Query gi|254780383|ref|YP_003064796.1| endonuclease III [Candidatus Liberibacter asiaticus str. psy62] Match_columns 227 No_of_seqs 149 out of 3690 Neff 6.6 Searched_HMMs 33803 Date Wed Jun 1 12:45:52 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780383.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >1kg2_A A/G-specific adenine g 99.9 5.3E-28 1.6E-32 208.8 7.8 108 117-227 15-127 (139) 2 >2abk_A Endonuclease III; DNA- 99.9 2E-25 5.8E-30 191.5 9.0 111 42-152 1-111 (111) 3 >1orn_A Endonuclease III; DNA 99.9 2.3E-25 6.7E-30 191.1 9.1 110 43-152 1-110 (110) 4 >1kea_A Possible G-T mismatche 99.9 3.1E-24 9.2E-29 183.4 8.5 109 43-151 2-110 (111) 5 >3fsp_A A/G-specific adenine g 99.9 1.4E-23 4E-28 179.1 7.9 109 44-153 2-110 (110) 6 >1pu6_A 3-methyladenine DNA gl 99.9 1.4E-23 4.1E-28 179.0 7.7 110 43-152 3-123 (123) 7 >1ngn_A Methyl-CPG binding pro 99.9 3.5E-24 1E-28 183.1 2.5 115 31-153 15-129 (129) 8 >1kg2_A A/G-specific adenine g 99.9 3.9E-22 1.2E-26 169.3 7.3 86 42-128 1-86 (86) 9 >1m3q_A 8-oxoguanine DNA glyco 99.8 1E-21 3.1E-26 166.4 5.8 110 43-152 2-132 (133) 10 >1mpg_A ALKA, 3-methyladenine 99.8 2.2E-21 6.5E-26 164.3 6.6 111 42-152 3-127 (127) 11 >1orn_A Endonuclease III; DNA 99.8 3.7E-20 1.1E-24 156.0 6.7 77 151-227 26-103 (116) 12 >2abk_A Endonuclease III; DNA- 99.8 4.3E-20 1.3E-24 155.6 5.8 76 152-227 22-97 (100) 13 >2h56_A DNA-3-methyladenine gl 99.8 1.5E-19 4.3E-24 152.0 4.9 112 104-216 32-156 (156) 14 >1kea_A Possible G-T mismatche 99.8 1.1E-18 3.3E-23 146.0 6.5 86 142-227 14-107 (110) 15 >3fhf_A Mjogg, N-glycosylase/D 99.8 1.3E-18 3.8E-23 145.6 6.8 101 43-149 2-109 (113) 16 >3fsp_A A/G-specific adenine g 99.7 2.8E-17 8.4E-22 136.6 6.4 74 150-223 30-108 (108) 17 >2h56_A DNA-3-methyladenine gl 99.6 7.1E-16 2.1E-20 127.1 4.6 77 47-126 1-77 (77) 18 >1pu6_A 3-methyladenine DNA gl 98.3 4.4E-07 1.3E-11 67.9 3.4 59 150-209 19-94 (95) 19 >3i0w_A 8-oxoguanine-DNA-glyco 97.6 1.9E-05 5.7E-10 56.9 1.7 29 125-153 30-58 (58) 20 >3fhg_A Mjogg, N-glycosylase/D 96.7 0.0094 2.8E-07 38.8 7.9 63 47-115 4-68 (73) 21 >2jhn_A ALKA, 3-methyladenine 96.4 0.0033 9.7E-08 41.9 3.8 39 76-118 96-134 (134) 22 >3i0w_A 8-oxoguanine-DNA-glyco 96.1 0.0076 2.2E-07 39.4 4.5 57 146-203 23-80 (84) 23 >2jhn_A ALKA, 3-methyladenine 96.0 0.0042 1.2E-07 41.1 2.6 26 126-151 29-54 (55) 24 >3i0w_A 8-oxoguanine-DNA-glyco 94.5 0.028 8.2E-07 35.6 3.0 39 74-117 28-66 (68) 25 >1ixr_A Holliday junction DNA 93.2 0.033 9.8E-07 35.1 1.3 69 80-151 59-130 (191) 26 >2bcq_A DNA polymerase lambda; 93.1 0.18 5.3E-06 30.2 4.9 60 87-149 19-78 (128) 27 >1cuk_A RUVA protein; DNA repa 92.8 0.21 6.2E-06 29.7 5.0 54 95-151 11-66 (79) 28 >2fmp_A DNA polymerase beta; n 92.7 0.21 6.3E-06 29.6 4.9 42 105-148 36-77 (119) 29 >2ztd_A Holliday junction ATP- 92.3 0.19 5.6E-06 30.0 4.2 26 125-150 41-66 (75) 30 >2w9m_A Polymerase X; SAXS, DN 92.3 0.04 1.2E-06 34.6 0.7 43 102-144 67-113 (118) 31 >1ixr_A Holliday junction DNA 92.0 0.23 6.7E-06 29.4 4.3 75 127-202 71-157 (191) 32 >1vdd_A Recombination protein 91.9 0.078 2.3E-06 32.6 1.8 28 125-152 9-36 (66) 33 >1jms_A Terminal deoxynucleoti 91.8 0.3 8.9E-06 28.6 4.8 44 104-149 58-101 (154) 34 >2ihm_A POL MU, DNA polymerase 91.4 0.28 8.4E-06 28.8 4.3 18 126-143 100-117 (129) 35 >2kp7_A Crossover junction end 91.3 0.25 7.4E-06 29.2 3.9 58 87-148 21-78 (87) 36 >3c1y_A DNA integrity scanning 91.2 0.14 4.1E-06 30.9 2.5 57 85-150 7-66 (74) 37 >1m3q_A 8-oxoguanine DNA glyco 91.1 0.3 8.8E-06 28.7 4.1 20 148-167 23-42 (89) 38 >2jhn_A ALKA, 3-methyladenine 90.3 0.73 2.2E-05 26.0 5.6 52 153-205 1-54 (61) 39 >2w9m_A Polymerase X; SAXS, DN 89.7 0.2 6E-06 29.8 2.2 44 105-149 34-78 (118) 40 >2ofk_A 3-methyladenine DNA gl 89.4 1.4 4.1E-05 24.1 6.4 74 48-121 31-111 (183) 41 >1z00_A DNA excision repair pr 89.2 0.26 7.8E-06 29.0 2.6 36 113-148 33-71 (89) 42 >2ztd_A Holliday junction ATP- 88.9 0.21 6.2E-06 29.7 1.9 61 126-187 7-69 (75) 43 >1cuk_A RUVA protein; DNA repa 88.4 0.21 6.3E-06 29.7 1.6 61 126-187 6-68 (79) 44 >1pzn_A RAD51, DNA repair and 88.4 0.76 2.3E-05 25.9 4.4 27 124-150 64-90 (95) 45 >1pzn_A RAD51, DNA repair and 88.3 0.49 1.5E-05 27.2 3.5 43 70-115 48-91 (95) 46 >1kft_A UVRC, excinuclease ABC 88.1 0.23 6.7E-06 29.5 1.6 36 113-148 38-76 (78) 47 >2jg6_A DNA-3-methyladenine gl 87.5 1.4 4.2E-05 24.1 5.4 74 48-121 31-111 (121) 48 >2edu_A Kinesin-like protein K 86.6 1.1 3.2E-05 24.9 4.4 58 82-148 33-90 (98) 49 >3bzc_A TEX; helix-turn-helix, 86.2 0.52 1.5E-05 27.0 2.6 56 84-148 5-60 (70) 50 >3bzc_A TEX; helix-turn-helix, 85.2 0.43 1.3E-05 27.6 1.8 24 125-148 7-30 (70) 51 >1s5l_U Photosystem II 12 kDa 84.6 0.45 1.3E-05 27.5 1.6 22 126-147 14-35 (87) 52 >2duy_A Competence protein com 83.8 0.42 1.3E-05 27.6 1.2 22 126-147 25-46 (75) 53 >2a1j_A DNA repair endonucleas 83.5 1.8 5.2E-05 23.5 4.3 42 68-113 15-56 (63) 54 >1b22_A DNA repair protein RAD 83.2 1 3.1E-05 25.0 3.0 36 77-115 46-81 (114) 55 >2bgw_A XPF endonuclease; hydr 81.9 0.57 1.7E-05 26.8 1.3 23 127-150 13-35 (49) 56 >1wcn_A Transcription elongati 80.8 1.6 4.6E-05 23.8 3.2 43 70-115 20-63 (70) 57 >3bz1_U Photosystem II 12 kDa 80.4 0.85 2.5E-05 25.6 1.7 61 76-149 20-80 (104) 58 >2nrt_A Uvrabc system protein 79.1 2.4 7E-05 22.6 3.7 24 71-94 26-49 (64) 59 >1kft_A UVRC, excinuclease ABC 78.7 0.81 2.4E-05 25.8 1.2 38 71-111 38-75 (78) 60 >1z00_B DNA repair endonucleas 77.0 3.4 0.0001 21.5 4.0 20 127-146 17-36 (71) 61 >2csb_A Topoisomerase V, TOP61 76.9 2.9 8.6E-05 22.0 3.6 90 79-188 47-137 (142) 62 >3c65_A Uvrabc system protein 76.1 0.62 1.8E-05 26.5 0.0 23 127-150 172-194 (226) 63 >1x2i_A HEF helicase/nuclease; 73.5 1.3 3.8E-05 24.4 1.1 23 127-150 13-35 (49) 64 >1a76_A Flap endonuclease-1 pr 70.5 1.7 5.2E-05 23.5 1.2 18 130-147 18-35 (65) 65 >1dgs_A DNA ligase; AMP comple 68.8 3.2 9.5E-05 21.7 2.2 71 69-147 27-100 (116) 66 >1exn_A 5'-exonuclease, 5'-nuc 64.9 2.3 7E-05 22.6 0.9 21 127-147 21-41 (80) 67 >2izo_A FEN1, flap structure-s 60.5 3.2 9.5E-05 21.7 1.0 18 130-147 18-35 (82) 68 >2zbk_B Type 2 DNA topoisomera 59.9 6.5 0.00019 19.7 2.4 22 127-148 28-49 (82) 69 >1t94_A Polymerase (DNA direct 59.9 6.2 0.00018 19.8 2.3 17 130-146 14-30 (70) 70 >3i1m_M 30S ribosomal protein 58.6 4.6 0.00014 20.7 1.5 20 127-146 16-35 (63) 71 >1b43_A Protein (FEN-1); nucle 58.5 3.6 0.00011 21.3 1.0 47 91-150 1-47 (77) 72 >3gfk_B DNA-directed RNA polym 58.5 4.6 0.00014 20.6 1.5 48 96-146 19-66 (79) 73 >1rxw_A Flap structure-specifi 57.9 3.7 0.00011 21.3 0.9 18 