++.| .+...||.--|++.---......|+-+||||+|+...++.. |.|++.|.+ .|.| +.+ T Consensus 101 eL~~vv~~iV~~nE~~FV~FfN~A~pItlrlH~leLLPGIGKK~~~~IleeR~k~~FeSFedi~~-------Rv~gi~dp 173 (205) T 2i5h_A 101 ELPYVIEHIIKQDEKKYVDFFNKADSITTRMHQLELLPGVGKKMMWAIIEERKKRPFESFEDIAQ-------RVKGIQRP 173 (205) T ss_dssp HHHHHHHHHHHTTHHHHHHHHC--CCBCSSSBGGGGSTTCCHHHHHHHHHHHHHSCCCSHHHHHH-------HSTTCCCH T ss_pred HHHHHHHHHHHHCCHHCCEEECCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHHHHHH-------HHCCCCCH T ss_conf 89999999999590201013246888618788887523505899999999965589889999998-------84467899 Q ss_pred --HHHHHHHHHHCCC Q ss_conf --9999999985478 Q gi|255764496|r 598 --KIACKIYNHFHKN 610 (616) Q Consensus 598 --~~A~~I~~~l~~~ 610 (616) -+|++|.+.+... T Consensus 174 ~~lia~Ri~~El~~~ 188 (205) T 2i5h_A 174 EKLIVSRIIYEIKNP 188 (205) T ss_dssp HHHHHHHHHHHHHCT T ss_pred HHHHHHHHHHHHCCC T ss_conf 999999999996499 No 76 >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* 3kzi_U* 3a0b_U* 3a0h_U* Probab=90.11 E-value=0.079 Score=31.14 Aligned_cols=26 Identities=12% Similarity=0.175 Sum_probs=16.1 Q ss_pred HHHHCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 89938988886278999899999999 Q gi|255764496|r 580 MISRSSPETLASIEGISKKIACKIYN 605 (616) Q Consensus 580 ~i~~As~eeL~~v~gi~~~~A~~I~~ 605 (616) +|-.||.+||.++|||++.+|++|.+ T Consensus 26 dlN~As~~eL~~lpGig~~~A~~Iv~ 51 (104) T 3bz1_U 26 DLNNTNIAAFIQYRGLYPTLAKLIVK 51 (104) T ss_dssp ETTSSCGGGGGGSTTTTHHHHHHHHH T ss_pred ECCCCCHHHHHHCCCCCHHHHHHHHH T ss_conf 78408999996589979999999997 No 77 >1yvu_A Hypothetical protein AQ_1447; RNAse H fold, RNA binding protein, gene regulation; 2.90A {Aquifex aeolicus VF5} SCOP: b.34.14.1 c.55.3.10 PDB: 2f8s_A 2f8t_A 2nub_A Probab=89.92 E-value=0.96 Score=23.33 Aligned_cols=101 Identities=13% Similarity=0.056 Sum_probs=55.2 Q ss_pred CCCEEEEEECCCCCCC----CCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHH-HHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 3516999707443775----4048888851687280323211024444554116-8998999999997753131112333 Q gi|255764496|r 378 IPKRIEIYDNSHIMGC----SAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDD-CAMMRMVLERRFSQLIKNEENLNFH 452 (616) Q Consensus 378 ~p~rIE~fDiSh~~G~----~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD-~~~m~Evi~RR~~r~~~~~~~l~~~ 452 (616) .+.-|.|+|+||-... ..+|+.++|.+.+ .-..|..... .-.+.++ ..+|.+++.- |.+ . T Consensus 494 ~~~miIGiDv~h~~~~~~~~~~~g~~~~~~~~g-~~~~~~~~~~---~~~~ee~~~~l~~~~l~~-y~~---~------- 558 (706) T 1yvu_A 494 KVDAFVGIDISRITRDGKTVNAVAFTKIFNSKG-ELVRYYLTSY---PAFGEKLTEKAIGDVFSL-LEK---L------- 558 (706) T ss_dssp CCSEEEEECEEECCCSSSCCCEEEEEEEECTTS-CEEEEEEEEE---CSCTTHHHHHHHHHHHHH-HHH---T------- T ss_pred CCEEEEEEEEEECCCCCCCCCEEEEEEEECCCC-CEEEEEEEEC---CCCHHHHHHHHHHHHHHH-HHH---H------- T ss_conf 952899999886378888663899999997999-7899999744---763688999999999999-999---6------- Q ss_pred CCCCCCCCCCCCCEEEE--ECC--HHHHHHHHHHHHHCCCCCCCCEEEEECCCC Q ss_conf 33333454579848998--098--589999999999758877871899971877 Q gi|255764496|r 453 PKKQEYSFPSWPDVVIL--DGG--KGQLSAAQGVLKKLNVENRITIISIAKGPK 502 (616) Q Consensus 453 ~~~~~~~~~~~PDLilI--DGG--kgQln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616) .+.+|+-|+| ||- ..-+.+.++++++++. ++.+|-+.|+.. T Consensus 559 -------n~~~P~rIiiyRDG~v~~~Ev~~ik~a~~~~~~--ki~~IvV~Kr~~ 603 (706) T 1yvu_A 559 -------GFKKGSKIVVHRDGRLYRDEVAAFKKYGELYGY--SLELLEIIKRNN 603 (706) T ss_dssp -------TCCTTCEEEEEESSCCCHHHHHHHHHHHHHHTC--EEEEEEEECSSC T ss_pred -------CCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCC--CEEEEEEECCCC T ss_conf -------599987799995887758999999999975499--689999980687 No 78 >2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ... Probab=89.28 E-value=0.33 Score=26.70 Aligned_cols=13 Identities=15% Similarity=0.151 Sum_probs=6.5 Q ss_pred HHHHHHHHHHCCC Q ss_conf 9999999997588 Q gi|255764496|r 476 LSAAQGVLKKLNV 488 (616) Q Consensus 476 ln~a~~vl~~l~i 488 (616) +......|.+.|. T Consensus 204 l~~~~~~l~~~g~ 216 (335) T 2bcq_A 204 FSRLLDSLRQEGF 216 (335) T ss_dssp HHHHHHHHHHTTC T ss_pred HHHHHHHHHHCCC T ss_conf 8877899986185 No 79 >1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A* Probab=88.32 E-value=1 Score=23.11 Aligned_cols=15 Identities=27% Similarity=0.481 Sum_probs=5.5 Q ss_pred CHHHHHHHHHHHHHH Q ss_conf 878999999999973 Q gi|255764496|r 127 SVDAVEKTINSLQRT 141 (616) Q Consensus 127 ~~~~~~~~l~~l~~~ 141 (616) +..++..+++-|... T Consensus 44 ~~~~v~~a~~~L~~~ 58 (218) T 1pu6_A 44 KFEAVLKSLENLKNA 58 (218) T ss_dssp CHHHHHHHHHHHHHT T ss_pred CHHHHHHHHHHHHHH T ss_conf 899999999999998 No 80 >1ywl_A Hypothetical UPF0213 protein EF2693; alpha and beta, structural genomics, northeast structural genomics consortium (NESG); NMR {Enterococcus faecalis} Probab=88.15 E-value=0.13 Score=29.58 Aligned_cols=65 Identities=20% Similarity=0.180 Sum_probs=41.7 Q ss_pred CCEEEEECCCCCEEEEEECHHHHHHHHHHCCCC-CCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHH Q ss_conf 862588869988889960125878887613788-7787999999734442999828719999999988 Q gi|255764496|r 10 PGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSN-NHTHRITHMISQINNIRFTVTCTEVEALLLEANM 76 (616) Q Consensus 10 pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~-~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~l 76 (616) -=||+....+|. +|||=+.||..|+.+|-++. ...-|+..- .-..=|=+....+-.+|+-+|..+ T Consensus 7 ~yVYIL~~~~~~-lY~G~T~dl~rRl~qHn~g~gak~Tr~~~~-~P~~Lvy~e~~~~~~~A~~~E~~i 72 (96) T 1ywl_A 7 HYFYVLLCQDGS-FYGGYTTEPERRLTEHNSGTGAKYTRLAKR-RPVIMIHTEKFETRSEATKAEAAF 72 (96) T ss_dssp EEEEEEECTTCC-CEEEEESCHHHHHHHHHHHHSCSSCSSCCS-SCCEEEEEEEESSHHHHHHHHHHH T ss_pred EEEEEEEECCCC-EEEEECCCHHHHHHHHHCCCCCCCCCCCCC-CCEEEEEEEECCCHHHHHHHHHHH T ss_conf 799999938899-999981999999999966488880335799-747999999698999999999999 No 81 >1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Probab=87.86 E-value=0.012 Score=37.15 Aligned_cols=97 Identities=16% Similarity=0.196 Sum_probs=49.6 Q ss_pred EEEECCCCCE-EEECCCCHHHHHHHHH-HHHHHHHHH----HHHHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHH Q ss_conf 4898179834-8857998999999988-787788788----989986432147710048887989999999980888989 Q gi|255764496|r 508 EKFFVKKGEA-LVLNMRDPILYFIQRL-RDEAHRFAI----TTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMI 581 (616) Q Consensus 508 e~~~~~~~~~-i~l~~~~~~l~~Lq~i-RDEaHRFAi----~~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i 581 (616) ..|.+.+|.. +..|-++--+++|.++ .|+.=.=|. -.|...-.....-+.+++.. ..|+..=--.||- + T Consensus 596 ~~f~~~~G~~lv~aDySQIELRilAhlS~D~~li~af~~g~Dih~~tA~~~f~~~~~~v~~--~~R~~AK~~nfgl---~ 670 (832) T 1bgx_T 596 RAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDP--LMRRAAKTINFGV---L 670 (832) T ss_dssp GGBCCCSSCCEEEEEESSHHHHHHHHTTTCTTHHHHHHHTCCHHHHHHHHHHTCCTTSCCT--THHHHHHHHHHHT---T T ss_pred CEEECCCCCEEEECCHHCCHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCH--HHHHHHHHHHHHH---H T ss_conf 3476699988982421006799999994698787654058707877799870997200687--8998989967447---6 Q ss_pred HHCCHHHHHHCCCCCHHHHHHHHHHHCC Q ss_conf 9389888862789998999999998547 Q gi|255764496|r 582 SRSSPETLASIEGISKKIACKIYNHFHK 609 (616) Q Consensus 582 ~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616) ..++..-|++..|++..-|+.+.+.|+. T Consensus 671 YG~g~~~La~~l~is~~EA~~~i~~f~~ 698 (832) T 1bgx_T 671 YGMSAHRLSQELAIPYEEAQAFIERYFQ 698 (832) T ss_dssp SCCCHHHHHHHSSCCHHHHHHHHHHHHH T ss_pred HCCCHHHHHHHCCCCHHHHHHHHHHHHH T ss_conf 3767778988619999999999999999 No 82 >2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix- hairpin-helix, HHH motif, three helix bundle; 2.30A {Methanopyrus kandleri} SCOP: a.60.2.4 a.60.2.4 a.60.2.4 a.60.2.4 a.267.1.1 PDB: 2csd_A Probab=87.07 E-value=1.4 Score=22.05 Aligned_cols=41 Identities=27% Similarity=0.409 Sum_probs=26.8 Q ss_pred CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCH Q ss_conf 100488879899999999808889899389888862789998 Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISK 597 (616) Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~ 597 (616) .|-.|-||...+...||++||++.++..|.++||..- |+.. T Consensus 469 slisirgidreraerllkkyggyskvreagveelred-gltd 509 (519) T 2csb_A 469 SLISIRGIDRERAERLLKKYGGYSKVREAGVEELRED-GLTD 509 (519) T ss_dssp HHHTSTTCCHHHHHHHHHHHTSHHHHHTSCHHHHHHT-TCCH T ss_pred HHEEECCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHC-CCCH T ss_conf 5100016568999999998378058888508999875-7748 No 83 >2w42_A PIWI, putative uncharacterized protein; RNAI, RISC, argonaute, PIWI domain, protein/DNA complex; 1.90A {Archaeoglobus fulgidus} PDB: 1ytu_A 2bgg_A 1w9h_A Probab=86.75 E-value=1.5 Score=21.93 Aligned_cols=106 Identities=10% Similarity=0.095 Sum_probs=51.5 Q ss_pred CCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC Q ss_conf 51699970744377540488888516872803232110244445541168998999999997753131112333333334 Q gi|255764496|r 379 PKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEY 458 (616) Q Consensus 379 p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~ 458 (616) +.-|-++|++|-.+...+|...+|...+ . +-.+++... ..+...-..|.+++.+......++. T Consensus 179 ~~miIG~dv~h~~~~~~~~~a~~~~~~g-~---~~~~~~~~~-~~~~e~~~~l~~~l~~~l~~~~~~~------------ 241 (427) T 2w42_A 179 SDIIIGTGATRIDNVNLFCFAMVFKKDG-T---MLWNEISPI-VTSSEYLTYLKSTIKKVVYGFKKSN------------ 241 (427) T ss_dssp CSEEEEEEEEESSSSEEEEEEEEECTTS-C---EEEEEECCC-EEGGGHHHHHHHHHHHHHHHHHHHC------------ T ss_pred CEEEEEEEEECCCCCEEEEEEEEECCCC-C---EEEEEEEEE-CCCCCHHHHHHHHHHHHHHHHHHHH------------ T ss_conf 7599999998179971789999991889-8---899999992-6973679999999999999999983------------ Q ss_pred CCCCCCCEEE-EECCH-H-----HHHHHHHHHHHCCC------CCCCCEEEEECCCC Q ss_conf 5457984899-80985-8-----99999999997588------77871899971877 Q gi|255764496|r 459 SFPSWPDVVI-LDGGK-G-----QLSAAQGVLKKLNV------ENRITIISIAKGPK 502 (616) Q Consensus 459 ~~~~~PDLil-IDGGk-g-----Qln~a~~vl~~l~i------~~~i~viglaK~~~ 502 (616) .+.+|+-|+ -++|+ + .+.+..+++++++. .-++.++.+.|... T Consensus 242 -~~~~p~rIvi~rdg~~~~~~~~e~~~i~~a~~~~~~~~~~~~~~k~~~I~v~k~~~ 297 (427) T 2w42_A 242 -PDWDVEKLTLHVSGKRPKMKDGETKILKETVEELKKQEMVSRDVKYAILHLNETHP 297 (427) T ss_dssp -TTCCCSEEEEEEESSCCSCHHHHHHHHHHHHHHHHHTTSSCTTCEEEEEEEEECCC T ss_pred -CCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCC T ss_conf -89998436999687562058899999999999997863678887479999993467 No 84 >1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix, fidelity, processivity, transferase; 2.30A {Sulfolobus solfataricus} SCOP: e.8.1.7 Probab=85.87 E-value=0.29 Score=27.09 Aligned_cols=36 Identities=31% Similarity=0.467 Sum_probs=29.5 Q ss_pred CCHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHH Q ss_conf 7100488879899999999808--889899389888862 Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLAS 591 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~ 591 (616) -++.+++|||+++.++| +.+| ++.++.++|.++|.+ T Consensus 184 lpl~~l~GiG~~~~~~L-~~~Gi~ti~dl~~~~~~~L~r 221 (221) T 1im4_A 184 LDIDEIPGIGSVLARRL-NELGIQKLRDILSKNYNELEK 221 (221) T ss_dssp CBGGGSTTCCHHHHHHH-HHTTCCBTTC----------- T ss_pred CCHHHHCCCCHHHHHHH-HHCCCCCHHHHHCCCHHHHCC T ss_conf 98754189479999999-992992099985799998119 No 85 >2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Probab=84.83 E-value=0.8 Score=23.91 Aligned_cols=14 Identities=7% Similarity=-0.080 Sum_probs=6.7 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 99999999973011 Q gi|255764496|r 131 VEKTINSLQRTFFL 144 (616) Q Consensus 131 ~~~~l~~l~~~f~l 144 (616) ..+++..|++.