Query gi|254780762|ref|YP_003065175.1| recombination protein RecR [Candidatus Liberibacter asiaticus str. psy62] Match_columns 201 No_of_seqs 130 out of 1674 Neff 5.3 Searched_HMMs 23785 Date Mon May 30 13:38:46 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780762.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1vdd_A Recombination protein R 100.0 0 0 529.2 15.6 194 6-201 3-196 (228) 2 1cuk_A RUVA protein; DNA repai 96.8 0.00074 3.1E-08 45.9 3.2 32 5-36 93-129 (203) 3 2ztd_A Holliday junction ATP-d 96.7 0.0009 3.8E-08 45.3 3.2 34 5-38 108-146 (212) 4 1ixr_A Holliday junction DNA h 96.6 0.00097 4.1E-08 45.1 3.0 33 5-37 92-129 (191) 5 1mw9_X DNA topoisomerase I; de 96.4 0.011 4.7E-07 38.0 7.2 64 127-200 93-156 (592) 6 2fcj_A Small toprim domain pro 93.8 0.44 1.9E-05 27.2 9.1 101 80-196 2-102 (119) 7 1lko_A Rubrerythrin all-iron(I 93.6 0.061 2.6E-06 33.0 3.9 58 23-80 112-182 (191) 8 1nnq_A Rubrerythrin; structura 93.2 0.08 3.4E-06 32.2 4.0 58 23-80 98-165 (171) 9 3fhg_A Mjogg, N-glycosylase/DN 93.1 0.055 2.3E-06 33.3 3.1 28 12-39 114-141 (207) 10 2gai_A DNA topoisomerase I; zi 92.7 0.3 1.3E-05 28.4 6.4 62 127-200 67-128 (633) 11 3i0w_A 8-oxoguanine-DNA-glycos 92.1 0.11 4.8E-06 31.2 3.7 33 10-42 206-238 (290) 12 1mpg_A ALKA, 3-methyladenine D 91.8 0.1 4.3E-06 31.5 3.1 32 9-40 201-232 (282) 13 1m3q_A 8-oxoguanine DNA glycos 91.7 0.11 4.7E-06 31.3 3.2 30 10-39 225-254 (317) 14 2abk_A Endonuclease III; DNA-r 91.6 0.15 6.1E-06 30.5 3.7 27 13-39 107-133 (211) 15 1z00_B DNA repair endonuclease 91.4 0.14 5.9E-06 30.6 3.5 47 1-47 1-56 (84) 16 3fhf_A Mjogg, N-glycosylase/DN 91.3 0.17 7.1E-06 30.1 3.8 32 8-39 24-56 (214) 17 1z00_A DNA excision repair pro 91.1 0.075 3.1E-06 32.4 1.8 30 6-35 10-39 (89) 18 1t6t_1 Putative protein; struc 91.1 0.91 3.8E-05 25.1 7.4 75 82-171 20-94 (118) 19 2jhn_A ALKA, 3-methyladenine D 90.9 0.16 6.7E-06 30.2 3.4 27 11-37 206-232 (295) 20 1orn_A Endonuclease III; DNA r 90.8 0.16 6.9E-06 30.2 3.4 25 14-38 112-136 (226) 21 2h56_A DNA-3-methyladenine gly 90.6 0.14 6.1E-06 30.5 2.9 32 9-40 132-163 (233) 22 1yuz_A Nigerythrin; rubrythrin 90.5 0.1 4.2E-06 31.6 2.0 57 23-79 133-196 (202) 23 1pu6_A 3-methyladenine DNA gly 90.4 0.1 4.4E-06 31.4 2.1 30 10-39 116-145 (218) 24 1kea_A Possible G-T mismatches 90.2 0.16 6.7E-06 30.2 2.8 22 13-34 113-134 (221) 25 1kg2_A A/G-specific adenine gl 90.1 0.22 9.3E-06 29.3 3.5 22 14-35 108-129 (225) 26 1i7d_A DNA topoisomerase III; 90.0 0.2 8.2E-06 29.6 3.2 55 137-199 93-150 (659) 27 2edu_A Kinesin-like protein KI 89.9 0.19 8.1E-06 29.7 3.1 22 14-35 39-60 (98) 28 3fsp_A A/G-specific adenine gl 89.5 0.27 1.1E-05 28.7 3.6 102 14-115 117-277 (369) 29 3n5n_X A/G-specific adenine DN 88.8 0.26 1.1E-05 28.8 3.1 22 13-34 127-148 (287) 30 2au3_A DNA primase; zinc ribbo 88.8 1.4 6.1E-05 23.8 8.5 86 82-183 244-329 (407) 31 1ryq_A DNA-directed RNA polyme 88.2 0.29 1.2E-05 28.5 3.0 41 55-95 9-51 (69) 32 2a1j_A DNA repair endonuclease 87.5 0.31 1.3E-05 28.3 2.8 33 15-47 4-42 (63) 33 2a1j_B DNA excision repair pro 87.5 0.51 2.2E-05 26.8 3.9 29 7-35 24-52 (91) 34 2fmp_A DNA polymerase beta; nu 86.5 0.35 1.5E-05 27.9 2.6 22 11-32 94-115 (335) 35 1vk6_A NADH pyrophosphatase; 1 86.1 0.15 6.3E-06 30.4 0.6 94 39-134 87-191 (269) 36 2ihm_A POL MU, DNA polymerase 86.1 0.48 2E-05 27.0 3.1 24 9-32 96-119 (360) 37 3lpe_B DNA-directed RNA polyme 85.5 0.29 1.2E-05 28.5 1.8 21 57-77 1-21 (59) 38 1nui_A DNA primase/helicase; z 85.1 1.2 4.9E-05 24.4 4.7 86 78-173 146-233 (255) 39 1x2i_A HEF helicase/nuclease; 84.9 0.68 2.9E-05 26.0 3.5 28 9-36 8-35 (75) 40 1kft_A UVRC, excinuclease ABC 84.6 0.5 2.1E-05 26.9 2.7 21 15-35 24-44 (78) 41 2w9m_A Polymerase X; SAXS, DNA 84.5 0.75 3.2E-05 25.7 3.5 19 14-32 96-114 (578) 42 1s5l_U Photosystem II 12 kDa e 84.3 0.23 9.7E-06 29.1 0.8 19 14-32 62-80 (134) 43 3bz1_U Photosystem II 12 kDa e 83.8 0.27 1.1E-05 28.7 1.0 19 14-32 32-50 (104) 44 2duy_A Competence protein come 83.5 0.5 2.1E-05 26.9 2.3 21 14-34 26-46 (75) 45 2bcq_A DNA polymerase lambda; 82.2 0.77 3.2E-05 25.6 2.8 20 13-32 94-113 (335) 46 1kft_A UVRC, excinuclease ABC 82.2 0.5 2.1E-05 26.9 1.9 22 14-35 55-76 (78) 47 2apo_B Ribosome biogenesis pro 79.5 0.4 1.7E-05 27.6 0.6 28 54-81 3-30 (60) 48 2aus_D NOP10, ribosome biogene 79.2 0.55 2.3E-05 26.6 1.2 27 54-80 2-28 (60) 49 2kp7_A Crossover junction endo 78.4 1.4 5.9E-05 23.9 3.1 23 15-37 58-80 (87) 50 2owo_A DNA ligase; protein/DNA 78.0 2.2 9.1E-05 22.6 4.0 69 15-117 544-612 (671) 51 1q57_A DNA primase/helicase; d 77.5 2.6 0.00011 22.1 4.3 85 81-173 86-170 (503) 52 3fbl_A Putative uncharacterize 77.2 1.3 5.5E-05 24.1 2.7 35 3-37 46-80 (82) 53 1ngn_A Methyl-CPG binding prot 76.5 1.7 7.2E-05 23.3 3.1 21 17-37 106-126 (155) 54 2i5h_A Hypothetical protein AF 75.6 0.91 3.8E-05 25.1 1.5 25 15-39 132-156 (205) 55 1jms_A Terminal deoxynucleotid 75.1 1.6 6.7E-05 23.5 2.7 19 13-31 119-137 (381) 56 1vq8_Y 50S ribosomal protein L 72.9 0.59 2.5E-05 26.4 0.0 21 15-35 48-68 (241) 57 2bgw_A XPF endonuclease; hydro 69.6 6.4 0.00027 19.4 6.2 56 103-164 80-135 (219) 58 2aq4_A DNA repair protein REV1 68.9 1.7 7.1E-05 23.3 1.6 24 10-33 234-259 (434) 59 1gku_B Reverse gyrase, TOP-RG; 67.6 2.3 9.8E-05 22.4 2.1 40 126-167 612-651 (1054) 60 3mfi_A DNA polymerase ETA; DNA 65.4 3.3 0.00014 21.4 2.5 30 6-35 294-327 (520) 61 3cng_A Nudix hydrolase; struct 65.3 0.5 2.1E-05 26.9 -1.7 77 56-134 2-92 (189) 62 1jyk_A LICC protein, CTP:phosp 64.7 8 0.00034 18.8 4.4 13 8-20 57-69 (254) 63 1dd9_A DNA primase, DNAG; topr 64.6 8 0.00034 18.8 8.2 92 77-184 158-252 (338) 64 2ziu_A MUS81 protein; helix-ha 63.6 4.5 0.00019 20.5 2.9 15 149-163 161-175 (311) 65 1d8b_A SGS1 RECQ helicase; fiv 63.1 2.3 9.8E-05 22.4 1.4 21 14-34 47-67 (81) 66 2nrt_A Uvrabc system protein C 61.6 6.5 0.00027 19.4 3.5 15 17-31 170-184 (220) 67 1t94_A Polymerase (DNA directe 61.6 3 0.00012 21.7 1.7 20 16-35 283-302 (459) 68 1vk2_A Uracil-DNA glycosylase 59.9 5 0.00021 20.2 2.6 45 46-92 16-61 (204) 69 3osn_A DNA polymerase IOTA; ho 59.4 7.3 0.00031 19.1 3.4 38 6-43 222-269 (420) 70 1rxw_A Flap structure-specific 57.5 4 0.00017 20.8 1.8 10 114-123 237-246 (336) 71 3bqs_A Uncharacterized protein 56.4 4.2 0.00018 20.7 1.8 28 16-43 5-32 (93) 72 1a5t_A Delta prime, HOLB; zinc 55.9 11 0.00047 17.8 5.8 118 8-144 9-142 (334) 73 1jx4_A DNA polymerase IV (fami 55.2 4.5 0.00019 20.5 1.8 36 7-42 168-212 (352) 74 1wud_A ATP-dependent DNA helic 55.1 9.2 0.00039 18.4 3.3 24 14-37 54-77 (89) 75 2i1q_A DNA repair and recombin 54.9 6.9 0.00029 19.2 2.7 32 15-46 3-41 (322) 76 1exn_A 5'-exonuclease, 5'-nucl 54.9 4.4 0.00018 20.6 1.7 15 83-97 144-158 (290) 77 2rhf_A DNA helicase RECQ; HRDC 54.9 8.4 0.00035 18.6 3.1 24 14-37 46-69 (77) 78 2exu_A Transcription initiatio 54.4 2.7 0.00011 22.0 0.5 88 56-150 3-111 (200) 79 3bq0_A POL IV, DBH, DNA polyme 54.3 3.4 0.00015 21.2 1.0 38 7-44 169-215 (354) 80 1gm5_A RECG; helicase, replica 54.3 3.3 0.00014 21.4 0.9 18 16-33 116-133 (780) 81 2izo_A FEN1, flap structure-sp 53.4 5.2 0.00022 20.1 1.8 33 107-143 226-261 (346) 82 3maj_A DNA processing chain A; 51.6 9 0.00038 18.4 2.8 46 142-196 132-178 (382) 83 1ui0_A Uracil-DNA glycosylase; 51.2 9.9 0.00042 18.2 3.0 54 49-104 2-55 (205) 84 1dgs_A DNA ligase; AMP complex 49.5 14 0.0006 17.1 5.0 62 15-115 539-600 (667) 85 2zj8_A DNA helicase, putative 48.5 10 0.00042 18.1 2.7 23 127-152 159-181 (720) 86 1a76_A Flap endonuclease-1 pro 48.4 6.8 0.00029 19.2 1.8 17 108-124 218-237 (326) 87 3nkl_A UDP-D-quinovosamine 4-d 48.3 12 0.00052 17.5 3.1 46 127-174 54-99 (141) 88 2rrd_A BLM HRDC domain, HRDC d 47.6 11 0.00045 18.0 2.7 25 14-38 63-87 (101) 89 3c65_A Uvrabc system protein C 45.6 3.6 0.00015 21.1 0.0 23 110-134 171-193 (226) 90 1ul1_X Flap endonuclease-1; pr 45.3 8.2 0.00035 18.7 1.8 13 19-31 236-248 (379) 91 3gqc_A DNA repair protein REV1 45.3 8.1 0.00034 18.8 1.8 37 7-43 305-350 (504) 92 3mr3_A DNA polymerase ETA; POL 44.4 8.7 0.00037 18.5 1.8 41 7-47 243-294 (435) 93 1jr3_A DNA polymerase III subu 42.5 18 0.00076 16.4 5.4 79 88-170 101-198 (373) 94 1am7_A Lysozyme; glycosidase, 41.2 19 0.00079 16.3 4.2 36 4-40 68-103 (158) 95 2gmg_A Hypothetical protein PF 40.9 9.9 0.00042 18.2 1.7 28 58-85 68-100 (105) 96 2zkq_m 40S ribosomal protein S 40.2 20 0.00082 16.2 4.8 90 12-111 25-128 (152) 97 1pzn_A RAD51, DNA repair and r 39.2 4.5 0.00019 20.5 -0.3 38 9-46 29-73 (349) 98 1iv0_A Hypothetical protein; r 37.6 18 0.00078 16.3 2.6 58 113-171 24-89 (98) 99 3k4g_A DNA-directed RNA polyme 36.6 22 0.00093 15.8 3.0 23 15-37 44-66 (86) 100 1ci4_A Protein (barrier-TO-aut 35.6 16 0.00066 16.8 2.0 31 17-47 20-63 (89) 101 1z3e_B DNA-directed RNA polyme 35.1 23 0.00098 15.7 3.4 29 9-37 31-63 (73) 102 1b22_A DNA repair protein RAD5 35.0 20 0.00083 16.2 2.4 12 21-32 31-42 (114) 103 2p6r_A Afuhel308 helicase; pro 34.2 18 0.00076 16.4 2.1 27 127-153 159-185 (702) 104 1xi4_A Clathrin heavy chain; a 34.1 9.8 0.00041 18.2 0.8 68 92-162 697-766 (1630) 105 1xpj_A Hypothetical protein; s 31.9 26 0.0011 15.3 4.6 62 127-190 30-101 (126) 106 3gfk_B DNA-directed RNA polyme 31.8 24 0.001 15.5 2.5 23 15-37 48-70 (79) 107 1bgx_T TAQ DNA polymerase; DNA 31.4 4.9 0.00021 20.2 -1.1 14 19-32 195-208 (832) 108 3io1_A Aminobenzoyl-glutamate 31.0 27 0.0011 15.2 3.5 28 135-162 169-196 (445) 109 2gnr_A Conserved hypothetical 30.4 11 0.00047 17.8 0.6 40 40-79 30-71 (145) 110 2va8_A SSO2462, SKI2-type heli 30.0 23 0.00098 15.7 2.1 21 127-151 166-186 (715) 111 1q8b_A Protein YJCS; structura 29.7 21 0.00087 16.0 1.8 54 40-100 25-78 (105) 112 2e18_A NH(3)-dependent NAD(+) 29.6 29 0.0012 15.1 5.2 19 106-124 142-160 (257) 113 3bbn_M Ribosomal protein S13; 29.4 3.1 0.00013 21.6 -2.5 69 13-111 60-128 (145) 114 1mc3_A Glucose-1-phosphate thy 29.3 29 0.0012 15.0 5.8 49 151-200 197-248 (296) 115 2kn9_A Rubredoxin; metalloprot 27.5 19 0.00081 16.2 1.4 27 57-83 27-74 (81) 116 1k8r_B Protein kinase BYR2; si 26.7 15 0.00063 16.9 0.7 28 61-88 48-76 (110) 117 1coo_A RNA polymerase alpha su 24.9 35 0.0015 14.5 3.2 24 15-38 56-79 (98) 118 6rxn_A Rubredoxin; electron tr 24.8 21 0.00088 16.0 1.1 23 59-81 6-42 (46) 119 2e1f_A Werner syndrome ATP-dep 24.4 35 0.0015 14.5 2.4 20 14-33 56-75 (103) 120 1l8d_A DNA double-strand break 24.0 36 0.0015 14.4 2.3 27 40-66 30-56 (112) 121 4rxn_A Rubredoxin; electron tr 23.7 21 0.00087 16.0 0.9 25 58-82 4-49 (54) 122 2avu_E Flagellar transcription 22.6 25 0.0011 15.5 1.2 41 43-83 120-168 (192) 123 2vje_A E3 ubiquitin-protein li 22.0 33 0.0014 14.6 1.7 18 66-83 5-22 (64) 124 3eln_A Cysteine dioxygenase ty 21.9 6.3 0.00027 19.5 -2.0 94 4-116 6-104 (200) 125 2vqe_M 30S ribosomal protein S 21.4 40 0.0017 14.1 2.2 75 12-112 14-96 (126) 126 2v3b_B Rubredoxin 2, rubredoxi 21.2 23 0.00097 15.7 0.8 24 59-82 5-49 (55) 127 2zix_A Crossover junction endo 20.4 6.5 0.00027 19.4 -2.2 11 152-162 161-171 (307) No 1 >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=100.00 E-value=0 Score=529.17 Aligned_cols=194 Identities=37% Similarity=0.685 Sum_probs=190.2 Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEE Q ss_conf 86679999999975689995379999999971998999999999999998518288999733456541003555567369 Q gi|254780762|r 6 TGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVI 85 (201) Q Consensus 6 ~~~~l~~LI~~l~kLPGIG~KsA~R~a~~Ll~~~~~~~~~l~~~l~~~~~~i~~C~~C~~l~~~~~C~iC~d~~Rd~~~l 85 (201) +|++|++||++|++|||||||||+|||||||+++++.+++|+++|.+++++|++|+.||+++++++|+||+|++||+++| T Consensus 3 ~p~~ie~LI~~l~kLPGIG~KsA~RlA~~LL~~~~~~~~~La~~i~~~k~~i~~C~~C~~lse~~~C~IC~D~~Rd~~~i 82 (228) T 1vdd_A 3 YPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTI 82 (228) T ss_dssp CCHHHHHHHHHHHTSTTCCHHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHCEECSSSCCEESSSSCHHHHCSSSCTTEE T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEE T ss_conf 95999999999966899988999999999981999999999999999998188386788716777766435777765458 Q ss_pred EEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCC Q ss_conf 99835889999975174013421012100200026811128899999851578554999946997868999999998201 Q gi|254780762|r 86 IVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKG 165 (201) Q Consensus 86 CVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~lk~ 165 (201) ||||++.|+++||+||.|+|+||||||+|||++|++|++|++++|++|+++ ++|||||||||+|||+||+||++.|++ T Consensus 83 CVVE~~~Dl~aIE~tg~y~G~YhVLgG~iSpldgigp~~l~i~~L~~Ri~~--~~EVIlA~~~t~EGe~Ta~yi~~~Lk~ 160 (228) T 1vdd_A 83 CVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQ--GMEVILATGTTVEGDATALYLQRLLEP 160 (228) T ss_dssp EEESSHHHHHHTTTTSSCCSEEEECSSCCBGGGTBCTTTSTTGGGGGGCCT--TCEEEECCCSSHHHHHHHHHHHHHHTT T ss_pred EEECCHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHCC--CCEEEEEECCCCCHHHHHHHHHHHHHH T ss_conf 997789999999860811269986687637234899410036999998635--867999817985518999999998544 Q ss_pred CCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 798088741467488206663479999998306479 Q gi|254780762|r 166 IDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRTVL 201 (201) Q Consensus 166 ~~ikitrla~GiP~G~~ley~D~~TL~~Al~~R~~l 201 (201) +++||||||+|||+||+|||+|+.||++||++|++| T Consensus 161 ~~ikiTRLA~GlP~G~~LeY~D~~TL~~Al~~R~~i 196 (228) T 1vdd_A 161 LGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTV 196 (228) T ss_dssp SSCEEEECCBCBCTTCCGGGSCHHHHHHHHHTCEEE T ss_pred CCCEEEEECCCCCCCCCHHHCCHHHHHHHHHCCCCC T ss_conf 497087610068778420016899999999808325 No 2 >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=96.76 E-value=0.00074 Score=45.91 Aligned_cols=32 Identities=22% Similarity=0.569 Sum_probs=23.5 Q ss_pred CCCHHHHHH-----HHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 686679999-----99997568999537999999997 Q gi|254780762|r 5 ITGKEIENL-----IKILARIPGFGPRSARRATLHLV 36 (201) Q Consensus 5 ~~~~~l~~L-----I~~l~kLPGIG~KsA~R~a~~Ll 36 (201) +.+..+-+. +..|+++||||+|+|+|+++.|- T Consensus 93 ~~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIilELk 129 (203) T 1cuk_A 93 MSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMK 129 (203) T ss_dssp SCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHH T ss_pred CCHHHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHH T ss_conf 7989999998718998860699877999999999999 No 3 >2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Probab=96.69 E-value=0.0009 Score=45.33 Aligned_cols=34 Identities=32% Similarity=0.595 Sum_probs=25.7 Q ss_pred CCCHHHHHHH-----HHHHHCCCCCHHHHHHHHHHHHHC Q ss_conf 6866799999-----999756899953799999999719 Q gi|254780762|r 5 ITGKEIENLI-----KILARIPGFGPRSARRATLHLVKK 38 (201) Q Consensus 5 ~~~~~l~~LI-----~~l~kLPGIG~KsA~R~a~~Ll~~ 38 (201) +.+..|-+.| ..|+++||||+|+|+||++-|=.. T Consensus 108 ~~~~~l~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdK 146 (212) T 2ztd_A 108 HDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDK 146 (212) T ss_dssp SCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHTTT T ss_pred CCHHHHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 999999999980899998517782488899999999754 No 4 >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=96.62 E-value=0.00097 Score=45.11 Aligned_cols=33 Identities=24% Similarity=0.438 Sum_probs=25.0 Q ss_pred CCCHHHHHHH-----HHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 6866799999-----99975689995379999999971 Q gi|254780762|r 5 ITGKEIENLI-----KILARIPGFGPRSARRATLHLVK 37 (201) Q Consensus 5 ~~~~~l~~LI-----~~l~kLPGIG~KsA~R~a~~Ll~ 37 (201) +.