130-147 17-34 (68) 74 >2zkq_m 40S ribosomal protein 57.6 4.9 0.00015 20.5 1.5 20 127-146 27-46 (88) 75 >3fhg_A Mjogg, N-glycosylase/D 57.4 5.7 0.00017 20.0 1.8 31 155-185 2-40 (65) 76 >1lb2_B DNA-directed RNA polym 57.1 5.9 0.00017 20.0 1.8 46 98-146 15-60 (84) 77 >1szp_A DNA repair protein RAD 56.9 4.8 0.00014 20.5 1.3 37 78-117 1-37 (56) 78 >2i5h_A Hypothetical protein A 50.0 7 0.00021 19.5 1.3 41 126-170 130-170 (205) 79 >1jx4_A DNA polymerase IV (fam 49.0 8.1 0.00024 19.0 1.5 33 78-115 18-50 (55) 80 >3bqs_A Uncharacterized protei 48.7 6.8 0.0002 19.5 1.0 41 127-167 3-43 (93) 81 >1t57_A Conserved protein MTH1 48.1 18 0.00052 16.7 3.1 106 56-163 55-171 (206) 82 >3e1s_A Exodeoxyribonuclease V 47.4 3.8 0.00011 21.2 -0.4 113 87-207 6-130 (149) 83 >3gzu_A Inner capsid protein V 47.3 10 0.0003 18.4 1.7 53 46-98 106-169 (321) 84 >1z3e_B DNA-directed RNA polym 46.6 9.2 0.00027 18.6 1.5 49 95-146 11-59 (73) 85 >2vqe_M 30S ribosomal protein 46.5 5.5 0.00016 20.1 0.3 20 127-146 16-35 (64) 86 >1d8b_A SGS1 RECQ helicase; fi 45.2 8.8 0.00026 18.8 1.2 21 122-142 42-62 (81) 87 >1ul1_X Flap endonuclease-1; p 43.2 5.5 0.00016 20.2 -0.1 30 130-168 31-60 (89) 88 >2aq4_A DNA repair protein REV 42.6 10 0.0003 18.3 1.2 18 130-147 4-21 (67) 89 >1f6f_A Placental lactogen; 4- 38.3 27 0.00079 15.5 5.4 63 104-166 124-193 (199) 90 >2yuk_A Myeloid/lymphoid or mi 38.3 13 0.0004 17.5 1.2 39 68-111 36-74 (90) 91 >2fj0_A JuvenIle hormone ester 36.9 28 0.00083 15.4 4.5 41 162-204 15-56 (64) 92 >2p4w_A Transcriptional regula 36.3 23 0.00067 16.0 2.1 40 156-195 1-40 (48) 93 >3fhf_A Mjogg, N-glycosylase/D 36.3 25 0.00075 15.7 2.4 38 148-185 32-76 (101) 94 >2b1e_A Exocyst complex compon 35.9 29 0.00086 15.3 7.2 72 22-98 29-104 (106) 95 >3fhg_A Mjogg, N-glycosylase/D 34.0 31 0.00092 15.1 3.7 22 125-146 41-62 (69) 96 >2rhf_A DNA helicase RECQ; HRD 33.2 15 0.00044 17.3 0.8 21 122-142 41-61 (77) 97 >2pft_A Exocytosis protein; he 32.9 32 0.00096 15.0 5.2 72 22-98 20-97 (102) 98 >1huw_A Human growth hormone; 32.0 33 0.00099 14.9 3.8 105 59-163 68-180 (191) 99 >1coo_A RNA polymerase alpha s 31.4 11 0.00033 18.0 -0.1 49 95-146 26-74 (98) 100 >2ziu_B Crossover junction end 28.6 17 0.00049 16.9 0.4 29 57-86 15-43 (100) 101 >2a6h_A DNA-directed RNA polym 27.6 35 0.001 14.7 1.9 49 94-145 130-178 (190) 102 >1c7v_A CAVP, calcium vector p 27.5 36 0.0011 14.7 1.9 59 70-131 10-68 (81) 103 >1l2l_A ADP-dependent glucokin 26.8 41 0.0012 14.3 3.9 74 79-171 3-78 (130) 104 >1bgx_T TAQ DNA polymerase; DN 26.4 8.7 0.00026 18.8 -1.4 16 127-142 152-167 (167) 105 >1wud_A ATP-dependent DNA heli 25.5 25 0.00074 15.7 0.9 22 122-143 49-70 (89) 106 >2cw6_A Hydroxymethylglutaryl- 25.5 11 0.00034 18.0 -0.9 20 16-35 20-39 (298) 107 >2ggm_A Centrin-2; EF-hand sup 25.1 44 0.0013 14.1 4.0 62 67-132 18-79 (87) 108 >2aja_A Ankyrin repeat family 24.8 44 0.0013 14.0 2.4 46 78-137 41-87 (156) 109 >1rq6_A 30S ribosomal protein 24.0 16 0.00047 17.1 -0.4 28 102-129 3-30 (62) 110 >1ua4_A Glucokinase, ADP-depen 23.4 47 0.0014 13.9 3.8 73 79-170 4-78 (132) 111 >2ziu_A MUS81 protein; helix-h 23.0 9.4 0.00028 18.6 -1.7 27 59-86 11-37 (82) 112 >1fpw_A Yeast frequenin, calci 22.2 37 0.0011 14.6 1.2 59 71-131 7-65 (74) 113 >3d48_P Prolactin, PRL; cytoki 21.1 52 0.0015 13.6 3.2 40 127-166 142-181 (188) 114 >2h7a_A Hypothetical protein Y 20.9 48 0.0014 13.8 1.5 21 81-101 63-83 (110) 115 >3f2b_A DNA-directed DNA polym 20.0 55 0.0016 13.4 1.7 32 134-169 1-32 (69) No 1 >>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} (A:1-23,A:110-225) Probab=99.95 E-value=5.3e-28 Score=208.81 Aligned_cols=108 Identities=25% Similarity=0.403 Sum_probs=96.1 Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCH-----HHHHHHHHHCCCHHHH Q ss_conf 42001000014567776432358888999987542100012104678776565407888-----9999999621884226 Q gi|254780383|r 117 NEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTP-----NKVEQSLLRIIPPKHQ 191 (227) Q Consensus 117 ~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~p~~~VDthv~Rv~~Rlgl~~~~~~-----~~~~~~l~~~~p~~~~ 191 (227) ++||. .+.-+|++|||||+|||++||+|+||+++|+|||||+||++|+|+++.+.. ...+..+...++...+ T Consensus 15 ~~~~~---~~~~eL~~LpGIG~ktAd~Illfa~~~~~~pVDthv~RVl~Rlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 91 (139) T 1kg2_A 15 DKYGR---KTLPEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENKLWSLSEQVTPAVGV 91 (139) T ss_dssp HHHCC---CCSGHHHTSTTCCHHHHHHHHHHHHCCSCCCCCHHHHHHHHHHHTCCSCTTSHHHHHHHHHHHHHHCCSTTH T ss_pred HHCCC---CCCCHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC T ss_conf 98199---879998628987278999999984498607679986775333025678996268999999987523861100 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCHHHCC Q ss_conf 789999999966516489989472840331768519 Q gi|254780383|r 192 YNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ 227 (227) Q Consensus 192 ~~~~~~li~~G~~iC~~~~P~C~~C~l~~~C~~~k~ 227 (227) .++|++||+||+.+|++++|+|+.|||++.|+++++ T Consensus 92 ~~~h~~L~~~Gr~vC~~r~P~C~~CpL~~~C~~~~~ 127 (139) T 1kg2_A 92 ERFNQAMMDLGAMICTRSKPKCSLCPLQNGCIAAAN 127 (139) T ss_dssp HHHHHHHHHHHHHTSCSSSCCGGGCTTTTTCHHHHH T ss_pred CHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCHHHHC T ss_conf 177799999978881499999998978333988776 No 2 >>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} (A:23-133) Probab=99.92 E-value=2e-25 Score=191.51 Aligned_cols=111 Identities=50% Similarity=0.852 Sum_probs=108.9 Q ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 77778689999999996333203567998998731762000101268999999997300379999997523554442001 Q gi|254780383|r 42 ELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDN 121 (227) Q Consensus 42 ~l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g 121 (227) +|.++|||++||++||||||++.++.+++.+|+++||||++++.++.+++++.|+++||++.||++|+++++.+.+.+++ T Consensus 1 el~~~d~~e~lv~~il~qq~~~~~a~~~~~~l~~~~~t~~~~~~~~~~~~~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~ 80 (111) T 2abk_A 1 ELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNG 80 (111) T ss_dssp SSCCSSHHHHHHHHHHTTTSCHHHHHHHHHHHTTTCCSHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHTTT T ss_pred CCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 88889879999999984536199999999988761488788754576667777674115677888999999999986041 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0000145677764323588889999875421 Q gi|254780383|r 122 KIPQTLEGLTRLPGIGRKGANVILSMAFGIP 152 (227) Q Consensus 122 ~vP~~~~~L~~LpGVG~ktA~~il~~~~~~p 152 (227) .