||- T Consensus 6 ~~ei~~~L~~~~~~ 19 (211) T 2abk_A 6 RLEILTRLRENNPH 19 (211) T ss_dssp HHHHHHHHHHHCSS T ss_pred HHHHHHHHHHHCCC T ss_conf 99999999997899 No 86 >1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A Probab=82.25 E-value=1.6 Score=21.83 Aligned_cols=45 Identities=18% Similarity=0.271 Sum_probs=37.1 Q ss_pred CCCHHHHHHHHH-HHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH Q ss_conf 879899999999-808889899389888862789998999999998 Q gi|255764496|r 562 GIGPLRKRLLLQ-SFGTVKMISRSSPETLASIEGISKKIACKIYNH 606 (616) Q Consensus 562 GIG~k~~~~Ll~-~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616) +|...-.+.|.. -|.|++.|..++.+||..+.|+...+|+.+.+. T Consensus 13 dvDe~iA~lLv~EGF~siEeIAy~~~~eL~~IegfDee~a~eL~~R 58 (70) T 1u9l_A 13 DIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRER 58 (70) T ss_dssp TCCHHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHH T ss_pred CCCHHHHHHHHHHCCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHH T ss_conf 8639999999986559799987599999976315589999999999 No 87 >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* Probab=80.74 E-value=2 Score=20.97 Aligned_cols=27 Identities=22% Similarity=0.279 Sum_probs=13.7 Q ss_pred CCCCCEEEEECCHHHHHHHHHHHHHCCC Q ss_conf 5798489980985899999999997588 Q gi|255764496|r 461 PSWPDVVILDGGKGQLSAAQGVLKKLNV 488 (616) Q Consensus 461 ~~~PDLilIDGGkgQln~a~~vl~~l~i 488 (616) ..+|- +-++++...-.....+.+++|+ T Consensus 269 weFP~-~~~e~~~~~~~l~r~l~ee~~i 295 (369) T 3fsp_A 269 WEFPS-CETDGADGKEKLEQMVGEQYGL 295 (369) T ss_dssp EECCE-EECSSSCTHHHHHHHHTTSSSC T ss_pred CCCCC-CCCCCCCCHHHHHHHHHHHCCC T ss_conf 62885-6657643077899888987088 No 88 >1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} SCOP: a.96.1.2 Probab=80.54 E-value=1.3 Score=22.38 Aligned_cols=12 Identities=33% Similarity=0.686 Sum_probs=4.2 Q ss_pred HHHHHHCCCCCC Q ss_conf 998751566435 Q gi|255764496|r 368 DFTKKFALPHIP 379 (616) Q Consensus 368 ~Lk~~L~L~~~p 379 (616) ++......++.| T Consensus 191 ~~G~~vC~~~~P 202 (221) T 1kea_A 191 DFSAIICAPRKP 202 (221) T ss_dssp HHHHHTSCSSSC T ss_pred HHHHHHCCCCCC T ss_conf 996887038899 No 89 >1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A* Probab=80.16 E-value=1.7 Score=21.55 Aligned_cols=16 Identities=6% Similarity=0.272 Sum_probs=9.3 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 7899999999997301 Q gi|255764496|r 128 VDAVEKTINSLQRTFF 143 (616) Q Consensus 128 ~~~~~~~l~~l~~~f~ 143 (616) ...++.+++.|.+.|| T Consensus 7 ~~~~~~i~~~L~~~y~ 22 (226) T 1orn_A 7 KQQIRYCLDEMAKMFP 22 (226) T ss_dssp HHHHHHHHHHHHHHCT T ss_pred HHHHHHHHHHHHHHCC T ss_conf 9999999999998779 No 90 >2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} Probab=79.77 E-value=1 Score=23.14 Aligned_cols=32 Identities=16% Similarity=0.187 Sum_probs=20.6 Q ss_pred CEEEECCCCHHHHHHHHHHHHHHHH----HHHHHHH Q ss_conf 3488579989999999887877887----8898998 Q gi|255764496|r 516 EALVLNMRDPILYFIQRLRDEAHRF----AITTHRK 547 (616) Q Consensus 516 ~~i~l~~~~~~l~~Lq~iRDEaHRF----Ai~~hRk 547 (616) +|+.-..|...+..|+.+.|++.+= +.+|.+- T Consensus 8 r~~Ps~~N~lfi~~L~e~~~~~~~k~~k~~~aY~kA 43 (87) T 2kp7_A 8 RPLPVCPNPLFVRWLTEWRDEAASRGRHTRFVFQKA 43 (87) T ss_dssp CCCCCSCCCHHHHHHHHHHHHHHHHTCTTHHHHHHH T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHH T ss_conf 999999889999999999999987073579999999 No 91 >1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B Probab=79.64 E-value=2.8 Score=19.97 Aligned_cols=56 Identities=11% Similarity=0.203 Sum_probs=44.0 Q ss_pred CCCHHCCCCCCHHHHHHHH-HHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC Q ss_conf 7710048887989999999-98088898993898888627899989999999985478 Q gi|255764496|r 554 YSPLDEINGIGPLRKRLLL-QSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616) Q Consensus 554 ~S~Ld~I~GIG~k~~~~Ll-~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616) ..+++++ +++..+...|- ....++..+.+.|.+||..++|+|++..+.|.+.|++. T Consensus 8 ~~~I~~L-~LS~R~~N~L~~~~I~tv~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~~~ 64 (73) T 1z3e_B 8 EMTIEEL-DLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEEL 64 (73) T ss_dssp TCBGGGS-CCBHHHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHHT T ss_pred CCCHHHH-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHC T ss_conf 6889884-69899999998948967999986899999747898660599999999984 No 92 >1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A Probab=78.91 E-value=2.1 Score=20.88 Aligned_cols=17 Identities=18% Similarity=0.221 Sum_probs=7.6 Q ss_pred HHHHHHHHHHCCCCCCC Q ss_conf 99999987515664351 Q gi|255764496|r 364 MILKDFTKKFALPHIPK 380 (616) Q Consensus 364 ~~l~~Lk~~L~L~~~p~ 380 (616) .+|-++.........|. T Consensus 182 ~~lv~~G~~iC~~~~P~ 198 (225) T 1kg2_A 182 QAMMDLGAMICTRSKPK 198 (225) T ss_dssp HHHHHHHHHTSCSSSCC T ss_pred HHHHHHHHHHCCCCCCC T ss_conf 99999978881599999 No 93 >3lti_A DNA-directed RNA polymerase subunit beta; BBM2, nucleotidyltransferase, transcription, transferase; HET: MLY MSE; 1.60A {Escherichia coli} PDB: 3e7h_A Probab=76.98 E-value=0.7 Score=24.35 Aligned_cols=21 Identities=38% Similarity=0.792 Sum_probs=13.9 Q ss_pred CCCCCCEEEEE------CCCCCEEEEEE Q ss_conf 86788625888------69988889960 Q gi|255764496|r 6 MPECPGVYQML------DIAGRVLYVGK 27 (616) Q Consensus 6 lP~~pGvY~~~------~~~~~iiYvGK 27 (616) -|.||||| |. ...|+.+|.+. T Consensus 2 ~~~SPGV~-F~~~~~k~~~~gk~ly~a~ 28 (296) T 3lti_A 2 HPMSPGVF-FDSDKGKTHSSGKVLYNAR 28 (296) T ss_dssp --CCCEEE-EEEC---------CCEEEE T ss_pred CCCCCEEE-EECCCCCCCCCCCEEEEEE T ss_conf 89798687-6046674467885799999 No 94 >3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A Probab=75.85 E-value=1.3 Score=22.28 Aligned_cols=55 Identities=9% Similarity=0.098 Sum_probs=37.5 Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCC Q ss_conf 710048887989999999980888989938988886278999899999999854786 Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNT 611 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~ 611 (616) +.|--|.|+||.+.+.|+.+...-.. =.|.++|.+|+|+|+++-++.--||+=.. T Consensus 508 ~lL~~VsGLgprkA~~iv~~r~~~g~--f~~R~~L~~v~~lG~k~F~q~AgFlrI~~ 562 (785) T 3bzc_A 508 ALLARISGLNSTLAQNIVAHRDANGA--FRTRDELKKVSRLGEKTFEQAAGFLRVMN 562 (785) T ss_dssp HHHHTSTTCCHHHHHHHHHHHHHHCC--CSSGGGGGGSTTCCHHHHHHHGGGEECTT T ss_pred HHHHCCCCCCHHHHHHHHHHHHHCCC--CCCHHHHHHCCCCCHHHHHHCCEEEEECC T ss_conf 77532578788999999999995799--57799997367866021765256777669 No 95 >3ofo_B 30S ribosomal protein S2; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_B* 2wwl_B 3ofp_B 3i1m_B 1vs7_B* 3e1a_B 3e1c_B 1vs5_B 3i1o_B 3i1q_B 3i1s_B 3i1z_B 3i21_B 3kc4_B 3or9_B 3ora_B 2qal_B* 1p87_B 2aw7_B 2avy_B ... Probab=75.80 E-value=3.6 Score=19.22 Aligned_cols=56 Identities=14% Similarity=0.210 Sum_probs=34.9 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCC Q ss_conf 999999775313111233333333454579848998098589999999999758877871899971877 Q gi|255764496|r 434 VLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPK 502 (616) Q Consensus 434 vi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616) .+.|.+.++.+.-..+ ..-..+||+++|-.-...-.|+.|+.. + .||++||+=-+- T Consensus 128 ~~~r~~~kL~~~~~Gi--------~~m~~~P~~vii~d~~~~~~ai~Ea~~-l----~IPvI~ivDTn~ 183 (218) T 3ofo_B 128 MRTRELEKLENSLGGI--------KDMGGLPDALFVIDADHEHIAIKEANN-L----GIPVFAIVDTNS 183 (218) T ss_dssp HHHHHHHHHTTTCSSS--------TTCCSCCSSEEEEETGGGHHHHHHHHH-T----TCCEEEECCTTS T ss_pred HHHHHHHHHHHHCCCC--------CCCCCCCCEEEECCCCHHHHHHHHHHH-C----CCCEEEEEECCC T ss_conf 7689999999960681--------113558734774285031799999998-5----997799850798 No 96 >3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} Probab=74.21 E-value=3.5 Score=19.32 Aligned_cols=56 Identities=11% Similarity=0.203 Sum_probs=44.2 Q ss_pred CCCHHCCCCCCHHHHHHHH-HHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC Q ss_conf 7710048887989999999-98088898993898888627899989999999985478 Q gi|255764496|r 554 YSPLDEINGIGPLRKRLLL-QSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616) Q Consensus 554 ~S~Ld~I~GIG~k~~~~Ll-~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616) ..+++++ +++..+...|- ...-++..+.+-|.+||..++|+|++..+.|.+.|..- T Consensus 15 ~~~I~~L-~LS~R~~n~L~~~gI~tv~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~~~ 71 (79) T 3gfk_B 15 EMTIEEL-DLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEEL 71 (79) T ss_dssp GCBGGGS-CCBHHHHHHHHHTTCCBHHHHTTCCHHHHTTSTTCHHHHHHHHHHHHHHT T ss_pred CCCHHHH-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHC T ss_conf 4959984-79899999998928967999986889999757898673799999999985 No 97 >1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19 Probab=70.08 E-value=3.6 Score=19.23 Aligned_cols=17 Identities=18% Similarity=0.200 Sum_probs=8.7 Q ss_pred CCCCHHHHHHHHHHHHH Q ss_conf 12203566555432345 Q gi|255764496|r 173 GEISSEKYMEFVHEAKK 189 (616) Q Consensus 173 ~~is~~~Y~~~v~~~~~ 189 (616) ..++.......|+++.. T Consensus 262 ~Glsqk~irklI~~al~ 278 (780) T 1gm5_A 262 SGISQKQMRKIFEENIP 278 (780) T ss_dssp TTBCHHHHHHHHHHHHH T ss_pred CCCCHHHHHHHHHHHHH T ss_conf 55669999999999998 No 98 >3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} PDB: 1lb2_B* 1xs9_D Probab=69.56 E-value=4.9 Score=18.22 Aligned_cols=56 Identities=11% Similarity=0.149 Sum_probs=43.8 Q ss_pred CCCCHHCCCCCCHHHHHHHHHHH--CCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC Q ss_conf 47710048887989999999980--88898993898888627899989999999985478 Q gi|255764496|r 553 AYSPLDEINGIGPLRKRLLLQSF--GTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616) Q Consensus 553 ~~S~Ld~I~GIG~k~~~~Ll~~F--gs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616) +..+++++ ++.. |...-|+.- .++..+.+.|.+||.+++|+|++..+.|.+.|... T Consensus 10 L~~~I~eL-~LSv-R~~N~Lk~~gI~tvgdLv~~se~dLl~i~NfG~kSl~EI~~~L~~~ 67 (86) T 3k4g_A 10 LLRPVDDL-ELTV-RSANCLXAEAIHYIGDLVQRTEVELLXTPNLGXXSLTEIXDVLASR 67 (86) T ss_dssp GGSBGGGG-CCCH-HHHHHHHHTTCCBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHTT T ss_pred HCCCHHHH-CCCH-HHHHHHCCCCCCCHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHC T ss_conf 71969872-7889-9998725543937999984899998178898772699999999985 No 99 >3bbn_B Ribosomal protein S2; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Probab=67.02 E-value=5.5 Score=17.87 Aligned_cols=54 Identities=19% Similarity=0.292 Sum_probs=33.8 Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 9999977531311123333333345457984899809858999999999975887787189997187 Q gi|255764496|r 435 LERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 435 i~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~ 501 (616) +.|++.++.+.-..+ ..-..+||+++|-+-..--.|+.|+.. .+||+|||+=-. T Consensus 137 ~~~~~~kl~k~~~Gi--------~~m~~~Pd~viv~d~~~~~~ai~Ea~~-----l~IPvI~ivDtn 190 (231) T 3bbn_B 137 VKRQLSHLQTYLGGI--------KYMTGLPDIVIIVDQQEEYTALRECIT-----LGIPTICLIDTN 190 (231) T ss_dssp HHHHHHHHTTSTTST--------TSCCSCCSEEEESCTTTTHHHHHHHHT-----TTCCEEECCCSS T ss_pred HHHHHHHHHHHCCCC--------CHHHCCCCEEEECCCCCCHHHHHHHHH-----CCCCEEEEECCC T ss_conf 768999998731463--------103129977985286322799999997-----399878874389 No 100 >1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A* 3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A* 3d4v_A* Probab=66.23 E-value=4.8 Score=18.27 Aligned_cols=54 Identities=11% Similarity=0.183 Sum_probs=28.1 Q ss_pred CCHHCCCCCCHHHHHH-HHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC Q ss_conf 7100488879899999-99980888989938988886278999899999999854 Q gi|255764496|r 555 SPLDEINGIGPLRKRL-LLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFH 608 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~-Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~ 608 (616) ..|..||||||.|..- +|..+|-.+-.-....-=...+.+++++....+.+.