++.|-+.| ..|+++||||+|+|+|+.+-|=. T Consensus 92 ~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~ 129 (191) T 1ixr_A 92 LPPRLLARALLEGDARLLTSASGVGRRLAERIALELKG 129 (191) T ss_dssp SCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHTT T ss_pred CCHHHHHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 99999999998399999501888468899999999986 No 5 >1mw9_X DNA topoisomerase I; decatenase enzyme, toprim domain; HET: DNA; 1.67A {Escherichia coli} SCOP: e.10.1.1 PDB: 1mw8_X* 1cy1_A* 1cy0_A* 1cy2_A* 1cy4_A* 1cy6_A* 1cy7_A* 1cy8_A* 1ecl_A 1cy9_A* 1cyy_A* Probab=96.39 E-value=0.011 Score=38.00 Aligned_cols=64 Identities=17% Similarity=0.286 Sum_probs=47.4 Q ss_pred HHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCC Q ss_conf 89999985157855499994699786899999999820179808874146748820666347999999830647 Q gi|254780762|r 127 IQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRTV 200 (201) Q Consensus 127 i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~lk~~~ikitrla~GiP~G~~ley~D~~TL~~Al~~R~~ 200 (201) +..|.+-+ ...++||+||.|.-|||.-+..|.+.++..+.++.|+-+ .-++...+.+||++... T Consensus 93 ~~~i~~l~--~~ad~Ii~AtD~DrEGE~I~~~I~~~~~~~~~~~~R~~~--------~~~t~~~I~~A~~n~~~ 156 (592) T 1mw9_X 93 VSELKQLA--EKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVF--------NEITKNAIRQAFNKPGE 156 (592) T ss_dssp HHHHHHHH--HTCSEEEECCCSSHHHHHHHHHHHHHHCSCGGGEEECCC--------SSCSHHHHHHHHHSCBC T ss_pred HHHHHHHH--HCCCEEEECCCCCCCHHHHHHHHHHHHCCCCCCEEEEEE--------CCCCHHHHHHHHHCCCC T ss_conf 99999998--379989989889704109999999984689986699995--------66899999999737774 No 6 >2fcj_A Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A* Probab=93.77 E-value=0.44 Score=27.25 Aligned_cols=101 Identities=10% Similarity=0.053 Sum_probs=65.4 Q ss_pred CCCCEEEEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHH Q ss_conf 56736999835889999975174013421012100200026811128899999851578554999946997868999999 Q gi|254780762|r 80 RDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYI 159 (201) Q Consensus 80 Rd~~~lCVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi 159 (201) |....+-|||-..|++++-+.|.- ...-+.+|- -...+ .++.|.+. ...++|||++.+.-.|+..+.-| T Consensus 2 kk~~~vIIVEG~~D~~al~q~g~~-~v~~~~~~~------~~~~~-~~~~l~~~---~~~~~Iil~~D~D~aG~k~~~~l 70 (119) T 2fcj_A 2 RRVEKVIIVEGRSDKQKVAAVLNE-PVVIVCTNG------TISDA-RLEELADE---LEGYDVYLLADADEAGEKLRRQF 70 (119) T ss_dssp CCCCEEEEESSHHHHHHHHHHBSS-CCEEEECCS------CCCHH-HHHHHHHH---TTTSEEEEECCSSHHHHHHHHHH T ss_pred CCCCEEEEEECHHHHHHHHHHCCC-CEEEECCCC------CCCHH-HHHHHHHH---HCCCEEEEECCCCHHHHHHHHHH T ss_conf 848979999488899999982798-729952786------47899-99999997---27986999738977999999999 Q ss_pred HHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHH Q ss_conf 9982017980887414674882066634799999983 Q gi|254780762|r 160 MDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIR 196 (201) Q Consensus 160 ~~~lk~~~ikitrla~GiP~G~~ley~D~~TL~~Al~ 196 (201) .+.|.+ .+-..++++. .++|-+....+.++++ T Consensus 71 ~~~L~~--a~~~~i~~~~---~~v~~~p~~~~~~~l~ 102 (119) T 2fcj_A 71 RRMFPE--AEHLYIDRAY---REVAAAPIWHLAQVLL 102 (119) T ss_dssp HHHCTT--SEEECCCTTT---CSTTTSCHHHHHHHHH T ss_pred HHHCCC--CCEEEECCCC---CCHHHCCHHHHHHHHH T ss_conf 986775--6389866776---3431199899999999 No 7 >1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix bundle, rubredoxin-like, electron transport; 1.63A {Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB: 1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A 1ryt_A Probab=93.56 E-value=0.061 Score=33.02 Aligned_cols=58 Identities=19% Similarity=0.276 Sum_probs=47.3 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH---------CCCCCCCCCCCCC----CCCCCCCCCCC Q ss_conf 9953799999999719989999999999999985---------1828899973345----65410035555 Q gi|254780762|r 23 FGPRSARRATLHLVKKKEQLLGPLAEAMANIYNK---------VCLCSICGNVDTT----DPCAICIDQQR 80 (201) Q Consensus 23 IG~KsA~R~a~~Ll~~~~~~~~~l~~~l~~~~~~---------i~~C~~C~~l~~~----~~C~iC~d~~R 80 (201) .|-+.+.++--+++...+.-...|...+..+.+. .-.|.+||++.+. +.|++|..+.- T Consensus 112 eGd~~~a~~f~~i~~~E~~H~~~f~~~l~~le~~~~~~~~~~~~~~C~~CG~i~~g~~~p~~CP~C~~~~~ 182 (191) T 1lko_A 112 EGYEEIARVFASIAVAEEFHEKRFLDFARNIKEGRVFLREQATKWRCRNCGYVHEGTGAPELCPACAHPKA 182 (191) T ss_dssp HTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSEEEEEEEEEETTTCCEEEEEECCSBCTTTCCBGG T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCHH T ss_conf 78999999999999999999999999999887688645578845789999860128999885979999659 No 8 >1nnq_A Rubrerythrin; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics, secsg; 2.35A {Pyrococcus furiosus} SCOP: a.25.1.1 g.41.5.1 PDB: 2hr5_A Probab=93.15 E-value=0.08 Score=32.24 Aligned_cols=58 Identities=21% Similarity=0.379 Sum_probs=47.2 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH-------CCCCCCCCCCCCC---CCCCCCCCCCC Q ss_conf 9953799999999719989999999999999985-------1828899973345---65410035555 Q gi|254780762|r 23 FGPRSARRATLHLVKKKEQLLGPLAEAMANIYNK-------VCLCSICGNVDTT---DPCAICIDQQR 80 (201) Q Consensus 23 IG~KsA~R~a~~Ll~~~~~~~~~l~~~l~~~~~~-------i~~C~~C~~l~~~---~~C~iC~d~~R 80 (201) .|-+.+.++.-+++...+.-...|-.++.++... +-.|++||++.+. +.||+|..|.- T Consensus 98 eG~~~~a~~f~~i~~~E~~H~~~~~~~l~~l~~~~~~~~~~~~vC~~CG~i~~g~~P~~CPvC~~p~~ 165 (171) T 1nnq_A 98 QGEKEAVRTTHYALEAEKIHAELYRKAKEKAEKGEDIEIKKVYICPICGYTAVDEAPEYCPVCGAPKE 165 (171) T ss_dssp TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCSCEEECTTTCCEEESCCCSBCTTTCCBGG T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCHH T ss_conf 68799999999999999999999999998755124567787358998939389999997979999676 No 9 >3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} Probab=93.08 E-value=0.055 Score=33.31 Aligned_cols=28 Identities=18% Similarity=0.050 Sum_probs=16.2 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHCC Q ss_conf 9999997568999537999999997199 Q gi|254780762|r 12 NLIKILARIPGFGPRSARRATLHLVKKK 39 (201) Q Consensus 12 ~LI~~l~kLPGIG~KsA~R~a~~Ll~~~ 39 (201) +..+.|.++||||+|||.=+..+....+ T Consensus 114 e~~~~L~~l~GIG~ktA~~~L~~~~~~~ 141 (207) T 3fhg_A 114 LARERLLNIKGIGMQEASHFLRNVGYFD 141 (207) T ss_dssp HHHHHHTTSTTCCHHHHHHHHHHTTCCS T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHCCCC T ss_conf 9999999878872999999999976887 No 10 >2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga maritima MSB8} PDB: 2gaj_A* Probab=92.69 E-value=0.3 Score=28.38 Aligned_cols=62 Identities=19% Similarity=0.224 Sum_probs=44.1 Q ss_pred HHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCC Q ss_conf 89999985157855499994699786899999999820179808874146748820666347999999830647 Q gi|254780762|r 127 IQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRTV 200 (201) Q Consensus 127 i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~lk~~~ikitrla~GiP~G~~ley~D~~TL~~Al~~R~~ 200 (201) ++.|.+.++. .|||+|+.|.-|||.-+..|.+.++. ..++.|+=+ .-++...+.+||.|.+. T Consensus 67 ~~~lk~l~k~---~~iiiAtD~DREGE~I~~~i~~~~~~-~~~v~R~~~--------s~lt~~~I~~A~~n~~~ 128 (633) T 2gai_A 67 VEKLKDLAKK---GELLIASDMDREGEAIAWHIARVTNT-LGRKNRIVF--------SEITPRVIREAVKNPRE 128 (633) T ss_dssp HHHHHHHHHH---SCEEECCCSSHHHHHHHHHHHHHHTC-TTSSCBCCC--------SSCCHHHHHHHHHSCBC T ss_pred HHHHHHHHCC---CCEEECCCCCCCHHHHHHHHHHHHCC-CCCCEEEEE--------CCCCHHHHHHHHHCCCC T ss_conf 9999998559---97999589983465999999998589-898168998--------13899999999858732 No 11 >3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A Probab=92.13 E-value=0.11 Score=31.18 Aligned_cols=33 Identities=21% Similarity=0.260 Sum_probs=24.7 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHCCHHH Q ss_conf 999999997568999537999999997199899 Q gi|254780762|r 10 IENLIKILARIPGFGPRSARRATLHLVKKKEQL 42 (201) Q Consensus 10 l~~LI~~l~kLPGIG~KsA~R~a~~Ll~~~~~~ 42 (201) .+++.+.|.+|||||||+|+=++++-+....-. T Consensus 206 ~~e~~~~L~~i~GIG~wtAd~ilLf~lg~~d~f 238 (290) T 3i0w_A 206 DNECHEELKKFMGVGPQVADCIMLFSMQKYSAF 238 (290) T ss_dssp HHHHHHHHTTSTTCCHHHHHHHHHHHHCCTTCC T ss_pred CHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCEE T ss_conf 067999998679948899999999967999967 No 12 >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=91.83 E-value=0.1 Score=31.53 Aligned_cols=32 Identities=28% Similarity=0.451 Sum_probs=27.4 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCH Q ss_conf 79999999975689995379999999971998 Q gi|254780762|r 9 EIENLIKILARIPGFGPRSARRATLHLVKKKE 40 (201) Q Consensus 9 ~l~~LI~~l~kLPGIG~KsA~R~a~~Ll~~~~ 40 (201) ..+++++.|.++|||||+||+-++++-+..+. T Consensus 201 ~~ee~~~~L~~l~GIGpWTA~~vll~~lg~~D 232 (282) T 1mpg_A 201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKD 232 (282) T ss_dssp CHHHHHHHHTTSTTCCHHHHHHHHHHHSCCSS T ss_pred CHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCC T ss_conf 88999999997679886999999999769988 No 13 >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=91.71 E-value=0.11 Score=31.29 Aligned_cols=30 Identities=30% Similarity=0.394 Sum_probs=17.9 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHCC Q ss_conf 999999997568999537999999997199 Q gi|254780762|r 10 IENLIKILARIPGFGPRSARRATLHLVKKK 39 (201) Q Consensus 10 l~~LI~~l~kLPGIG~KsA~R~a~~Ll~~~ 39 (201) .+++.+.|.+|||||||+|.=+.++=+... T Consensus 225 ~~e~~~~L~~l~GIG~wtAd~ilLf~lg~~ 254 (317) T 1m3q_A 225 YEEAHKALCILPGVGTKVADCICLMALDKP 254 (317) T ss_dssp HHHHHHHHTTSTTCCHHHHHHHHHHHSCCT T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHCCCC T ss_conf 799999998548948899999999857999 No 14 >2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Probab=91.55 E-value=0.15 Score=30.50 Aligned_cols=27 Identities=19% Similarity=0.159 Sum_probs=20.8 Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHCC Q ss_conf 999997568999537999999997199 Q gi|254780762|r 13 LIKILARIPGFGPRSARRATLHLVKKK 39 (201) Q Consensus 13 LI~~l~kLPGIG~KsA~R~a~~Ll~~~ 39 (201) ..+.|.+|||||+|||.-+..+-.+.+ T Consensus 107 ~~~~L~~LpGVG~kTA~~il~~a~~~~ 133 (211) T 2abk_A 107 DRAALEALPGVGRKTANVVLNTAFGWP 133 (211) T ss_dssp CHHHHHHSTTCCHHHHHHHHHHHHCCC T ss_pred CHHHHHHCCCCCHHHHHHHHHHHHCCC T ss_conf 299987178873699999999873588 No 15 >1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Probab=91.45 E-value=0.14 Score=30.60 Aligned_cols=47 Identities=17% Similarity=0.279 Sum_probs=31.8 Q ss_pred CCCCCCCHH---HHHHHHHHHHCCCCCHHHHHHHHHH------HHHCCHHHHHHHH Q ss_conf 986668667---9999999975689995379999999------9719989999999 Q gi|254780762|r 1 MQKKITGKE---IENLIKILARIPGFGPRSARRATLH------LVKKKEQLLGPLA 47 (201) Q Consensus 1 M~~~~~~~~---l~~LI~~l~kLPGIG~KsA~R~a~~------Ll~~~~~~~~~l~ 47 (201) |.+...++. =....+.|.++||||+|.++++.-+ |.+.+.+++..+. T Consensus 1 ~~~~~~~e~~~~n~~~~~~L~~iPGIg~k~~~~Ll~~f~sl~~i~~AS~eeL~~v~ 56 (84) T 1z00_B 1 MDSETLPESEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSIL 56 (84) T ss_dssp CCSCCCGGGGTSCHHHHHHHHTCSSCCHHHHHHHHHHSSCHHHHHHSCHHHHHHHH T ss_pred CCCCCCHHHHHHCCHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHCC T ss_conf 97430018888321199999838999999999999996699999859999998875 No 16 >3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} PDB: 3knt_A* Probab=91.30 E-value=0.17 Score=30.07 Aligned_cols=32 Identities=6% Similarity=0.091 Sum_probs=19.2 Q ss_pred HHHHHHHHHHHHCCCCCHHHH-HHHHHHHHHCC Q ss_conf 679999999975689995379-99999997199 Q gi|254780762|r 8 KEIENLIKILARIPGFGPRSA-RRATLHLVKKK 39 (201) Q Consensus 8 ~~l~~LI~~l~kLPGIG~KsA-~R~a~~Ll~~~ 39 (201) +.++++++.|..++--+.+.. +-+++.+|.+. T Consensus 24 ~~i~~~~~~f~~~~~~~~~~~F~~Lv~~ILsqq 56 (214) T 3fhf_A 24 DIIDKRIQEFKSFKNKSNEEWFKELCFCILTAN 56 (214) T ss_dssp HHHHHHHHHHHGGGGSCHHHHHHHHHHHHHHTT T ss_pred HHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCC T ss_conf 999999998515677654888999999997365 No 17 >1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Probab=91.11 E-value=0.075 Score=32.44 Aligned_cols=30 Identities=3% Similarity=0.093 Sum_probs=26.5 Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 866799999999756899953799999999 Q gi|254780762|r 6 TGKEIENLIKILARIPGFGPRSARRATLHL 35 (201) Q Consensus 6 ~~~~l~~LI~~l~kLPGIG~KsA~R~a~~L 35 (201) ....+++++..|..+||||+++|++++-+. T Consensus 10 ~~~~~~~~~~~L~~I~gIG~~~a~~L~~~F 39 (89) T 1z00_A 10 EQDFVSRVTECLTTVKSVNKTDSQTLLTTF 39 (89) T ss_dssp HHHHHHHHHHHHTTSSSCCHHHHHHHHHHT T ss_pred HCCHHHHHHHHHCCCCCCCHHHHHHHHHHH T ss_conf 367499999987589975999999999994 No 18 >1t6t_1 Putative protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 1.80A {Aquifex aeolicus VF5} SCOP: c.136.1.1 Probab=91.11 E-value=0.91 Score=25.14 Aligned_cols=75 Identities=16% Similarity=0.285 Sum_probs=55.5 Q ss_pred CCEEEEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHH Q ss_conf 73699983588999997517401342101210020002681112889999985157855499994699786899999999 Q gi|254780762|r 82 ASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMD 161 (201) Q Consensus 82 ~~~lCVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~ 161 (201) .+.+.|||-..|+.+.-+.| |++.--+.|..++ ...+.+. ...++|||++.+.--|+.-+.=+.+ T Consensus 20 ~~~viiVEG~~D~~aL~~~G-i~n~va~~Gt~~~-------------~~~~~l~-~~~~~Vil~~D~D~aG~~~~~k~~~ 84 (118) T 1t6t_1 20 REAVILVEGKNDKKALSKFS-IKNVIDLSGKRYA-------------DVVDMLE-GKWEKVILLFDLDTHGERINQKMKE 84 (118) T ss_dssp TTSEEEESSHHHHHHHHTTT-CCCEEECTTSCHH-------------HHHHHHT-TTCSEEEECCCSSHHHHHHHHHHHH T ss_pred CCCEEEECCHHHHHHHHHCC-CCHHHHCCCCCHH-------------HHHHHHH-HCCCEEEEEECCCHHHHHHHHHHHH T ss_conf 99789973899999999816-5232301686559-------------9999998-6489389986788889999999999 Q ss_pred HHCCCCCEEE Q ss_conf 8201798088 Q gi|254780762|r 162 KLKGIDVKIT 171 (201) Q Consensus 162 ~lk~~~ikit 171 (201) .|...++++. T Consensus 85 ~L~~~g~~v~ 94 (118) T 1t6t_1 85 LLSSQGFLVD 94 (118) T ss_dssp HHHHTTCEEE T ss_pred HHHHCCCCCC T ss_conf 9998779137 No 19 >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=90.92 E-value=0.16 Score=30.25 Aligned_cols=27 Identities=19% Similarity=0.196 Sum_probs=13.6 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 999999975689995379999999971 Q gi|254780762|r 11 ENLIKILARIPGFGPRSARRATLHLVK 37 (201) Q Consensus 11 ~~LI~~l~kLPGIG~KsA~R~a~~Ll~ 37 (201) +++++.|.++|||||+||+=++++-+. T Consensus 206 ~e~~~~L~~i~GIGpWTA~~ill~~lg 232 (295) T 2jhn_A 206 EEAYEYLTSFKGIGRWTAELVLSIALG 232 (295) T ss_dssp HHHHHHHHTSTTCCHHHHHHHHHHTTC T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHCC T ss_conf 888889984599488999999998169 No 20 >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=90.82 E-value=0.16 Score=30.15 Aligned_cols=25 Identities=20% Similarity=0.284 Sum_probs=19.1 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHC Q ss_conf 9999756899953799999999719 Q gi|254780762|r 14 IKILARIPGFGPRSARRATLHLVKK 38 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a~~Ll~~ 38 (201) .+.|.+|||||++||.=+..