+|.++++|.+|||||+|||++||+|+||+| T Consensus 81 ~~~~~~~~L~~l~GIG~~tA~~vll~~~g~P 111 (111) T 2abk_A 81 EVPEDRAALEALPGVGRKTANVVLNTAFGWP 111 (111) T ss_dssp SCCSCHHHHHHSTTCCHHHHHHHHHHHHCCC T ss_pred CHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC T ss_conf 1367799999898606359999999985671 No 3 >>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} (A:28-137) Probab=99.92 E-value=2.3e-25 Score=191.12 Aligned_cols=110 Identities=47% Similarity=0.791 Sum_probs=107.4 Q ss_pred CCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 77786899999999963332035679989987317620001012689999999973003799999975235544420010 Q gi|254780383|r 43 LYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNK 122 (227) Q Consensus 43 l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~ 122 (227) +.++|||++||++||||||+++++.+++.+|+++||||++++.++.+++.+.|+++||+++||++|+++++.+.++|+|. T Consensus 1 ~~~~dpfe~Li~~Il~Qqt~~~~a~~~~~~l~~~~~~~~~~~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~~~~~~~~~ 80 (110) T 1orn_A 1 LVHRNPFELLIAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGE 80 (110) T ss_dssp SCCSSHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCCSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHHHHHHHSTTS T ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCHHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCC T ss_conf 99899799999999981086999999999998604998998607899999999973249999999999878999993998 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 000145677764323588889999875421 Q gi|254780383|r 123 IPQTLEGLTRLPGIGRKGANVILSMAFGIP 152 (227) Q Consensus 123 vP~~~~~L~~LpGVG~ktA~~il~~~~~~p 152 (227) +|.++++|++|||||+|||+++|+|+||+| T Consensus 81 ~~~~~~~L~~l~GIG~~ta~~~llf~~~~P 110 (110) T 1orn_A 81 VPRDRDELMKLPGVGRKTANVVVSVAFGVP 110 (110) T ss_dssp CCSCHHHHTTSTTCCHHHHHHHHHHHHCCC T ss_pred CCCCHHHHHHCCCCCHHHHHHHHHHHHCCC T ss_conf 988899997587975258999999985788 No 4 >>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} (A:29-139) Probab=99.91 E-value=3.1e-24 Score=183.43 Aligned_cols=109 Identities=19% Similarity=0.455 Sum_probs=106.2 Q ss_pred CCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 77786899999999963332035679989987317620001012689999999973003799999975235544420010 Q gi|254780383|r 43 LYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNK 122 (227) Q Consensus 43 l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~ 122 (227) .+.+|||+.||++||+|||+++++.+++.+|+++||||++++.++.++++++|+++||+++||++|+++++.+.+.+++. T Consensus 2 r~~~d~fe~Lv~~Il~qq~s~~~a~~~~~~l~~~~~~~~~l~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~~~~~~~~~ 81 (111) T 1kea_A 2 RHTRDPYVILITEILLRRTTAGHVKKIYDKFFVKYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGR 81 (111) T ss_dssp GGCCCHHHHHHHHHHTTTSCHHHHHHHHHHHHHHCCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHHHTTS T ss_pred CCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC T ss_conf 98998799999999983196999999999999978899999839988999998976889999999999999888751599 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00014567776432358888999987542 Q gi|254780383|r 123 IPQTLEGLTRLPGIGRKGANVILSMAFGI 151 (227) Q Consensus 123 vP~~~~~L~~LpGVG~ktA~~il~~~~~~ 151 (227) +|+.+++|++|||||+|||+++|+|++|+ T Consensus 82 ~~~~~~~L~~l~GIG~~tA~~~llf~~gr 110 (111) T 1kea_A 82 VPRNRKAILDLPGVGKYTCAAVMCLAFGK 110 (111) T ss_dssp CCSCHHHHHTSTTCCHHHHHHHHHHTTCC T ss_pred CCCHHHHHHCCCCCCHHHHHHHHHHHCCC T ss_conf 97304676508987616899999986388 No 5 >>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A* (A:34-143) Probab=99.89 E-value=1.4e-23 Score=179.11 Aligned_cols=109 Identities=17% Similarity=0.321 Sum_probs=103.2 Q ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 77868999999999633320356799899873176200010126899999999730037999999752355444200100 Q gi|254780383|r 44 YYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKI 123 (227) Q Consensus 44 ~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~v 123 (227) .+.|||+.||++||+|||++..+.+++.+|+++||||+.++.++.+++.++|+++||+++|+++|..++..+ +++++.+ T Consensus 2 ~~~dpfe~Li~~Il~q~~s~~~a~~~~~rl~~~~~t~~~~~~~~~~~l~~~l~~~g~~~~k~~~i~~~~~~~-~~~~~~~ 80 (110) T 3fsp_A 2 KDRDPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVK-TRYGGKV 80 (110) T ss_dssp SCCCHHHHHHHHHHTTTSCHHHHHHHHHHHHHHCCSHHHHHTSCHHHHHHTTTTSSCTHHHHHHHHHHHHHH-HHHTTCC T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHH-HHHCCCC T ss_conf 899879999999986108788999999999997799999977899999999872671999999999899986-8637989 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 001456777643235888899998754210 Q gi|254780383|r 124 PQTLEGLTRLPGIGRKGANVILSMAFGIPT 153 (227) Q Consensus 124 P~~~~~L~~LpGVG~ktA~~il~~~~~~p~ 153 (227) |..+++|++|||||+|||++||+|++|+|. T Consensus 81 ~~~~~~L~~lpGIG~~tA~~vll~~~g~pe 110 (110) T 3fsp_A 81 PDDPDEFSRLKGVGPYTVGAVLSLAYGVPE 110 (110) T ss_dssp CCSHHHHHTSTTCCHHHHHHHHHHHHCCCC T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 988999951112689999999999715887 No 6 >>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} (A:23-145) Probab=99.89 E-value=1.4e-23 Score=179.04 Aligned_cols=110 Identities=25% Similarity=0.319 Sum_probs=104.5 Q ss_pred CCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC-------CCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 77786899999999963332035679989987317-------62000101268999999997300379999997523554 Q gi|254780383|r 43 LYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIA-------DTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHIL 115 (227) Q Consensus 43 l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~y-------pt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i 115 (227) ..-+|||+.||++||||||+++++.+++.+|+++| |||+++++++++++.++|+++||++.||++|+++++.+ T Consensus 3 ~~~~d~fe~Li~~il~qq~~~~~a~~~~~~l~~~~g~~~~~~pt~~~l~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~~ 82 (123) T 1pu6_A 3 WPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNI 82 (123) T ss_dssp STTTTSHHHHHHHHHTTTSCHHHHHHHHHHHHHTTSSCSCHHHHHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHH T ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHH T ss_conf 99998799999999946698999999999999987520124899999977999999999998799589999999999999 Q ss_pred HHHHCC----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 442001----0000145677764323588889999875421 Q gi|254780383|r 116 INEFDN----KIPQTLEGLTRLPGIGRKGANVILSMAFGIP 152 (227) Q Consensus 116 ~~~~~g----~vP~~~~~L~~LpGVG~ktA~~il~~~~~~p 152 (227) .