+. T Consensus 207 ~~L~~l~GIGpWTA~~vll~~lg~~D~fp~~Dl~l~~~~~~l~~~~~~~~ae~w~ 261 (282) T 1mpg_A 207 KTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWK 261 (282) T ss_dssp HHHTTSTTCCHHHHHHHHHHHSCCSSCCCTTCHHHHHHSTTCCHHHHHHHHGGGT T ss_pred HHHHHCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCC T ss_conf 9999767988699999999976998838743499998741089999999998556 No 101 >3ecd_A Serine hydroxymethyltransferase 2; ssgcid, decode, bupsa00008A, cytoplasm, one-carbon metabolism, pyridoxal phosphate; 1.60A {Burkholderia pseudomallei} Probab=65.01 E-value=6 Score=17.60 Aligned_cols=26 Identities=12% Similarity=0.284 Sum_probs=16.7 Q ss_pred CCEEEEECCH-H-HHHHHHHHHHHCCCC Q ss_conf 8489980985-8-999999999975887 Q gi|255764496|r 464 PDVVILDGGK-G-QLSAAQGVLKKLNVE 489 (616) Q Consensus 464 PDLilIDGGk-g-Qln~a~~vl~~l~i~ 489 (616) =-+++||-.. | --..|..+|++.||. T Consensus 320 nH~vlvd~~~~g~~g~~a~~~Le~~gI~ 347 (425) T 3ecd_A 320 NHLLLVDLRPKGLKGAQVEQALERAGIT 347 (425) T ss_dssp SSEEEEECGGGTCCHHHHHHHHHHTTEE T ss_pred CCEEEEECCCCCCCHHHHHHHHHHCCEE T ss_conf 5479996366688689999999971958 No 102 >2vqe_B 30S ribosomal protein S2; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: c.23.15.1 PDB: 1gix_E* 1hnw_B* 1hnx_B* 1hnz_B* 1hr0_B 1ibk_B* 1ibl_B* 1ibm_B 1j5e_B 1jgo_E* 1jgp_E* 1jgq_E* 1ml5_E* 1n32_B* 1n33_B* 1n34_B 1n36_B 1xmo_B* 1xmq_B* 1xnq_B* ... Probab=63.87 E-value=6.3 Score=17.46 Aligned_cols=38 Identities=21% Similarity=0.295 Sum_probs=28.2 Q ss_pred CCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCC Q ss_conf 4579848998098589999999999758877871899971877 Q gi|255764496|r 460 FPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPK 502 (616) Q Consensus 460 ~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616) ...+||+|+|=.-..-..|+.++.. + +||+|||+=-+- T Consensus 155 m~~~Pd~v~v~d~~~~~~AI~EA~~-l----~IPvIaivDTn~ 192 (256) T 2vqe_B 155 LKRLPDAIFVVDPTKEAIAVREARK-L----FIPVIALADTDS 192 (256) T ss_dssp CSSCCSEEEESCTTTTHHHHHHHHH-T----TCCCEECCCTTS T ss_pred CCCCCCEEEECCCCHHHHHHHHHHH-H----CCCEEEEECCCC T ss_conf 2468977996377500889999998-5----895577613898 No 103 >1rv3_A Serine hydroxymethyltransferase, cytosolic; one-carbon metabolism; HET: GLY PLP; 2.40A {Oryctolagus cuniculus} SCOP: c.67.1.4 PDB: 1rv4_A* 1rvu_A* 1rvy_A* 1ls3_A* 1cj0_A* 1bj4_A* 1eji_A* Probab=63.71 E-value=6.3 Score=17.44 Aligned_cols=24 Identities=25% Similarity=0.534 Sum_probs=16.5 Q ss_pred CCEEEEE----CCHHHHHHHHHHHHHCCCC Q ss_conf 8489980----9858999999999975887 Q gi|255764496|r 464 PDVVILD----GGKGQLSAAQGVLKKLNVE 489 (616) Q Consensus 464 PDLilID----GGkgQln~a~~vl~~l~i~ 489 (616) =-+++|| |.-|+ .|.+.|++.||. T Consensus 355 nHlvlvdl~~~g~~g~--~a~~~Le~~gI~ 382 (483) T 1rv3_A 355 NHLILVDLRSKGTDGG--RAEKVLEACSIA 382 (483) T ss_dssp SSEEEEEGGGGTCCHH--HHHHHHHHTTEE T ss_pred CCEEEEECCCCCCCHH--HHHHHHHHCCCE T ss_conf 7369986021378799--999999986948 No 104 >2gkg_A Response regulator homolog; social motility, receiver domain, signalling, high resolutio signaling protein; 1.00A {Myxococcus xanthus} PDB: 2i6f_A 2nt4_A 2nt3_A Probab=63.00 E-value=6.5 Score=17.35 Aligned_cols=39 Identities=18% Similarity=0.282 Sum_probs=24.9 Q ss_pred CCCCEEEEECC----HHHHHHHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 79848998098----58999999999975887787189997187 Q gi|255764496|r 462 SWPDVVILDGG----KGQLSAAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 462 ~~PDLilIDGG----kgQln~a~~vl~~l~i~~~i~viglaK~~ 501 (616) ..||||++|=. ..=+..+.++-...... .+||+.++-.+ T Consensus 48 ~~pdliilD~~lp~~~~G~~l~~~ir~~~~~~-~iPii~lt~~~ 90 (127) T 2gkg_A 48 DRPDLVVLAVDLSAGQNGYLICGKLKKDDDLK-NVPIVIIGNPD 90 (127) T ss_dssp HCCSEEEEESBCGGGCBHHHHHHHHHHSTTTT-TSCEEEEECGG T ss_pred CCCCEEEEECCCCCCCCHHHHHHHHHHCCCCC-CCCEEEEECCC T ss_conf 79999999757776888999999998388889-98389996898 No 105 >2jba_A Phosphate regulon transcriptional regulatory protein PHOB; transcription factor, sensory transduction, phosphate regulation; 1.45A {Escherichia coli} PDB: 2jba_B 1b00_A 2iyn_A 2jb9_A 1zes_A Probab=57.78 E-value=7.9 Score=16.73 Aligned_cols=77 Identities=16% Similarity=0.098 Sum_probs=41.0 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH--HHHHHCCCCCCCCEEEEECCC Q ss_conf 11689989999999977531311123333333345457984899809858999999--999975887787189997187 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQ--GVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~--~vl~~l~i~~~i~viglaK~~ 501 (616) .||-..+++++.+.++..-=+-.....+......-....|||||+|-.-+.++... +.++.......+|++-++-.. T Consensus 8 VDDd~~~~~~l~~~L~~~G~~v~~a~~~~~al~~l~~~~~dlii~D~~mp~~~G~~l~~~ir~~~~~~~~piI~ls~~~ 86 (127) T 2jba_A 8 VEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVVMLTARG 86 (127) T ss_dssp ECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHTTCSSSCCSEEEEESEETTEEHHHHHHHHHTSTTTTTSCEEEEEETT T ss_pred EECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCC T ss_conf 9799999999999999879999998999999999971799999981889996289999999847877999099998989 No 106 >2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structure initiative; 1.80A {Bacteroides fragilis YCH46} Probab=57.01 E-value=8.1 Score=16.64 Aligned_cols=73 Identities=14% Similarity=0.115 Sum_probs=34.2 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEE--------CCHHHHHHHHHHHHHCCCCCCCCEEEE Q ss_conf 168998999999997753131112333333334545798489980--------985899999999997588778718999 Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILD--------GGKGQLSAAQGVLKKLNVENRITIISI 497 (616) Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilID--------GGkgQln~a~~vl~~l~i~~~i~vigl 497 (616) ||-.++++++.+.+...--+-.....+...-..-....|||+|+| +|..=+..+.++-+. .- .+|||-+ T Consensus 10 DDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlillDl~mP~~~~~G~dGl~~l~~ir~~-~~--~ipvI~l 86 (140) T 2qr3_A 10 DDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLREENPEVVLLDMNFTSGINNGNEGLFWLHEIKRQ-YR--DLPVVLF 86 (140) T ss_dssp CSCHHHHHHHHHHHTTTSSEEEEECCHHHHHHHHHHSCEEEEEEETTTTC-----CCHHHHHHHHHHH-CT--TCCEEEE T ss_pred ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHH-CC--CCCEEEE T ss_conf 79999999999999978999999899999999997279999999168877776775199999999986-89--9828999 Q ss_pred ECCC Q ss_conf 7187 Q gi|255764496|r 498 AKGP 501 (616) Q Consensus 498 aK~~ 501 (616) .-.. T Consensus 87 T~~~ 90 (140) T 2qr3_A 87 TAYA 90 (140) T ss_dssp EEGG T ss_pred ECCC T ss_conf 7899 No 107 >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 Probab=56.83 E-value=8.2 Score=16.62 Aligned_cols=17 Identities=35% Similarity=0.552 Sum_probs=9.9 Q ss_pred CHHCCCCCCHHHHHHHH Q ss_conf 10048887989999999 Q gi|255764496|r 556 PLDEINGIGPLRKRLLL 572 (616) Q Consensus 556 ~Ld~I~GIG~k~~~~Ll 572 (616) .|..||||||.|..-++ T Consensus 211 ~L~~i~GIGpWTA~~il 227 (295) T 2jhn_A 211 YLTSFKGIGRWTAELVL 227 (295) T ss_dssp HHHTSTTCCHHHHHHHH T ss_pred HHHHCCCCCHHHHHHHH T ss_conf 99845994889999999 No 108 >3gl9_A Response regulator; beta-sheet, surrounded by alpha helices, BOTH sides, signaling protein; HET: BFD; 1.80A {Thermotoga maritima} PDB: 3dgf_C 3dge_C Probab=54.20 E-value=8.9 Score=16.38 Aligned_cols=76 Identities=16% Similarity=0.092 Sum_probs=36.3 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH--HHHHHHHCCCCCCCCEEEEECCC Q ss_conf 16899899999999775313111233333333454579848998098589999--99999975887787189997187 Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSA--AQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~--a~~vl~~l~i~~~i~viglaK~~ 501 (616) ||-..+++++.+.+.+.-=+-.....+...-..-....|||||+|---+.++- +.+.+++..-...+|++.+.-.. T Consensus 9 DD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~~~~~~pdliilD~~mP~~~G~el~~~ir~~~~~~~iPiI~lT~~~ 86 (122) T 3gl9_A 9 DDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLXIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKG 86 (122) T ss_dssp CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHTTBCCSEEEECSCCSSSCHHHHHHHHHTSTTTTTSCEEEEESCC T ss_pred ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCC T ss_conf 699999999999999879999998999999999983799999851028999889999999838878999899982799 No 109 >3c3m_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein structure initiative; HET: MSE; 1.70A {Methanoculleus marisnigri JR1} Probab=54.13 E-value=8.1 Score=16.66 Aligned_cols=75 Identities=16% Similarity=0.106 Sum_probs=36.0 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH---HHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 1689989999999977531311123333333345457984899809858999---999999975887787189997187 Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLS---AAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln---~a~~vl~~l~i~~~i~viglaK~~ 501 (616) ||-..+++++.+-+...-=+-.....+...-..-....|||||+|-.-+.++ .+..+-..... ..+||+.++-.. T Consensus 10 DD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~~~~pdliilD~~mP~~dG~el~~~ir~~~~~-~~ipvI~ls~~~ 87 (138) T 3c3m_A 10 DDSPMIVDVFVTMLERGGYRPITAFSGEECLEALNATPPDLVLLDIMMEPMDGWETLERIKTDPAT-RDIPVLMLTAKP 87 (138) T ss_dssp CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHSTTT-TTSCEEEEESSC T ss_pred ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHCCCC-CCCCEEEEECCC T ss_conf 799999999999999879999998999999999753899899970678999889999999848655-899879986379 No 110 >1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A Probab=53.98 E-value=6.6 Score=17.28 Aligned_cols=97 Identities=12% Similarity=0.068 Sum_probs=41.9 Q ss_pred CCCCCHHHHCCCCCEEEEEEEEEECCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHEECCCCC-HHHHHHH Q ss_conf 454201110001883478899842474541011356677789978988877754321378981231026888-5787666 Q gi|255764496|r 239 YNRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAE-ETSLLEI 317 (616) Q Consensus 239 ~~d~Dvi~i~~~~~~~~I~vl~vR~G~i~g~~~f~~~~~~~~~~~eil~~fI~qyY~~~~iP~~Iiv~~~~~-~~~~l~~ 317 (616) -+..|++++...+.+- ...||=+|.+.-.....++ +....+++.. + ++ -+|||+-..+. |-+.-.. T Consensus 86 E~~~Dl~aIE~tg~y~--G~YhVLgG~iSpldgigp~---~l~i~~L~~R-i-----~~--~~EVIlA~~~t~EGe~Ta~ 152 (228) T 1vdd_A 86 EEPGDVIALERSGEYR--GLYHVLHGVLSPMNGVGPD---KLHIKPLLPR-V-----GQ--GMEVILATGTTVEGDATAL 152 (228) T ss_dssp SSHHHHHHTTTTSSCC--SEEEECSSCCBGGGTBCTT---TSTTGGGGGG-C-----CT--TCEEEECCCSSHHHHHHHH T ss_pred CCHHHHHHHHHCCCCC--EEEEECCCCCCCCCCCCCC---CCCHHHHHHH-H-----CC--CCEEEEEECCCCCHHHHHH T ss_conf 7899999998608112--6998668763723489941---0036999998-6-----35--8679998179855189999 Q ss_pred HHHHHC-CCCCCCC-----CCCCCCHHHHHH-HHHHHHH Q ss_conf 543201-3433321-----256552667899-9999999 Q gi|255764496|r 318 SFFKQY-GYKVKIT-----VPKQGEKRKIIE-QALINAH 349 (616) Q Consensus 318 ~L~~k~-g~kV~i~-----~P~rG~kk~Ll~-lA~~NA~ 349 (616) +|.+.. +..++|. .|.-|+ .+.+| ..+.+|- T Consensus 153 yi~~~Lk~~~ikiTRLA~GlP~G~~-LeY~D~~TL~~Al 190 (228) T 1vdd_A 153 YLQRLLEPLGAAISRIAYGVPVGGS-LEYTDEVTLGRAL 190 (228) T ss_dssp HHHHHHTTSSCEEEECCBCBCTTCC-GGGSCHHHHHHHH T ss_pred HHHHHHHHCCCEEEEECCCCCCCCC-HHHCCHHHHHHHH T ss_conf 9999854449708761006877842-0016899999999 No 111 >3kbq_A Protein TA0487; structural genomics, CINA, protein structure initiative, MCSG, PSI-2, midwest center for structural genomics; 2.00A {Thermoplasma acidophilum} Probab=53.57 E-value=9.2 Score=16.27 Aligned_cols=14 Identities=21% Similarity=0.302 Sum_probs=7.5 Q ss_pred CCCCCEEEEEECCC Q ss_conf 64351699970744 Q gi|255764496|r 376 PHIPKRIEIYDNSH 389 (616) Q Consensus 376 ~~~p~rIE~fDiSh 389 (616) ...|.--+.++|++ T Consensus 119 A~~P~ga~~i~N~~ 132 (172) T 3kbq_A 119 AKIPPSCRPIENPV 132 (172) T ss_dssp GEECTTEEEECCSS T ss_pred HCCCCCCEEEECCC T ss_conf 43842253441788 No 112 >3i42_A Response regulator receiver domain protein (CHEY- like); structural genomics, PSI-2, protein structure initiative; 2.15A {Methylobacillus flagellatus KT} Probab=53.34 E-value=8 Score=16.71 Aligned_cols=76 Identities=12% Similarity=0.034 Sum_probs=36.4 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHH--HHHHHHCCCCCCCCEEEEECCC Q ss_conf 168998999999997753131112333333334545798489980985899999--9999975887787189997187 Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAA--QGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a--~~vl~~l~i~~~i~viglaK~~ 501 (616) ||-...