+-... T Consensus 112 ~~~L~~LpGVG~kTA~~il~~a~~~ 136 (226) T 1orn_A 112 RDELMKLPGVGRKTANVVVSVAFGV 136 (226) T ss_dssp HHHHTTSTTCCHHHHHHHHHHHHCC T ss_pred HHHHHHCCCCCHHHHHHHHHHHHCC T ss_conf 9999748775367999999998168 No 21 >2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} Probab=90.61 E-value=0.14 Score=30.50 Aligned_cols=32 Identities=22% Similarity=0.337 Sum_probs=27.3 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCH Q ss_conf 79999999975689995379999999971998 Q gi|254780762|r 9 EIENLIKILARIPGFGPRSARRATLHLVKKKE 40 (201) Q Consensus 9 ~l~~LI~~l~kLPGIG~KsA~R~a~~Ll~~~~ 40 (201) +.+++++.|.++|||||+||+=+.+|-+..+. T Consensus 132 ~~~e~~~~L~~ikGIGpWTA~~illf~lgr~D 163 (233) T 2h56_A 132 EATTVIEKLTAIKGIGQWTAEMFMMFSLGRLD 163 (233) T ss_dssp CHHHHHHHHHTSTTCCHHHHHHHHHHTTCCSC T ss_pred CHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCC T ss_conf 88899999880688487899999999689997 No 22 >1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIRON center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_A Probab=90.50 E-value=0.1 Score=31.58 Aligned_cols=57 Identities=23% Similarity=0.401 Sum_probs=39.8 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH----HHCCCCCCCCCCCCC---CCCCCCCCCC Q ss_conf 99537999999997199899999999999999----851828899973345---6541003555 Q gi|254780762|r 23 FGPRSARRATLHLVKKKEQLLGPLAEAMANIY----NKVCLCSICGNVDTT---DPCAICIDQQ 79 (201) Q Consensus 23 IG~KsA~R~a~~Ll~~~~~~~~~l~~~l~~~~----~~i~~C~~C~~l~~~---~~C~iC~d~~ 79 (201) .|-+.+.++.-.++...+.-.+.|..++.+++ ..+-.|..||++.+. +.|++|.-+. T Consensus 133 eGd~~~a~~f~~i~~~E~~H~~~f~~~le~l~~~~~~~~~~C~~CG~i~~g~~p~~CP~C~~~~ 196 (202) T 1yuz_A 133 EGNSKAVHVFTRAKLAESVHAERYLAAYNDIDAPDDDKFHLCPICGYIHKGEDFEKCPICFRPK 196 (202) T ss_dssp HTCHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCSCCEEECSSSCCEEESSCCSBCTTTCCBG T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCEECCCCCCCCCCCCCCH T ss_conf 6989999999999999999999999999987377888067889999852499899899999874 No 23 >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=90.41 E-value=0.1 Score=31.45 Aligned_cols=30 Identities=23% Similarity=0.112 Sum_probs=17.7 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHCC Q ss_conf 999999997568999537999999997199 Q gi|254780762|r 10 IENLIKILARIPGFGPRSARRATLHLVKKK 39 (201) Q Consensus 10 l~~LI~~l~kLPGIG~KsA~R~a~~Ll~~~ 39 (201) .++..+.|.+|||||+|||.=+..+-+..+ T Consensus 116 ~~~~~~~L~~lpGIG~kTA~~il~~~~~~~ 145 (218) T 1pu6_A 116 QEVTREWLLDQKGIGKESADAILCYACAKE 145 (218) T ss_dssp HHCCHHHHHTSTTCCHHHHHHHHHHTTCCS T ss_pred CHHHHHHHHCCCCCCHHHHHHHHHHHCCCC T ss_conf 467999998489966999999999987998 No 24 >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=90.16 E-value=0.16 Score=30.21 Aligned_cols=22 Identities=18% Similarity=0.252 Sum_probs=16.6 Q ss_pred HHHHHHHCCCCCHHHHHHHHHH Q ss_conf 9999975689995379999999 Q gi|254780762|r 13 LIKILARIPGFGPRSARRATLH 34 (201) Q Consensus 13 LI~~l~kLPGIG~KsA~R~a~~ 34 (201) ..+.|.+|||||+|||.=+..+ T Consensus 113 ~~~eL~~LPGVG~ktA~~vl~~ 134 (221) T 1kea_A 113 NRKAILDLPGVGKYTCAAVMCL 134 (221) T ss_dssp CHHHHHTSTTCCHHHHHHHHHH T ss_pred HHHHHHCCCCCCHHHHHHHHHH T ss_conf 2888744898765679999998 No 25 >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=90.12 E-value=0.22 Score=29.28 Aligned_cols=22 Identities=23% Similarity=0.302 Sum_probs=16.6 Q ss_pred HHHHHHCCCCCHHHHHHHHHHH Q ss_conf 9999756899953799999999 Q gi|254780762|r 14 IKILARIPGFGPRSARRATLHL 35 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a~~L 35 (201) .+.|.+|||||+|||.=+..+- T Consensus 108 ~~~L~~LpGVG~kTA~~il~~a 129 (225) T 1kg2_A 108 FEEVAALPGVGRSTAGAILSLS 129 (225) T ss_dssp HHHHHTSTTCCHHHHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHHHHH T ss_conf 9999758987478999999985 No 26 >1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex, single-stranded DNA, isomerase/DNA complex; HET: DNA; 2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A* 2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A* Probab=90.03 E-value=0.2 Score=29.62 Aligned_cols=55 Identities=20% Similarity=0.229 Sum_probs=39.7 Q ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHCC---CCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCC Q ss_conf 78554999946997868999999998201---7980887414674882066634799999983064 Q gi|254780762|r 137 KKIRELIFAISATIEGQTTAHYIMDKLKG---IDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRT 199 (201) Q Consensus 137 ~~i~EVIlA~~~t~EGe~Ta~yi~~~lk~---~~ikitrla~GiP~G~~ley~D~~TL~~Al~~R~ 199 (201) .+++|||+||.|.-|||+-+..|.+.++. .+.+|.|+-+- + +....+.+||++.+ T Consensus 93 k~ad~iiiAtD~DREGE~I~~~i~~~~~~~~~~~~~v~R~~fs-----~---iT~~~I~~A~~n~~ 150 (659) T 1i7d_A 93 HEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLIN-----D---LNPQAVERAIDRLR 150 (659) T ss_dssp HHCSEEEEECCSSHHHHHHHHHHHHHTTCCHHHHHTCEECCCS-----C---CSHHHHHHHHTTCE T ss_pred HCCCEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEEEEE-----C---CCHHHHHHHHHCCC T ss_conf 7099899837898245699999999956222468745899971-----6---88999999997457 No 27 >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=89.95 E-value=0.19 Score=29.67 Aligned_cols=22 Identities=18% Similarity=0.220 Sum_probs=19.5 Q ss_pred HHHHHHCCCCCHHHHHHHHHHH Q ss_conf 9999756899953799999999 Q gi|254780762|r 14 IKILARIPGFGPRSARRATLHL 35 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a~~L 35 (201) ++.|.+|||||++.|++++-|= T Consensus 39 ~~eL~~lpgIg~~~A~~Iv~~R 60 (98) T 2edu_A 39 ARDLRSLQRIGPKKAQLIVGWR 60 (98) T ss_dssp HHHHHHSTTCCHHHHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHHHHH T ss_conf 9999647998999999999999 No 28 >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=89.46 E-value=0.27 Score=28.65 Aligned_cols=102 Identities=14% Similarity=0.183 Sum_probs=52.6 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHCC----------------------------------------HHHHHHHHHHHHHH Q ss_conf 99997568999537999999997199----------------------------------------89999999999999 Q gi|254780762|r 14 IKILARIPGFGPRSARRATLHLVKKK----------------------------------------EQLLGPLAEAMANI 53 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a~~Ll~~~----------------------------------------~~~~~~l~~~l~~~ 53 (201) .+.|.+|||||++||--++.+-...+ .+...++.++|.++ T Consensus 117 ~~~L~~LpGVG~~TA~ail~~a~~~~~~~vD~nv~Rv~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nqalmdl 196 (369) T 3fsp_A 117 PDEFSRLKGVGPYTVGAVLSLAYGVPEPAVDGNVMRVLSRLFLVTDDIAKPSTRKRFEQIVREIMAYENPGAFNEALIEL 196 (369) T ss_dssp HHHHHTSTTCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHTTCCSCTTSHHHHHHHHHHHHHHCCSSSHHHHHHHHHHH T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCCCCEECCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHH T ss_conf 99985242258899999999861488612248513567543044688875114677887530358767756889999997 Q ss_pred HHHCCC--CCCCCCCCCCCCCCCCCC------C---CC-C----CCEEEEEECHHHHHHHH---HHCCEEEEEEEHHHHC Q ss_conf 985182--889997334565410035------5---55-6----73699983588999997---5174013421012100 Q gi|254780762|r 54 YNKVCL--CSICGNVDTTDPCAICID------Q---QR-D----ASVIIVVEDVADLWALE---RSKAVNALYHVLGGSL 114 (201) Q Consensus 54 ~~~i~~--C~~C~~l~~~~~C~iC~d------~---~R-d----~~~lCVVE~~~Di~~IE---~t~~y~G~YhVLgG~i 114 (201) -..|+. -+.|..=--.+.|.--.. | .+ . .-..+|+.+..+-+-++ ..|.+.|+|..=+|.+ T Consensus 197 G~~iC~~~~P~C~~CPl~~~C~~~~~~~~~~~P~k~kK~~~~~~~~~~~i~~~~~~~iLl~kR~~~gll~GLweFP~~~~ 276 (369) T 3fsp_A 197 GALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRKRDSTGLLANLWEFPSCET 276 (369) T ss_dssp HHHTSCSSSCCTTTCTTGGGCHHHHHTCGGGCSCCCCCCCCEEEEEEEEEEECSSSEEEEEECCSSSTTTTCEECCEEEC T ss_pred HHHHCCCCCCCCCCCCCHHHCHHHCCCCHHHCCCCCCCCCCCCCCHHHHHHHCHHHHHHHHHCCCCCCCCCCCCCCCCCC T ss_conf 56415689998988985332776527997656788778876532046766412178889986255444578762885665 Q ss_pred C Q ss_conf 2 Q gi|254780762|r 115 S 115 (201) Q Consensus 115 s 115 (201) . T Consensus 277 e 277 (369) T 3fsp_A 277 D 277 (369) T ss_dssp S T ss_pred C T ss_conf 7 No 29 >3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices, helix-hairpin-helix motif, iron-sulfur cluste hydrolase; 2.30A {Homo sapiens} Probab=88.85 E-value=0.26 Score=28.76 Aligned_cols=22 Identities=18% Similarity=0.211 Sum_probs=16.5 Q ss_pred HHHHHHHCCCCCHHHHHHHHHH Q ss_conf 9999975689995379999999 Q gi|254780762|r 13 LIKILARIPGFGPRSARRATLH 34 (201) Q Consensus 13 LI~~l~kLPGIG~KsA~R~a~~ 34 (201) ..+.+.+|||||++||.-+..+ T Consensus 127 ~~e~l~~LPGVG~kTA~aIl~~ 148 (287) T 3n5n_X 127 AETLQQLLPGVGRYTAGAIASI 148 (287) T ss_dssp HHHHHHHSTTCCHHHHHHHHHH T ss_pred HHHHCCCCCCCCHHHHHHHHHH T ss_conf 1544046887568999999998 No 30 >2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus} Probab=88.82 E-value=1.4 Score=23.79 Aligned_cols=86 Identities=19% Similarity=0.229 Sum_probs=58.8 Q ss_pred CCEEEEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHH Q ss_conf 73699983588999997517401342101210020002681112889999985157855499994699786899999999 Q gi|254780762|r 82 ASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMD 161 (201) Q Consensus 82 ~~~lCVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~ 161 (201) ...+-|||-..|++++.+.|. +..--.+|..++ ++. +..| . ...++||+++...-.|+.-+.-+.+ T Consensus 244 ~~~viivEG~~D~l~l~~~Gi-~n~va~~Gt~lt------~~~--~~~L-~----~~~~~vvl~~D~D~AG~~A~~k~~~ 309 (407) T 2au3_A 244 EGFAILVEGYFDLLRLFSEGI-RNVVAPLGTALT------QNQ--ANLL-S----KFTKKVYILYDGDDAGRKAMKSAIP 309 (407) T ss_dssp HTCEEECSSHHHHHHHHHTTC-CSEEEESSSSCC------HHH--HHHH-H----TTCSEEEEECCSSHHHHHHHHHHHH T ss_pred CCCCEEECCCCHHHHHHHCCC-CCEEECCCCCCC------HHH--HHHH-H----CCCCEEEEECCCCHHHHHHHHHHHH T ss_conf 543253036303999986697-645741577683------899--9998-6----1167158845886999999999999 Q ss_pred HHCCCCCEEEEEECCCCCCCCH Q ss_conf 8201798088741467488206 Q gi|254780762|r 162 KLKGIDVKITRLAYGIPMGSEL 183 (201) Q Consensus 162 ~lk~~~ikitrla~GiP~G~~l 183 (201) .|...++++..+- +|-|-+. T Consensus 310 ~l~~~g~~v~vv~--lP~gkDp 329 (407) T 2au3_A 310 LLLSAGVEVYPVY--LPEGYDP 329 (407) T ss_dssp HHHHTTCEEEEEC--CCTTCCH T ss_pred HHHHCCCEEEEEE--CCCCCCH T ss_conf 9875176048997--9899895 No 31 >1ryq_A DNA-directed RNA polymerase, subunit E''; structural genomics, zinc, PSI, protein structure initiative; 1.38A {Pyrococcus furiosus} SCOP: g.41.9.3 Probab=88.18 E-value=0.29 Score=28.51 Aligned_cols=41 Identities=17% Similarity=0.409 Sum_probs=26.1 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCC--CCCCCCEEEEEECHHHHH Q ss_conf 85182889997334565410035--555673699983588999 Q gi|254780762|r 55 NKVCLCSICGNVDTTDPCAICID--QQRDASVIIVVEDVADLW 95 (201) Q Consensus 55 ~~i~~C~~C~~l~~~~~C~iC~d--~~Rd~~~lCVVE~~~Di~ 95 (201) .+-+-|..|+.+.+.+.|++|.+ .+-|.+=+-+|-+|.+=| T Consensus 9 ~~~rAC~~C~~i~~~~~CPnCgs~~~S~~w~G~I~I~dPe~S~ 51 (69) T 1ryq_A 9 SSEKACRHCHYITSEDRCPVCGSRDLSEEWFDLVIIVDVENSE 51 (69) T ss_dssp --CEEETTTCBEESSSSCTTTCCCCEESCEEEEEEESCGGGCH T ss_pred CCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHH T ss_conf 3023475198765799797984986777715189996767889 No 32 >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=87.52 E-value=0.31 Score=28.25 Aligned_cols=33 Identities=21% Similarity=0.423 Sum_probs=25.2 Q ss_pred HHHHHCCCCCHHHHHHHHHH------HHHCCHHHHHHHH Q ss_conf 99975689995379999999------9719989999999 Q gi|254780762|r 15 KILARIPGFGPRSARRATLH------LVKKKEQLLGPLA 47 (201) Q Consensus 15 ~~l~kLPGIG~KsA~R~a~~------Ll~~~~~~~~~l~ 47 (201) +.|.++||||+|.++++.-+ |.+.+.+++.++. T Consensus 4 d~L~~IPGIg~~~~~~Ll~~fgSi~~l~~as~eeL~~v~ 42 (63) T 2a1j_A 4 DFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSIL 42 (63) T ss_dssp HHHHTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHHH T ss_pred HHHHCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHCC T ss_conf 888529998899999999986799999879999998786 No 33 >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=87.49 E-value=0.51 Score=26.82 Aligned_cols=29 Identities=3% Similarity=0.098 Sum_probs=25.2 Q ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 66799999999756899953799999999 Q gi|254780762|r 7 GKEIENLIKILARIPGFGPRSARRATLHL 35 (201) Q Consensus 7 ~~~l~~LI~~l~kLPGIG~KsA~R~a~~L 35 (201) ...+.+++..|..+||||++.|++++-+. T Consensus 24 ~~~~~~~~~~L~~I~gIGk~~A~~L~~~F 52 (91) T 2a1j_B 24 QDFVSRVTECLTTVKSVNKTDSQTLLTTF 52 (91) T ss_dssp HHHHHHHHHHHTTSTTCCHHHHHHHHHHH T ss_pred CCCHHHHHHHHCCCCCCCHHHHHHHHHHH T ss_conf 79099999986468885999999999995 No 34 >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=86.49 E-value=0.35 Score=27.92 Aligned_cols=22 Identities=36% Similarity=0.724 Sum_probs=17.4 Q ss_pred HHHHHHHHHCCCCCHHHHHHHH Q ss_conf 9999999756899953799999 Q gi|254780762|r 11 ENLIKILARIPGFGPRSARRAT 32 (201) Q Consensus 11 ~~LI~~l~kLPGIG~KsA~R~a 32 (201) ..+++.|.++||||||+|+++. T Consensus 94 ~~~l~~l~~I~GvGpk~a~~l~ 115 (335) T 2fmp_A 94 SSSINFLTRVSGIGPSAARKFV 115 (335) T ss_dssp HHHHHHHTTSTTCCHHHHHHHH T ss_pred HHHHHHHHHCCCCCHHHHHHHH T ss_conf 4678998745687989999999 No 35 >1vk6_A NADH pyrophosphatase; 1790429, structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics; HET: MSE; 2.20A {Escherichia coli K12} SCOP: d.113.1.4 d.113.1.4 g.41.14.1 PDB: 2gb5_A Probab=86.12 E-value=0.15 Score=30.41 Aligned_cols=94 Identities=18% Similarity=0.313 Sum_probs=63.3 Q ss_pred CHHH--HHHHHHHHHHHHHHCCCCCCCCCCCC---CC---CCCCCCCCC---CCCCEEEEEECHHHHHHHHHHCCEEEEE Q ss_conf 9899--99999999999985182889997334---56---541003555---5673699983588999997517401342 Q gi|254780762|r 39 KEQL--LGPLAEAMANIYNKVCLCSICGNVDT---TD---PCAICIDQQ---RDASVIIVVEDVADLWALERSKAVNALY 107 (201) Q Consensus 39 ~~~~--~~~l~~~l~~~~~~i~~C~~C~~l~~---~~---~C~iC~d~~---Rd~~~lCVVE~~~Di~~IE~t~~y~G~Y 107 (201) +... +-.-|.+|..-..+-++|+.||.-+. .+ .|+-|.... -+...+++|.+...+.-.-+.....|.| T Consensus 87 ~~~~~~l~~~a~~l~~w~~~~rfC~~CG~~~~~~~~~~~~~C~~C~~~~yP~~~p~vivli~~~~~iLL~R~~~~~~g~W 166 (269) T 1vk6_A 87 DVGLFQLAGRGVQLAEFYRSHKYCGYCGHEMYPSKTEWAMLCSHCRERYYPQIAPCIIVAIRRDDSILLAQHTRHRNGVH 166 (269) T ss_dssp CHHHHHHHHHHHHHHHHHHTTSBCTTTCCBEEECSSSSCEEESSSSCEECCCCEEEEEEEEEETTEEEEEEETTTCSSCC T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCEEEEEEEECCEEEEEEECCCCCCCE T ss_conf 99999999999999999872986866798774367980488989988568876865999998399899997336899857 Q ss_pred EEHHHHCCCCCCCCHHHCCHHHHHHHH Q ss_conf 101210020002681112889999985 Q gi|254780762|r 108 HVLGGSLSPLDRIGPEDIGIQSLIERI 134 (201) Q Consensus 108 hVLgG~ispl~g~~p~~l~i~~L~~ri 134 (201) -+.||.+.| |-.+++--..++.+=. T Consensus 167 slPgGfVE~--GEt~eeAa~REv~EEt 191 (269) T 1vk6_A 167 TVLAGFVEV--GETLEQAVAREVMEES 191 (269) T ss_dssp BCEEEECCT--TCCHHHHHHHHHHHHH T ss_pred EECCCCCCC--CCCHHHHHHHHHHHHC T ss_conf 601665438--9989999889876522 No 36 >2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Probab=86.12 E-value=0.48 Score=27.04 Aligned_cols=24 Identities=25% Similarity=0.382 Sum_probs=19.0 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHH Q ss_conf 799999999756899953799999 Q gi|254780762|r 9 EIENLIKILARIPGFGPRSARRAT 32 (201) Q Consensus 9 ~l~~LI~~l~kLPGIG~KsA~R~a 32 (201) +....+..|.