++++| ..|+.+++|.+|||||+|||+++|+|++|+| T Consensus 83 ~~~~~~l~~~~~~~~~~~L~~l~GIG~~tA~~illf~l~~P 123 (123) T 1pu6_A 83 LKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACAKE 123 (123) T ss_dssp HHHHSSHHHHHHHCCHHHHHTSTTCCHHHHHHHHHHTTCCS T ss_pred HHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHCCCC T ss_conf 98663103799467999998489966999999999987998 No 7 >>1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} (A:1-129) Probab=99.89 E-value=3.5e-24 Score=183.06 Aligned_cols=115 Identities=13% Similarity=0.208 Sum_probs=102.6 Q ss_pred HHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99997679998777786899999999963332035679989987317620001012689999999973003799999975 Q gi|254780383|r 31 LFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIIS 110 (227) Q Consensus 31 ~L~~~yp~~~~~l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~ 110 (227) .+.+.|+ +..+....|||+.||++||||||+++++++++.+|+++|+||++++.++.++++++|+++||+++||++|++ T Consensus 15 ~l~~~~~-~~~~~~~~~pfe~Li~~Il~Qq~s~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~G~~~~Ka~~i~~ 93 (129) T 1ngn_A 15 PPRSPFN-LVQEILFHDPWKLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIK 93 (129) T ss_dssp CCCCTTC-CTHHHHTTSHHHHHHHHHHHTTSCHHHHHHHHHHHHHHSCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHH T ss_pred CCCCCCC-HHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCCHHHHHHHHHHH T ss_conf 9998642-146551598589999999986186999999999999988799999716758689898124479999999999 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2355444200100001456777643235888899998754210 Q gi|254780383|r 111 LSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPT 153 (227) Q Consensus 111 ~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~p~ 153 (227) +++.+++ +.+++|++|||||+|||++||+|+||+|- T Consensus 94 ~a~~~~~-------e~~~~L~~l~GIG~~tA~~vll~~~grP~ 129 (129) T 1ngn_A 94 FSDEYLT-------KQWRYPIELHGIGKYGNDSYRIFCVNEWK 129 (129) T ss_dssp HHHHHHH-------SCCSSGGGSTTCCHHHHHHHHHHTSSCGG T ss_pred HHHHHHH-------HHHHHHHHCCCCCHHHHHHHHHHHCCCCC T ss_conf 9824666-------34766562799668999999999769988 No 8 >>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} (A:24-109) Probab=99.86 E-value=3.9e-22 Score=169.31 Aligned_cols=86 Identities=12% Similarity=0.142 Sum_probs=82.5 Q ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 77778689999999996333203567998998731762000101268999999997300379999997523554442001 Q gi|254780383|r 42 ELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDN 121 (227) Q Consensus 42 ~l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g 121 (227) |++++|||++||++||||||+|++|.+++.+|+++||||+++++++.++|+++|+|+|||+ ||++|+++|+.|+++||| T Consensus 1 W~~~~dp~~~Lia~iLsq~T~~~~~~~~~~~L~~~~~t~~~l~~a~~~~l~~~i~~~G~~~-Ka~~i~~~a~~i~~~~~g 79 (86) T 1kg2_A 1 WQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVATLHGG 79 (86) T ss_dssp GGSSCCHHHHHHHHHHHTSSCHHHHHHHHHHHHHHCSSHHHHHHSCHHHHHHHHTTSCCTH-HHHHHHHHHHHHHHHSTT T ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHCCHHH-HHHHHHHHHHHHHHHCCC T ss_conf 9989986999999999811849999999999999879999998608999999988468999-999999999999886079 Q ss_pred CCHHHHH Q ss_conf 0000145 Q gi|254780383|r 122 KIPQTLE 128 (227) Q Consensus 122 ~vP~~~~ 128 (227) +||.+++ T Consensus 80 ~vP~~~e 86 (86) T 1kg2_A 80 KFPETFE 86 (86) T ss_dssp SCCCSHH T ss_pred CCCCHHH T ss_conf 9972899 No 9 >>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} (A:123-255) Probab=99.85 E-value=1e-21 Score=166.42 Aligned_cols=110 Identities=15% Similarity=0.114 Sum_probs=97.2 Q ss_pred CCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCC-----------CHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 77786899999999963332035679989987317620001012-----------6899999999730037999999752 Q gi|254780383|r 43 LYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAI-----------GEKKLQNYIRTIGIYRKKSENIISL 111 (227) Q Consensus 43 l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a-----------~~~el~~~ir~~G~~~~KAk~I~~~ 111 (227) +...|||++||++||+|||+++++++++.+|+++|+++...+.. ..++..+.++++|++++||++|+++ T Consensus 2 l~~~dpfe~Li~~Il~Qq~~~~~a~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~ka~~i~~~ 81 (133) T 1m3q_A 2 LLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSAS 81 (133) T ss_dssp CCCCCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSCEEEEETTEEEECCCCHHHHTSTTHHHHHHHTTCTTHHHHHHHH T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHCCHHHHHHHCCCHHHHHHHHHH T ss_conf 45788899999999998865999999999999980987667786543478999999736889999864747899999999 Q ss_pred HHHHHHHHCCCC----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 355444200100----------00145677764323588889999875421 Q gi|254780383|r 112 SHILINEFDNKI----------PQTLEGLTRLPGIGRKGANVILSMAFGIP 152 (227) Q Consensus 112 a~~i~~~~~g~v----------P~~~~~L~~LpGVG~ktA~~il~~~~~~p 152 (227) |+.+.++|+|.+ ++.+++|++|||||+|||++||+|+||+| T Consensus 82 a~~~~~~~~g~~~~~~~~~~~~~~~~~~L~~lpGIG~~tA~~ill~~l~rp 132 (133) T 1m3q_A 82 ARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKP 132 (133) T ss_dssp HHHHHHTSCSHHHHHHTTTSCHHHHHHHHTTSTTCCHHHHHHHHHHHSCCT T ss_pred HHHHHHCCCCCCCHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCCC T ss_conf 999874245435799771399899999998468837999999999967999 No 10 >>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} (A:105-231) Probab=99.84 E-value=2.2e-21 Score=164.27 Aligned_cols=111 Identities=18% Similarity=0.214 Sum_probs=98.7 Q ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCC---------CHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 777786899999999963332035679989987317620001012---------68999999997300379999997523 Q gi|254780383|r 42 ELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAI---------GEKKLQNYIRTIGIYRKKSENIISLS 112 (227) Q Consensus 42 ~l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a---------~~~el~~~ir~~G~~~~KAk~I~~~a 112 (227) ++...|||+.||++||+|||+++++.+++.+|+++|++++..... ..+.+++.++++||+++||++|+++| T Consensus 3 ~~~~~~pfe~lv~~Il~Qq~~~~~a~~~~~~l~~~~g~~~~~~~~~~~~p~~~~~~~~~~~~~~~~g~~~~ka~~i~~~a 82 (127) T 1mpg_A 3 LPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLA 82 (127) T ss_dssp CCCCSCHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHCCBCSSCTTCBCCCCHHHHHTCCHHHHHHTTSCHHHHHHHHHHH T ss_pred CCCCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHCCCHHHHHHCCCCHHHHHHHHHHH T ss_conf 89989989999999996723299999999999998588767687656799899997699999975288665899999999 Q ss_pred HHHHH-----HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 55444-----20010000145677764323588889999875421 Q gi|254780383|r 113 HILIN-----EFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIP 152 (227) Q Consensus 113 ~~i~~-----~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~p 152 (227) +.