++++.+.+.++-=.-.....+...-..-....||+||+|-.-+.++-. .+.++.......+|++.+.-.. T Consensus 10 DD~~~~~~~l~~~L~~~G~~v~~a~~g~eAl~~l~~~~~dlillD~~mP~~~G~el~~~lr~~~~~~~~pii~lt~~~ 87 (127) T 3i42_A 10 EDYQAAAETFKELLEMLGFQADYVMSGTDALHAMSTRGYDAVFIDLNLPDTSGLALVKQLRALPMEKTSKFVAVSGFA 87 (127) T ss_dssp CSCHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHHHSCCSEEEEESBCSSSBHHHHHHHHHHSCCSSCCEEEEEECC- T ss_pred ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCEEEEEECCC T ss_conf 578999999999999879999998999999999980899999862789998459999999847678999499997888 No 113 >1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} SCOP: a.96.1.2 PDB: 3iho_A Probab=52.59 E-value=9.5 Score=16.16 Aligned_cols=81 Identities=9% Similarity=0.022 Sum_probs=46.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH-H-HH-CCCC----HHCCCCCCHH--HHHHHHHHHCCHHHHHHCCHHHHHHCCCCCH Q ss_conf 99999887877887889899864-3-21-4771----0048887989--9999999808889899389888862789998 Q gi|255764496|r 527 LYFIQRLRDEAHRFAITTHRKRR-K-KA-AYSP----LDEINGIGPL--RKRLLLQSFGTVKMISRSSPETLASIEGISK 597 (616) Q Consensus 527 l~~Lq~iRDEaHRFAi~~hRk~r-~-k~-~~S~----Ld~I~GIG~k--~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~ 597 (616) -.++|+-+|++=.=+...-.++- . .. .... .+-|.++|-- +.+.|.+-. +.+..-+.++|.++||||+ T Consensus 38 ~ILsqqT~~~~v~~v~~~l~~~~pt~~~la~a~~~el~~~i~~lG~~~~KAk~I~~~a---~~~vp~~~~~l~~LpGVG~ 114 (155) T 1ngn_A 38 TIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFS---DEYLTKQWRYPIELHGIGK 114 (155) T ss_dssp HHHHTTSCHHHHHHHHHHHHHHSCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHH---HHHHHSCCSSGGGSTTCCH T ss_pred HHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---HHHHHHHHHCCCCCCCCCH T ss_conf 9998709699999999999998889999987349999999720026879999999997---1665442331675898219 Q ss_pred HHHHHHHHHHCCC Q ss_conf 9999999985478 Q gi|255764496|r 598 KIACKIYNHFHKN 610 (616) Q Consensus 598 ~~A~~I~~~l~~~ 610 (616) ..|..+.-+...+ T Consensus 115 ytad~~~if~~~~ 127 (155) T 1ngn_A 115 YGNDSYRIFCVNE 127 (155) T ss_dssp HHHHHHHHHTSSC T ss_pred HHHHHHHHHHCCC T ss_conf 9999999998799 No 114 >3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum} Probab=52.32 E-value=9.6 Score=16.13 Aligned_cols=77 Identities=13% Similarity=0.064 Sum_probs=42.8 Q ss_pred CHHHHHHHHHHHHHHHHHHCCC-CCCCCCCCC-CCCCCCCCCCEEEEE----CCHHHHHHHHHHHHHCCCCCCCCEEEEE Q ss_conf 1168998999999997753131-112333333-334545798489980----9858999999999975887787189997 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNE-ENLNFHPKK-QEYSFPSWPDVVILD----GGKGQLSAAQGVLKKLNVENRITIISIA 498 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~-~~l~~~~~~-~~~~~~~~PDLilID----GGkgQln~a~~vl~~l~i~~~i~vigla 498 (616) .||-..+++++..-+..+-... -....+... ........|||||+| ||-+-...+..+-..... ..+|||.+. T Consensus 10 VDD~~~~r~~l~~~L~~~G~~~v~~a~~g~eal~~l~~~~~~dlii~D~~mP~~~~g~~l~~~ir~~~~~-~~~piI~lT 88 (140) T 3lua_A 10 IDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIFKDLDSITLIIMDIAFPVEKEGLEVLSAIRNNSRT-ANTPVIIAT 88 (140) T ss_dssp ECSCHHHHHHHHHHHHHHCCCEEEEECSHHHHHTTTTTCCCCSEEEECSCSSSHHHHHHHHHHHHHSGGG-TTCCEEEEE T ss_pred EECCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHCCCCCCEEEEECCCCCCCCHHHHHHHHHHCCCC-CCCCEEEEE T ss_conf 9499999999999998679908999899999999997389985999868999999888999987644246-899889982 Q ss_pred CCCC Q ss_conf 1877 Q gi|255764496|r 499 KGPK 502 (616) Q Consensus 499 K~~~ 502 (616) -... T Consensus 89 ~~~~ 92 (140) T 3lua_A 89 KSDN 92 (140) T ss_dssp SCCC T ss_pred CCCC T ss_conf 7999 No 115 >2etv_A Iron(III) ABC transporter, periplasmic iron- binding protein, putative; TM0189, structural genomics; HET: MLY; 1.70A {Thermotoga maritima MSB8} SCOP: c.92.2.4 Probab=50.15 E-value=7.9 Score=16.75 Aligned_cols=20 Identities=15% Similarity=0.210 Sum_probs=13.0 Q ss_pred CCEEEEECCHHHHHHHHHHH Q ss_conf 84899809858999999999 Q gi|255764496|r 464 PDVVILDGGKGQLSAAQGVL 483 (616) Q Consensus 464 PDLilIDGGkgQln~a~~vl 483 (616) ||.|++.++-.+........ T Consensus 232 PDvI~v~~~~~~~~~~~~l~ 251 (346) T 2etv_A 232 PEYIFIDENGLSLVLDDYSX 251 (346) T ss_dssp CSEEEEEGGGHHHHHHHHHH T ss_pred CCEEEEECCCCCHHHHHHHH T ss_conf 89999968985447888764 No 116 >3cvo_A Methyltransferase-like protein of unknown function; YP_167254.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE PG4; 1.80A {Silicibacter pomeroyi dss-3} Probab=48.68 E-value=5.6 Score=17.80 Aligned_cols=24 Identities=29% Similarity=0.443 Sum_probs=16.0 Q ss_pred CCCEEEEECCHHHHHHHHHHHHHCC Q ss_conf 9848998098589999999999758 Q gi|255764496|r 463 WPDVVILDGGKGQLSAAQGVLKKLN 487 (616) Q Consensus 463 ~PDLilIDGGkgQln~a~~vl~~l~ 487 (616) -||||||||.-- ...+..++..+. T Consensus 122 ~~DlIlIDGR~R-~aC~l~~~~~lk 145 (202) T 3cvo_A 122 HPDVVLVDGRFR-VGCALATAFSIT 145 (202) T ss_dssp CCSEEEECSSSH-HHHHHHHHHHCS T ss_pred CCCEEEECCHHH-HHHHHHHHHHCC T ss_conf 887899756378-999999999669 No 117 >1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} SCOP: a.60.3.1 PDB: 2jzb_A Probab=47.62 E-value=11 Score=15.63 Aligned_cols=55 Identities=13% Similarity=0.174 Sum_probs=38.6 Q ss_pred CCHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC Q ss_conf 71004888798999999998-088898993898888627899989999999985478 Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616) .+++++ ++...+...|-+. ..++..+.+-|.+||..++|+|++.-+.|.+.|... T Consensus 24 ~~I~eL-~LSvRs~N~L~~~gI~tvgdLv~~se~dLl~~~n~G~KSl~EIk~~L~~~ 79 (98) T 1coo_A 24 RPVDDL-ELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 79 (98) T ss_dssp SBGGGG-TCCTTTHHHHHTTTCCBHHHHHTSCHHHHTTSTTCCHHHHHHHHHHHHHT T ss_pred CCHHHH-CCCHHHHHHHHHHCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHC T ss_conf 969882-77899999873817938999985799999758897687899999999985 No 118 >3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12} Probab=46.07 E-value=12 Score=15.47 Aligned_cols=76 Identities=16% Similarity=0.112 Sum_probs=42.2 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH--HHHHHHHCCCCCCCCEEEEECCCC Q ss_conf 116899899999999775313111233333333454579848998098589999--999999758877871899971877 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSA--AQGVLKKLNVENRITIISIAKGPK 502 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~--a~~vl~~l~i~~~i~viglaK~~~ 502 (616) .||-..+++++.+.+.+.--+-.....+...-..-....|||+++|-.-+.++- +.+.+++.+- .+|++-++-... T Consensus 13 VDD~~~~r~~l~~~L~~~g~~v~~a~~g~~Al~~l~~~~~dlvi~D~~mP~~dG~~~~~~ir~~~~--~~piI~lt~~~~ 90 (130) T 3eod_A 13 VEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLGGFTPDLMICDIAMPRMNGLKLLEHIRNRGD--QTPVLVISATEN 90 (130) T ss_dssp ECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHTTCCCSEEEECCC-----CHHHHHHHHHTTC--CCCEEEEECCCC T ss_pred EECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEHHHHCCCCCCHHHHHHHHHHHCC--CCCEEEEECCCC T ss_conf 969899999999999988999999899999999985289887457421799989999999996098--998999989999 No 119 >3cg4_A Response regulator receiver domain protein (CHEY- like); structural genomics, unknown function, uncharacterized protein; HET: MSE; 1.61A {Methanospirillum hungatei jf-1} Probab=45.63 E-value=12 Score=15.42 Aligned_cols=75 Identities=16% Similarity=0.131 Sum_probs=35.6 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH---HHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 1689989999999977531311123333333345457984899809858999---999999975887787189997187 Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLS---AAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln---~a~~vl~~l~i~~~i~viglaK~~ 501 (616) ||-.++++++.+-+...-=.-.....+...-..-....|||||+|-.-+.++ .+. .+++......+||+-+.-.. T Consensus 14 DD~~~~r~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~dliilD~~mP~~~G~el~~-~ir~~~~~~~ipiI~lT~~~ 91 (142) T 3cg4_A 14 DDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLKKGFSGVVLLDIMMPGMDGWDTIR-AILDNSLEQGIAIVMLTAKN 91 (142) T ss_dssp CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHTCCCEEEEEESCCSSSCHHHHHH-HHHHTTCCTTEEEEEEECTT T ss_pred ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHH-HHHHCCCCCCCEEEEEECCC T ss_conf 7989999999999998799999989999999999717999999838999986899999-99857556899599997889 No 120 >2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp} Probab=45.51 E-value=12 Score=15.41 Aligned_cols=75 Identities=13% Similarity=0.160 Sum_probs=37.6 Q ss_pred CHHHHHHHHHHHHHHHHHHCC---------CCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH--HHHHHHHCCCCCCCC Q ss_conf 116899899999999775313---------111233333333454579848998098589999--999999758877871 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKN---------EENLNFHPKKQEYSFPSWPDVVILDGGKGQLSA--AQGVLKKLNVENRIT 493 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~---------~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~--a~~vl~~l~i~~~i~ 493 (616) .||-...++++.+-+++.--. ++.+.. -..........||||++|-.-+..+- +.+.+++......+| T Consensus 13 VDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~-l~~~~~~~~~~~dliilD~~mP~~~G~el~~~ir~~~~~~~ip 91 (143) T 2qvg_A 13 LEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDM-LYGRNKENKIHPKLILLDINIPKMNGIEFLKELRDDSSFTDIE 91 (143) T ss_dssp ECCCHHHHHHHHHHHHHHCTTCCEEEESSHHHHHHH-HHTCTTCCCCCCSEEEEETTCTTSCHHHHHHHHTTSGGGTTCE T ss_pred EECCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHH-HHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCE T ss_conf 979999999999999976998499998999999999-9841233037987899648788997279999998577779991 Q ss_pred EEEEECC Q ss_conf 8999718 Q gi|255764496|r 494 IISIAKG 500 (616) Q Consensus 494 viglaK~ 500 (616) ||.+.=. T Consensus 92 iI~lS~~ 98 (143) T 2qvg_A 92 VFVLTAA 98 (143) T ss_dssp EEEEESC T ss_pred EEEEECC T ss_conf 9999788 No 121 >1mb3_A Cell division response regulator DIVK; signal transduction protein, structural proteomics in europe, spine, structural genomics; 1.41A {Caulobacter vibrioides} SCOP: c.23.1.1 PDB: 1m5u_A 1mav_A 1mb0_A 1m5t_A Probab=44.69 E-value=9.1 Score=16.30 Aligned_cols=39 Identities=18% Similarity=0.242 Sum_probs=23.4 Q ss_pred CCCEEEEECCHHHHHHH--HHHHHHCCCCCCCCEEEEECCC Q ss_conf 98489980985899999--9999975887787189997187 Q gi|255764496|r 463 WPDVVILDGGKGQLSAA--QGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 463 ~PDLilIDGGkgQln~a--~~vl~~l~i~~~i~viglaK~~ 501 (616) .||+||+|-.-+.++-. .+.+++..-...+|++.++-.. T Consensus 45 ~pdlillD~~mp~~~G~el~~~ir~~~~~~~iPii~ls~~~ 85 (124) T 1mb3_A 45 KPDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFA 85 (124) T ss_dssp CCSEEEEESBCSSSBHHHHHHHHHHSTTTTTSCEEEEC--- T ss_pred CCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCC T ss_conf 99999978999998479999999828877999689998989 No 122 >2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, PSI-2, protein structure initiative; 2.00A {Desulfuromonas acetoxidans dsm 684} Probab=43.46 E-value=7.1 Score=17.08 Aligned_cols=38 Identities=21% Similarity=0.322 Sum_probs=22.3 Q ss_pred CCCEEEEECCHHHHHH--HHHHHHHCCCCCCCCEEEEECC Q ss_conf 9848998098589999--9999997588778718999718 Q gi|255764496|r 463 WPDVVILDGGKGQLSA--AQGVLKKLNVENRITIISIAKG 500 (616) Q Consensus 463 ~PDLilIDGGkgQln~--a~~vl~~l~i~~~i~viglaK~ 500 (616) .|||||+|---+.++- +.+.+++..-...