++||||||+|+++. T Consensus 96 ~~~~~l~~l~~i~GvGpk~a~~l~ 119 (360) T 2ihm_A 96 ERYQTMKLFTQVFGVGVKTANRWY 119 (360) T ss_dssp HHHHHHHHHHTSTTCCHHHHHHHH T ss_pred HHHHHHHHHHHCCCCCHHHHHHHH T ss_conf 157999999757787899999999 No 37 >3lpe_B DNA-directed RNA polymerase subunit E''; transcription regulation, SPT4, SPT5, NUSG, archaea, evoluti directed RNA polymerase; 1.90A {Methanocaldococcus jannaschii} Probab=85.51 E-value=0.29 Score=28.52 Aligned_cols=21 Identities=24% Similarity=0.675 Sum_probs=18.2 Q ss_pred CCCCCCCCCCCCCCCCCCCCC Q ss_conf 182889997334565410035 Q gi|254780762|r 57 VCLCSICGNVDTTDPCAICID 77 (201) Q Consensus 57 i~~C~~C~~l~~~~~C~iC~d 77 (201) ++-|..|+.+.+.+.|+.|.+ T Consensus 1 LkAC~~C~~i~~~~~Cp~C~s 21 (59) T 3lpe_B 1 MRACLKCKYLTNDEICPICHS 21 (59) T ss_dssp CEEETTTCBEESSSBCTTTCC T ss_pred CCCCCCCCCCCCCCCCCCCCC T ss_conf 937231957717898969489 No 38 >1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA- directed RNA polymerase, primosome, late protein; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2 Probab=85.09 E-value=1.2 Score=24.44 Aligned_cols=86 Identities=14% Similarity=0.143 Sum_probs=54.0 Q ss_pred CCCCCCEEEEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHC--CHHHHHHHHCCCCCCEEEEEECCCCCHHHH Q ss_conf 555673699983588999997517401342101210020002681112--889999985157855499994699786899 Q gi|254780762|r 78 QQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDI--GIQSLIERIEVKKIRELIFAISATIEGQTT 155 (201) Q Consensus 78 ~~Rd~~~lCVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l--~i~~L~~ri~~~~i~EVIlA~~~t~EGe~T 155 (201) ...+...|.|||-..|++++.+.+.-...-... +.++... ......+. ...+++||||+...-.|+.- T Consensus 146 ~~~~~~~v~I~EGe~Dalsl~~~~~~~~~~~s~--------~~~~~~~~~~~~~~~~~--~~~~~~Iii~~DnD~aG~~a 215 (255) T 1nui_A 146 LWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSL--------GHGASAAKKTCAANYEY--FDQFEQIILMFDMDEAGRKA 215 (255) T ss_dssp GCCCBSCCEEESSHHHHHHHHHHHTTCSCEECC--------TTTTTTHHHHHHHTHHH--HTTBSCEEEECCSSHHHHHH T ss_pred HCCCCCEEEEEECHHHHHHHHHHHCCCCCCCCC--------CCCCCHHHHHHHHHHHH--HCCCCEEEEECCCCHHHHHH T ss_conf 126887799991468899999861268851024--------65531002332566665--31556599967999999999 Q ss_pred HHHHHHHHCCCCCEEEEE Q ss_conf 999999820179808874 Q gi|254780762|r 156 AHYIMDKLKGIDVKITRL 173 (201) Q Consensus 156 a~yi~~~lk~~~ikitrl 173 (201) +.-+.+.|....+++-.+ T Consensus 216 a~k~~~~l~~~~~~iv~~ 233 (255) T 1nui_A 216 VEEAAQVLPAGKVRVAVL 233 (255) T ss_dssp HHHHHHHSCTTTEEECCC T ss_pred HHHHHHHCCCCCEEEEEC T ss_conf 999999746787999618 No 39 >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=84.94 E-value=0.68 Score=25.97 Aligned_cols=28 Identities=25% Similarity=0.221 Sum_probs=21.9 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 7999999997568999537999999997 Q gi|254780762|r 9 EIENLIKILARIPGFGPRSARRATLHLV 36 (201) Q Consensus 9 ~l~~LI~~l~kLPGIG~KsA~R~a~~Ll 36 (201) .-+.....|..+||||++.|.+++-|.= T Consensus 8 ~~~~~~~~L~~IpgIG~~~a~~L~~~F~ 35 (75) T 1x2i_A 8 LAERQRLIVEGLPHVSATLARRLLKHFG 35 (75) T ss_dssp HHHHHHHHHTTSTTCCHHHHHHHHHHHC T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHHHHC T ss_conf 9999999984899942999999999968 No 40 >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=84.59 E-value=0.5 Score=26.87 Aligned_cols=21 Identities=24% Similarity=0.385 Sum_probs=15.9 Q ss_pred HHHHHCCCCCHHHHHHHHHHH Q ss_conf 999756899953799999999 Q gi|254780762|r 15 KILARIPGFGPRSARRATLHL 35 (201) Q Consensus 15 ~~l~kLPGIG~KsA~R~a~~L 35 (201) ..|..+|||||++|+++.-+. T Consensus 24 S~L~~IpGIG~k~ak~Ll~~F 44 (78) T 1kft_A 24 SSLETIEGVGPKRRQMLLKYM 44 (78) T ss_dssp CGGGGCTTCSSSHHHHHHHHH T ss_pred CCCCCCCCCCHHHHHHHHHHH T ss_conf 826569993299999999992 No 41 >2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Probab=84.50 E-value=0.75 Score=25.69 Aligned_cols=19 Identities=26% Similarity=0.449 Sum_probs=14.8 Q ss_pred HHHHHHCCCCCHHHHHHHH Q ss_conf 9999756899953799999 Q gi|254780762|r 14 IKILARIPGFGPRSARRAT 32 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a 32 (201) +..|.++||||||+|+++. T Consensus 96 ~~~l~~I~GvGpk~A~~l~ 114 (578) T 2w9m_A 96 LLDLLGVRGLGPKKIRSLW 114 (578) T ss_dssp HHHHTTSTTCCHHHHHHHH T ss_pred HHHHHCCCCCCHHHHHHHH T ss_conf 9998478986899999999 No 42 >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=84.33 E-value=0.23 Score=29.14 Aligned_cols=19 Identities=21% Similarity=0.280 Sum_probs=17.0 Q ss_pred HHHHHHCCCCCHHHHHHHH Q ss_conf 9999756899953799999 Q gi|254780762|r 14 IKILARIPGFGPRSARRAT 32 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a 32 (201) ++.|.+||||||+.|+|++ T Consensus 62 ~~eL~~lpGig~~~A~~Iv 80 (134) T 1s5l_U 62 IAAFIQYRGLYPTLAKLIV 80 (134) T ss_dssp GGGGGGSTTCTHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHH T ss_conf 9999771034699999999 No 43 >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=83.79 E-value=0.27 Score=28.70 Aligned_cols=19 Identities=21% Similarity=0.280 Sum_probs=16.8 Q ss_pred HHHHHHCCCCCHHHHHHHH Q ss_conf 9999756899953799999 Q gi|254780762|r 14 IKILARIPGFGPRSARRAT 32 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a 32 (201) .+.|.+|||||+..|+|++ T Consensus 32 ~~eL~~lpGig~~~A~~Iv 50 (104) T 3bz1_U 32 IAAFIQYRGLYPTLAKLIV 50 (104) T ss_dssp GGGGGGSTTTTHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHH T ss_conf 9999658997999999999 No 44 >2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} SCOP: a.60.2.7 Probab=83.53 E-value=0.5 Score=26.91 Aligned_cols=21 Identities=38% Similarity=0.618 Sum_probs=18.0 Q ss_pred HHHHHHCCCCCHHHHHHHHHH Q ss_conf 999975689995379999999 Q gi|254780762|r 14 IKILARIPGFGPRSARRATLH 34 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a~~ 34 (201) .+.|.++||||++.|+|++-| T Consensus 26 ~~eL~~lpGig~~~A~~Iv~~ 46 (75) T 2duy_A 26 LEELMALPGIGPVLARRIVEG 46 (75) T ss_dssp HHHHTTSTTCCHHHHHHHHHT T ss_pred HHHHHHCCCCCHHHHHHHHHC T ss_conf 999977789899999999985 No 45 >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=82.22 E-value=0.77 Score=25.62 Aligned_cols=20 Identities=20% Similarity=0.383 Sum_probs=16.4 Q ss_pred HHHHHHHCCCCCHHHHHHHH Q ss_conf 99999756899953799999 Q gi|254780762|r 13 LIKILARIPGFGPRSARRAT 32 (201) Q Consensus 13 LI~~l~kLPGIG~KsA~R~a 32 (201) .+..|.++||||||+|+++. T Consensus 94 ~~~~l~~I~GvGpk~a~~l~ 113 (335) T 2bcq_A 94 VLELFSNIWGAGTKTAQMWY 113 (335) T ss_dssp HHHHHHTSTTCCHHHHHHHH T ss_pred HHHHHHCCCCCCHHHHHHHH T ss_conf 15665118876889999999 No 46 >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=82.22 E-value=0.5 Score=26.88 Aligned_cols=22 Identities=23% Similarity=0.463 Sum_probs=19.7 Q ss_pred HHHHHHCCCCCHHHHHHHHHHH Q ss_conf 9999756899953799999999 Q gi|254780762|r 14 IKILARIPGFGPRSARRATLHL 35 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a~~L 35 (201) ++.|.+.||||++.|+++.-|| T Consensus 55 ~eeL~~v~GIg~~~A~~I~~~l 76 (78) T 1kft_A 55 VEEIAKVPGISQGLAEKIFWSL 76 (78) T ss_dssp HHHHTTSSSTTSHHHHHHHHHH T ss_pred HHHHHCCCCCCHHHHHHHHHHH T ss_conf 9999807998999999999996 No 47 >2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A Probab=79.53 E-value=0.4 Score=27.55 Aligned_cols=28 Identities=18% Similarity=0.386 Sum_probs=23.7 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 9851828899973345654100355556 Q gi|254780762|r 54 YNKVCLCSICGNVDTTDPCAICIDQQRD 81 (201) Q Consensus 54 ~~~i~~C~~C~~l~~~~~C~iC~d~~Rd 81 (201) +..++.|+.|+.+|-.+.|+.|..+... T Consensus 3 r~kirkC~~C~~YTL~~~Cp~CG~~t~~ 30 (60) T 2apo_B 3 EMRMKKCPKCGLYTLKEICPKCGEKTVI 30 (60) T ss_dssp CCCCEECTTTCCEESSSBCSSSCSBCBC T ss_pred HHHHHHCCCCCCEECCCCCCCCCCCCCC T ss_conf 6666518746665354537678784676 No 48 >2aus_D NOP10, ribosome biogenesis protein NOP10; isomerase, structural protein, isomerase/structural protein complex; 2.10A {Pyrococcus abyssi} PDB: 3lwr_B 3lwo_B* 3lwq_B* 3lwp_B 3lwv_B 3hax_C* 2hvy_C* 3hay_C* 2ey4_E 3hjw_B* 2rfk_B* 3hjy_B Probab=79.16 E-value=0.55 Score=26.61 Aligned_cols=27 Identities=19% Similarity=0.668 Sum_probs=23.3 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 985182889997334565410035555 Q gi|254780762|r 54 YNKVCLCSICGNVDTTDPCAICIDQQR 80 (201) Q Consensus 54 ~~~i~~C~~C~~l~~~~~C~iC~d~~R 80 (201) +..|+.|+.|+.+|-.+.|+.|..+.. T Consensus 2 k~~irkC~~C~~YTLk~~CP~CG~~t~ 28 (60) T 2aus_D 2 RFRIRKCPKCGRYTLKETCPVCGEKTK 28 (60) T ss_dssp --CCEECTTTCCEESSSBCTTTCSBCE T ss_pred CHHHHCCCCCCCEECCCCCCCCCCCCC T ss_conf 224114874666635563767878557 No 49 >2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} Probab=78.45 E-value=1.4 Score=23.86 Aligned_cols=23 Identities=26% Similarity=0.250 Sum_probs=19.0 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 99975689995379999999971 Q gi|254780762|r 15 KILARIPGFGPRSARRATLHLVK 37 (201) Q Consensus 15 ~~l~kLPGIG~KsA~R~a~~Ll~ 37 (201) +.+..|||||++.|+++--+|-+ T Consensus 58 ~~l~~l~GIG~~i~~ki~e~L~~ 80 (87) T 2kp7_A 58 KEAKILQHFGDRLCRMLDEKLKQ 80 (87) T ss_dssp HHHHTCTTTCHHHHHHHHHHHHH T ss_pred HHHHHCCCCCHHHHHHHHHHHHH T ss_conf 99972799778999999999999 No 50 >2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Probab=78.00 E-value=2.2 Score=22.60 Aligned_cols=69 Identities=17% Similarity=0.092 Sum_probs=35.7 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECHHHH Q ss_conf 99975689995379999999971998999999999999998518288999733456541003555567369998358899 Q gi|254780762|r 15 KILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADL 94 (201) Q Consensus 15 ~~l~kLPGIG~KsA~R~a~~Ll~~~~~~~~~l~~~l~~~~~~i~~C~~C~~l~~~~~C~iC~d~~Rd~~~lCVVE~~~Di 94 (201) +.|..+||||+++|+.+.-|+-. +...++.+.|....-++ . .+... T Consensus 544 eeL~~I~gIG~~~A~si~~ff~~---~~n~~~i~~L~~~G~~~---------~----------------------~~~~~ 589 (671) T 2owo_A 544 EELQKVPDVGIVVASHVHNFFAE---ESNRNVISELLAEGVHW---------P----------------------APIVI 589 (671) T ss_dssp HHHTTSTTCCHHHHHHHHHHHTC---HHHHHHHHHHHHHTCBC---------C----------------------CC--- T ss_pred HHHHCCCCCCHHHHHHHHHHHCC---HHHHHHHHHHHHHCCCC---------C----------------------CCCCC T ss_conf 99964498169999999999749---89999999999848885---------6----------------------64334 Q ss_pred HHHHHHCCEEEEEEEHHHHCCCC Q ss_conf 99975174013421012100200 Q gi|254780762|r 95 WALERSKAVNALYHVLGGSLSPL 117 (201) Q Consensus 95 ~~IE~t~~y~G~YhVLgG~ispl 117 (201) ..-+..+.+.|+-||+-|.++.+ T Consensus 590 ~~~~~~~~l~gk~~ViTG~l~~~ 612 (671) T 2owo_A 590 NAEEIDSPFAGKTVVLTGSLSQM 612 (671) T ss_dssp ----------------------- T ss_pred CCCCCCCCCCCCEEEEEECCCCC T ss_conf 54345897689889994068999 No 51 >1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2 Probab=77.52 E-value=2.6 Score=22.11 Aligned_cols=85 Identities=15% Similarity=0.191 Sum_probs=55.4 Q ss_pred CCCEEEEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHH Q ss_conf 67369998358899999751740134210121002000268111288999998515785549999469978689999999 Q gi|254780762|r 81 DASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIM 160 (201) Q Consensus 81 d~~~lCVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~ 160 (201) ....+.|||-..|++++-+.+... +.| +|.-.|.+...-.+...++.+ .++++|||++...-.|..-+.-+. T Consensus 86 ~~~~v~i~EGe~Dals~~~~~~~~--~~~----~~~~~~~~~~~~~~~~~~~~l--~~~~~v~l~~D~D~~G~~~~~~~~ 157 (503) T 1q57_A 86 GGKKIVVTEGEIDMLTVMELQDCK--YPV----VSLGHGASAAKKTCAANYEYF--DQFEQIILMFDMDEAGRKAVEEAA 157 (503) T ss_dssp SEEEEEEESSHHHHHHHTTTTTTC--SCE----EEESSTTTTHHHHHHTTHHHH--HTEEEEEEECCSSHHHHHHHHHHH T ss_pred CCCEEEEECCHHHHHHHHHHCCCC--CCC----CCCCCCCCHHHHHHHHHHHHH--CCCCEEEEECCCCHHHHHHHHHHH T ss_conf 999899988679999999964888--750----215753124688999989871--688989996289989999999999 Q ss_pred HHHCCCCCEEEEE Q ss_conf 9820179808874 Q gi|254780762|r 161 DKLKGIDVKITRL 173 (201) Q Consensus 161 ~~lk~~~ikitrl 173 (201) +.+....+++..+ T Consensus 158 ~~~~~~~~~~~~~ 170 (503) T 1q57_A 158 QVLPAGKVRVAVL 170 (503) T ss_dssp HHSCGGGEEECCC T ss_pred HHCCCCEEEEEEC T ss_conf 7557760799866 No 52 >3fbl_A Putative uncharacterized protein; AFV1, archaeal virus, extremophiles, lipothrixviridae, structural protein, DNA-binding protein; 1.95A {Acidianus filamentous virus 1} Probab=77.18 E-value=1.3 Score=24.10 Aligned_cols=35 Identities=14% Similarity=0.266 Sum_probs=30.5 Q ss_pred CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 66686679999999975689995379999999971 Q gi|254780762|r 3 KKITGKEIENLIKILARIPGFGPRSARRATLHLVK 37 (201) Q Consensus 3 ~~~~~~~l~~LI~~l~kLPGIG~KsA~R~a~~Ll~ 37 (201) ++|..+.+++.|.+|+.-.||...+||++|-|+-. T Consensus 46 sdmiaeyinnaisafssrtgisqetaqkiadfits 80 (82) T 3fbl_A 46 SDMIAEYINNAISAFSSRTGISQETAQKIADFITS 80 (82) T ss_dssp HHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHC T ss_conf 78999999889998760246449999999998723 No 53 >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=76.53 E-value=1.7 Score=23.29 Aligned_cols=21 Identities=14% Similarity=0.214 Sum_probs=11.3 Q ss_pred HHHCCCCCHHHHHHHHHHHHH Q ss_conf 975689995379999999971 Q gi|254780762|r 17 LARIPGFGPRSARRATLHLVK 37 (201) Q Consensus 17 l~kLPGIG~KsA~R~a~~Ll~ 37 (201) +.+|||||+++|.-+..|..+ T Consensus 106 l~~LpGVG~ytad~~~if~~~ 126 (155) T 1ngn_A 106 PIELHGIGKYGNDSYRIFCVN 126 (155) T ss_dssp GGGSTTCCHHHHHHHHHHTSS T ss_pred CCCCCCCCHHHHHHHHHHHCC T ss_conf 675898219999999999879 No 54 >2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} SCOP: e.71.1.1 Probab=75.64 E-value=0.91 Score=25.14 Aligned_cols=25 Identities=20% Similarity=0.263 Sum_probs=18.2 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHCC Q ss_conf 9997568999537999999997199 Q gi|254780762|r 15 KILARIPGFGPRSARRATLHLVKKK 39 (201) Q Consensus 15 ~~l~kLPGIG~KsA~R~a~~Ll~~~ 39 (201) .+|.-|||||+|+|+.|.--==+.+ T Consensus 132 H~leLLPGIGKK~~~~IleeR~k~~ 156 (205) T 2i5h_A 132 HQLELLPGVGKKMMWAIIEERKKRP 156 (205) T ss_dssp BGGGGSTTCCHHHHHHHHHHHHHSC T ss_pred HHHHHCCCCCHHHHHHHHHHHCCCC T ss_conf 8887523505899999999965589 No 55 >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=75.05 E-value=1.6 Score=23.50 Aligned_cols=19 Identities=21% Similarity=0.417 Sum_probs=12.7 Q ss_pred HHHHHHHCCCCCHHHHHHH Q ss_conf 9999975689995379999 Q gi|254780762|r 13 LIKILARIPGFGPRSARRA 31 (201) Q Consensus 13 LI~~l~kLPGIG~KsA~R~ 31 (201) .+..|.++||||||+|+++ T Consensus 119 ~l~~l~~I~GiGpk~a~~l 137 (381) T 1jms_A 119 SFKLFTSVFGVGLKTAEKW 137 (381) T ss_dssp HHHHHHTSTTCCHHHHHHH T ss_pred HHHHHHHCCCCCHHHHHHH T ss_conf 8899873778789999999 No 56 >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=72.93 E-value=0.59 Score=26.42 Aligned_cols=21 Identities=29% Similarity=0.419 Sum_probs=15.9 Q ss_pred HHHHHCCCCCHHHHHHHHHHH Q ss_conf 999756899953799999999 Q gi|254780762|r 15 KILARIPGFGPRSARRATLHL 35 (201) Q Consensus 15 ~~l~kLPGIG~KsA~R~a~~L 35 (201) +.|.++||+|+|+|+++.-.| T Consensus 48 ~~L~~~~g~g~k~a~~i~~~i 68 (241) T 1vq8_Y 48 SALADVSGIGNALAARIKADV 68 (241) T ss_dssp --------------------- T ss_pred HHHHHCCCCCHHHHHHHHHHH T ss_conf 999746895799999999998 No 57 >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=69.56 E-value=6.4 Score=19.42 Aligned_cols=56 Identities=14% Similarity=0.039 Sum_probs=27.3 Q ss_pred EEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHC Q ss_conf 01342101210020002681112889999985157855499994699786899999999820 Q gi|254780762|r 103 VNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLK 164 (201) Q Consensus 103 y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~lk 164 (201) .+-.|.|-|+..++...+.++.+ ..++..-....+ -.|+ .|.+-+-||.|+..+.