+.+ .+++.+|..+++|++|||||+|||++||+|+||+. T Consensus 83 ~~~~~~~l~~~~~~~~~~~~~~L~~lpGIG~~tA~~vll~~~gr~ 127 (127) T 1mpg_A 83 NAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAK 127 (127) T ss_dssp HHHHHTCSCSSCCSCHHHHHHHHTTSTTCCHHHHHHHHHHHSCCS T ss_pred HHHHCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCCC T ss_conf 999829942134467899999998658978999999999857998 No 11 >>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} (A:1-27,A:138-226) Probab=99.81 E-value=3.7e-20 Score=155.96 Aligned_cols=77 Identities=39% Similarity=0.730 Sum_probs=73.0 Q ss_pred HHHHHCCCHHHHHHHHHHHHCCC-CHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCHHHCC Q ss_conf 21000121046787765654078-889999999621884226789999999966516489989472840331768519 Q gi|254780383|r 151 IPTIGVDTHIFRISNRIGLAPGK-TPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ 227 (227) Q Consensus 151 ~p~~~VDthv~Rv~~Rlgl~~~~-~~~~~~~~l~~~~p~~~~~~~~~~li~~G~~iC~~~~P~C~~C~l~~~C~~~k~ 227 (227) -.+|+|||||+||++||||++++ ++++++..+++++|.+.|++||++||+||+.||++++|+|+.|||++.|++|++ T Consensus 26 ~~ai~VDthV~RV~~Rlg~i~~~~~~~~~~~~l~~~ip~~~~~~~~~~Li~lGr~vC~ar~P~C~~CPL~~~C~~~~~ 103 (116) T 1orn_A 26 CEAIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIPKEEWSITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREGKK 103 (116) T ss_dssp CCCCCCCHHHHHHHHHHTSSCTTCCHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHTSCSSCCCGGGCTTGGGCHHHHH T ss_pred CCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHCHHHHC T ss_conf 998788843577999838666543046999999983865443799999999999883489999998978021778763 No 12 >>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} (A:1-22,A:134-211) Probab=99.80 E-value=4.3e-20 Score=155.58 Aligned_cols=76 Identities=53% Similarity=1.066 Sum_probs=73.9 Q ss_pred HHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCHHHCC Q ss_conf 1000121046787765654078889999999621884226789999999966516489989472840331768519 Q gi|254780383|r 152 PTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ 227 (227) Q Consensus 152 p~~~VDthv~Rv~~Rlgl~~~~~~~~~~~~l~~~~p~~~~~~~~~~li~~G~~iC~~~~P~C~~C~l~~~C~~~k~ 227 (227) .+|+|||||+||++|+||++++++++++..+++++|.+.|.+||++||+||+.+|++++|+|+.|||++.|++|++ T Consensus 22 ~a~~VDthv~RV~~Rlg~v~~~~~~~~e~~l~~~lp~~~~~~~h~aLi~lGr~vC~~r~P~C~~CpL~~~C~~~~~ 97 (100) T 2abk_A 22 TTIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPAEFKVDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEK 97 (100) T ss_dssp CCCCCCHHHHHHHHHHCSSCCSSHHHHHHHHHHHSCGGGTTTHHHHHHHHHHHTSCSSSCCGGGCTTGGGCCCTTC T ss_pred CCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC T ss_conf 9423568999999970677542046788888604870358999999999845442599999999979142888678 No 13 >>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} (A:1-49,A:127-233) Probab=99.78 E-value=1.5e-19 Score=151.99 Aligned_cols=112 Identities=13% Similarity=0.094 Sum_probs=89.8 Q ss_pred HHHHHHHHHHHH-----HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCHHHHHHHHHHHHCCC--CH Q ss_conf 999997523554-----4420010000145677764323588889999875421-000121046787765654078--88 Q gi|254780383|r 104 KSENIISLSHIL-----INEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIP-TIGVDTHIFRISNRIGLAPGK--TP 175 (227) Q Consensus 104 KAk~I~~~a~~i-----~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~p-~~~VDthv~Rv~~Rlgl~~~~--~~ 175 (227) +--..++++..+ -+.++|.+|.++++|++|||||+|||++||+|+||+| +||||+|+.|+..|+++...+ +. T Consensus 32 ~~~~~~~~~~~~~~~~~~el~~g~~pe~~~~LlsLPGIGpkTA~~ILlfalgrpdvfpVdD~~iRr~~r~~~~~~~~~~~ 111 (156) T 2h56_A 32 RLFQFIEIAGEVQLPTKPELEGAEATTVIEKLTAIKGIGQWTAEXFXXFSLGRLDVLSVGDVGLQRGAKWLYGNGEGDGK 111 (156) T ss_dssp HHHHHHHHHCCEEEECCSHHTTSCHHHHHHHHHTSTTCCHHHHHHHHHHTTCCSCCCCTTCHHHHHHHHHHHSSSCSCHH T ss_pred HHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCH T ss_conf 99999998699867898926665355788888873897878999999851689977864579999999998288889989 Q ss_pred HHHHHHHHHCCCHHHH-----HHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 9999999621884226-----7899999999665164899894728 Q gi|254780383|r 176 NKVEQSLLRIIPPKHQ-----YNAHYWLVLHGRYVCKARKPQCQSC 216 (227) Q Consensus 176 ~~~~~~l~~~~p~~~~-----~~~~~~li~~G~~iC~~~~P~C~~C 216 (227) .+++..++.+.|...| .++|++||++|+.+|++++|.| +| T Consensus 112 ~~~~~~~e~~~P~~~~~~~~L~~~~~alidlGr~vC~~r~Pc~-~C 156 (156) T 2h56_A 112 KLLIYHGKAWAPYETVACLYLWKAAGTFAEEYRSLEELLHHGN-QC 156 (156) T ss_dssp HHHHHHHGGGTTCHHHHHHHHHHHHTHHHHHCSSHHHHSCC----- T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCC-CC T ss_conf 9999998707899999999999408995043211887607767-89 No 14 >>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} (A:1-28,A:140-221) Probab=99.76 E-value=1.1e-18 Score=146.00 Aligned_cols=86 Identities=22% Similarity=0.367 Sum_probs=73.4 Q ss_pred HHHHHHHH----HHHHHHCCCHHHHHHHHHHHHCCCC----HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 89999875----4210001210467877656540788----899999996218842267899999999665164899894 Q gi|254780383|r 142 NVILSMAF----GIPTIGVDTHIFRISNRIGLAPGKT----PNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQC 213 (227) Q Consensus 142 ~~il~~~~----~~p~~~VDthv~Rv~~Rlgl~~~~~----~~~~~~~l~~~~p~~~~~~~~~~li~~G~~iC~~~~P~C 213 (227) +.||.|-- +.|+|+|||||+||++|+|+++.++ ..+++..+.+++|.+.|.+||++||+||+.+|++++|+| T Consensus 14 ~~~~~~~~~~~~~~~~~~VDtnv~RV~~Rl~~v~~~~~~~~~~~l~~~~~~~lp~~~~~~~h~aLi~lG~~vC~~k~P~C 93 (110) T 1kea_A 14 STILTFWNTDRRDFPAAMVDANFVRVINRYFGGSYENLNYNHKALWELAETLVPGGKCRDFNLGLMDFSAIICAPRKPKC 93 (110) T ss_dssp HHHHHHHHHSCCCCGCCCCCHHHHHHHHHHHCGGGTTCCTTSHHHHHHHHHHSCTTCHHHHHHHHHHHHHHTSCSSSCCG T ss_pred HHHHHHHHHCCCCCCCCEECCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 99999998669999930224388878998637788982166999999998628813299999999998588603989999 Q ss_pred CCCCCHHHCHHHCC Q ss_conf 72840331768519 Q gi|254780383|r 214 QSCIISNLCKRIKQ 227 (227) Q Consensus 214 ~~C~l~~~C~~~k~ 227 (227) ++|||++.