+||+-++-. T Consensus 52 ~pdliilD~~mP~~dG~el~~~ir~~~~~~~iPiI~lS~~ 91 (147) T 2zay_A 52 HPHLIITEANMPKISGMDLFNSLKKNPQTASIPVIALSGR 91 (147) T ss_dssp CCSEEEEESCCSSSCHHHHHHHHHTSTTTTTSCEEEEESS T ss_pred CCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCCEEEEECC T ss_conf 9999998599999975189999984855689718997268 No 123 >3n0l_A Serine hydroxymethyltransferase; alpha beta class, 3-layer(ABA) sandwich, CSGI transferase, structural genomics; HET: MSE; 1.80A {Campylobacter jejuni} Probab=41.43 E-value=14 Score=14.98 Aligned_cols=24 Identities=13% Similarity=0.129 Sum_probs=12.9 Q ss_pred CEEEEEC-CHH-HHHHHHHHHHHCCC Q ss_conf 4899809-858-99999999997588 Q gi|255764496|r 465 DVVILDG-GKG-QLSAAQGVLKKLNV 488 (616) Q Consensus 465 DLilIDG-Gkg-Qln~a~~vl~~l~i 488 (616) -+++||- .+| -=..|...|++.|| T Consensus 313 H~vlvd~~~~~~~G~~a~~~Le~~gI 338 (417) T 3n0l_A 313 HLVLMSFLDREFSGKDADLALGNAGI 338 (417) T ss_dssp SEEEEECTTSSSCHHHHHHHHHHTTE T ss_pred EEEEEECCCCCCCHHHHHHHHHHCCE T ss_conf 17888601135769999999987593 No 124 >1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket, two component system; 1.90A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 1pey_A 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A 2jvj_A 2jvk_A 2jvi_A 1f51_E Probab=39.92 E-value=11 Score=15.58 Aligned_cols=74 Identities=18% Similarity=0.168 Sum_probs=34.5 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH--HHHHHHHCCCCCCCCEEEEECC Q ss_conf 116899899999999775313111233333333454579848998098589999--9999997588778718999718 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSA--AQGVLKKLNVENRITIISIAKG 500 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~--a~~vl~~l~i~~~i~viglaK~ 500 (616) -||=..+++++.+-+.+.--+-.....+...-..-....||||++|-.-+.++- +.+.+++..- .+|++-+.-. T Consensus 9 VDD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~~~~~~~dliilD~~mP~~~G~el~~~ir~~~~--~~pii~lt~~ 84 (124) T 1srr_A 9 VDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDE--NIRVIIMTAY 84 (124) T ss_dssp ECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHHCCSEEEEESCCTTCCHHHHHHHHHHHCT--TCEEEEEESS T ss_pred EECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCC--CCCEEEEECC T ss_conf 979999999999999986998999599899999998079988998536999988999999996099--9989999888 No 125 >1zgz_A Torcad operon transcriptional regulatory protein TORR; two-component system, gene regulation, transcription factor, TMAO respiratory system; 1.80A {Escherichia coli} SCOP: c.23.1.1 Probab=38.53 E-value=12 Score=15.35 Aligned_cols=38 Identities=16% Similarity=0.170 Sum_probs=22.7 Q ss_pred CCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 984899809858999999999975887787189997187 Q gi|255764496|r 463 WPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 463 ~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~ 501 (616) .|||||+|-.-+.++-. +.++.+--...+|++-++-.. T Consensus 46 ~~dliilD~~mP~~dG~-e~~~~~r~~~~~piI~lt~~~ 83 (122) T 1zgz_A 46 SVDLILLDINLPDENGL-MLTRALRERSTVGIILVTGRS 83 (122) T ss_dssp CCSEEEEESCCSSSCHH-HHHHHHHTTCCCEEEEEESSC T ss_pred CCCEEEEECCCCCCCHH-HHHHHHHHCCCCCEEEEECCC T ss_conf 99899997898997728-999999847999399998369 No 126 >1d8b_A SGS1 RECQ helicase; five helices, three-helical bundle flanked by two helices, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.60.8.1 Probab=38.51 E-value=14 Score=14.90 Aligned_cols=16 Identities=6% Similarity=0.187 Sum_probs=7.5 Q ss_pred CHHCCCCCCHHHHHHH Q ss_conf 1004888798999999 Q gi|255764496|r 556 PLDEINGIGPLRKRLL 571 (616) Q Consensus 556 ~Ld~I~GIG~k~~~~L 571 (616) .|..|+|||+++.++- T Consensus 49 eL~~I~Gvg~~k~~kY 64 (81) T 1d8b_A 49 AFATLGTVEDKYRRRF 64 (81) T ss_dssp HHGGGSCCCHHHHHHG T ss_pred HHCCCCCCCHHHHHHH T ss_conf 9827999998999999 No 127 >1gp8_A Protein (scaffolding protein); coat protein-binding domain, helix- loop-helix motif, viral protein; NMR {Enterobacteria phage P22} SCOP: j.58.1.1 PDB: 2gp8_A Probab=38.31 E-value=14 Score=15.05 Aligned_cols=30 Identities=27% Similarity=0.315 Sum_probs=24.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999863338888889999999 Q gi|255764496|r 198 LKEKIARNMNQATLKEDYESAIIHRDRLAA 227 (616) Q Consensus 198 ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~a 227 (616) -+..++++|+.|+.+-+-|.-.+++-++.. T Consensus 9 n~~ai~kqm~aaa~kgdvetyrklka~lkg 38 (40) T 1gp8_A 9 NKDAIRKQMDAAASKGDVETYRKLKAKLKG 38 (40) T ss_dssp HHHHHHHHHHHHHTTSCHHHHHHHHHHHTT T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHCC T ss_conf 089999999987414649999999998636 No 128 >3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices, helix-hairpin-helix motif, iron-sulfur cluste hydrolase; 2.30A {Homo sapiens} Probab=37.61 E-value=16 Score=14.57 Aligned_cols=20 Identities=25% Similarity=0.134 Sum_probs=11.9 Q ss_pred CCCCHHHHHHHHHHHHHHHH Q ss_conf 37887899999999997301 Q gi|255764496|r 124 PFASVDAVEKTINSLQRTFF 143 (616) Q Consensus 124 Pf~~~~~~~~~l~~l~~~f~ 143 (616) .|.+...+..+-+.|...|. T Consensus 8 ~~~~~~~~~~~~~~Ll~Wy~ 27 (287) T 3n5n_X 8 LFRDVAEVTAFRGSLLSWYD 27 (287) T ss_dssp SCCCHHHHHHHHHHHHHHHH T ss_pred CCCCHHHHHHHHHHHHHHHH T ss_conf 22888999999999999999 No 129 >2h31_A Multifunctional protein ADE2; alpha-beta-alpha, ligase, lyase; 2.80A {Homo sapiens} Probab=36.99 E-value=13 Score=15.21 Aligned_cols=29 Identities=24% Similarity=0.292 Sum_probs=20.7 Q ss_pred CCE-EEEECCHHHHHHHHHHHHHCCCCCCCCEEEEE Q ss_conf 848-99809858999999999975887787189997 Q gi|255764496|r 464 PDV-VILDGGKGQLSAAQGVLKKLNVENRITIISIA 498 (616) Q Consensus 464 PDL-ilIDGGkgQln~a~~vl~~l~i~~~i~vigla 498 (616) |.+ |-+-|+-++|.-+..++ . ..||||+- T Consensus 322 ~~v~ia~aG~sa~L~g~va~~-----t-~~PVIgvP 351 (425) T 2h31_A 322 PTVFVAVAGRSNGLGPVMSGN-----T-AYPVISCP 351 (425) T ss_dssp CEEEEEECCSSCCHHHHHHHH-----C-SSCEEECC T ss_pred CEEEEEECCCCCCCHHHHHHC-----C-CCCEEECC T ss_conf 779998466322434553323-----6-89979767 No 130 >1g8l_A Molybdopterin biosynthesis MOEA protein; molybdenum cofactor biosynthesis, metal binding protein; 1.95A {Escherichia coli} SCOP: b.85.6.1 b.103.1.1 c.57.1.2 PDB: 1fc5_A 1g8r_A 2nqu_A 2nro_A 2nqq_A 2nqk_A 2nqr_A 2nqm_A 2nqs_A 2nrp_A 2nqv_A 2nrs_A 2nqn_A Probab=36.90 E-value=16 Score=14.50 Aligned_cols=100 Identities=20% Similarity=0.163 Sum_probs=59.3 Q ss_pred EEEEEECCCCCHHHHHHHHCCCCC-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCH--H Q ss_conf 888851687280323211024444-5541168998999999997753131112333333334545798489980985--8 Q gi|255764496|r 398 CMVVVGENGFVKNQYRKFNLHPND-VKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGK--G 474 (616) Q Consensus 398 s~Vvf~~g~~~K~~YR~f~Ik~~~-v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGk--g 474 (616) +.|+=.|+-.-...-+.+...... ..-.||...+++.+.+-.++ -|+||+=||- | T Consensus 199 g~i~dsN~~~l~a~l~~~G~~~~~~~~~~Dd~~~i~~~~~~~~~~----------------------~DiiIttGG~S~G 256 (411) T 1g8l_A 199 GQIYDTNRLAVHLMLEQLGCEVINLGIIRDDPHALRAAFIEADSQ----------------------ADVVISSGGVSVG 256 (411) T ss_dssp SCEECCHHHHHHHHHHHTTCEEEEEEEECSCHHHHHHHHHHHHHH----------------------CSEEEECSSSCSS T ss_pred CEEEECCHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHC----------------------CCEEEECCCCCCC T ss_conf 719834589999999977998997464268699999998754420----------------------3558851575568 Q ss_pred HHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEE-EECCCCH Q ss_conf 99999999997588778718999718776766348981798348-8579989 Q gi|255764496|r 475 QLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEAL-VLNMRDP 525 (616) Q Consensus 475 Qln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i-~l~~~~~ 525 (616) .-..+.++|+++| .+.+-+++=+..+-+. +-..++.++ -|+-+.- T Consensus 257 ~~D~v~~~l~~~G---~i~f~~v~ikPGkp~~---~~~~~~~~v~gLPGnPv 302 (411) T 1g8l_A 257 EADYTKTILEELG---EIAFWKLAIKPGKPFA---FGKLSNSWFCGLPGNPV 302 (411) T ss_dssp SCSHHHHHHHHHS---EEEEEEBSEESCCEEE---EEECSSSEEEECCSSHH T ss_pred CCHHHHHHHHHCC---CEEEEEEEEECCCCEE---EEEECCCCCCCCCCCCH T ss_conf 2066899999759---7699987686366469---99970564327988858 No 131 >2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus} Probab=35.88 E-value=17 Score=14.39 Aligned_cols=40 Identities=10% Similarity=0.106 Sum_probs=24.6 Q ss_pred CCCEEEEECCHHHH---HHHHHHHHHCCCCCCCCEEEEECCCCC Q ss_conf 98489980985899---999999997588778718999718776 Q gi|255764496|r 463 WPDVVILDGGKGQL---SAAQGVLKKLNVENRITIISIAKGPKR 503 (616) Q Consensus 463 ~PDLilIDGGkgQl---n~a~~vl~~l~i~~~i~viglaK~~~r 503 (616) .||+||+|-.-+.. ..+..+ ++..-...+|++.++-.+.. T Consensus 45 ~pdlvllD~~lp~~~G~~l~~~l-r~~~~~~~~pii~~t~~~~~ 87 (119) T 2j48_A 45 QPIVILMAWPPPDQSCLLLLQHL-REHQADPHPPLVLFLGEPPV 87 (119) T ss_dssp CCSEEEEECSTTCCTHHHHHHHH-HHTCCCSSCCCEEEESSCCS T ss_pred CCCEEEEECCCCCCCHHHHHHHH-HHCCCCCCCEEEEEECCHHH T ss_conf 99989996379999999999999-82888898649999771889 No 132 >1vi6_A 30S ribosomal protein S2P; structural genomics, ribosome; 1.95A {Archaeoglobus fulgidus} SCOP: c.23.15.1 PDB: 1vi5_A Probab=33.65 E-value=18 Score=14.14 Aligned_cols=36 Identities=14% Similarity=0.250 Sum_probs=28.2 Q ss_pred CCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCC Q ss_conf 79848998098589999999999758877871899971877 Q gi|255764496|r 462 SWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPK 502 (616) Q Consensus 462 ~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616) ..||+++|=+-.-.-+|+.++.+ + +||+|||+=-+- T Consensus 114 ~~P~~viv~dp~~d~~ai~Ea~~-l----~IP~I~ivDTn~ 149 (208) T 1vi6_A 114 REPEVVFVNDPAIDKQAVSEATA-V----GIPVVALCDSNN 149 (208) T ss_dssp CCCSEEEESCTTTTHHHHHHHHH-T----TCCEEEEECTTC T ss_pred CCCCCCEEECCCCCHHHHHHHHH-C----CCCEEEEECCCC T ss_conf 46766077767753799999998-0----996588724999 No 133 >3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon metabolism, pyridoxal phosphate, structural genomics; HET: LLP; 1.50A {Mycobacterium tuberculosis} Probab=32.37 E-value=19 Score=14.00 Aligned_cols=24 Identities=29% Similarity=0.505 Sum_probs=16.0 Q ss_pred CCEEEEE----CCHHHHHHHHHHHHHCCCC Q ss_conf 8489980----9858999999999975887 Q gi|255764496|r 464 PDVVILD----GGKGQLSAAQGVLKKLNVE 489 (616) Q Consensus 464 PDLilID----GGkgQln~a~~vl~~l~i~ 489 (616) =-+++|| |.-|+ .|.+.|++.||. T Consensus 337 nH~vlvdl~~~g~~g~--~a~~~Le~agI~ 364 (447) T 3h7f_A 337 VHLVLVDLRDSPLDGQ--AAEDLLHEVGIT 364 (447) T ss_dssp SSEEEEECTTSSCCHH--HHHHHHHHTTEE T ss_pred CCEEEEECCCCCCCHH--HHHHHHHHCCEE T ss_conf 5257532345799999--999999971918 No 134 >3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, hydrolase; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A* Probab=32.15 E-value=6.8 Score=17.23 Aligned_cols=30 Identities=23% Similarity=0.319 Sum_probs=16.9 Q ss_pred CCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 79834885799899999998878778878898998643 Q gi|255764496|r 513 KKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRK 550 (616) Q Consensus 513 ~~~~~i~l~~~~~~l~~Lq~iRDEaHRFAi~~hRk~r~ 550 (616) .+++.+.++... +.+=.|-||+|-|+..-+ T Consensus 473 ~dg~~v~~~~~~--------l~~l~laYA~TvHKsQGs 502 (574) T 3e1s_A 473 FDGNVVELTGAE--------LFNLQLGYALTVHRAQGS 502 (574) T ss_dssp ETTEEEEECGGG--------GTTEEECSEEEHHHHTTC T ss_pred ECCEEEEECHHH--------HCCEEEEEEEEEECCCCC T ss_conf 899699976788--------277039999367422004 No 135 >3gbx_A Serine hydroxymethyltransferase; structural genomics, IDP01011, cytoplasm, one-carbon metabolism, pyridoxal phosphate; HET: MSE; 1.80A {Salmonella typhimurium} PDB: 1dfo_A* 3g8m_A* 1eqb_A* Probab=31.36 E-value=20 Score=13.89 Aligned_cols=26 Identities=23% Similarity=0.316 Sum_probs=15.2 Q ss_pred CCEEEEECCHHHH--HHHHHHHHHCCCC Q ss_conf 8489980985899--9999999975887 Q gi|255764496|r 464 PDVVILDGGKGQL--SAAQGVLKKLNVE 489 (616) Q Consensus 464 PDLilIDGGkgQl--n~a~~vl~~l~i~ 489 (616) =-++|||=..-.+ ..|...|++.