+ T Consensus 80 ~~~~~lIEg~~~~~~~~~~~~~~-~~~l~~~~~~~~-~~vi----~t~~~~eta~~l~~l~~ 135 (219) T 2bgw_A 80 ETVFIIVEGPPVPRRYRGRERSL-YAAMAALQLDYG-IRLM----NTMDPKGTALVIESLAR 135 (219) T ss_dssp SEEEEEEESCSSCGGGTTTHHHH-HHHHHHHHHHSC-CEEE----EESSHHHHHHHHHHHHH T ss_pred CCEEEEECCCCCCCCCCCCHHHH-HHHHHHHHHHCC-CEEE----EECCCHHHHHHHHHHHH T ss_conf 45389954787310025657899-999999998679-7499----93351067889999998 No 58 >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=68.86 E-value=1.7 Score=23.35 Aligned_cols=24 Identities=25% Similarity=0.392 Sum_probs=18.0 Q ss_pred HHHHHH--HHHHCCCCCHHHHHHHHH Q ss_conf 999999--997568999537999999 Q gi|254780762|r 10 IENLIK--ILARIPGFGPRSARRATL 33 (201) Q Consensus 10 l~~LI~--~l~kLPGIG~KsA~R~a~ 33 (201) .++++. .++.|||||+++++|+.- T Consensus 234 ~~~fl~~lpv~~LpGIG~~~~~kL~~ 259 (434) T 2aq4_A 234 SEEFWSSFKLDDLPGVGHSTLSRLES 259 (434) T ss_dssp CHHHHTTCCGGGSTTCCHHHHHHHHH T ss_pred HHHHCCCCCCCCCCCCCHHHHHHHHH T ss_conf 22303666721066867899999998 No 59 >1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B* Probab=67.56 E-value=2.3 Score=22.38 Aligned_cols=40 Identities=20% Similarity=0.250 Sum_probs=30.2 Q ss_pred CHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCC Q ss_conf 889999985157855499994699786899999999820179 Q gi|254780762|r 126 GIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGID 167 (201) Q Consensus 126 ~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~lk~~~ 167 (201) +|+.|.+.. ...+=||..|.|..|||-.|--++++|..-+ T Consensus 612 riealrkla--hdaefvivgtdpdtegekiawdlknllsgcg 651 (1054) T 1gku_B 612 RIEALRKLA--HDAEFVIVGTDPDTEGEKIAWDLKNLLSGCG 651 (1054) T ss_dssp HHHHHHHHH--HHHSEEEECCCSSHHHHHHHHHHHHHHTTSS T ss_pred HHHHHHHHH--CCCCEEEEECCCCCCCCHHHHHHHHHHCCCC T ss_conf 999999750--4670899807988764315556887750023 No 60 >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=65.39 E-value=3.3 Score=21.41 Aligned_cols=30 Identities=7% Similarity=0.042 Sum_probs=22.2 Q ss_pred CCHHHHHHHH----HHHHCCCCCHHHHHHHHHHH Q ss_conf 8667999999----99756899953799999999 Q gi|254780762|r 6 TGKEIENLIK----ILARIPGFGPRSARRATLHL 35 (201) Q Consensus 6 ~~~~l~~LI~----~l~kLPGIG~KsA~R~a~~L 35 (201) .+....++++ .+++|||||+|+++|+.-.| T Consensus 294 ~~~~~~~~L~~~~lpI~~i~GIG~~~~~kL~~~L 327 (520) T 3mfi_A 294 KNDCLLDFLDCGKFEITSFWTLGGVLGKELIDVL 327 (520) T ss_dssp CGGGHHHHHTSSSCCGGGSTTCSSHHHHHHHHHT T ss_pred CHHHHHHHHHHCCCCCCEECCCCHHHHHHHHHHH T ss_conf 8478999987357980100674789999999985 No 61 >3cng_A Nudix hydrolase; structural genomics, APC7497, PSI-2, protein structure initiative, midwest center for structural genomics; 2.00A {Nitrosomonas europaea atcc 19718} Probab=65.32 E-value=0.5 Score=26.87 Aligned_cols=77 Identities=16% Similarity=0.200 Sum_probs=50.1 Q ss_pred HCCCCCCCCCCCC-----CC-----CCCCCCCCCCCC---CEEEEEECHHHHHHHHHH-CCEEEEEEEHHHHCCCCCCCC Q ss_conf 5182889997334-----56-----541003555567---369998358899999751-740134210121002000268 Q gi|254780762|r 56 KVCLCSICGNVDT-----TD-----PCAICIDQQRDA---SVIIVVEDVADLWALERS-KAVNALYHVLGGSLSPLDRIG 121 (201) Q Consensus 56 ~i~~C~~C~~l~~-----~~-----~C~iC~d~~Rd~---~~lCVVE~~~Di~~IE~t-~~y~G~YhVLgG~ispl~g~~ 121 (201) .+++|+.||.-.+ .+ .|+-|.-..... ...+||++...+.-+.+. .-++|.|-.-||.+.+ |-. T Consensus 2 ~~~yCp~CG~~~~~~~~~g~~~~~~~C~~C~~~~y~~p~v~v~~ii~~~~~vLLv~r~~~~~~g~W~lPGG~ve~--GEs 79 (189) T 3cng_A 2 HMKFCSQCGGEVILRIPEGDTLPRYICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFMEN--NET 79 (189) T ss_dssp -CCBCTTTCCBCEEECCTTCSSCEEEETTTTEEECCCCEEEEEEEEEETTEEEEEEESSSSSTTCEECSEEECCT--TCC T ss_pred CCEECCCCCCCCEECCCCCCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCEECCCCCCCC--CCC T ss_conf 760584678756403468897247537999976089998599999984992889963689999858288423568--989 Q ss_pred HHHCCHHHHHHHH Q ss_conf 1112889999985 Q gi|254780762|r 122 PEDIGIQSLIERI 134 (201) Q Consensus 122 p~~l~i~~L~~ri 134 (201) |++--+.++.+=. T Consensus 80 ~eeaa~REv~EEt 92 (189) T 3cng_A 80 LVQGAARETLEEA 92 (189) T ss_dssp HHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHH T ss_conf 9999889988754 No 62 >1jyk_A LICC protein, CTP:phosphocholine cytidylytransferase; 3D structure, CTP:phosphocholine cytidylyltransferase; 1.50A {Streptococcus pneumoniae} SCOP: c.68.1.13 PDB: 1jyl_A* Probab=64.74 E-value=8 Score=18.80 Aligned_cols=13 Identities=31% Similarity=0.240 Sum_probs=8.2 Q ss_pred HHHHHHHHHHHHC Q ss_conf 6799999999756 Q gi|254780762|r 8 KEIENLIKILARI 20 (201) Q Consensus 8 ~~l~~LI~~l~kL 20 (201) +-|+..++.|++. T Consensus 57 plI~~~i~~l~~~ 69 (254) T 1jyk_A 57 PLIEYQIEFLKEK 69 (254) T ss_dssp EHHHHHHHHHHHT T ss_pred EHHHHHHHHHHHC T ss_conf 8899999999986 No 63 >1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein, transferase; HET: DNA; 1.60A {Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A* 1eqn_A* 3b39_A* Probab=64.58 E-value=8 Score=18.78 Aligned_cols=92 Identities=22% Similarity=0.273 Sum_probs=57.2 Q ss_pred CCCCCCCEEEEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHHH Q ss_conf 55556736999835889999975174013421012100200026811128899999851578554999946997868999 Q gi|254780762|r 77 DQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTA 156 (201) Q Consensus 77 d~~Rd~~~lCVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta 156 (201) ..-|..+.+.|||-..|+++.-+.| ++-.--.+|..++ .+++ .++.|. .++|++++...--|..-+ T Consensus 158 ~~i~~~~~viivEG~~Dvi~l~q~G-i~n~VA~~GTa~t------~~~~---~~l~r~----~~~i~l~~D~D~AG~~A~ 223 (338) T 1dd9_A 158 QDNAEPNRLLVVEGYMDVVALAQYG-INYAVASLGTSTT------ADHI---QLLFRA----TNNVICCYDGDRAGRDAA 223 (338) T ss_dssp HTCSSCSCEEEESSHHHHHHHHHTT-CCCEEECCC-CCC------HHHH---HHHHHH----CSEEEEEEESSHHHHHHH T ss_pred HHHCCCCCEEEEECHHHHHHHHHHC-CCCCCCCCCCCCC------HHHH---HHHHHC----CCCEEEEECCCCCCHHHH T ss_conf 7522567279983579999998704-2245555454754------5889---987622----785699845765430457 Q ss_pred H-HHHHHHCC--CCCEEEEEECCCCCCCCHH Q ss_conf 9-99998201--7980887414674882066 Q gi|254780762|r 157 H-YIMDKLKG--IDVKITRLAYGIPMGSELD 184 (201) Q Consensus 157 ~-yi~~~lk~--~~ikitrla~GiP~G~~le 184 (201) . -+...++. .++.+.- --+|-|-+.+ T Consensus 224 ~r~~~~~l~~~~~g~~v~v--~~lp~g~DPD 252 (338) T 1dd9_A 224 WRALETALPYMTDGRQLRF--MFLPDGEDPD 252 (338) T ss_dssp HHHHHHHGGGCCTTCEEEE--EEECTTCCHH T ss_pred HHHHHHHHHHHCCCCEEEE--EECCCCCCHH T ss_conf 7489997665048975999--9799997979 No 64 >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=63.55 E-value=4.5 Score=20.49 Aligned_cols=15 Identities=13% Similarity=0.209 Sum_probs=8.6 Q ss_pred CCCHHHHHHHHHHHH Q ss_conf 978689999999982 Q gi|254780762|r 149 TIEGQTTAHYIMDKL 163 (201) Q Consensus 149 t~EGe~Ta~yi~~~l 163 (201) |-.-+.|+.||..+. T Consensus 161 T~s~~eTa~~L~~l~ 175 (311) T 2ziu_A 161 VQDAKESAAYLTIMT 175 (311) T ss_dssp CSSHHHHHHHHHHHH T ss_pred CCCHHHHHHHHHHHH T ss_conf 357899999999999 No 65 >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=63.13 E-value=2.3 Score=22.38 Aligned_cols=21 Identities=14% Similarity=0.093 Sum_probs=17.6 Q ss_pred HHHHHHCCCCCHHHHHHHHHH Q ss_conf 999975689995379999999 Q gi|254780762|r 14 IKILARIPGFGPRSARRATLH 34 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a~~ 34 (201) .+.|..++|+|++.++|+-+| T Consensus 47 ~~eL~~I~Gvg~~k~~kY~~F 67 (81) T 1d8b_A 47 DSAFATLGTVEDKYRRRFKYF 67 (81) T ss_dssp HHHHGGGSCCCHHHHHHGGGT T ss_pred HHHHCCCCCCCHHHHHHHHHH T ss_conf 999827999998999999999 No 66 >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=61.63 E-value=6.5 Score=19.40 Aligned_cols=15 Identities=33% Similarity=0.837 Sum_probs=5.4 Q ss_pred HHHCCCCCHHHHHHH Q ss_conf 975689995379999 Q gi|254780762|r 17 LARIPGFGPRSARRA 31 (201) Q Consensus 17 l~kLPGIG~KsA~R~ 31 (201) |..+||||||+.+++ T Consensus 170 Ld~I~GIG~k~~~~L 184 (220) T 2nrt_A 170 LDNVPGIGPIRKKKL 184 (220) T ss_dssp HTTSTTCCHHHHHHH T ss_pred CHHCCCCCHHHHHHH T ss_conf 100379699999999 No 67 >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=61.56 E-value=3 Score=21.69 Aligned_cols=20 Identities=10% Similarity=0.190 Sum_probs=16.1 Q ss_pred HHHHCCCCCHHHHHHHHHHH Q ss_conf 99756899953799999999 Q gi|254780762|r 16 ILARIPGFGPRSARRATLHL 35 (201) Q Consensus 16 ~l~kLPGIG~KsA~R~a~~L 35 (201) .++++||||+++++|+.-+= T Consensus 283 pv~~l~GIG~~~~~~L~~~g 302 (459) T 1t94_A 283 PIRKVSGIGKVTEKMLKALG 302 (459) T ss_dssp BGGGCTTSCHHHHHHHHHTT T ss_pred CCCEECCCCCHHHHHHHHHC T ss_conf 83533688841378898707 No 68 >1vk2_A Uracil-DNA glycosylase TM0511; structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics, hydrolase; 1.90A {Thermotoga maritima} SCOP: c.18.1.2 PDB: 1l9g_A Probab=59.90 E-value=5 Score=20.16 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=28.2 Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEE-CHH Q ss_conf 99999999985182889997334565410035555673699983-588 Q gi|254780762|r 46 LAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVE-DVA 92 (201) Q Consensus 46 l~~~l~~~~~~i~~C~~C~~l~~~~~C~iC~d~~Rd~~~lCVVE-~~~ 92 (201) -.++|..+.+.|+.|..|. +.......+...-+.+ +.||||. .|. T Consensus 16 ~~~~l~~L~~~i~~C~~C~-L~~~~~~~V~g~G~~~-a~imiVgeaPg 61 (204) T 1vk2_A 16 REELMEIVSERVKKCTACP-LHLNRTNVVVGEGNLD-TRIVFVGEGPG 61 (204) T ss_dssp HHHHHHHHHHHHHHCCSSG-GGGTCSSCCCCEECTT-CSEEEEESCCC T ss_pred HHHHHHHHHHHHHCCCCCC-CCCCCCCCCCCCCCCC-CCEEEEECCCC T ss_conf 9999999999986187897-9889988256889999-99999989974 No 69 >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=59.40 E-value=7.3 Score=19.05 Aligned_cols=38 Identities=24% Similarity=0.394 Sum_probs=25.6 Q ss_pred CCHHHHHHHHH---HHHCCCCCHHHHHHHHH-------HHHHCCHHHH Q ss_conf 86679999999---97568999537999999-------9971998999 Q gi|254780762|r 6 TGKEIENLIKI---LARIPGFGPRSARRATL-------HLVKKKEQLL 43 (201) Q Consensus 6 ~~~~l~~LI~~---l~kLPGIG~KsA~R~a~-------~Ll~~~~~~~ 43 (201) .|......+.. ++.|||||+++++++.- .|.+.+...+ T Consensus 222 ~~~~~~~~L~~l~pv~~l~GiG~~~~~~L~~~Gi~ti~dl~~~~~~~L 269 (420) T 3osn_A 222 LPESCQHLIHSLNHIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKIL 269 (420) T ss_dssp CGGGHHHHHHHCSSGGGSTTCCHHHHHHHHHTTCCSHHHHHHSCHHHH T ss_pred CHHHHHHHHHCCCCHHHHCCCCHHHHHHHHHHCCCCHHHHHCCCHHHH T ss_conf 668899998566768885688878999986425660998752755369 No 70 >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=57.51 E-value=4 Score=20.80 Aligned_cols=10 Identities=10% Similarity=0.202 Sum_probs=4.8 Q ss_pred CCCCCCCCHH Q ss_conf 0200026811 Q gi|254780762|r 114 LSPLDRIGPE 123 (201) Q Consensus 114 ispl~g~~p~ 123 (201) ++.+.|+||. T Consensus 237 ~~gv~giG~k 246 (336) T 1rxw_A 237 NEGVKGVGVK 246 (336) T ss_dssp BCCCTTCCHH T ss_pred CCCCCCCCHH T ss_conf 8999996889 No 71 >3bqs_A Uncharacterized protein; 10114F, NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.42A {Listeria monocytogenes str} PDB: 3bqt_A 3mab_A Probab=56.37 E-value=4.2 Score=20.66 Aligned_cols=28 Identities=18% Similarity=0.192 Sum_probs=20.1 Q ss_pred HHHHCCCCCHHHHHHHHHHHHHCCHHHH Q ss_conf 9975689995379999999971998999 Q gi|254780762|r 16 ILARIPGFGPRSARRATLHLVKKKEQLL 43 (201) Q Consensus 16 ~l~kLPGIG~KsA~R~a~~Ll~~~~~~~ 43 (201) .|+.||+||+++++.+.--=+...++.. T Consensus 5 ~L~~LPNig~~~e~~L~~iGI~~~~~L~ 32 (93) T 3bqs_A 5 NLSELPNIGKVLEQDLIKAGIKTPVELK 32 (93) T ss_dssp CGGGSTTCCHHHHHHHHHTTCCSHHHHH T ss_pred HHHHCCCCCHHHHHHHHHCCCCCHHHHH T ss_conf 7724899999999999993999899998 No 72 >1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E* Probab=55.91 E-value=11 Score=17.79 Aligned_cols=118 Identities=14% Similarity=0.194 Sum_probs=52.3 Q ss_pred HHHHHHHHHHH--HCC---------CCCHHH-HHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCC---CCCC-CC Q ss_conf 67999999997--568---------999537-99999999719989999999999999985182889997---3345-65 Q gi|254780762|r 8 KEIENLIKILA--RIP---------GFGPRS-ARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGN---VDTT-DP 71 (201) Q Consensus 8 ~~l~~LI~~l~--kLP---------GIG~Ks-A~R~a~~Ll~~~~~~~~~l~~~l~~~~~~i~~C~~C~~---l~~~-~~ 71 (201) +..++|...+. +|| |+|+.+ |..+|-.|+-.+.. .-..|..|.. +... .+ T Consensus 9 ~~~~~L~~~~~~~~l~ha~L~~G~~G~GK~~~a~~~a~~llc~~~~--------------~~~~c~~c~~c~~i~~~~hp 74 (334) T 1a5t_A 9 PDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQ--------------GHKSCGHCRGCQLMQAGTHP 74 (334) T ss_dssp HHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCB--------------TTBCCSCSHHHHHHHHTCCT T ss_pred HHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCC--------------CCCCCCCCHHHHHHHCCCCC T ss_conf 9999999999869956036358999988999999999997087998--------------88888666899999757999 Q ss_pred CCCCCCCCCCCCEEEEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEE Q ss_conf 4100355556736999835889999975174013421012100200026811128899999851578554999 Q gi|254780762|r 72 CAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIF 144 (201) Q Consensus 72 C~iC~d~~Rd~~~lCVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIl 144 (201) --....+..+.+.| -|+...++...=....+.|.|-|+ .|...|...++. -.+|++-+.+..-.-++| T Consensus 75 d~~~i~~~~~~~~i-~i~~iR~l~~~~~~~~~~~~~kii--iI~~ad~m~~~a--~nalLK~lEeP~~~~~fi 142 (334) T 1a5t_A 75 DYYTLAPEKGKNTL-GVDAVREVTEKLNEHARLGGAKVV--WVTDAALLTDAA--ANALLKTLEEPPAETWFF 142 (334) T ss_dssp TEEEECCCTTCSSB-CHHHHHHHHHHTTSCCTTSSCEEE--EESCGGGBCHHH--HHHHHHHHTSCCTTEEEE T ss_pred CEEEECCHHCCCCC-CHHHHHHHHHHHHHCCCCCCCEEE--EECCHHHCCHHH--HHHHHHHHHCCCCCCEEE T ss_conf 74543212104657-899999999986426446895799--977845448656--899999986597331343 No 73 >1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family, transferase/DNA complex; HET: DNA MSE ADI; 1.70A {Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB: 1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A* 1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A* 2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ... Probab=55.24 E-value=4.5 Score=20.46 Aligned_cols=36 Identities=22% Similarity=0.397 Sum_probs=22.7 Q ss_pred CHHHHHHHHH--HHHCCCCCHHHHHHHHH-------HHHHCCHHH Q ss_conf 6679999999--97568999537999999-------997199899 Q gi|254780762|r 7 GKEIENLIKI--LARIPGFGPRSARRATL-------HLVKKKEQL 42 (201) Q Consensus 7 ~~~l~~LI~~--l~kLPGIG~KsA~R~a~-------~Ll~~~~~~ 42 (201) +..+++++.. +++|||||+|+++++.- .|.+.+.+. T Consensus 168 ~~~~~~~L~~lpv~~l~Gig~~~~~~L~~~Gi~ti~dl~~~~~~~ 212 (352) T 1jx4_A 168 DEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDK 212 (352) T ss_dssp HHHHHHHHHHSBGGGSTTCCHHHHHHHHTTTCCBGGGGGSSCHHH T ss_pred CCCCCCCCCCCCEEEECCCCCHHHHHHHHHCCCCHHHHHCCCHHH T ss_conf 432000002676024148870468899984686825413279789 No 74 >1wud_A ATP-dependent DNA helicase RECQ; DNA-binding domain, HRDC, hydrolase; 2.20A {Escherichia coli} SCOP: a.60.8.1 Probab=55.14 E-value=9.2 Score=18.38 Aligned_cols=24 Identities=17% Similarity=0.229 Sum_probs=19.4 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 999975689995379999999971 Q gi|254780762|r 14 IKILARIPGFGPRSARRATLHLVK 37 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a~~Ll~ 37 (201) .+.|.++||||++.++|+--.+|. T Consensus 54 ~~eL~~I~Gvg~~k~~~yG~~iL~ 77 (89) T 1wud_A 54 ASEMLSVNGVGMRKLERFGKPFMA 77 (89) T ss_dssp HHHHHTSTTCCHHHHHHHHHHHHH T ss_pred HHHHCCCCCCCHHHHHHHHHHHHH T ss_conf 999807999899999999999999 No 75 >2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ewa_A* 3ew9_A* 3etl_A* 2gdj_A* Probab=54.90 E-value=6.9 Score=19.24 Aligned_cols=32 Identities=22% Similarity=0.440 Sum_probs=24.6 Q ss_pred HHHHHCCCCCHHHHHHH-------HHHHHHCCHHHHHHH Q ss_conf 99975689995379999-------999971998999999 Q gi|254780762|r 15 KILARIPGFGPRSARRA-------TLHLVKKKEQLLGPL 46 (201) Q Consensus 15 ~~l~kLPGIG~KsA~R~-------a~~Ll~~~~~~~~~l 46 (201) +.