|+||++ T Consensus 94 ~~CPL~~~C~~~~~ 107 (110) T 1kea_A 94 EKCGMSKLCSYYEK 107 (110) T ss_dssp GGCTTTTTCHHHHT T ss_pred CCCCCCCCCCCCCC T ss_conf 88989101937277 No 15 >>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} (A:38-150) Probab=99.76 E-value=1.3e-18 Score=145.58 Aligned_cols=101 Identities=19% Similarity=0.119 Sum_probs=91.0 Q ss_pred CCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHC Q ss_conf 777868999999999633320356799899873176200010126899999999730--037999999752355444200 Q gi|254780383|r 43 LYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIG--IYRKKSENIISLSHILINEFD 120 (227) Q Consensus 43 l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G--~~~~KAk~I~~~a~~i~~~~~ 120 (227) +...|||+.||++||+|||+++++.+++.+|+++|+++ +.+++++++++.| |+++||++|+++++.+.++++ T Consensus 2 ~~~~dpfe~Lv~~Il~Qq~s~~~a~~~~~~l~~~~~~~------~~~~~~~~~~~~g~~~~~~ka~~l~~~a~~~~~~~~ 75 (113) T 3fhf_A 2 KSNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFLTL------PREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDI 75 (113) T ss_dssp SCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHTTHHHHS------CHHHHHHHHHHTTCTTHHHHHHHHHHHGGGCCHHHH T ss_pred CCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCC------CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 75478999999999614586999999999999998718------976799999994524667889999999999988767 Q ss_pred CCCHHH-----HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 100001-----45677764323588889999875 Q gi|254780383|r 121 NKIPQT-----LEGLTRLPGIGRKGANVILSMAF 149 (227) Q Consensus 121 g~vP~~-----~~~L~~LpGVG~ktA~~il~~~~ 149 (227) |.+|.. +++|++|||||+|||+++|+|+. T Consensus 76 ~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~f~~ 109 (113) T 3fhf_A 76 VESFENEKVAREFLVRNIKGIGYKEASHFLRNVG 109 (113) T ss_dssp HHHSSSHHHHHHHHHHHSTTCCHHHHHHHHHHTT T ss_pred HHHCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHC T ss_conf 7760688976399998785832999999999967 No 16 >>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A* (A:1-33,A:144-218) Probab=99.69 E-value=2.8e-17 Score=136.56 Aligned_cols=74 Identities=26% Similarity=0.481 Sum_probs=67.8 Q ss_pred HHHHHHCCCHHHHHHHHHHHHCC-----CCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCH Q ss_conf 42100012104678776565407-----888999999962188422678999999996651648998947284033176 Q gi|254780383|r 150 GIPTIGVDTHIFRISNRIGLAPG-----KTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCK 223 (227) Q Consensus 150 ~~p~~~VDthv~Rv~~Rlgl~~~-----~~~~~~~~~l~~~~p~~~~~~~~~~li~~G~~iC~~~~P~C~~C~l~~~C~ 223 (227) +.|-|+|||||+||++|+|++++ +++.+++..+.+++|.+.+.++|++||+||+.||++++|+|+.|||++.|+ T Consensus 30 ~~~~i~VDtnV~RVl~Rlg~v~~~~~~~~t~~~i~~~l~~liP~~~~~~~h~aLi~lGr~vC~~k~P~C~~CPL~~~Ck 108 (108) T 3fsp_A 30 DLPWPAVDGNVMRVLSRLFLVTDDIAKPSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQ 108 (108) T ss_dssp CCGGCCCCHHHHHHHHHHTTCCSCTTSHHHHHHHHHHHHHHCCSSSHHHHHHHHHHHHHHTSCSSSCCTTTCTTGGGCH T ss_pred CCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHCH T ss_conf 8998652571898889860557887650378999988740366457789999999955300058999898898633277 No 17 >>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} (A:50-126) Probab=99.59 E-value=7.1e-16 Score=127.14 Aligned_cols=77 Identities=13% Similarity=0.130 Sum_probs=73.7 Q ss_pred CHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHH Q ss_conf 68999999999633320356799899873176200010126899999999730037999999752355444200100001 Q gi|254780383|r 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQT 126 (227) Q Consensus 47 ~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~ 126 (227) |||++||++||||||+++++.+++.+|+++||+++.++++..+++++.|+++||+++||++|+++|+.+++ |++|.+ T Consensus 1 dpf~~Li~~Ilsqqts~~~a~~~~~rl~~~~~~~~~~~~~~~~~~~~~ir~~G~~~~Ka~~i~~~a~~i~~---g~ip~t 77 (77) T 2h56_A 1 NPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHVES---GRLDFT 77 (77) T ss_dssp CHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHTSCCCCTHHHHTSCHHHHHHTTCCHHHHHHHHHHHHHHHT---TSSCHH T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHHHCHHHHHHHHHHHHHH---CCCCCH T ss_conf 98999999998170039999999999999860023688998637999987776410001689999999981---665310 No 18 >>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} (A:1-22,A:146-218) Probab=98.30 E-value=4.4e-07 Score=67.94 Aligned_cols=59 Identities=8% Similarity=0.107 Sum_probs=48.9 Q ss_pred HH-HHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHH----------------HHHHHHHHHHHHHHHHCCCC Q ss_conf 42-10001210467877656540788899999996218842----------------26789999999966516489 Q gi|254780383|r 150 GI-PTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPK----------------HQYNAHYWLVLHGRYVCKAR 209 (227) Q Consensus 150 ~~-p~~~VDthv~Rv~~Rlgl~~~~~~~~~~~~l~~~~p~~----------------~~~~~~~~li~~G~~iC~~~ 209 (227) |. .+|+||+|+.|+++|+|+... ++++++..+++.+|.+ .+.+||.+|+.||+..|+.+ T Consensus 19 ~~~~VFVVDaYTrRLf~rLG~~~e-~Ydelq~~fe~~L~~d~~~~~~~~~~e~~l~~lyqefHALIVE~gK~~ckkK 94 (95) T 1pu6_A 19 NAPAVMVVDKYSYLFLKKLGIEIE-DYDELQHFFEKGVQENLNSALALYENTISLAQLYARFHGXIVEFSKQKLELK 94 (95) T ss_dssp TSCTCCCCCHHHHHHHHHTTCCCC-SHHHHHHHHHHHHHTTHHHHHHTTTTCSCHHHHHHHHHHHHHHHHHHHHHTC T ss_pred CCCCCCCCCHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 899906204259999999089889-9999999999886898999887750002089999999999999869877898 No 19 >>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A (A:111-127,A:196-236) Probab=97.62 E-value=1.9e-05 Score=56.89 Aligned_cols=29 Identities=21% Similarity=0.358 Sum_probs=26.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 01456777643235888899998754210 Q gi|254780383|r 125 QTLEGLTRLPGIGRKGANVILSMAFGIPT 153 (227) Q Consensus 125 ~~~~~L~~LpGVG~ktA~~il~~~~~~p~ 153 (227) +.+++|.++||||+|||++||+|++++|. T Consensus 30 ea~~~L~~i~GIGpwTAdciLLF~L~RPn 58 (58) T 3i0w_A 30 ECHEELKKFMGVGPQVADCIMLFSMQKYS 58 (58) T ss_dssp HHHHHHTTSTTCCHHHHHHHHHHHHCCTT T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHCCCCC T ss_conf 67899982688129999999998648988 No 20 >>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} (A:29-101) Probab=96.73 E-value=0.0094 Score=38.77 Aligned_cols=63 Identities=22% Similarity=0.305 Sum_probs=52.6 Q ss_pred CHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHH--HHHHHHHHHHHHHHHH Q ss_conf 68999999999633320356799899873176200010126899999999730--0379999997523554 Q gi|254780383|r 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIG--IYRKKSENIISLSHIL 115 (227) Q Consensus 47 ~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G--~~~~KAk~I~~~a~~i 115 (227) +-|.-|+-|||.+|++.....++...|-. .+...+.+||.+.++.+| |+|+||++|.+.=+.