||. T Consensus 319 ~H~vLvdl~~~g~~G~~a~~~Le~~gI~ 346 (420) T 3gbx_A 319 NHLFLLDLVDKNLTGKEADAALGRANIT 346 (420) T ss_dssp SSEEEEECGGGTCCHHHHHHHHHHTTEE T ss_pred CCEEEEECCCCCCCHHHHHHHHHHHCEE T ss_conf 7468752356799889999999982958 No 136 >3kht_A Response regulator; PSI-II, structural genomics, protein structure initiative, NEW YORK SGX research center for structural genomics; 2.10A {Hahella chejuensis kctc 2396} Probab=30.85 E-value=20 Score=13.83 Aligned_cols=79 Identities=13% Similarity=0.168 Sum_probs=39.7 Q ss_pred CCCCEEEEECCHHHHHH--HHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHHHHHHHHHHHHHH Q ss_conf 79848998098589999--9999997588778718999718776766348981798348857998999999988787788 Q gi|255764496|r 462 SWPDVVILDGGKGQLSA--AQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHR 539 (616) Q Consensus 462 ~~PDLilIDGGkgQln~--a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l~~Lq~iRDEaHR 539 (616) ..|||||+|-.-+.++- +.+.+++......+||+.++-....... +..+-..-..+...+-.+.--|+.+|+.=..| T Consensus 50 ~~~dliilD~~mP~~~G~el~~~ir~~~~~~~iPiI~lS~~~~~~~~-~~a~~~Ga~~~l~KP~~~~~eL~~~i~~~l~~ 128 (144) T 3kht_A 50 AKYDLIILDIGLPIANGFEVMSAVRKPGANQHTPIVILTDNVSDDRA-KQCMAAGASSVVDKSSNNVTDFYGRIYAIFSY 128 (144) T ss_dssp CCCSEEEECTTCGGGCHHHHHHHHHSSSTTTTCCEEEEETTCCHHHH-HHHHHTTCSEEEECCTTSHHHHHHHHHHHHHH T ss_pred CCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCHHHH-HHHHHCCCCEEEECCCCCHHHHHHHHHHHHHH T ss_conf 79999998699999999999999983787899918999888999999-99998699999969999999999999999998 Q ss_pred HH Q ss_conf 78 Q gi|255764496|r 540 FA 541 (616) Q Consensus 540 FA 541 (616) |- T Consensus 129 ~~ 130 (144) T 3kht_A 129 WL 130 (144) T ss_dssp HH T ss_pred HC T ss_conf 66 No 137 >1zh2_A KDP operon transcriptional regulatory protein KDPE; two-component system, gene regulation, transcription factor, KDP potassium transport system; 2.00A {Escherichia coli} SCOP: c.23.1.1 PDB: 1zh4_A Probab=30.77 E-value=11 Score=15.60 Aligned_cols=36 Identities=22% Similarity=0.351 Sum_probs=21.9 Q ss_pred CCCEEEEECCHHHH---HHHHHHHHHCCCCCCCCEEEEECCCC Q ss_conf 98489980985899---99999999758877871899971877 Q gi|255764496|r 463 WPDVVILDGGKGQL---SAAQGVLKKLNVENRITIISIAKGPK 502 (616) Q Consensus 463 ~PDLilIDGGkgQl---n~a~~vl~~l~i~~~i~viglaK~~~ 502 (616) .|||||+|=.-+.+ ..+.. ++. ...+|++-+.-... T Consensus 45 ~~dlil~D~~mp~~~G~~l~~~-ir~---~~~ipiI~lt~~~~ 83 (121) T 1zh2_A 45 KPDLIILDLGLPDGDGIEFIRD-LRQ---WSAVPVIVLSARSE 83 (121) T ss_dssp CCSEEEEESEETTEEHHHHHHH-HHT---TCCCCEEEEESCCS T ss_pred CCCEEEEECCCCCCCHHHHHHH-HHH---HCCCEEEEEECCCC T ss_conf 9999998099999897999999-997---47990999978599 No 138 >3bqs_A Uncharacterized protein; 10114F, NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.42A {Listeria monocytogenes str} PDB: 3bqt_A 3mab_A Probab=30.43 E-value=20 Score=13.78 Aligned_cols=31 Identities=23% Similarity=0.329 Sum_probs=17.5 Q ss_pred CCCHHCCCCCCHHHHHHHHHHHC--CHHHHHHCC Q ss_conf 77100488879899999999808--889899389 Q gi|255764496|r 554 YSPLDEINGIGPLRKRLLLQSFG--TVKMISRSS 585 (616) Q Consensus 554 ~S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As 585 (616) -|.|.++|+|||+..+.|-+ -| |++.++... T Consensus 3 m~~L~~LPNig~~~e~~L~~-iGI~~~~~L~~~g 35 (93) T 3bqs_A 3 LANLSELPNIGKVLEQDLIK-AGIKTPVELKDVG 35 (93) T ss_dssp CSCGGGSTTCCHHHHHHHHH-TTCCSHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHHH-CCCCCHHHHHHCC T ss_conf 67772489999999999999-3999899998679 No 139 >1jlj_A Gephyrin; globular alpha/beta fold, structural protein; 1.60A {Homo sapiens} SCOP: c.57.1.1 PDB: 1ihc_A Probab=29.94 E-value=21 Score=13.72 Aligned_cols=30 Identities=17% Similarity=0.336 Sum_probs=22.7 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHH Q ss_conf 11689989999999977531311123333333345457984899809858 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKG 474 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkg 474 (616) +||...+++.+.+...+ .-.||||.-||-| T Consensus 60 pDd~~~I~~~l~~~~~~--------------------~~~DlViTTGGtg 89 (189) T 1jlj_A 60 PDEIEEIKETLIDWCDE--------------------KELNLILTTGGTG 89 (189) T ss_dssp CSCHHHHHHHHHHHHHT--------------------SCCSEEEEESCCS T ss_pred CCCHHHHHHHHHHHHHC--------------------CCCCEEEECCCCC T ss_conf 89789999999998752--------------------3776899767556 No 140 >3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV} Probab=29.11 E-value=21 Score=13.63 Aligned_cols=76 Identities=16% Similarity=0.094 Sum_probs=37.5 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH---HHHHHH--HHCCCCCCCCEEEEEC Q ss_conf 11689989999999977531311123333333345457984899809858999---999999--9758877871899971 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLS---AAQGVL--KKLNVENRITIISIAK 499 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln---~a~~vl--~~l~i~~~i~viglaK 499 (616) -||-..+++++.+-+.++--+-.....+...-..-....||+|++|..-+.++ .+.++- ..-+.. .+|++.+.- T Consensus 20 VDD~~~~r~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlii~D~~mp~~~G~el~~~ir~~~~~~~~-~~pii~lt~ 98 (143) T 3m6m_D 20 ADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMAEEDYDAVIVDLHMPGMNGLDMLKQLRVMQASGMR-YTPVVVLSA 98 (143) T ss_dssp ECSSHHHHHHHHHHHHC--CEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHHHHTTCC-CCCEEEEES T ss_pred EECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCC-CCEEEEEEC T ss_conf 9588999999999999879999998999999999752899999983888999889999999862843358-993999978 Q ss_pred CC Q ss_conf 87 Q gi|255764496|r 500 GP 501 (616) Q Consensus 500 ~~ 501 (616) .. T Consensus 99 ~~ 100 (143) T 3m6m_D 99 DV 100 (143) T ss_dssp CC T ss_pred CC T ss_conf 89 No 141 >1uz5_A MOEA protein, 402AA long hypothetical molybdopterin biosynthesis MOEA protein; MOEA molybdopterin, MOCF biosynthesis; 2.05A {Pyrococcus horikoshii} SCOP: b.85.6.1 b.103.1.1 c.57.1.2 Probab=28.97 E-value=21 Score=13.61 Aligned_cols=99 Identities=18% Similarity=0.230 Sum_probs=59.8 Q ss_pred EEEEECCCCCHHHHHHHHCCCCCC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECC--HHH Q ss_conf 888516872803232110244445-54116899899999999775313111233333333454579848998098--589 Q gi|255764496|r 399 MVVVGENGFVKNQYRKFNLHPNDV-KTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGG--KGQ 475 (616) Q Consensus 399 ~Vvf~~g~~~K~~YR~f~Ik~~~v-~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGG--kgQ 475 (616) .|+=.|+-.-...-+.+....... .-.||...+++.+..-..+ -|+||+-|| .|. T Consensus 203 ~i~dsN~~~l~a~l~~~G~~~~~~~~~~D~~~~i~~~i~~~~~~----------------------~DivIttGG~S~G~ 260 (402) T 1uz5_A 203 QIYDINGRALCDAINELGGEGIFMGVARDDKESLKALIEKAVNV----------------------GDVVVISGGASGGT 260 (402) T ss_dssp CEECCHHHHHHHHHHHHTSEEEEEEEECSSHHHHHHHHHHHHHH----------------------CSEEEEECCC---- T ss_pred CEEECCHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHCCCC----------------------CCEEEEECCCCCCC T ss_conf 68445599999999866972776266685689999987632223----------------------54478754755885 Q ss_pred HHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEE-EECCCCH Q ss_conf 9999999997588778718999718776766348981798348-8579989 Q gi|255764496|r 476 LSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEAL-VLNMRDP 525 (616) Q Consensus 476 ln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i-~l~~~~~ 525 (616) -..+.++|.++|- +-+-+++=+..+-+.. -..++.++ -|+-+.. T Consensus 261 ~D~v~~~l~~~G~---~~f~~v~~kPGkP~~~---~~~~~~~v~gLPGnP~ 305 (402) T 1uz5_A 261 KDLTASVIEELGE---VKVHGIAIQPGKPTII---GVIKGKPVFGLPGYPT 305 (402) T ss_dssp -CHHHHHHHHHSE---EEEECBSEESCTTCEE---EEETTEEEEEECSSHH T ss_pred CHHHHHHHHHCCC---EEEEEEEEECCCCEEE---EECCCCEEEECCCCCH T ss_conf 2349999997597---7997676870675589---7507756994898858 No 142 >2a7v_A Serine hydroxymethyltransferase; structural genomics, structural genomics consortium, SGC; 2.04A {Homo sapiens} SCOP: c.67.1.4 PDB: 3ou5_A Probab=27.89 E-value=22 Score=13.48 Aligned_cols=26 Identities=27% Similarity=0.395 Sum_probs=16.1 Q ss_pred CCEEEEECC-HH-HHHHHHHHHHHCCCC Q ss_conf 848998098-58-999999999975887 Q gi|255764496|r 464 PDVVILDGG-KG-QLSAAQGVLKKLNVE 489 (616) Q Consensus 464 PDLilIDGG-kg-Qln~a~~vl~~l~i~ 489 (616) =-|+|||=. +| .=..|..+|+..||. T Consensus 365 nHlvlvdl~~~g~~G~~a~~~Le~~gI~ 392 (490) T 2a7v_A 365 NHLVLVDLRPKGLDGARAERVLELVSIT 392 (490) T ss_dssp SSEEEEECTTTTCCHHHHHHHHHHTTEE T ss_pred CEEEEEECCCCCCCHHHHHHHHHHCCEE T ss_conf 7069985454588678999999986907 No 143 >3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A Probab=27.22 E-value=11 Score=15.80 Aligned_cols=22 Identities=18% Similarity=0.120 Sum_probs=10.8 Q ss_pred EEEECCCCHHHHHHHHHHHHHHH Q ss_conf 37703788789999999999730 Q gi|255764496|r 120 SYFGPFASVDAVEKTINSLQRTF 142 (616) Q Consensus 120 ~yfGPf~~~~~~~~~l~~l~~~f 142 (616) -+++||..+. +-.+=..|+++. T Consensus 26 f~i~Ple~G~-g~TlGnaLRRvL 47 (329) T 3lu0_A 26 VTLEPLERGF-GHTLGNALRRIL 47 (329) T ss_dssp EEECCCCTTC-HHHHHHHHHHHT T ss_pred EEEECCCCCC-HHHHHHHHHHHH T ss_conf 9997688862-636688999998 No 144 >2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus} Probab=27.11 E-value=23 Score=13.39 Aligned_cols=36 Identities=31% Similarity=0.428 Sum_probs=23.0 Q ss_pred CCEEEEEC----------CHH-----HHHHHHHHHHHCCCCCCCCEEEEEC Q ss_conf 84899809----------858-----9999999999758877871899971 Q gi|255764496|r 464 PDVVILDG----------GKG-----QLSAAQGVLKKLNVENRITIISIAK 499 (616) Q Consensus 464 PDLilIDG----------Gkg-----Qln~a~~vl~~l~i~~~i~viglaK 499 (616) ||+|+||- +.+ ++..+...|+.+-...+|||+.+|- T Consensus 311 ~~~vviDyl~~~~~~~~~~~~~~~~~~i~~i~~~Lk~lA~~~~i~vi~~sq 361 (444) T 2q6t_A 311 VGLIIIDYLQLMSGPGSGKSGENRQQEIAAISRGLKALARELGIPIIALSQ 361 (444) T ss_dssp CCEEEEECGGGCBCC-------CHHHHHHHHHHHHHHHHHHHTSCEEEEEE T ss_pred CCEEEEEEHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCEEEEEEC T ss_conf 785999624542145567764209999999999999999973987999851 No 145 >3f6p_A Transcriptional regulatory protein YYCF; unphosphorelated, receiver domain, cytoplasm, DNA-binding, phosphoprotein, transcription regulation; 1.95A {Bacillus subtilis} PDB: 2zwm_A Probab=27.06 E-value=23 Score=13.38 Aligned_cols=75 Identities=16% Similarity=0.085 Sum_probs=34.4 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECC Q ss_conf 1168998999999997753131112333333334545798489980985899999999997588778718999718 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKG 500 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~ 500 (616) -||-..+++++.+.+...--+-.....+...-..-....|||||+|=.-+.++-. +.+..+.-...+|++-+.-. T Consensus 8 VDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlii~D~~mP~~~G~-e~~~~~r~~~~~~ii~lt~~ 82 (120) T 3f6p_A 8 VDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGV-EVCREVRKKYDMPIIMLTAK 82 (120) T ss_dssp ECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHTTCCSEEEEETTSTTTHHH-HHHHHHHTTCCSCEEEEEES T ss_pred EECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCHH-HHHHHHHHCCCCCEEEEECC T ss_conf 9399999999999999889999998999999999971899999982999999999-99999981689958999767 No 146 >3er9_B Poly(A) polymerase catalytic subunit; polyadenylate polymerase, translocation, single tranded RNA poly(A) polymerase, RNA protein complex, processivity, heterodimer; HET: 3AT; 2.06A {Vaccinia virus WR} PDB: 3er8_C* 3erc_C* 2ga9_D* 2gaf_D Probab=26.82 E-value=20 Score=13.84 Aligned_cols=30 Identities=27% Similarity=0.414 Sum_probs=21.1 Q ss_pred EECHHHHHHHHHHCCCCCCCHHHHHHHHHC Q ss_conf 601258788876137887787999999734 Q gi|255764496|r 26 GKAYNLQKRIKSYMHSNNHTHRITHMISQI 55 (616) Q Consensus 26 GKaknL~~Rv~syf~~~~~~~k~~~l~~~~ 55 (616) |-...++.||-+||.+..+..|+.++..-+ T Consensus 69 ~s~~eIk~RI~~YFsKQ~~~~kiG~i~tIi 98 (479) T 3er9_B 69 TSASEIKDRILSYFSKQTQTYNIGKLFTII 98 (479) T ss_dssp CCHHHHHHHHHHHTTGGGGCCCHHHHHHHH T ss_pred CCHHHHHHHHHHHHHHCCHHHHHHHHHEEE T ss_conf 998999999999974054033320002130 No 147 >3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus} Probab=26.67 E-value=23 Score=13.33 Aligned_cols=37 Identities=19% Similarity=0.233 Sum_probs=22.0 Q ss_pred CCCCEEEEECCHHHH---HHHHHHHHHCCCCCCCCEEEEEC Q ss_conf 798489980985899---99999999758877871899971 Q gi|255764496|r 462 SWPDVVILDGGKGQL---SAAQGVLKKLNVENRITIISIAK 499 (616) Q Consensus 462 ~~PDLilIDGGkgQl---n~a~~vl~~l~i~~~i~viglaK 499 (616) ..