|..||||||++.+|+ +..|+..++.++.+. T Consensus 3 ~~l~~~~g~~~~~~~kL~~ag~~t~~~l~~~~~~~l~~~ 41 (322) T 2i1q_A 3 DNLTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDI 41 (322) T ss_dssp --CTTSTTCCHHHHHHHHHHTCCSHHHHHTCCHHHHHTS T ss_pred CCHHCCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHH T ss_conf 630027998999999999869960999973999999987 No 76 >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=54.87 E-value=4.4 Score=20.56 Aligned_cols=15 Identities=13% Similarity=0.133 Sum_probs=8.2 Q ss_pred CEEEEEECHHHHHHH Q ss_conf 369998358899999 Q gi|254780762|r 83 SVIIVVEDVADLWAL 97 (201) Q Consensus 83 ~~lCVVE~~~Di~~I 97 (201) ..+.||....|...+ T Consensus 144 ~~v~IvS~DkD~~QL 158 (290) T 1exn_A 144 DHVWLISTDGDWDTL 158 (290) T ss_dssp SCEEEECSCGGGGGG T ss_pred CEEEEEECCCCHHHH T ss_conf 758999358864441 No 77 >2rhf_A DNA helicase RECQ; HRDC, D. radiodurans, ATP-binding, hydrolase, nucleotide-binding; HET: DNA; 1.10A {Deinococcus radiodurans R1} Probab=54.86 E-value=8.4 Score=18.65 Aligned_cols=24 Identities=21% Similarity=0.459 Sum_probs=19.6 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 999975689995379999999971 Q gi|254780762|r 14 IKILARIPGFGPRSARRATLHLVK 37 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a~~Ll~ 37 (201) .+.|..+||||++.++|+.-.+|. T Consensus 46 ~~eL~~I~Gig~~k~~~yG~~il~ 69 (77) T 2rhf_A 46 LAELAEVPGLGEKRIEAYGERILD 69 (77) T ss_dssp HHHHTTSTTTCHHHHHHHHHHHHH T ss_pred HHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 999807999799999999999999 No 78 >2exu_A Transcription initiation protein SPT4/SPT5; helixs surrounding beta sheet; 2.23A {Saccharomyces cerevisiae} Probab=54.43 E-value=2.7 Score=21.98 Aligned_cols=88 Identities=16% Similarity=0.279 Sum_probs=51.8 Q ss_pred HCCCCCCCCCCCCCC-----CCCCCCC------------CCCCCCEEEEEECHHHHHHHHHHCCE---EEEEEEHHHHCC Q ss_conf 518288999733456-----5410035------------55567369998358899999751740---134210121002 Q gi|254780762|r 56 KVCLCSICGNVDTTD-----PCAICID------------QQRDASVIIVVEDVADLWALERSKAV---NALYHVLGGSLS 115 (201) Q Consensus 56 ~i~~C~~C~~l~~~~-----~C~iC~d------------~~Rd~~~lCVVE~~~Di~~IE~t~~y---~G~YhVLgG~is 115 (201) +-+-|..|+.+.+.+ -|+.|.+ .+-+.+=+-+|-+|.+=|.-...+.= .|.|-|= T Consensus 3 ~~rAC~~C~lI~t~~qf~~~gCpnC~~~~~~~~~~~~~~tS~~f~G~i~i~dP~~SwvAk~l~i~~~vpG~YAl~----- 77 (200) T 2exu_A 3 SERACMLCGIVQTTNEFNRDGCPNCQGIFEEAGVSTMECTSPSFEGLVGMCKPTKSWVAKWLSVDHSIAGMYAIK----- 77 (200) T ss_dssp CEEEETTTCBEEEHHHHHHHCCTTTHHHHHHHTCCSGGGEESCEEEEEEESCTTTCHHHHHTTCTTSCSEEEEEE----- T ss_pred CCCHHHHCCCEECHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHCCCCCCCCEEEEE----- T ss_conf 460455199550142413579999700231466653455676713189996852739999857877789737999----- Q ss_pred CCCCCCHHHCCHHHHHH-HHCCCCCCEEEEEECCCC Q ss_conf 00026811128899999-851578554999946997 Q gi|254780762|r 116 PLDRIGPEDIGIQSLIE-RIEVKKIRELIFAISATI 150 (201) Q Consensus 116 pl~g~~p~~l~i~~L~~-ri~~~~i~EVIlA~~~t~ 150 (201) ..|.-|+++. +.|.+ |-+++.=+.-|.|..-+. T Consensus 78 -V~g~lp~~i~-~~l~~y~~rd~s~~~sIw~Vrc~~ 111 (200) T 2exu_A 78 -VDGRLPAEVV-ELLPHYKPRDGSGSATIWGVRCRP 111 (200) T ss_dssp -ECSCCCHHHH-TTCTTCCCTTSCSCCCEEEEEECT T ss_pred -ECCCCCHHHH-HHHHHCCCCCCCCCCCEEEEECCC T ss_conf -5174998899-999972789887887579997578 No 79 >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=54.29 E-value=3.4 Score=21.25 Aligned_cols=38 Identities=26% Similarity=0.464 Sum_probs=23.7 Q ss_pred CHHHHHHHHH--HHHCCCCCHHHHHHHHH-------HHHHCCHHHHH Q ss_conf 6679999999--97568999537999999-------99719989999 Q gi|254780762|r 7 GKEIENLIKI--LARIPGFGPRSARRATL-------HLVKKKEQLLG 44 (201) Q Consensus 7 ~~~l~~LI~~--l~kLPGIG~KsA~R~a~-------~Ll~~~~~~~~ 44 (201) +..+.+.... ++.+||||+|+++++.- .|.+.+.+.+. T Consensus 169 ~~~~~~~l~~lpv~~l~GiG~~~~~~L~~~Gi~t~~dl~~~~~~~l~ 215 (354) T 3bq0_A 169 PTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELE 215 (354) T ss_dssp GGGHHHHHHHCBSTTSTTCCHHHHHHHTTTTCCBGGGGGGSCHHHHH T ss_pred CHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHH T ss_conf 06799999861066615964789999998189699995458987899 No 80 >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=54.25 E-value=3.3 Score=21.39 Aligned_cols=18 Identities=17% Similarity=0.342 Sum_probs=14.5 Q ss_pred HHHHCCCCCHHHHHHHHH Q ss_conf 997568999537999999 Q gi|254780762|r 16 ILARIPGFGPRSARRATL 33 (201) Q Consensus 16 ~l~kLPGIG~KsA~R~a~ 33 (201) .++.|+|||||.|++++- T Consensus 116 ~i~~lkGVGpk~a~~L~k 133 (780) T 1gm5_A 116 DIQYAKGVGPNRKKKLKK 133 (780) T ss_dssp CSSSSSSCCHHHHHHHHT T ss_pred CCCCCCCCCHHHHHHHHH T ss_conf 860178815999999997 No 81 >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=53.36 E-value=5.2 Score=20.06 Aligned_cols=33 Identities=27% Similarity=0.454 Sum_probs=14.9 Q ss_pred EEEHHHH---CCCCCCCCHHHCCHHHHHHHHCCCCCCEEE Q ss_conf 2101210---020002681112889999985157855499 Q gi|254780762|r 107 YHVLGGS---LSPLDRIGPEDIGIQSLIERIEVKKIRELI 143 (201) Q Consensus 107 YhVLgG~---ispl~g~~p~~l~i~~L~~ri~~~~i~EVI 143 (201) |-+|+|. +.-..|+||.. --+|++.- +++++|+ T Consensus 226 ~~iL~G~dyn~~gv~giG~kt--A~kli~~~--~sle~i~ 261 (346) T 2izo_A 226 IGILIGTDYNPDGIRGIGPER--ALKIIKKY--GKIEKAM 261 (346) T ss_dssp HHHHHCCSSSTTCSTTCCHHH--HHHHHHHS--SCC---- T ss_pred HHHHCCCCCCCCCCCCCCHHH--HHHHHHHH--CCHHHHH T ss_conf 998458656866689837999--99999993--9999999 No 82 >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=51.60 E-value=9 Score=18.44 Aligned_cols=46 Identities=24% Similarity=0.243 Sum_probs=30.9 Q ss_pred EEEEECCCCCHHHHHHHHHHHHCCCC-CEEEEEECCCCCCCCHHHHHHHHHHHHHH Q ss_conf 99994699786899999999820179-80887414674882066634799999983 Q gi|254780762|r 142 LIFAISATIEGQTTAHYIMDKLKGID-VKITRLAYGIPMGSELDYLDDGTIFEAIR 196 (201) Q Consensus 142 VIlA~~~t~EGe~Ta~yi~~~lk~~~-ikitrla~GiP~G~~ley~D~~TL~~Al~ 196 (201) |+=+-+||..|...+..+...|...+ +-||-+|+|+ |......|++ T Consensus 132 IVGsR~~s~yg~~~a~~l~~~la~~g~~VVSGlA~GI---------D~~AH~~aL~ 178 (382) T 3maj_A 132 IVGSRNASGAGLKFAGQLAADLGAAGFVVISGLARGI---------DQAAHRASLS 178 (382) T ss_dssp EECCSSCCHHHHHHHHHHHHHHHHHTCEEEECCCTTH---------HHHHHHHHTT T ss_pred EECCCCCCHHHHHHHHHHHHHHHHCCEEEECCCCCCC---------CHHHHHHHHC T ss_conf 9779999976999999999999878979981565682---------1899874032 No 83 >1ui0_A Uracil-DNA glycosylase; base excision repair, iron/sulfer cluster, thermophIle, riken structural genomics/proteomics initiative, RSGI; 1.50A {Thermus thermophilus} SCOP: c.18.1.2 PDB: 1ui1_A Probab=51.21 E-value=9.9 Score=18.16 Aligned_cols=54 Identities=7% Similarity=0.131 Sum_probs=29.1 Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECHHHHHHHHHHCCEE Q ss_conf 99999985182889997334565410035555673699983588999997517401 Q gi|254780762|r 49 AMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVN 104 (201) Q Consensus 49 ~l~~~~~~i~~C~~C~~l~~~~~C~iC~d~~Rd~~~lCVVE~~~Di~~IE~t~~y~ 104 (201) .|.++.+.|+.|..|. +.....=.+-.+-..+ +.|+||...-+...-+.-..|. T Consensus 2 ~l~~L~~~i~~C~~C~-L~~~~~~~V~g~G~~~-a~imiVg~aPg~~e~~~g~pf~ 55 (205) T 1ui0_A 2 TLELLQAQAQNCTACR-LMEGRTRVVFGEGNPD-AKLMIVGEGPGEEEDKTGRPFV 55 (205) T ss_dssp CHHHHHHHHTTCCSSG-GGTTCSSCCCCEECTT-CSEEEEESCCCHHHHHHSCSSC T ss_pred CHHHHHHHHHCCCCCC-CCCCCCCCCCCCCCCC-CCEEEEECCCCHHHHHCCCCCC T ss_conf 8899999986788899-9889978554789999-9999995887607762088646 No 84 >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=49.51 E-value=14 Score=17.13 Aligned_cols=62 Identities=23% Similarity=0.236 Sum_probs=37.9 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECHHHH Q ss_conf 99975689995379999999971998999999999999998518288999733456541003555567369998358899 Q gi|254780762|r 15 KILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADL 94 (201) Q Consensus 15 ~~l~kLPGIG~KsA~R~a~~Ll~~~~~~~~~l~~~l~~~~~~i~~C~~C~~l~~~~~C~iC~d~~Rd~~~lCVVE~~~Di 94 (201) +.|..++|||+++|+.+.-|+-. ....++.+.|....-+. . .. T Consensus 539 e~L~~I~GIG~~~A~si~~~f~~---~~~~~~i~~L~~~g~~~---------~----------~~--------------- 581 (667) T 1dgs_A 539 EELIEVEEVGELTARAILETLKD---PAFRDLVRRLKEAGVSM---------E----------SK--------------- 581 (667) T ss_dssp HHHHTSTTCCHHHHHHHHHHHHC---HHHHHHHHHHHHTTCCC---------B----------CC--------------- T ss_pred HHHHCCCCCCHHHHHHHHHHHCC---HHHHHHHHHHHHCCCCC---------C----------CC--------------- T ss_conf 99857799489999999999759---99999999999759987---------7----------65--------------- Q ss_pred HHHHHHCCEEEEEEEHHHHCC Q ss_conf 999751740134210121002 Q gi|254780762|r 95 WALERSKAVNALYHVLGGSLS 115 (201) Q Consensus 95 ~~IE~t~~y~G~YhVLgG~is 115 (201) .+..+.+.|+-||+-|.++ T Consensus 582 --~~~~~~l~gk~~v~TG~l~ 600 (667) T 1dgs_A 582 --EEVSDLLSGLTFVLTGELS 600 (667) T ss_dssp --------------------- T ss_pred --CCCCCCCCCCEEEEECCCC T ss_conf --5558856898899985747 No 85 >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=48.45 E-value=10 Score=18.14 Aligned_cols=23 Identities=22% Similarity=0.381 Sum_probs=11.6 Q ss_pred HHHHHHHHCCCCCCEEEEEECCCCCH Q ss_conf 89999985157855499994699786 Q gi|254780762|r 127 IQSLIERIEVKKIRELIFAISATIEG 152 (201) Q Consensus 127 i~~L~~ri~~~~i~EVIlA~~~t~EG 152 (201) ++.+..++.. .--++++++|+.. T Consensus 159 le~~~~~~~~---~~~~i~lSAt~~~ 181 (720) T 2zj8_A 159 LEVILAHMLG---KAQIIGLSATIGN 181 (720) T ss_dssp HHHHHHHHBT---TBEEEEEECCCSC T ss_pred HHHHHHCCCC---CCHHEEECCCCCC T ss_conf 9987620334---2121010045798 No 86 >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=48.42 E-value=6.8 Score=19.25 Aligned_cols=17 Identities=18% Similarity=0.260 Sum_probs=7.9 Q ss_pred EEHHHHC-C-C-CCCCCHHH Q ss_conf 1012100-2-0-00268111 Q gi|254780762|r 108 HVLGGSL-S-P-LDRIGPED 124 (201) Q Consensus 108 hVLgG~i-s-p-l~g~~p~~ 124 (201) -+|+|.= + | +.|+||.. T Consensus 218 ~il~g~d~n~~gi~giG~k~ 237 (326) T 1a76_A 218 AIFMGTDYNPGGVKGIGFKR 237 (326) T ss_dssp HHHHCCTTSTTTTTTCCHHH T ss_pred HHEECCCCCCCCCCCCCHHH T ss_conf 80279645788999424999 No 87 >3nkl_A UDP-D-quinovosamine 4-dehydrogenase; alpha-beta fold, structural genomics, PSI-2, protein structu initiative; HET: MSE GOL; 1.90A {Vibrio fischeri} Probab=48.34 E-value=12 Score=17.49 Aligned_cols=46 Identities=17% Similarity=0.283 Sum_probs=33.1 Q ss_pred HHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCEEEEEE Q ss_conf 899999851578554999946997868999999998201798088741 Q gi|254780762|r 127 IQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLA 174 (201) Q Consensus 127 i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~lk~~~ikitrla 174 (201) .+.|.+.+++..++|||+|.+...+-+. .-|.+.+++.+++|..+. T Consensus 54 ~~~l~~~i~~~~i~~viia~p~~~~~~~--~~l~~~~~~~~i~i~~vP 99 (141) T 3nkl_A 54 PKYLERLIKKHCISTVLLAVPSASQVQK--KVIIESLAKLHVEVLTIP 99 (141) T ss_dssp GGGHHHHHHHHTCCEEEECCTTSCHHHH--HHHHHHHHTTTCEEEECC T ss_pred HHHHHHHHHHCCCCEEEEECCCCCHHHH--HHHHHHHHCCCCCEEECC T ss_conf 8787788864686389994588899999--999998750597237778 No 88 >2rrd_A BLM HRDC domain, HRDC domain from bloom syndrome protein; DNA helicase, RECQ family, HRDC DOMA binding protein; NMR {Homo sapiens} Probab=47.65 E-value=11 Score=17.96 Aligned_cols=25 Identities=12% Similarity=0.206 Sum_probs=19.6 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHC Q ss_conf 9999756899953799999999719 Q gi|254780762|r 14 IKILARIPGFGPRSARRATLHLVKK 38 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a~~Ll~~ 38 (201) ++.|.++||+|++.++|+.-.+|.. T Consensus 63 ~~eL~~I~Gv~~~k~~~yG~~il~~ 87 (101) T 2rrd_A 63 PEVLLQIDGVTEDKLEKYGAEVISV 87 (101) T ss_dssp HHHHHTSTTCCHHHHHHTHHHHHHH T ss_pred HHHHHCCCCCCHHHHHHHHHHHHHH T ss_conf 9998267787999999999999999 No 89 >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=45.57 E-value=3.6 Score=21.15 Aligned_cols=23 Identities=13% Similarity=0.326 Sum_probs=13.5 Q ss_pred HHHHCCCCCCCCHHHCCHHHHHHHH Q ss_conf 1210020002681112889999985 Q gi|254780762|r 110 LGGSLSPLDRIGPEDIGIQSLIERI 134 (201) Q Consensus 110 LgG~ispl~g~~p~~l~i~~L~~ri 134 (201) +...|.-+.|+||.. ...|++.. T Consensus 171 ~~S~Ld~I~GIG~~~--~~~Ll~~F 193 (226) T 3c65_A 171 FHSVLDDIPGVGEKR--KKALLNYF 193 (226) T ss_dssp ------------------------- T ss_pred CCCCCCCCCCCCHHH--HHHHHHHC T ss_conf 037110268869999--99999981 No 90 >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=45.32 E-value=8.2 Score=18.71 Aligned_cols=13 Identities=38% Similarity=0.670 Sum_probs=5.6 Q ss_pred HCCCCCHHHHHHH Q ss_conf 5689995379999 Q gi|254780762|r 19 RIPGFGPRSARRA 31 (201) Q Consensus 19 kLPGIG~KsA~R~ 31 (201) .+||||+|+|-++ T Consensus 236 gv~giG~ktA~kl 248 (379) T 1ul1_X 236 SIRGIGPKRAVDL 248 (379) T ss_dssp CCTTCCHHHHHHH T ss_pred CCCCCCHHHHHHH T ss_conf 6788668999999 No 91 >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=45.30 E-value=8.1 Score=18.77 Aligned_cols=37 Identities=19% Similarity=0.324 Sum_probs=24.5 Q ss_pred CHHHHHHHHH--HHHCCCCCHHHHHHHH-------HHHHHCCHHHH Q ss_conf 6679999999--9756899953799999-------99971998999 Q gi|254780762|r 7 GKEIENLIKI--LARIPGFGPRSARRAT-------LHLVKKKEQLL 43 (201) Q Consensus 7 ~~~l~~LI~~--l~kLPGIG~KsA~R~a-------~~Ll~~~~~~~ 43 (201) +..+.+++.. ++.|||||+++++|+. ..|.+.+.+.+ T Consensus 305 ~~~~~~fL~~lpv~~lpGIG~~~~~kL~~lGI~Ti~DL~~l~~~~L 350 (504) T 3gqc_A 305 PEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKL 350 (504) T ss_dssp GGGHHHHHHHSBGGGSTTCCHHHHHHHHHTTCCBHHHHTTSCHHHH T ss_pred HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCHHHHHCCCHHHH T ss_conf 8998898864133344787878999998616850999855999999 No 92 >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=44.42 E-value=8.7 Score=18.54 Aligned_cols=41 Identities=17% Similarity=0.246 Sum_probs=23.9 Q ss_pred CHHHHHHHH--HHHHCCCCCHHH-HHHHHHH-------HHHCCHHHH-HHHH Q ss_conf 667999999--997568999537-9999999-------971998999-9999 Q gi|254780762|r 7 GKEIENLIK--ILARIPGFGPRS-ARRATLH-------LVKKKEQLL-GPLA 47 (201) Q Consensus 7 ~~~l~~LI~--~l~kLPGIG~Ks-A~R~a~~-------Ll~~~~~~~-~~l~ 47 (201) |..+.+++. .+++|||||+|. ++++..+ |...+.+.+ ..|. T Consensus 243 ~~~~~~~l~~lpi~~l~GiG~k~~~~~L~~~gi~ti~dl~~~~~~~L~~~~G 294 (435) T 3mr3_A 243 HGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFG 294 (435) T ss_dssp GGGHHHHHHTCBGGGSTTCSSHHHHHHHHHHTCCBGGGGGGSCHHHHHHHHC T ss_pred HHHHHHHHHHCCCCEECCCCHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHHC T ss_conf 7899999983767760776757899999995894789987399989999978 No 93 >1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B* Probab=42.46 E-value=18 Score=16.42 Aligned_cols=79 Identities=14% Similarity=0.213 Sum_probs=41.8 Q ss_pred EECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEE-EEEECC------------------ Q ss_conf 8358899999751740134210121002000268111288999998515785549-999469------------------ Q gi|254780762|r 88 VEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIREL-IFAISA------------------ 148 (201) Q Consensus 88 VE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EV-IlA~~~------------------ 148 (201) |+...++...=....+.|.|-|+ .|...|+.+++. ...|++-+++..-.