+ T Consensus 4 ~lF~EL~FCILTanssA~~g~kaq~~lg~------gf~~~s~eel~~~L~~~g~RF~n~rA~yIve~R~l~ 68 (73) T 3fhg_A 4 VWFRELTLCLLTANSSFISAYQALNCLGQ------KIYYANEEEIRNILKSCKYRFYNLKAKYIIMAREKV 68 (73) T ss_dssp HHHHHHHHHHHHTTSCHHHHHHHHHHHGG------GGGTCCHHHHHHHHHHTTCTTHHHHHHHHHHHHHHH T ss_pred CHHHHHHHHHHCCCCCHHHHHHHHHHHHH------HHHCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 09999999996687719999999999999------882599999999999846402788999999999999 No 21 >>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A (A:1-66,A:131-198) Probab=96.41 E-value=0.0033 Score=41.86 Aligned_cols=39 Identities=28% Similarity=0.323 Sum_probs=34.0 Q ss_pred CCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 1762000101268999999997300379999997523554442 Q gi|254780383|r 76 IADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINE 118 (227) Q Consensus 76 ~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~ 118 (227) -||+|+.|+.+++++| +.+||..+||++|+++|+.+.++ T Consensus 96 aFPTPEqLA~as~EeL----RacGlsyRKA~YI~~lAqaVadk 134 (134) T 2jhn_A 96 GFPTQEAILKAGVEGL----RECGLSRRKAELIVEIAKEENLE 134 (134) T ss_dssp CCCCHHHHHHHHHHHH----HHTTCCHHHHHHHHHHHTCSSGG T ss_pred CCCCHHHHHCCCHHHH----HHHCCCCHHHHHHHHCCCCHHHH T ss_conf 5589999974999998----54102300456655201101133 No 22 >>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A (A:81-110,A:237-290) Probab=96.15 E-value=0.0076 Score=39.41 Aligned_cols=57 Identities=19% Similarity=0.152 Sum_probs=37.7 Q ss_pred HHHHHHH-HHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHH Q ss_conf 9875421-000121046787765654078889999999621884226789999999966 Q gi|254780383|r 146 SMAFGIP-TIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGR 203 (227) Q Consensus 146 ~~~~~~p-~~~VDthv~Rv~~Rlgl~~~~~~~~~~~~l~~~~p~~~~~~~~~~li~~G~ 203 (227) -|+.|.. +|||||||.||+.+.-.-..+++.+++....+.+-+ ..+-+++.|-.+.| T Consensus 23 ~~~~~~~~AfPVDthI~rI~~~~Y~~t~k~y~~i~~f~re~fG~-yAG~AQqyLFyy~R 80 (84) T 3i0w_A 23 DFGEGIRIAFPVDTWVKKAMMSLYVAPDVSLKKIRDFGREKFGS-LSGFAQQYLFYYAR 80 (84) T ss_dssp HHTTTCCCCCCCCHHHHHHHHHHTSCTTCCHHHHHHHHHHHHGG-GHHHHHHHHHHHHH T ss_pred HHCCCCCCEEEEEHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCC-HHHHHHHHHHHHHH T ss_conf 96799888677529999999996699999999999999987307-59999999999676 No 23 >>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A (A:112-130,A:199-234) Probab=96.00 E-value=0.0042 Score=41.12 Aligned_cols=26 Identities=46% Similarity=0.654 Sum_probs=24.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 14567776432358888999987542 Q gi|254780383|r 126 TLEGLTRLPGIGRKGANVILSMAFGI 151 (227) Q Consensus 126 ~~~~L~~LpGVG~ktA~~il~~~~~~ 151 (227) -++.|.+++|||+.||+++|.|++++ T Consensus 29 vi~~Lt~IkGIG~WTAem~LmF~LgR 54 (55) T 2jhn_A 29 AYEYLTSFKGIGRWTAELVLSIALGK 54 (55) T ss_dssp HHHHHHTSTTCCHHHHHHHHHHTTCC T ss_pred HHHHHHHCCCCCHHHHHHHHHHCCCC T ss_conf 78898753782899999999861598 No 24 >>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A (A:128-195) Probab=94.55 E-value=0.028 Score=35.61 Aligned_cols=39 Identities=13% Similarity=0.087 Sum_probs=32.2 Q ss_pred HHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 73176200010126899999999730037999999752355444 Q gi|254780383|r 74 FEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILIN 117 (227) Q Consensus 74 ~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~ 117 (227) |-.||+|+.|+.+++++| +.+||- .||++|+++|+.+.+ T Consensus 28 ~~~FP~pe~la~~~~~~L----r~~g~g-~RA~yI~~~a~~i~~ 66 (68) T 3i0w_A 28 YYAFPTVDKLHEFTEKDF----EECTAG-FRAKYLKDTVDRIYN 66 (68) T ss_dssp EECCCCHHHHTTCCHHHH----HHTTCG-GGHHHHHHHHHHHHT T ss_pred HHCCCCHHHHHCCCHHHH----HHCCHH-HHHHHHHHHHHHHHC T ss_conf 303499999971899998----750267-899999999999972 No 25 >>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} (A:) Probab=93.15 E-value=0.033 Score=35.10 Aligned_cols=69 Identities=19% Similarity=0.141 Sum_probs=38.2 Q ss_pred CHHHCCCCHHHHHHHHHHH-HHHHHHHHHHHHHHH--HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0001012689999999973-003799999975235--54442001000014567776432358888999987542 Q gi|254780383|r 80 PQKMLAIGEKKLQNYIRTI-GIYRKKSENIISLSH--ILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGI 151 (227) Q Consensus 80 ~e~l~~a~~~el~~~ir~~-G~~~~KAk~I~~~a~--~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~ 151 (227) ...+....+.++-..+-.+ |.-..+|..|...-. .+.+ ...-.|.+.|.++||||+|||.-|.....++ T Consensus 59 l~GF~~~~er~~F~~L~~V~GIGpk~Al~iL~~~~~~el~~---aI~~~d~~~L~~ipGIG~KtA~rIi~eLk~k 130 (191) T 1ixr_A 59 LYGFPDEENLALFELLLSVSGVGPKVALALLSALPPRLLAR---ALLEGDARLLTSASGVGRRLAERIALELKGK 130 (191) T ss_dssp EEEESSHHHHHHHHHHHSSSCCCHHHHHHHHHHSCHHHHHH---HHHTTCHHHHTTSTTCCHHHHHHHHHHHTTT T ss_pred EECCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHH---HHHCCCHHHHCCCCCCCHHHHHHHHHHHHHH T ss_conf 77108289999999985758847788999985599999999---9982899985138884568899999999864 No 26 >>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} (A:1-128) Probab=93.09 E-value=0.18 Score=30.16 Aligned_cols=60 Identities=17% Similarity=0.232 Sum_probs=37.5 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 689999999973003799999975235544420010000145677764323588889999875 Q gi|254780383|r 87 GEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAF 149 (227) Q Consensus 87 ~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~ 149 (227) -.+++.++..--|-. -|+.....++..| +.+...| .+.+++.+|||||+++|+.|--+.- T Consensus 19 ~L~~la~~~e~~g~~-~r~~aY~kAa~~i-~~lp~~I-~s~~~~~~lpgIG~~ia~~I~E~l~ 78 (128) T 2bcq_A 19 KLEVLAKAYSVQGDK-WRALGYAKAINAL-KSFHKPV-TSYQEACSIPGIGKRMAEKIIEILE 78 (128) T ss_dssp HHHHHHHHHHHTTCH-HHHHHHHHHHHHH-HSCCSCC-CCHHHHHTSTTCCHHHHHHHHHHHH T ss_pred HHHHHHHHHHHCCCC-HHHHHHHHHHHHH-HHCCCCC-CCHHHHHCCCCCCHHHHHHHHHHHH T ss_conf 999999999984995-8999999999999-8598665-8999982799964899999999997 No 27 >>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:66-144) Probab=92.83 E-value=0.21 Score=29.70 Aligned_cols=54 Identities=28% Similarity=0.345 Sum_probs=28.4 Q ss_pred HHHHHHHHHHHHHHHHHHH--HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9973003799999975235--54442001000014567776432358888999987542 Q gi|254780383|r 95 IRTIGIYRKKSENIISLSH--ILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGI 151 (227) Q Consensus 95 ir~~G~~~~KAk~I~~~a~--~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~ 151 (227) +.-.|.-...|-.|..... .+.+ -..-.|.+.|.++||||+|||.-|....