|||||+|---+.+ ..+.. ++.......+||+-+.= T Consensus 46 ~~pdliilD~~mP~~dG~el~~~-ir~~~~~~~iPiI~lT~ 85 (133) T 3nhm_A 46 HPPDVLISDVNMDGMDGYALCGH-FRSEPTLKHIPVIFVSG 85 (133) T ss_dssp SCCSEEEECSSCSSSCHHHHHHH-HHHSTTTTTCCEEEEES T ss_pred CCCCEEEECCCCCCCCHHHHHHH-HHHCCCCCCCCEEEEEC T ss_conf 79999997599999999999999-98288889987899707 No 148 >2pl1_A Transcriptional regulatory protein PHOP; CHEY-like fold, response regulator, beryllium fluoride, transcription factor, activated, virulence; 1.90A {Escherichia coli} SCOP: c.23.1.1 PDB: 2pkx_A Probab=26.57 E-value=24 Score=13.32 Aligned_cols=74 Identities=18% Similarity=0.229 Sum_probs=34.6 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHH---HHHHHHHHHCCCCCCCCEEEEECCCC Q ss_conf 168998999999997753131112333333334545798489980985899---99999999758877871899971877 Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQL---SAAQGVLKKLNVENRITIISIAKGPK 502 (616) Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQl---n~a~~vl~~l~i~~~i~viglaK~~~ 502 (616) ||-..+++++.+.+...--+-.....+...-..-....|||||+|=.-+.+ ..+. .+++.+- .+|++-++-... T Consensus 7 dDd~~~~~~l~~~L~~~G~~v~~a~~~~~al~~l~~~~~dlii~D~~mp~~dG~e~~~-~lr~~~~--~~pii~lt~~~~ 83 (121) T 2pl1_A 7 EDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIR-RWRSNDV--SLPILVLTARES 83 (121) T ss_dssp CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHH-HHHHTTC--CSCEEEEESCCC T ss_pred ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCCHHHHH-HHHHCCC--CCCEEEEECCCC T ss_conf 6899999999999998799999989999999996458998999889999987478999-9996399--981899978899 No 149 >3hdv_A Response regulator; PSI-II, structural genomics, protein structure initiative, NEW YORK SGX research center for structural genomics; 2.09A {Pseudomonas putida KT2440} Probab=26.54 E-value=24 Score=13.32 Aligned_cols=75 Identities=15% Similarity=0.086 Sum_probs=33.6 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC-CCCCCCCEEEEECCHHHHHHH--HHHHHHCCCCCCCCEEEEECC Q ss_conf 1168998999999997753131112333333334-545798489980985899999--999997588778718999718 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEY-SFPSWPDVVILDGGKGQLSAA--QGVLKKLNVENRITIISIAKG 500 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~-~~~~~PDLilIDGGkgQln~a--~~vl~~l~i~~~i~viglaK~ 500 (616) .||-..+++++.+.+...--+-.....+...... .....|||||+|..-+.++-. .+.++...- ..+|++-+.-. T Consensus 13 VDD~~~~r~~l~~~L~~~G~~v~~a~~~~~a~~~l~~~~~~dlii~D~~mP~~~G~el~~~ir~~~~-~~~piI~lT~~ 90 (136) T 3hdv_A 13 VDDNAVNREALILYLKSRGIDAVGADGAEEARLYLHYQKRIGLMITDLRMQPESGLDLIRTIRASER-AALSIIVVSGD 90 (136) T ss_dssp ECSCHHHHHHHHHHHHHTTCCEEEESSHHHHHHHHHHCTTEEEEEECSCCSSSCHHHHHHHHHTSTT-TTCEEEEEESS T ss_pred EECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHCCC-CCCEEEEEECC T ss_conf 9799999999999999879999998999999999975799988998798999989999999995579-99919999888 No 150 >2db7_A Hairy/enhancer-OF-split related with YRPW motif 1; structural genomics, unknown function, DNA binding protein, NPPSFA; 1.90A {Homo sapiens} SCOP: a.273.1.1 Probab=26.48 E-value=18 Score=14.19 Aligned_cols=44 Identities=18% Similarity=0.199 Sum_probs=28.4 Q ss_pred HHHHHHHHHHH-HHHHHH--CCCCHHCCCCCCHH--HHHHHHHHHCCHH Q ss_conf 77887889899-864321--47710048887989--9999999808889 Q gi|255764496|r 536 EAHRFAITTHR-KRRKKA--AYSPLDEINGIGPL--RKRLLLQSFGTVK 579 (616) Q Consensus 536 EaHRFAi~~hR-k~r~k~--~~S~Ld~I~GIG~k--~~~~Ll~~Fgs~~ 579 (616) .+|.+|..|+. -=+.=+ ....|..++||.+. .+.+||.|..+-- T Consensus 11 d~~~~a~~yra~GF~ECa~EVsRyL~~~eg~d~~d~~r~RLl~HL~~C~ 59 (64) T 2db7_A 11 DAHALAMDYRSLGFRECLAEVARYLSIIEGLDASDPLRVRLVSHLNNYA 59 (64) T ss_dssp CHHHHHHTHHHHHHHHHHHHHHHHHHHTSCCCTTCHHHHHHHHHHHHHH T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 8799999999704999999999995036888976389999999999999 No 151 >3n2l_A OPRT, oprtase, orotate phosphoribosyltransferase; pyrimidine ribonucleotide biosynthesis, infectious diseases; 2.10A {Vibrio cholerae} Probab=26.22 E-value=22 Score=13.49 Aligned_cols=32 Identities=41% Similarity=0.558 Sum_probs=25.4 Q ss_pred EEEEE---CCHHHHHHHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 89980---9858999999999975887787189997187 Q gi|255764496|r 466 VVILD---GGKGQLSAAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 466 LilID---GGkgQln~a~~vl~~l~i~~~i~viglaK~~ 501 (616) ++++| ||+..++++.+++++.| |++.+|++-. T Consensus 176 ~vivDR~~gg~~~~~a~~~~~~~~g----i~~~Sl~tl~ 210 (238) T 3n2l_A 176 LVAIDRQEKGKGELSAIQEVERDFG----CAVISIVSLT 210 (238) T ss_dssp EEEEECCCBCSSSSBHHHHHHHHHC----CEEEEEEEHH T ss_pred EEEEECCCCCCCCHHHHHHHHHHCC----CEEEEEEEHH T ss_conf 9986502155420228999999749----8299981399 No 152 >3cnb_A DNA-binding response regulator, MERR family; signal receiver domain, DNA binding protein, protein structure initiative, PSI-2; 2.00A {Colwellia psychrerythraea 34H} Probab=25.72 E-value=24 Score=13.21 Aligned_cols=74 Identities=18% Similarity=0.147 Sum_probs=35.5 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCC--CCCCCCCCCCCCCCCCCEEEEECCHHHH---HHHHHHHHHCCCCCCCCEEEEECC Q ss_conf 16899899999999775313111--2333333334545798489980985899---999999997588778718999718 Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEEN--LNFHPKKQEYSFPSWPDVVILDGGKGQL---SAAQGVLKKLNVENRITIISIAKG 500 (616) Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~--l~~~~~~~~~~~~~~PDLilIDGGkgQl---n~a~~vl~~l~i~~~i~viglaK~ 500 (616) ||-..+++++.+-+.++...-+- ...+...-..-....|||||+|---+.+ ..+.+ ++...-...+||+.+.-. T Consensus 15 DD~~~~~~~l~~~L~~~~~~~~v~~a~~g~eAl~~~~~~~pDlillD~~mP~~dG~el~~~-ir~~~~~~~ipvI~lt~~ 93 (143) T 3cnb_A 15 EDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLLHTVKPDVVMLDLMMVGMDGFSICHR-IKSTPATANIIVIAMTGA 93 (143) T ss_dssp CSCHHHHHHHHHHHHHHCTTCEEEEECSHHHHHHHHHHTCCSEEEEETTCTTSCHHHHHHH-HHTSTTTTTSEEEEEESS T ss_pred ECCHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHH-HHHCCCCCCCEEEEEECC T ss_conf 1999999999999982789808999899999999997279999998088899986999999-984788899849999848 No 153 >2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics, protein structure initiative; 2.89A {Clostridium difficile 630} Probab=25.19 E-value=20 Score=13.81 Aligned_cols=35 Identities=14% Similarity=0.326 Sum_probs=20.4 Q ss_pred CCCCEEEEE----CCHHHHHHHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 798489980----9858999999999975887787189997187 Q gi|255764496|r 462 SWPDVVILD----GGKGQLSAAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 462 ~~PDLilID----GGkgQln~a~~vl~~l~i~~~i~viglaK~~ 501 (616) ..|||||+| |+-| +..+.+ +.+. ..+|++-++-.. T Consensus 47 ~~~dlillD~~mP~~dG-~el~~~-~~~~---~~~piI~lt~~~ 85 (136) T 2qzj_A 47 NKYDLIFLEIILSDGDG-WTLCKK-IRNV---TTCPIVYMTYIN 85 (136) T ss_dssp CCCSEEEEESEETTEEH-HHHHHH-HHTT---CCCCEEEEESCC T ss_pred CCCCEEEECCCCCCCCC-HHHHHH-HHHC---CCCCEEEEEEEC T ss_conf 79999997799989986-079999-9836---999899999628 No 154 >1xl7_A COT, peroxisomal carnitine O-octanoyltransferase; selenomethionine, hepes; HET: EPE; 2.00A {Mus musculus} SCOP: c.43.1.3 c.43.1.3 PDB: 1xl8_A* 1xmd_A* 1xmc_A* Probab=23.64 E-value=27 Score=12.95 Aligned_cols=34 Identities=15% Similarity=0.148 Sum_probs=20.0 Q ss_pred HHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHH Q ss_conf 58999999999999863-----------33888888999999998 Q gi|255764496|r 196 HNLKEKIARNMNQATLK-----------EDYESAIIHRDRLAALS 229 (616) Q Consensus 196 ~~ii~~L~~~M~~aS~~-----------l~FE~Aa~~RD~I~aL~ 229 (616) .++...|+.-+..++.. ++-...|..|..+.++. T Consensus 215 ~el~~ql~~I~~~~~~~~~~~~vg~LTt~~R~~Wa~~R~~L~~~~ 259 (612) T 1xl7_A 215 PELLRQLTYIHKKCSNEPVGPSIAALTSEERTRWAKAREYLISLD 259 (612) T ss_dssp HHHHHHHHHHHHHHHTSCCCCCGGGGGGSCHHHHHHHHHHHHHHC T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCC T ss_conf 999999999996254578888856045776119999999976079 No 155 >1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A Probab=23.63 E-value=27 Score=12.95 Aligned_cols=40 Identities=13% Similarity=0.316 Sum_probs=23.7 Q ss_pred CCCCCEEEEECCHHH---HHHHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 579848998098589---99999999975887787189997187 Q gi|255764496|r 461 PSWPDVVILDGGKGQ---LSAAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 461 ~~~PDLilIDGGkgQ---ln~a~~vl~~l~i~~~i~viglaK~~ 501 (616) ...|||||+|---+. +..+..+-+.-.. ..|||+-+.-.. T Consensus 59 ~~~pdlillD~~mP~~~G~el~~~ir~~~~~-~~iPvI~lT~~~ 101 (149) T 1i3c_A 59 SPRPNLILLDLNLPKKDGREVLAEIKQNPDL-KRIPVVVLTTSH 101 (149) T ss_dssp CCCCSEEEECSCCSSSCHHHHHHHHHHCTTT-TTSCEEEEESCC T ss_pred CCCCCEEEEECCCCCCCHHHHHHHHHHCCCC-CCCCEEEEECCC T ss_conf 6898889984899998649999999858044-799889995689 No 156 >1qkk_A DCTD, C4-dicarboxylate transport transcriptional regulatory protein; receiver domain, 2-component signal transduction; 1.7A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1l5z_A 1l5y_A Probab=23.30 E-value=27 Score=12.90 Aligned_cols=73 Identities=11% Similarity=0.068 Sum_probs=33.3 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH---HHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 1689989999999977531311123333333345457984899809858999---999999975887787189997187 Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLS---AAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln---~a~~vl~~l~i~~~i~viglaK~~ 501 (616) ||=..+++.+.+-+.+.--.-.....+......-....||+||+|=.-+.++ .+.+ +++.+- .+|||-+.-.. T Consensus 10 DDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dliilD~~mP~~dGle~~~~-ir~~~~--~~pvI~lT~~~ 85 (155) T 1qkk_A 10 DDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRK-ILALDP--DLPMILVTGHG 85 (155) T ss_dssp CSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTCCTTCCSEEEEESCCSSSCHHHHHHH-HHHHCT--TSCEEEEECGG T ss_pred ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEECCCCCCCCCHHHHHHH-HHHHCC--CCCEEEEECCC T ss_conf 59999999999999987998999789999999853269877765457899989999999-997298--99489897989 No 157 >2is8_A Molybdopterin biosynthesis enzyme, MOAB; globular alpha/beta fold, structural genomics, NPPSFA; 1.64A {Thermus thermophilus HB8} Probab=23.16 E-value=27 Score=12.88 Aligned_cols=42 Identities=19% Similarity=0.327 Sum_probs=24.4 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCH--HHHHHHHHHHHHC Q ss_conf 1168998999999997753131112333333334545798489980985--8999999999975 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGK--GQLSAAQGVLKKL 486 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGk--gQln~a~~vl~~l 486 (616) +||...+.+++...... .-.||||.-||. |+-....+++.++ T Consensus 44 ~Dd~~~i~~~l~~~~~~--------------------~~~DlVittGG~g~~~~D~t~~ai~~~ 87 (164) T 2is8_A 44 PDEPPMIKKVLRLWADR--------------------EGLDLILTNGGTGLAPRDRTPEATREL 87 (164) T ss_dssp CSCHHHHHHHHHHHHHT--------------------SCCSEEEEESCCSSSTTCCHHHHHHTT T ss_pred CCCHHHHHHHHHHHHHC--------------------CCCCEEEECCCCCCCCCCCCHHHHHHH T ss_conf 98889999999999845--------------------498689967861389985658889998 No 158 >3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901} Probab=22.90 E-value=20 Score=13.76 Aligned_cols=73 Identities=10% Similarity=0.146 Sum_probs=34.8 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCCCCCCCCCEEEEECCH----HHHHHHHHHHHHCCCCCCCCEEEEEC Q ss_conf 1168998999999997753131112333333-334545798489980985----89999999999758877871899971 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKK-QEYSFPSWPDVVILDGGK----GQLSAAQGVLKKLNVENRITIISIAK 499 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~-~~~~~~~~PDLilIDGGk----gQln~a~~vl~~l~i~~~i~viglaK 499 (616) -||-..+++++.+-+++.--+-.....+... ........|||||+|=.- .=+..+..+ .+. . .+||+-+.