-+ |++++. T Consensus 101 i~~ir~~~~~~~~~~~~~~~kvi--iide~d~l~~~a--~n~Llk~lEep~~~~~~il~t~~~~~~~~ti~SRc~~i~~~ 176 (373) T 1jr3_A 101 VEDTRDLLDNVQYAPARGRFKVY--LIDEVHMLSRHS--FNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLK 176 (373) T ss_dssp SSCHHHHHHHTTSCCSSSSSEEE--EEECGGGSCHHH--HHHHHHHHHSCCSSEEEEEEESCGGGSCHHHHTTSEEEECC T ss_pred HHHHHHHHHHHHHCCCCCCCEEE--EEECCCCCCHHH--HHHHHHHHHCCCCCEEEEEECCCHHHCHHHHHHHHHHCCCC T ss_conf 99999999998546657997699--986836389999--99999998578867389884487565428999654310113 Q ss_pred CCCHHHHHHHHHHHHCCCCCEE Q ss_conf 9786899999999820179808 Q gi|254780762|r 149 TIEGQTTAHYIMDKLKGIDVKI 170 (201) Q Consensus 149 t~EGe~Ta~yi~~~lk~~~iki 170 (201) .+.-+--..++...++..++++ T Consensus 177 ~~~~~~~~~~l~~i~~~e~~~~ 198 (373) T 1jr3_A 177 ALDVEQIRHQLEHILNEEHIAH 198 (373) T ss_dssp CCCHHHHHHHHHHHHHHHTCCB T ss_pred CCCHHHHHHHHHHHHHHCCCCC T ss_conf 4670778999999999819998 No 94 >1am7_A Lysozyme; glycosidase, transglycosylase, evolution; HET: TRN; 2.30A {Enterobacteria phage lambda} SCOP: d.2.1.4 PDB: 1d9u_A* 3d3d_A* Probab=41.21 E-value=19 Score=16.29 Aligned_cols=36 Identities=19% Similarity=0.419 Sum_probs=26.0 Q ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCH Q ss_conf 6686679999999975689995379999999971998 Q gi|254780762|r 4 KITGKEIENLIKILARIPGFGPRSARRATLHLVKKKE 40 (201) Q Consensus 4 ~~~~~~l~~LI~~l~kLPGIG~KsA~R~a~~Ll~~~~ 40 (201) |+.+.+++.+...+ .||..+|.+=.|+|++||+... T Consensus 68 Qfl~~Tw~~~~~~l-gl~~F~P~~QD~~a~~Ll~~r~ 103 (158) T 1am7_A 68 QLLSRXXDAYRKQL-GLKDFSPKSQDAVALQQIKERG 103 (158) T ss_dssp TBCHHHHHHHHHHH-TCCCCCHHHHHHHHHHHHHHTT T ss_pred HHHHHHHHHHHHHC-CCCCCCHHHHHHHHHHHHHHCC T ss_conf 75346799999963-9999985889999999999726 No 95 >2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structural genomics, PSI; NMR {Pyrococcus furiosus dsm 3638} SCOP: a.4.5.82 Probab=40.88 E-value=9.9 Score=18.16 Aligned_cols=28 Identities=21% Similarity=0.484 Sum_probs=18.3 Q ss_pred CCCCCCCCCCCC-----CCCCCCCCCCCCCCEE Q ss_conf 828899973345-----6541003555567369 Q gi|254780762|r 58 CLCSICGNVDTT-----DPCAICIDQQRDASVI 85 (201) Q Consensus 58 ~~C~~C~~l~~~-----~~C~iC~d~~Rd~~~l 85 (201) -.|..||+.-.+ ..|+-|.++.=+.-.. T Consensus 68 p~CrkCGfvF~d~~kkPSRCP~CKSE~Ie~P~F 100 (105) T 2gmg_A 68 AQCRKCGFVFKAEINIPSRCPKCKSEWIEEPRF 100 (105) T ss_dssp CBBTTTCCBCCCCSSCCSSCSSSCCCCBCCCCE T ss_pred HHHCCCCCEECCCCCCCCCCCCCCCCCCCCCCE T ss_conf 202308577478899999899988746249823 No 96 >2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M 3jyv_M* Probab=40.17 E-value=20 Score=16.18 Aligned_cols=90 Identities=20% Similarity=0.142 Sum_probs=53.5 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHH--------CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 99999975689995379999999971--------9989999999999999985182889997334565410035555673 Q gi|254780762|r 12 NLIKILARIPGFGPRSARRATLHLVK--------KKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDAS 83 (201) Q Consensus 12 ~LI~~l~kLPGIG~KsA~R~a~~Ll~--------~~~~~~~~l~~~l~~~~~~i~~C~~C~~l~~~~~C~iC~d~~Rd~~ 83 (201) .+.-+|..+-|||+++|..+.-.+=- ..++.+..+.+.|.+-.+.--+ -+++.-. .| -.+.. T Consensus 25 ~v~~aLt~I~GIG~~~A~~Ic~~lgI~~~~kvg~Lt~~ql~kl~~~I~~~~~~~ip---~w~~nr~------~d-~~~g~ 94 (152) T 2zkq_m 25 KIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIMQNPRQYKIP---DWFLNRQ------KD-VKDGK 94 (152) T ss_dssp BHHHHGGGSTTCCHHHHHHHHHHHTCCTTSBTTTSCHHHHHHHHHHHHTTCSCCSC---CCSSCSS------SC-CCCCS T ss_pred EEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC---HHHHHHH------HH-HHCCC T ss_conf 88765002106589999999999389954301519999999999998500011575---5877656------66-50453 Q ss_pred EEEEEECHH------HHHHHHHHCCEEEEEEEHH Q ss_conf 699983588------9999975174013421012 Q gi|254780762|r 84 VIIVVEDVA------DLWALERSKAVNALYHVLG 111 (201) Q Consensus 84 ~lCVVE~~~------Di~~IE~t~~y~G~YhVLg 111 (201) -..+||+.. |+...=+.+.|+|+=|..| T Consensus 95 ~~hli~~dL~~~~~~dI~rl~~i~syRG~RH~~g 128 (152) T 2zkq_m 95 YSQVLANGLDNKLREDLERLKKIRAHRGLRHFWG 128 (152) T ss_dssp SCCCSSHHHHHHHHHHHHHHHHSSCHHHHHHHHT T ss_pred CEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 1022076799999997999998605889998758 No 97 >1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11 Probab=39.23 E-value=4.5 Score=20.49 Aligned_cols=38 Identities=21% Similarity=0.407 Sum_probs=27.5 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHH-------HHHHHCCHHHHHHH Q ss_conf 799999999756899953799999-------99971998999999 Q gi|254780762|r 9 EIENLIKILARIPGFGPRSARRAT-------LHLVKKKEQLLGPL 46 (201) Q Consensus 9 ~l~~LI~~l~kLPGIG~KsA~R~a-------~~Ll~~~~~~~~~l 46 (201) ..++-++.|..|||||+..|+|+. -.|+..++..+.+. T Consensus 29 ~~~~~~~~l~~l~gv~~~~~~kL~~aG~~t~~~l~~~~~~~L~~~ 73 (349) T 1pzn_A 29 KKEKIIRSIEDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEV 73 (349) T ss_dssp ------CCSSCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHH T ss_pred CCHHCCCCHHHCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH T ss_conf 210001576337996999999999869972999970899999986 No 98 >1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus} SCOP: c.55.3.8 Probab=37.57 E-value=18 Score=16.35 Aligned_cols=58 Identities=9% Similarity=0.158 Sum_probs=35.8 Q ss_pred HCCCCCCCCH--HHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHH------HHHHHHHHCCCCCEEE Q ss_conf 0020002681--112889999985157855499994699786899------9999998201798088 Q gi|254780762|r 113 SLSPLDRIGP--EDIGIQSLIERIEVKKIRELIFAISATIEGQTT------AHYIMDKLKGIDVKIT 171 (201) Q Consensus 113 ~ispl~g~~p--~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~T------a~yi~~~lk~~~ikit 171 (201) .-+|+.-+.- .+-.++.|.+.+++.++..+++.++-+++|..+ ..|..+ |+..++.|. T Consensus 24 ~A~pl~~i~~~~~~~~~~~l~~li~e~~i~~iVvGlP~~~dG~~~~~~~~v~~f~~~-L~~~~~pv~ 89 (98) T 1iv0_A 24 LASGRGYLVRKTLEEDVEALLDFVRREGLGKLVVGLPLRTDLKESAQAGKVLPLVEA-LRARGVEVE 89 (98) T ss_dssp SCCCEEEEECCCHHHHHHHHHHHHHHHTCCEEEEECCCCCCSSSCCCSSTTHHHHHH-HHHTTCEEE T ss_pred EEECEEEEECCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCHHHHHHHHHHHH-HHHCCCCEE T ss_conf 781778898258568999999999971857499158977899919899999999999-863799999 No 99 >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=36.63 E-value=22 Score=15.82 Aligned_cols=23 Identities=22% Similarity=0.190 Sum_probs=18.7 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 99975689995379999999971 Q gi|254780762|r 15 KILARIPGFGPRSARRATLHLVK 37 (201) Q Consensus 15 ~~l~kLPGIG~KsA~R~a~~Ll~ 37 (201) +.|.++|++|+||.+.+--.|-+ T Consensus 44 ~dLl~i~NfG~kSl~EI~~~L~~ 66 (86) T 3k4g_A 44 VELLXTPNLGXXSLTEIXDVLAS 66 (86) T ss_dssp HHHHTSTTCCHHHHHHHHHHHHT T ss_pred HHHCCCCCCCHHHHHHHHHHHHH T ss_conf 99817889877269999999998 No 100 >1ci4_A Protein (barrier-TO-autointegration factor (BAF) ); DNA binding protein, retroviral integration, preintegration complex; 1.90A {Homo sapiens} SCOP: a.60.5.1 PDB: 1qck_A 2bzf_A 2ezx_A 2ezy_A 2ezz_A 2odg_A Probab=35.61 E-value=16 Score=16.82 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=21.4 Q ss_pred HHHCCCCCHHHHHHHH-------------HHHHHCCHHHHHHHH Q ss_conf 9756899953799999-------------999719989999999 Q gi|254780762|r 17 LARIPGFGPRSARRAT-------------LHLVKKKEQLLGPLA 47 (201) Q Consensus 17 l~kLPGIG~KsA~R~a-------------~~Ll~~~~~~~~~l~ 47 (201) ...|||||+.-++|+. |-+++.+++..++-. T Consensus 20 V~~l~GIG~~lg~~L~~kGfdKAy~vLGqfLvl~kde~~F~~Wl 63 (89) T 1ci4_A 20 VGSLAGIGEVLGKKLEERGFDKAYVVLGQFLVLKKDEDLFREWL 63 (89) T ss_dssp GGGSTTCCHHHHHHHHHTTCCSHHHHHHHHHHTTTCHHHHHHHH T ss_pred CCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHH T ss_conf 43147864899999998585399999999998566499999999 No 101 >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=35.10 E-value=23 Score=15.66 Aligned_cols=29 Identities=14% Similarity=0.331 Sum_probs=20.6 Q ss_pred HHHHHH----HHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 799999----99975689995379999999971 Q gi|254780762|r 9 EIENLI----KILARIPGFGPRSARRATLHLVK 37 (201) Q Consensus 9 ~l~~LI----~~l~kLPGIG~KsA~R~a~~Ll~ 37 (201) ++.+|+ +.|.++||+|+||-+.+--.|-+ T Consensus 31 tv~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~~ 63 (73) T 1z3e_B 31 TVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE 63 (73) T ss_dssp BHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHH T ss_pred CHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 799998689999974789866059999999998 No 102 >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=35.00 E-value=20 Score=16.15 Aligned_cols=12 Identities=8% Similarity=0.285 Sum_probs=6.8 Q ss_pred CCCCHHHHHHHH Q ss_conf 899953799999 Q gi|254780762|r 21 PGFGPRSARRAT 32 (201) Q Consensus 21 PGIG~KsA~R~a 32 (201) +|||+.+++++. T Consensus 31 ~Gvg~~~i~KL~ 42 (114) T 1b22_A 31 CGINANDVKKLE 42 (114) T ss_dssp TTCSHHHHHHHH T ss_pred CCCCHHHHHHHH T ss_conf 899999999999 No 103 >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=34.16 E-value=18 Score=16.41 Aligned_cols=27 Identities=15% Similarity=0.213 Sum_probs=15.3 Q ss_pred HHHHHHHHCCCCCCEEEEEECCCCCHH Q ss_conf 899999851578554999946997868 Q gi|254780762|r 127 IQSLIERIEVKKIRELIFAISATIEGQ 153 (201) Q Consensus 127 i~~L~~ri~~~~i~EVIlA~~~t~EGe 153 (201) ++.++.|.....-.=-++++++|+... T Consensus 159 le~~l~~~~~~~~~~~ii~lSat~~~~ 185 (702) T 2p6r_A 159 LEILVTKMRRMNKALRVIGLSATAPNV 185 (702) T ss_dssp HHHHHHHHHHHCTTCEEEEEECCCTTH T ss_pred HHHHHHHHHCCCCCHHHHCCCCCCCHH T ss_conf 999998630134320120013676248 No 104 >1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis/exocytosis complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A Probab=34.06 E-value=9.8 Score=18.19 Aligned_cols=68 Identities=15% Similarity=0.240 Sum_probs=44.9 Q ss_pred HHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEE--EEEECCCCCHHHHHHHHHHH Q ss_conf 899999751740134210121002000268111288999998515785549--99946997868999999998 Q gi|254780762|r 92 ADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIREL--IFAISATIEGQTTAHYIMDK 162 (201) Q Consensus 92 ~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EV--IlA~~~t~EGe~Ta~yi~~~ 162 (201) .=+..+|+-+.|.|+|+.||..++.... .++.+.=...-++-++++|| |.--|..-+.|-+-+|+++. T Consensus 697 ~lI~lFE~~k~~EgLyyfLgsivn~s~D---pdVhfKYIeAa~k~gQ~~EvERI~resn~YdpekvKnfLKea 766 (1630) T 1xi4_A 697 SLIELFESFKSFEGLFYFLGSIVNFSQD---PDVHFKYIQAACKTGQIKEVERICRESNCYDPERVKNFLKEA 766 (1630) T ss_pred HHHHHHHHCCCCHHHHHHHHHHCCCCCC---CHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCHHHHHHHHHCC T ss_conf 9999999647630389998876155668---128999999998728579999997056778989999998418 No 105 >1xpj_A Hypothetical protein; structural genomics, MCSG, protein structure initiative, PSI, midwest center for structural genomics, unknown function; HET: TLA; 2.30A {Vibrio cholerae} SCOP: c.108.1.18 Probab=31.94 E-value=26 Score=15.33 Aligned_cols=62 Identities=19% Similarity=0.247 Sum_probs=41.0 Q ss_pred HHHHHHHHCCCCCCEEEEEECCCCC---------HHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHH-HHHHHH Q ss_conf 8999998515785549999469978---------689999999982017980887414674882066-634799 Q gi|254780762|r 127 IQSLIERIEVKKIRELIFAISATIE---------GQTTAHYIMDKLKGIDVKITRLAYGIPMGSELD-YLDDGT 190 (201) Q Consensus 127 i~~L~~ri~~~~i~EVIlA~~~t~E---------Ge~Ta~yi~~~lk~~~ikitrla~GiP~G~~le-y~D~~T 190 (201) ++.+. .+++.+ -+|||-|+=... ++.+.....+.|+..+|+..+|-.|-|.++.-+ |+|+-. T Consensus 30 Ie~i~-~l~~~G-~~Iii~TaR~~~~~~~~~~~~~~~~~~~T~~wL~~~gi~yd~L~~gKP~~~~~d~yIDDka 101 (126) T 1xpj_A 30 IEQLR-EYHQLG-FEIVISTARNMRTYEGNVGKINIHTLPIITEWLDKHQVPYDEILVGKPWCGHDGFYIDDRA 101 (126) T ss_dssp HHHHH-HHHHTT-CEEEEEECTTTTTTTTCHHHHHHHTHHHHHHHHHHTTCCCSEEEECCCCCCTTCEEECTTE T ss_pred HHHHH-HHHHCC-CEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCEEEECCC T ss_conf 99999-999789-9899997774334577677766758999999999829980589868998777998844897 No 106 >3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} Probab=31.81 E-value=24 Score=15.55 Aligned_cols=23 Identities=13% Similarity=0.290 Sum_probs=17.7 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 99975689995379999999971 Q gi|254780762|r 15 KILARIPGFGPRSARRATLHLVK 37 (201) Q Consensus 15 ~~l~kLPGIG~KsA~R~a~~Ll~ 37 (201) +.|.++||+|+||.+.+--.|-. T Consensus 48 ~dLl~i~n~G~kSl~EI~~~L~~ 70 (79) T 3gfk_B 48 EDMMKVRNLGRKSLEEVKAKLEE 70 (79) T ss_dssp HHHTTSTTCHHHHHHHHHHHHHH T ss_pred HHHHHCCCCCHHHHHHHHHHHHH T ss_conf 99975789867379999999998 No 107 >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=31.43 E-value=4.9 Score=20.20 Aligned_cols=14 Identities=29% Similarity=0.636 Sum_probs=8.1 Q ss_pred HCCCCCHHHHHHHH Q ss_conf 56899953799999 Q gi|254780762|r 19 RIPGFGPRSARRAT 32 (201) Q Consensus 19 kLPGIG~KsA~R~a 32 (201) -.||||+|||.++. T Consensus 195 Gv~giG~ktA~~ll 208 (832) T 1bgx_T 195 GVKGIGEKTARKLL 208 (832) T ss_dssp CCCCSSSCTTTTTG T ss_pred CCCCCCHHHHHHHH T ss_conf 86655747799998 No 108 >3io1_A Aminobenzoyl-glutamate utilization protein; peptidase_M20D superfamily, protein structure initiative II, NYSGXRC, structural genomics; 2.50A {Klebsiella pneumoniae subsp} Probab=31.05 E-value=27 Score=15.23 Aligned_cols=28 Identities=11% Similarity=0.100 Sum_probs=16.1 Q ss_pred CCCCCCEEEEEECCCCCHHHHHHHHHHH Q ss_conf 1578554999946997868999999998 Q gi|254780762|r 135 EVKKIRELIFAISATIEGQTTAHYIMDK 162 (201) Q Consensus 135 ~~~~i~EVIlA~~~t~EGe~Ta~yi~~~ 162 (201) +..---.|.+.+.|.-|+-.-+.++.+. T Consensus 169 ~~~~~G~v~~~f~p~EE~~~g~~~~i~~ 196 (445) T 3io1_A 169 AAQLNGVIKLIFQPAEEGTRGARAMVAA 196 (445) T ss_dssp GGGCCSEEEEEEESCTTTTCHHHHHHHT T ss_pred CCCCCCEEEEEECCCCCCCHHHHHHHHH T ss_conf 2035967998411543122138999973 No 109 >2gnr_A Conserved hypothetical protein; 13815350, structural genomics, PSI, protein structure initiative; 1.80A {Sulfolobus solfataricus P2} SCOP: b.40.4.15 PDB: 3irb_A Probab=30.41 E-value=11 Score=17.82 Aligned_cols=40 Identities=15% Similarity=0.222 Sum_probs=29.9 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCC--CCCCCCCCCCCC Q ss_conf 8999999999999998518288999733--456541003555 Q gi|254780762|r 40 EQLLGPLAEAMANIYNKVCLCSICGNVD--TTDPCAICIDQQ 79 (201) Q Consensus 40 ~~~~~~l~~~l~~~~~~i~~C~~C~~l~--~~~~C~iC~d~~ 79 (201) .....+|-+++.+=+--.++|+.|+.+. -...|+-|.... T Consensus 30 g~~~~~f~~al~~grL~~~rC~~Cg~~~~Ppr~~Cp~C~s~~ 71 (145) T 2gnr_A 30 GPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSYCEHCFVKI 71 (145) T ss_dssp HHHHHHHHHHHHTTCCEEEECTTTCCEEESCCSEETTTTEEC T ss_pred CCCHHHHHHHHHCCEEEEEECCCCCCEEECCCCCCCCCCCCC T ss_conf 900899999877493999987999958839601177999987 No 110 >2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-binding, nucleotide-binding; 2.30A {Sulfolobus solfataricus} Probab=30.05 E-value=23 Score=15.67 Aligned_cols=21 Identities=33% Similarity=0.434 Sum_probs=10.5 Q ss_pred HHHHHHHHCCCCCCEEEEEECCCCC Q ss_conf 8999998515785549999469978 Q gi|254780762|r 127 IQSLIERIEVKKIRELIFAISATIE 151 (201) Q Consensus 127 i~~L~~ri~~~~i~EVIlA~~~t~E 151 (201) ++.++.|... --++++++|+. T Consensus 166 le~il~~~~~----~~~i~lsat~~ 186 (715) T 2va8_A 166 VESVTIRAKR----RNLLALSATIS 186 (715) T ss_dssp HHHHHHHHHT----SEEEEEESCCT T ss_pred HHHHHHHCCC----HHHHHHCCCCC T ss_conf 7777664232----03333124468 No 111 >1q8b_A Protein YJCS; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 1.90A {Bacillus subtilis} SCOP: d.58.4.6 Probab=29.74 E-value=21 Score=16.02 Aligned_cols=54 Identities=9% Similarity=0.011 Sum_probs=41.2 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECHHHHHHHHHH Q ss_conf 8999999999999998518288999733456541003555567369998358899999751 Q gi|254780762|r 40 EQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERS 100 (201) Q Consensus 40 ~~~~~~l~~~l~~~~~~i~~C~~C~~l~~~~~C~iC~d~~Rd~~~lCVVE~~~Di~~IE~t 100 (201) ....+++.+.+.++......-+-|-.+. ++.|.. |.+.++++|.+.|..+++.- T Consensus 25 ~~~~~e~~~~l~~l~~~tr~E~GCl~y~------~~~d~~-~p~~f~~~E~w~~~~a~~~H 78 (105) T 1q8b_A 25 DKDLNEIMKEFKKLEEETNKEEGCITFH------AYPLEP-SERKIMLWEIWENEEAVKIH 78 (105) T ss_dssp CSCHHHHHHHHHHHHHHHTTSTTEEEEE------EEECCG-GGCEEEEEEEESSHHHHHHH T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCEEEE------EEECCC-CCCEEEEEEEECCHHHHHHH T ss_conf 6579999999999999983699958999------996699-99889999998999999999 No 112 >2e18_A NH(3)-dependent NAD(+) synthetase; ligase, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.10A {Pyrococcus horikoshii OT3} Probab=29.63 E-value=29 Score=15.07 Aligned_cols=19 Identities=5% Similarity=0.064 Sum_probs=9.2 Q ss_pred EEEEHHHHCCCCCCCCHHH Q ss_conf 4210121002000268111 Q gi|254780762|r 106 LYHVLGGSLSPLDRIGPED 124 (201) Q Consensus 106 ~YhVLgG~ispl~g~~p~~ 124 (201) .|.-..+.++|+-+....+ T Consensus 142 ~~gd~~~~~~Pl~dL~K~e 160 (257) T 2e18_A 142 KWGDGASDYAPIINLYKTE 160 (257) T ss_dssp TTSTTCSSBCTTTTSCHHH T ss_pred CCCCCCCCCCCCCCCCHHH T ss_conf 5675457765456884999 No 113 >3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa} Probab=29.42 E-value=3.1 Score=21.59 Aligned_cols=69 Identities=17% Similarity=0.259 Sum_probs=47.6 Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECHH Q ss_conf 99999756899953799999999719989999999999999985182889997334565410035555673699983588 Q gi|254780762|r 13 LIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVA 92 (201) Q Consensus 13 LI~~l~kLPGIG~KsA~R~a~~Ll~~~~~~~~~l~~~l~~~~~~i~~C~~C~~l~~~~~C~iC~d~~Rd~~~lCVVE~~~ 92 (201) +.-+|.++-|||+++|..+.-.+ .-+ +...+.++|++.=.+- +..| +.-. T Consensus 60 V~~ALT~IyGIG~~~A~~Ic~~l-gId--------------------~kkv~dLteeel~~i~-~~rr--------~~~~ 109 (145) T 3bbn_M 60 VEYSLQYIHGIGRSRSRQILLDL-NFD--------------------NKVTKDLSEEEVIILR-KEKR--------FNRV 109 (145) T ss_dssp TTTGGGGSTTCCSSTTTGGGTTT-TCC--------------------SCBTTSCCSSTTHHHH-SSCC--------CCST T ss_pred EEEHHHHHHCCCHHHHHHHHHHC-CCC--------------------HHHHHHCCHHHHHHHH-HHHH--------HHHH T ss_conf 21235567463889999999985-997--------------------4667654787999999-9999--------9899 Q ss_pred HHHHHHHHCCEEEEEEEHH Q ss_conf 9999975174013421012 Q gi|254780762|r 93 DLWALERSKAVNALYHVLG 111 (201) Q Consensus 93 Di~~IE~t~~y~G~YhVLg 111 (201) |+...-+.+.|+|.=|..| T Consensus 110 dIkRLk~I~sYRG~RH~~g 128 (145) T 3bbn_M 110 AIERLKEIRCYRGIRHKLG 128 (145) T ss_dssp TTHHHHCCCCSCCTTTTTT T ss_pred HHHHHHHHHHHHHHHHHCC T ss_conf 9999998500554455249 No 114 >1mc3_A Glucose-1-phosphate thymidylyltransferase; glucose-1-phosphate thymidylytransferase, RFFH; HET: TTP; 2.60A {Escherichia coli} SCOP: c.68.1.6 Probab=29.26 E-value=29 Score=15.03 Aligned_cols=49 Identities=16% Similarity=0.212 Sum_probs=34.1 Q ss_pred CHHHHHHHHHHHHCCCCCEEEEEECCC---CCCCCHHHHHHHHHHHHHHCCCC Q ss_conf 868999999998201798088741467---48820666347999999830647 Q gi|254780762|r 151 EGQTTAHYIMDKLKGIDVKITRLAYGI---PMGSELDYLDDGTIFEAIRSRTV 200 (201) Q Consensus 151 EGe~Ta~yi~~~lk~~~ikitrla~Gi---P~G~~ley~D~~TL~~Al~~R~~ 200 (201) |=|.|- .+..++++-.+.+..+.+|. -+|+-=+|.+..+.-++++.|+. T Consensus 197 E~eitD-~~~~~i~~~~~~~~~~~~~~~W~D~Gt~~~l~~a~~~v~~~e~~q~ 248 (296) T 1mc3_A 197 ELEITS-INQMYLEAGNLTVELLGRGFAWLDTGTHDSLIEASTFVQTVEKRQG 248 (296) T ss_dssp SCCHHH-HHHHHHHTTCEEEEECCTTCEEEECCSHHHHHHHHHHHHHHHHHHS T ss_pred CCCHHH-HHHHHHHCCCCEEEEECCCCEEECCCCHHHHHHHHHHHHHHHHHCC T ss_conf 745689-9999998499559995489889868898999999999999998739 No 115 >2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious disease, electron transport; NMR {Mycobacterium tuberculosis} Probab=27.46 E-value=19 Score=16.22 Aligned_cols=27 Identities=22% Similarity=0.377 Sum_probs=18.5 Q ss_pred CCCCCCCCCCCCC---------------------CCCCCCCCCCCCCC Q ss_conf 1828899973345---------------------65410035555673 Q gi|254780762|r 57 VCLCSICGNVDTT---------------------DPCAICIDQQRDAS 83 (201) Q Consensus 57 i~~C~~C~~l~~~---------------------~~C~iC~d~~Rd~~ 83 (201) +-.|..|+.+-+. =.|++|..++.+.. T Consensus 27 ~y~C~~CgyiYDp~~GD~~~gippGT~F~dLP~dw~CP~Cga~K~~F~ 74 (81) T 2kn9_A 27 LFRCIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAAKSDFE 74 (81) T ss_dssp EEEETTTCCEEETTTCBTTTTBCTTCCTTTSCTTCCCTTTCCCGGGEE T ss_pred EEECCCCCEEECCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCHHHCE T ss_conf 598299993876665884568798897657898886929998378877 No 116 >1k8r_B Protein kinase BYR2; signal transduction, cancer, GTPase, ubiquitin fold, signaling protein; HET: GNP; 3.00A {Schizosaccharomyces pombe} SCOP: d.15.1.5 PDB: 1i35_A Probab=26.70 E-value=15 Score=16.94 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=22.0 Q ss_pred CCCCCCCCCCCCCCCCCCCC-CCCEEEEE Q ss_conf 89997334565410035555-67369998 Q gi|254780762|r 61 SICGNVDTTDPCAICIDQQR-DASVIIVV 88 (201) Q Consensus 61 ~~C~~l~~~~~C~iC~d~~R-d~~~lCVV 88 (201) ..|..+++.+...||.+++| .++.|+.+ T Consensus 48 ~~~r~L~D~EL~~IC~~~~R~ER~RLIL~ 76 (110) T 1k8r_B 48 SRIKLITEEEFKQICFNSSSPERDRLIIV 76 (110) T ss_dssp SSEEECCCC-------------CCCEEEE T ss_pred CCEEEECHHHHHHHHCCCCCCCCCCEEEE T ss_conf 43678517889999808984325606987 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=24.92 E-value=35 Score=14.52 Aligned_cols=24 Identities=21% Similarity=0.288 Sum_probs=18.2 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHC Q ss_conf 999756899953799999999719 Q gi|254780762|r 15 KILARIPGFGPRSARRATLHLVKK 38 (201) Q Consensus 15 ~~l~kLPGIG~KsA~R~a~~Ll~~ 38 (201) +.|.++|++|+||-+.+--.|-.. T Consensus 56 ~dLl~~~n~G~KSl~EIk~~L~~~ 79 (98) T 1coo_A 56 VELLKTPNLGKKSLTEIKDVLASR 79 (98) T ss_dssp HHHTTSTTCCHHHHHHHHHHHHHT T ss_pred HHHHHCCCCCHHHHHHHHHHHHHC T ss_conf 999758897687899999999985 No 118 >6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1 Probab=24.82 E-value=21 Score=15.99 Aligned_cols=23 Identities=22% Similarity=0.703 Sum_probs=16.2 Q ss_pred CCCCCCCCCCC---------C-----CCCCCCCCCCC Q ss_conf 28899973345---------6-----54100355556 Q gi|254780762|r 59 LCSICGNVDTT---------D-----PCAICIDQQRD 81 (201) Q Consensus 59 ~C~~C~~l~~~---------~-----~C~iC~d~~Rd 81 (201) .|..||.+-+. + .|++|..++.+ T Consensus 6 ~C~~CgyiYdp~~GdGt~F~~lp~dw~CP~C~a~K~~ 42 (46) T 6rxn_A 6 VCNVCGYEYDPAEHDNVPFDQLPDDWCCPVCGVSKDQ 42 (46) T ss_dssp EETTTCCEECGGGGTTCCGGGSCTTCBCTTTCCBGGG T ss_pred ECCCCCEEECCCCCCCCCHHHCCCCCCCCCCCCCHHH T ss_conf 9699992877743799887788988768499883887 No 119 >2e1f_A Werner syndrome ATP-dependent helicase; HRDC domain, hydrolase; 2.00A {Homo sapiens} SCOP: a.60.8.1 PDB: 2e1e_A Probab=24.42 E-value=35 Score=14.46 Aligned_cols=20 Identities=20% Similarity=0.232 Sum_probs=16.4 Q ss_pred HHHHHHCCCCCHHHHHHHHH Q ss_conf 99997568999537999999 Q gi|254780762|r 14 IKILARIPGFGPRSARRATL 33 (201) Q Consensus 14 I~~l~kLPGIG~KsA~R~a~ 33 (201) ++.|..++|+|++.++|+.- T Consensus 56 ~~eL~~I~G~g~~k~~ryG~ 75 (103) T 2e1f_A 56 VENVKRIDGVSEGKAAMLAP 75 (103) T ss_dssp HHHHTTSTTCCHHHHHHTHH T ss_pred HHHHHCCCCCCHHHHHHHHH T ss_conf 99993789989999999989 No 120 >1l8d_A DNA double-strand break repair RAD50 ATPase; zinc finger, DNA repair, recombination, HOOK motif, replication; HET: DNA CIT; 2.20A {Pyrococcus furiosus} SCOP: h.4.12.1 Probab=24.02 E-value=36 Score=14.41 Aligned_cols=27 Identities=22% Similarity=0.551 Sum_probs=21.8 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 899999999999999851828899973 Q gi|254780762|r 40 EQLLGPLAEAMANIYNKVCLCSICGNV 66 (201) Q Consensus 40 ~~~~~~l~~~l~~~~~~i~~C~~C~~l 66 (201) .....++-.+|.++++-=..||.||.- T Consensus 30 ~~~i~elkKal~ELk~a~GkCPvCgre 56 (112) T 1l8d_A 30 KNKIGDLKTAIEELKKAKGKCPVCGRE 56 (112) T ss_dssp HHHHHHHHHHHHHHTTCSEECTTTCCE T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCC T ss_conf 878999999999999747879988993 No 121 >4rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.20A {Clostridium pasteurianum} SCOP: g.41.5.1 PDB: 5rxn_A 1bfy_A 1fhh_A 1fhm_A 1irn_A 1iro_A 1r0f_A 1r0g_A 1r0h_A 1r0i_A 1r0j_A 1t9q_A 1c09_A 1b2j_A 1b13_A 1smm_A 1smu_A 1smw_A 1be7_A 1t9o_A ... Probab=23.66 E-value=21 Score=16.02 Aligned_cols=25 Identities=20% Similarity=0.688 Sum_probs=16.9 Q ss_pred CCCCCCCCCCCCC---------------------CCCCCCCCCCCC Q ss_conf 8288999733456---------------------541003555567 Q gi|254780762|r 58 CLCSICGNVDTTD---------------------PCAICIDQQRDA 82 (201) Q Consensus 58 ~~C~~C~~l~~~~---------------------~C~iC~d~~Rd~ 82 (201) -.|..||.+-+.. .|++|..++.+. T Consensus 4 y~C~~CgyiYdp~~Gd~~~gi~pGT~F~~LP~dw~CP~C~a~K~~F 49 (54) T 4rxn_A 4 YTCTVCGYIYDPEDGDPDDGVNPGTDFKDIPDDWVCPLCGVGKDEF 49 (54) T ss_dssp EEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCCBGGGE T ss_pred EECCCCCCEECCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCHHHC T ss_conf 5939999087755488456879899978889988893998938992 No 122 >2avu_E Flagellar transcriptional activator FLHC; C4-type zinc finger, transcription activator; 3.00A {Escherichia coli} SCOP: e.64.1.1 Probab=22.58 E-value=25 Score=15.46 Aligned_cols=41 Identities=17% Similarity=0.455 Sum_probs=26.4 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCC--CCC-CC-----CCCCCCCCCCCCC Q ss_conf 99999999999985182889997--334-56-----5410035555673 Q gi|254780762|r 43 LGPLAEAMANIYNKVCLCSICGN--VDT-TD-----PCAICIDQQRDAS 83 (201) Q Consensus 43 ~~~l~~~l~~~~~~i~~C~~C~~--l~~-~~-----~C~iC~d~~Rd~~ 83 (201) +-.|+..+..=--.+..|..|+. ++. .+ .|++|.-|+|-.+ T Consensus 120 Aw~LvRf~ds~~L~l~~C~~Cgg~fv~~~~~~~~~f~C~lC~~psRagk 168 (192) T 2avu_E 120 AWTLVRFVESGLLQLSSCNCCGGNFITHAHQPVGSFACSLCQPPSRAVK 168 (192) T ss_dssp HHHHHHHHHTTSEEEEECTTTCCEEEEESSCCSSCCCCTTC-------- T ss_pred HHHHHHHHHCCCEEECCCCCCCCCEECCCCCCCCCCCCCCCCCHHHCCC T ss_conf 9999999725871256578789951556666676873899998000566 No 123 >2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A Probab=22.01 E-value=33 Score=14.64 Aligned_cols=18 Identities=22% Similarity=0.859 Sum_probs=13.3 Q ss_pred CCCCCCCCCCCCCCCCCC Q ss_conf 334565410035555673 Q gi|254780762|r 66 VDTTDPCAICIDQQRDAS 83 (201) Q Consensus 66 l~~~~~C~iC~d~~Rd~~ 83 (201) +++.+.|.||.+..+|.. T Consensus 5 ~~~~~~C~IC~~~~~~~~ 22 (64) T 2vje_A 5 LNAIEPCVICQGRPKNGC 22 (64) T ss_dssp CGGGSCCTTTSSSCSCEE T ss_pred CCCCCCCCCCCCCCCCCE T ss_conf 898996906697787889 No 124 >3eln_A Cysteine dioxygenase type 1; peroxysulfenate, non-heme dioxygenases, Fe2+ metalloenzyme, taurine, thioether, iron, metal- binding; 1.42A {Rattus norvegicus} SCOP: b.82.1.19 PDB: 2gh2_A 2b5h_A 2atf_A* 2q4s_A 2ic1_A Probab=21.88 E-value=6.3 Score=19.48 Aligned_cols=94 Identities=11% Similarity=0.078 Sum_probs=46.3 Q ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHH----HHHHHCCCCCCCCCCCCCCCCCCCC-CC Q ss_conf 668667999999997568999537999999997199899999999999----9998518288999733456541003-55 Q gi|254780762|r 4 KITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMA----NIYNKVCLCSICGNVDTTDPCAICI-DQ 78 (201) Q Consensus 4 ~~~~~~l~~LI~~l~kLPGIG~KsA~R~a~~Ll~~~~~~~~~l~~~l~----~~~~~i~~C~~C~~l~~~~~C~iC~-d~ 78 (201) -|.|++|++||+.|.++..-..- +.+.++.+.++.. +..+-+.+.+ ..-...+. +. T Consensus 6 ~~~p~~l~~Li~~L~~~~~~~~~------------~~~~v~~ll~~y~sn~~dw~~y~~~~~-------~~YtRnlv~~~ 66 (200) T 3eln_A 6 LLKPRTLADLIRILHELFAGDEV------------NVEEVQAVLEAYESNPAEWALYAKFDQ-------YRYTRNLVDQG 66 (200) T ss_dssp CCCCSSHHHHHHHHHHHTSSSSC------------CHHHHHHHHHHSCCCHHHHGGGCCCCS-------SSCEEEEEECG T ss_pred CCCHHHHHHHHHHHHHHHCCCCC------------CHHHHHHHHHHCCCCHHHHHHHCCCCC-------CCEEEEEEECC T ss_conf 36878899999999987514689------------999999999984299899997613684-------54388998759 Q ss_pred CCCCCEEEEEECHHHHHHHHHHCCEEEEEEEHHHHCCC Q ss_conf 55673699983588999997517401342101210020 Q gi|254780762|r 79 QRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSP 116 (201) Q Consensus 79 ~Rd~~~lCVVE~~~Di~~IE~t~~y~G~YhVLgG~isp 116 (201) +-+.+++.++=.|...-.|-.-+.-.|.+-||.|.+.- T Consensus 67 ~~~fel~li~W~pGq~SpIHdH~~s~c~~~vl~G~l~e 104 (200) T 3eln_A 67 NGKFNLMILCWGEGHGSSIHDHTDSHCFLKLLQGNLKE 104 (200) T ss_dssp GGTCEEEEEEECTTCBCCEECCTTCEEEEEEEESCEEE T ss_pred CCCEEEEEEECCCCCCCCCCCCCCCCEEEEEECCEEEE T ss_conf 99889999963899978676688873599960564999 No 125 >2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ... Probab=21.35 E-value=40 Score=14.07 Aligned_cols=75 Identities=21% Similarity=0.070 Sum_probs=46.9 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHH--------HCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 9999997568999537999999997--------19989999999999999985182889997334565410035555673 Q gi|254780762|r 12 NLIKILARIPGFGPRSARRATLHLV--------KKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDAS 83 (201) Q Consensus 12 ~LI~~l~kLPGIG~KsA~R~a~~Ll--------~~~~~~~~~l~~~l~~~~~~i~~C~~C~~l~~~~~C~iC~d~~Rd~~ 83 (201) .+.-+|.++-|||+++|..+...+= ...++.+..|.+.+.+ ..+.+ .|-.| T Consensus 14 ~v~~aLt~I~GIG~~~A~~Ic~~lGId~~~kvg~Lt~~qi~~l~~~i~~-----------~~~i~-------~~L~~--- 72 (126) T 2vqe_M 14 RVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVEN-----------TWKLE-------GELRA--- 72 (126) T ss_dssp BHHHHHTTSSSCCSHHHHHHTTTTTCCTTSBGGGCCHHHHHHHHHHHHT-----------TSCCH-------HHHHH--- T ss_pred EEEEEECCEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHC-----------CCCCH-------HHHHH--- T ss_conf 8787620434838999999999859796630163999999999999831-----------45114-------78999--- Q ss_pred EEEEEECHHHHHHHHHHCCEEEEEEEHHH Q ss_conf 69998358899999751740134210121 Q gi|254780762|r 84 VIIVVEDVADLWALERSKAVNALYHVLGG 112 (201) Q Consensus 84 ~lCVVE~~~Di~~IE~t~~y~G~YhVLgG 112 (201) +...|+...=+.+.|+|+=|..|= T Consensus 73 -----~~~~~i~rl~~i~syrG~RH~~gL 96 (126) T 2vqe_M 73 -----EVAANIKRLMDIGCYRGLRHRRGL 96 (126) T ss_dssp -----HHHHHHHHHHHTTCHHHHHHHTTC T ss_pred -----HHHHHHHHHHHHCCHHHHHHCCCC T ss_conf -----999989998874312123340699 No 126 >2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur protein, oxidoreductase, electron transfer, electron transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas aeruginosa} Probab=21.19 E-value=23 Score=15.68 Aligned_cols=24 Identities=25% Similarity=0.524 Sum_probs=16.7 Q ss_pred CCCCCCCCCCCC---------------------CCCCCCCCCCCC Q ss_conf 288999733456---------------------541003555567 Q gi|254780762|r 59 LCSICGNVDTTD---------------------PCAICIDQQRDA 82 (201) Q Consensus 59 ~C~~C~~l~~~~---------------------~C~iC~d~~Rd~ 82 (201) .|..||.+-+.. .|++|..++.+. T Consensus 5 ~C~~CgyiYd~~~Gd~~~~i~pGT~F~~lP~dw~CP~C~a~K~~F 49 (55) T 2v3b_B 5 QCVVCGFIYDEALGLPEEGIPAGTRWEDIPADWVCPDCGVGKIDF 49 (55) T ss_dssp EETTTCCEEETTTCBTTTTBCTTCCGGGSCTTCCCTTTCCCGGGE T ss_pred ECCCCCEEECCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCHHHC T ss_conf 929999188855588456869899968888987695999838889 No 127 >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=20.38 E-value=6.5 Score=19.40 Aligned_cols=11 Identities=18% Similarity=0.117 Sum_probs=4.0 Q ss_pred HHHHHHHHHHH Q ss_conf 68999999998 Q gi|254780762|r 152 GQTTAHYIMDK 162 (201) Q Consensus 152 Ge~Ta~yi~~~ 162 (201) -+-|+.||..+ T Consensus 161 ~~eTa~~L~~l 171 (307) T 2zix_A 161 IKESAAYLALL 171 (307) T ss_dssp HHHHTHHHHHH T ss_pred HHHHHHHHHHH T ss_conf 99999999999 Done!