- T Consensus 11 VDD~~~~~~~l~~~L~~~g~~v~~a~~g~eAl~~l~~~~~~dlillD~~mp~g~dG~e~~~~i-r~~--~-~~PvI~lT~ 86 (140) T 3h5i_A 11 VEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVSGGWYPDLILMDIELGEGMDGVQTALAI-QQI--S-ELPVVFLTA 86 (140) T ss_dssp ECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHTTCCCSEEEEESSCSSSCCHHHHHHHH-HHH--C-CCCEEEEES T ss_pred EECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHH-HHC--C-CCCEEEEEC T ss_conf 959899999999999987999999898999999998469998999726653357899999999-856--9-998999989 Q ss_pred CC Q ss_conf 87 Q gi|255764496|r 500 GP 501 (616) Q Consensus 500 ~~ 501 (616) .. T Consensus 87 ~~ 88 (140) T 3h5i_A 87 HT 88 (140) T ss_dssp SS T ss_pred CC T ss_conf 99 No 159 >2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92, PSI-2; 2.10A {Neptuniibacter caesariensis} Probab=22.75 E-value=28 Score=12.83 Aligned_cols=74 Identities=18% Similarity=0.003 Sum_probs=37.1 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHH--HHHHHHCCCCCCCCEEEEECC Q ss_conf 1168998999999997753131112333333334545798489980985899999--999997588778718999718 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAA--QGVLKKLNVENRITIISIAKG 500 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a--~~vl~~l~i~~~i~viglaK~ 500 (616) .||-..+++.+.+.+.+.--+-.....+......-....|||||+|=.-+.++-. .+.+++..- .+|+|=+.-. T Consensus 13 VDDd~~~~~~l~~~L~~~g~~v~~a~~~~~Al~~l~~~~~dliilD~~mp~~~G~~~l~~ir~~~~--~~piI~lt~~ 88 (154) T 2rjn_A 13 VDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALKGTSVQLVISDMRMPEMGGEVFLEQVAKSYP--DIERVVISGY 88 (154) T ss_dssp ECSCHHHHHHHHHHHHTTTCEEEEESCHHHHHHHHTTSCCSEEEEESSCSSSCHHHHHHHHHHHCT--TSEEEEEECG T ss_pred EECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCCHHHHHHHHHHCC--CCCEEEEECC T ss_conf 979999999999999987998999899999999986289988996688888881899999998588--9978999866 No 160 >2a9o_A Response regulator; essential protein, YYCF/YYCG homolog, signaling protein; 1.65A {Streptococcus pneumoniae} SCOP: c.23.1.1 PDB: 1nxo_A 1nxs_A 1nxv_A 1nxw_A 1nxx_A 1nxp_A 2a9p_A 2a9q_A 1nxt_A* 2a9r_A* Probab=22.69 E-value=16 Score=14.49 Aligned_cols=36 Identities=25% Similarity=0.410 Sum_probs=19.8 Q ss_pred CCCEEEEECCHHH---HHHHHHHHHHCCCCCCCCEEEEECCCC Q ss_conf 9848998098589---999999999758877871899971877 Q gi|255764496|r 463 WPDVVILDGGKGQ---LSAAQGVLKKLNVENRITIISIAKGPK 502 (616) Q Consensus 463 ~PDLilIDGGkgQ---ln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616) .|||||+|=.-+. +..+.+ +... ..+|++-+.-... T Consensus 45 ~~dliilD~~mp~~dG~~~l~~-~~~~---~~~pvi~lt~~~~ 83 (120) T 2a9o_A 45 QPDIIILDLMLPEIDGLEVAKT-IRKT---SSVPILMLSAKDS 83 (120) T ss_dssp CCSEEEECSSCSSSCHHHHHHH-HHHH---CCCCEEEEESCCS T ss_pred CCCEEEECCCCCCCCHHHHHHH-HHHC---CCCCEEEEECCCC T ss_conf 9989998299999899999999-8865---9981999979899 No 161 >3opy_B 6-phosphofructo-1-kinase beta-subunit; ATP binding, fructose-6-phosphate bindi magnesium binding, citrate binding, ADP binding; HET: ATP; 3.05A {Pichia pastoris} Probab=22.29 E-value=28 Score=12.77 Aligned_cols=37 Identities=22% Similarity=0.160 Sum_probs=26.6 Q ss_pred CCEEEEECCHHHHHHHHHHHHHCCCC--CCCCEEEEECC Q ss_conf 84899809858999999999975887--78718999718 Q gi|255764496|r 464 PDVVILDGGKGQLSAAQGVLKKLNVE--NRITIISIAKG 500 (616) Q Consensus 464 PDLilIDGGkgQln~a~~vl~~l~i~--~~i~viglaK~ 500 (616) =|-+++=||=|=+..|.+.-++..-. ..|||+||-|- T Consensus 663 Id~LivIGGdgS~~~a~~L~~~~~~~~~~~I~vVgIPkT 701 (941) T 3opy_B 663 FDGLILVGGFEAFISLHQLERARINYPSLRIPLVLIPAT 701 (941) T ss_dssp CSEEEEEESHHHHHHHHHHHHGGGTCGGGCSCEEEEEBC T ss_pred CCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCEEEECCC T ss_conf 997999167589999999999775424679737971144 No 162 >2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* 2gho_A 1hqm_A ... Probab=22.28 E-value=15 Score=14.71 Aligned_cols=39 Identities=15% Similarity=0.082 Sum_probs=17.1 Q ss_pred CCCCEEEEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHH Q ss_conf 9984599981235678437703788789999999999730 Q gi|255764496|r 103 HKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTF 142 (616) Q Consensus 103 ~~~p~l~~~r~~~~~~~~yfGPf~~~~~~~~~l~~l~~~f 142 (616) -++|.+...-....-+.-+.|||..+. +..+=..|+++. T Consensus 6 ~~~~~~~~~~~~~~Yg~F~i~Pl~~G~-g~TlGnaLRRvL 44 (315) T 2a6h_A 6 LKAPVFTVRTQGREYGEFVLEPLERGF-GVTLGNPLRRIL 44 (315) T ss_dssp TSCCEEEEEEETTTEEEEEEEEECTTC-HHHHHHHHHHHH T ss_pred CCCCEEEEEECCCCEEEEEEECCCCCC-HHHHHHHHHHHH T ss_conf 688566888668856899996688972-304678999999 No 163 >2ixs_A SDAI restriction endonuclease; hydrolase, domain architecture; HET: EPE; 2.0A {Streptomyces diastaticus} Probab=22.05 E-value=28 Score=12.73 Aligned_cols=18 Identities=11% Similarity=-0.044 Sum_probs=12.6 Q ss_pred EEEECCCCCHHHHHHHHC Q ss_conf 885168728032321102 Q gi|255764496|r 400 VVVGENGFVKNQYRKFNL 417 (616) Q Consensus 400 Vvf~~g~~~K~~YR~f~I 417 (616) ++|...-++++.+|+|-- T Consensus 275 lvfVTAF~dR~~fkk~~~ 292 (323) T 2ixs_A 275 LVFVNCFENREAMRQWLP 292 (323) T ss_dssp EEEEEEESSHHHHGGGGG T ss_pred EEEEEECCCHHHHHHHHH T ss_conf 699985689899999999 No 164 >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} SCOP: a.96.1.3 d.129.1.2 PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A* 2nol_A* 3ktu_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* ... Probab=21.46 E-value=29 Score=12.65 Aligned_cols=16 Identities=19% Similarity=0.220 Sum_probs=8.4 Q ss_pred CCHHCCCCCCHHHHHH Q ss_conf 7100488879899999 Q gi|255764496|r 555 SPLDEINGIGPLRKRL 570 (616) Q Consensus 555 S~Ld~I~GIG~k~~~~ 570 (616) ..|..||||||++..- T Consensus 230 ~~L~~l~GIG~wtAd~ 245 (317) T 1m3q_A 230 KALCILPGVGTKVADC 245 (317) T ss_dssp HHHTTSTTCCHHHHHH T ss_pred HHHHHCCCCCHHHHHH T ss_conf 9998548948899999 No 165 >2rhf_A DNA helicase RECQ; HRDC, D. radiodurans, ATP-binding, hydrolase, nucleotide-binding; HET: DNA; 1.10A {Deinococcus radiodurans R1} Probab=21.39 E-value=29 Score=12.64 Aligned_cols=47 Identities=21% Similarity=0.333 Sum_probs=23.1 Q ss_pred CHHHHHHHHHHHHH------HHHHHHHHHHHHH---HH--CCCCHHCCCCCCHHHHHH Q ss_conf 89999999887877------8878898998643---21--477100488879899999 Q gi|255764496|r 524 DPILYFIQRLRDEA------HRFAITTHRKRRK---KA--AYSPLDEINGIGPLRKRL 570 (616) Q Consensus 524 ~~~l~~Lq~iRDEa------HRFAi~~hRk~r~---k~--~~S~Ld~I~GIG~k~~~~ 570 (616) .+++.-|...|.+- ..|.|-....++. .. ....|.+|+|||+++.++ T Consensus 5 ~~L~~~L~~~R~~~A~~~~vp~~~I~~d~~L~~ia~~~P~t~~eL~~I~Gig~~k~~~ 62 (77) T 2rhf_A 5 ADLSEALRELRRELMKETGYSAFVVFTNATLEALAARQPRTLAELAEVPGLGEKRIEA 62 (77) T ss_dssp HHHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHCCCSHHHHTTSTTTCHHHHHH T ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCHHHHHCCCCCCHHHHHH T ss_conf 9999999999999998769896565789999999983978999980799979999999 No 166 >2x8r_A Glycosyl hydrolase; peptidoglycan cleavage, endo-N-acetylmuramidases, motif; 1.70A {Aspergillus fumigatus} Probab=21.32 E-value=29 Score=12.63 Aligned_cols=14 Identities=29% Similarity=0.275 Sum_probs=7.8 Q ss_pred CEEEEECCHHHHHH Q ss_conf 48998098589999 Q gi|255764496|r 465 DVVILDGGKGQLSA 478 (616) Q Consensus 465 DLilIDGGkgQln~ 478 (616) ||=+..|...||.. T Consensus 193 D~n~f~G~~~~l~~ 206 (210) T 2x8r_A 193 DSDKFNGPMTQLRK 206 (210) T ss_dssp EEEEEESCHHHHHH T ss_pred CCCEECCCHHHHHH T ss_conf 75656799999998 No 167 >1wud_A ATP-dependent DNA helicase RECQ; DNA-binding domain, HRDC, hydrolase; 2.20A {Escherichia coli} SCOP: a.60.8.1 Probab=21.12 E-value=30 Score=12.60 Aligned_cols=14 Identities=21% Similarity=0.432 Sum_probs=7.1 Q ss_pred CHHCCCCCCHHHHH Q ss_conf 10048887989999 Q gi|255764496|r 556 PLDEINGIGPLRKR 569 (616) Q Consensus 556 ~Ld~I~GIG~k~~~ 569 (616) .|..|+|||+++.+ T Consensus 56 eL~~I~Gvg~~k~~ 69 (89) T 1wud_A 56 EMLSVNGVGMRKLE 69 (89) T ss_dssp HHHTSTTCCHHHHH T ss_pred HHCCCCCCCHHHHH T ss_conf 98079998999999 No 168 >3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, protein structure initiative; 2.40A {Rhodospirillum rubrum atcc 11170} Probab=20.92 E-value=30 Score=12.58 Aligned_cols=40 Identities=13% Similarity=0.205 Sum_probs=23.6 Q ss_pred CCCCCEEEEECCHHHH---HHHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 5798489980985899---9999999975887787189997187 Q gi|255764496|r 461 PSWPDVVILDGGKGQL---SAAQGVLKKLNVENRITIISIAKGP 501 (616) Q Consensus 461 ~~~PDLilIDGGkgQl---n~a~~vl~~l~i~~~i~viglaK~~ 501 (616) ...|||||+|-.-+.+ ..+. .+++..-...+||+-+.-.. T Consensus 57 ~~~~dlIilD~~mP~~dG~el~~-~ir~~~~~~~iPvI~lTa~~ 99 (152) T 3heb_A 57 AGRAQLVLLDLNLPDMTGIDILK-LVKENPHTRRSPVVILTTTD 99 (152) T ss_dssp TTCBEEEEECSBCSSSBHHHHHH-HHHHSTTTTTSCEEEEESCC T ss_pred CCCCCEEEEECCCCCCCHHHHHH-HHHHCCCCCCCCEEEEECCC T ss_conf 06999899868999998899999-99848777999589997769 No 169 >2i2c_A Probable inorganic polyphosphate/ATP-NAD kinase 1; NADP bound of lmnadk1, transferase; HET: DTA PG4; 1.85A {Listeria monocytogenes egd-e} PDB: 2i1w_A* 2i2a_A* 2i2b_A* 2i29_A* 2i2d_A* 2i2e_A* 2i2f_A* 2q5f_A* Probab=20.69 E-value=30 Score=12.54 Aligned_cols=12 Identities=25% Similarity=0.205 Sum_probs=5.2 Q ss_pred HHHHHHHHHHHH Q ss_conf 888889999999 Q gi|255764496|r 216 ESAIIHRDRLAA 227 (616) Q Consensus 216 E~Aa~~RD~I~a 227 (616) |+|..++.+|.. T Consensus 11 ~~s~~i~~~i~~ 22 (272) T 2i2c_A 11 EKSDLLRLNMIA 22 (272) T ss_dssp HHHHHHHHHHHH T ss_pred HHHHHHHHHHHH T ss_conf 899999999999 No 170 >3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB} Probab=20.34 E-value=31 Score=12.49 Aligned_cols=75 Identities=12% Similarity=0.100 Sum_probs=36.3 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH---HHHHHHHHCCCCCCCCEEEEECC Q ss_conf 11689989999999977531311123333333345457984899809858999---99999997588778718999718 Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLS---AAQGVLKKLNVENRITIISIAKG 500 (616) Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln---~a~~vl~~l~i~~~i~viglaK~ 500 (616) .||-..+++++.+.+...-=+-.....+...-..-....|||||+|---+.++ .+..+-..... ..+|||-|.-. T Consensus 13 VDDd~~~~~~l~~~L~~~G~~v~~a~~~~~al~~l~~~~~DlillD~~mP~~dG~el~~~ir~~~~~-~~iPiI~lTa~ 90 (154) T 3gt7_A 13 VEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYALCRWLKGQPDL-RTIPVILLTIL 90 (154) T ss_dssp ECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHTTCCCSEEEEESCCSSSCHHHHHHHHHHSTTT-TTSCEEEEECC T ss_pred EECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHCCCC-CCCEEEEEECC T ss_conf 9799999999999999879999998999999999983899999980899999887999999858455-79959999826 No 171 >1k68_A Phytochrome response regulator RCPA; phosphorylated aspartate, CHEY homologue, homodimer, (beta/alpha)5, signaling protein; HET: PHD; 1.90A {Tolypothrix SP} SCOP: c.23.1.1 Probab=20.10 E-value=31 Score=12.46 Aligned_cols=75 Identities=13% Similarity=0.239 Sum_probs=35.4 Q ss_pred HHHHHHHHHHHHHHHHHHC---------CCCCCCCCCCCCCCCCCCCCCEEEEECCHHH---HHHHHHHHHHCCCCCCCC Q ss_conf 1689989999999977531---------3111233333333454579848998098589---999999999758877871 Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIK---------NEENLNFHPKKQEYSFPSWPDVVILDGGKGQ---LSAAQGVLKKLNVENRIT 493 (616) Q Consensus 426 DD~~~m~Evi~RR~~r~~~---------~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQ---ln~a~~vl~~l~i~~~i~ 493 (616) ||-..+++++.+-+.+.-- .++.+..-...........|||||+|-.-+. +..+..+-..-.. ..|| T Consensus 9 dDd~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~~~~~pdliilD~~mP~~dG~el~~~ir~~~~~-~~iP 87 (140) T 1k68_A 9 EDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLXLNLPKKDGREVLAEIKSDPTL-KRIP 87 (140) T ss_dssp CCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCGGGGSCCCCSEEEECSSCSSSCHHHHHHHHHHSTTG-GGSC T ss_pred ECCHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHCCCC-CCCC T ss_conf 799999999999999679981899989999999999862454404799689998899998559999999838665-8998 Q ss_pred EEEEECCC Q ss_conf 89997187 Q gi|255764496|r 494 IISIAKGP 501 (616) Q Consensus 494 viglaK~~ 501 (616) |+-+.-.. T Consensus 88 vi~ls~~~ 95 (140) T 1k68_A 88 VVVLSTSI 95 (140) T ss_dssp EEEEESCC T ss_pred EEEEECCC T ss_conf 99995789 Done!