-++ T Consensus 11 ~~V~GIGpk~Al~iLs~~~~~el~~---aI~~~D~~~L~~ipGIG~KtAerii~eLk~K 66 (79) T 1cuk_A 11 IKTNGVGPKLALAILSGMSAQQFVN---AVEREEVGALVKLPGIGKKTAERLIVEMKDR 66 (79) T ss_dssp HHSSSCCHHHHHHHHHHSCHHHHHH---HHHTTCHHHHHTSTTCCHHHHHHHHHHHHHH T ss_pred HCCCCCCHHHHHHHHCCCCHHHHHH---HHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 3478848999999975799999999---9992899998419998899999999999988 No 28 >>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} (A:1-119) Probab=92.74 E-value=0.21 Score=29.64 Aligned_cols=42 Identities=21% Similarity=0.343 Sum_probs=22.5 Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99997523554442001000014567776432358888999987 Q gi|254780383|r 105 SENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMA 148 (227) Q Consensus 105 Ak~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~ 148 (227) +.....++..| +.+.-.| .+.+++.+|||||+++|+.|--+. T Consensus 36 ~~aY~rAa~~l-~~~p~~i-~s~~~~~~lpgiG~~ia~~I~e~l 77 (119) T 2fmp_A 36 YNAYRKAASVI-AKYPHKI-KSGAEAKKLPGVGTKIAEKIDEFL 77 (119) T ss_dssp HHHHHHHHHHH-HHCSSCC-CCHHHHHTSTTCCHHHHHHHHHHH T ss_pred HHHHHHHHHHH-HHCCCCC-CCHHHHHCCCCCCHHHHHHHHHHH T ss_conf 99999999999-8599554-789998479996489999999999 No 29 >>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A (A:80-154) Probab=92.31 E-value=0.19 Score=30.02 Aligned_cols=26 Identities=35% Similarity=0.626 Sum_probs=16.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 01456777643235888899998754 Q gi|254780383|r 125 QTLEGLTRLPGIGRKGANVILSMAFG 150 (227) Q Consensus 125 ~~~~~L~~LpGVG~ktA~~il~~~~~ 150 (227) .|.+.|.++||||+|||.-|+....+ T Consensus 41 ~D~~~L~~ipGIG~KtA~rii~ELk~ 66 (75) T 2ztd_A 41 GNVAALTRVPGIGKRGAERMVLELRD 66 (75) T ss_dssp TCHHHHHTSTTCCHHHHHHHHHHHTT T ss_pred CCHHHHHCCCCCCHHHHHHHHHHHHC T ss_conf 68899850888356889999999841 No 30 >>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:1-118) Probab=92.29 E-value=0.04 Score=34.57 Aligned_cols=43 Identities=14% Similarity=0.289 Sum_probs=25.1 Q ss_pred HHHHHHHHHHHHH----HHHHHCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 7999999752355----444200100001456777643235888899 Q gi|254780383|r 102 RKKSENIISLSHI----LINEFDNKIPQTLEGLTRLPGIGRKGANVI 144 (227) Q Consensus 102 ~~KAk~I~~~a~~----i~~~~~g~vP~~~~~L~~LpGVG~ktA~~i 144 (227) ..-|..|.++... -+++.....|.+..+|.+++|||++||... T Consensus 67 ~~~a~kI~E~l~tG~~~~le~l~~~~~~~l~~l~~i~GiGp~ta~~l 113 (118) T 2w9m_A 67 KGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLGVRGLGPKKIRSL 113 (118) T ss_dssp HHHHHHHHHHHHHSSCHHHHHHHHHSCHHHHHHTTSTTCCHHHHHHH T ss_pred HHHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHCCCCCCHHHHHHH T ss_conf 89999999999849828899987025178999857898789999999 No 31 >>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} (A:) Probab=91.99 E-value=0.23 Score=29.45 Aligned_cols=75 Identities=20% Similarity=0.262 Sum_probs=44.6 Q ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHH-HHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCH----------HHHHHH Q ss_conf 45677764323588889999-87542-1000121046787765654078889999999621884----------226789 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILS-MAFGI-PTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPP----------KHQYNA 194 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~-~~~~~-p~~~VDthv~Rv~~Rlgl~~~~~~~~~~~~l~~~~p~----------~~~~~~ 194 (227) +..|.++||||+|+|-.+|. |.... -.......+.++.+-=|+ ..++.+++-.+|+.-++. ....+. T Consensus 71 F~~L~~V~GIGpk~Al~iL~~~~~~el~~aI~~~d~~~L~~ipGI-G~KtA~rIi~eLk~k~~~~~~~~~~~~~~~~~e~ 149 (191) T 1ixr_A 71 FELLLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGV-GRRLAERIALELKGKVPPHLLAGEKVESEAAEEA 149 (191) T ss_dssp HHHHHSSSCCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTC-CHHHHHHHHHHHTTTSCSCC-------------- T ss_pred HHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHCCCHHHHCCCCCC-CHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHH T ss_conf 999857588477889999855999999999982899985138884-5688999999998642521001123355568999 Q ss_pred HHHHHHHH Q ss_conf 99999996 Q gi|254780383|r 195 HYWLVLHG 202 (227) Q Consensus 195 ~~~li~~G 202 (227) -.+|+.+| T Consensus 150 ~~aL~~LG 157 (191) T 1ixr_A 150 VMALAALG 157 (191) T ss_dssp -------- T ss_pred HHHHHHCC T ss_conf 99999869 No 32 >>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} (A:1-66) Probab=91.92 E-value=0.078 Score=32.59 Aligned_cols=28 Identities=39% Similarity=0.623 Sum_probs=21.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0145677764323588889999875421 Q gi|254780383|r 125 QTLEGLTRLPGIGRKGANVILSMAFGIP 152 (227) Q Consensus 125 ~~~~~L~~LpGVG~ktA~~il~~~~~~p 152 (227) +-.+.|.+|||||+|||.=+..+....| T Consensus 9 ~LI~~l~~LPGIG~KsA~Rla~~lL~~~ 36 (66) T 1vdd_A 9 SLIRELSRLPGIGPKSAQRLAFHLFEQP 36 (66) T ss_dssp HHHHHHHTSTTCCHHHHHHHHHHHSSSC T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHCCC T ss_conf 9999996789988999999999997299 No 33 >>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} (A:1-154) Probab=91.85 E-value=0.3 Score=28.62 Aligned_cols=44 Identities=16% Similarity=0.263 Sum_probs=25.1 Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999975235544420010000145677764323588889999875 Q gi|254780383|r 104 KSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAF 149 (227) Q Consensus 104 KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~ 149 (227) |+.....++..| +.+.-.| .+.+++.+|||||+++|+.|--+.- T Consensus 58 r~~aYr~Aa~~l-~~~p~~I-~s~~~l~~lpgIG~~ia~~I~E~l~ 101 (154) T 1jms_A 58 SCLAFMRASSVL-KSLPFPI-TSMKDTEGIPCLGDKVKSIIEGIIE 101 (154) T ss_dssp HHHHHHHHHHHH-HTCSSCC-CSGGGGTTCSSCCHHHHHHHHHHHH T ss_pred HHHHHHHHHHHH-HHCCCCC-CCHHHHHCCCCCCHHHHHHHHHHHH T ss_conf 799999999999-8599777-9999983799964999999999999 No 34 >>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} (A:1-129) Probab=91.40 E-value=0.28 Score=28.80 Aligned_cols=18 Identities=39% Similarity=0.495 Sum_probs=8.7 Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 145677764323588889 Q gi|254780383|r 126 TLEGLTRLPGIGRKGANV 143 (227) Q Consensus 126 ~~~~L~~LpGVG~ktA~~ 143 (227) ...+|.+++|||++||.. T Consensus 100 ~l~~l~~i~GvG~~~a~~ 117 (129) T 2ihm_A 100 TMKLFTQVFGVGVKTANR 117 (129) T ss_dssp HHHHHHTSTTCCHHHHHH T ss_pred HHHHHHHCCCCCHHHHHH T ss_conf 999998555778899999 No 35 >>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} (A:) Probab=91.32 E-value=0.25 Score=29.16 Aligned_cols=58 Identities=7% Similarity=-0.034 Sum_probs=36.1 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 68999999997300379999997523554442001000014567776432358888999987 Q gi|254780383|r 87 GEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMA 148 (227) Q Consensus 87 ~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~ 148 (227) -.+++.+....-|-++ +.....++..| ..+...| .+.++|.+|||||+++|+.|.-+. T Consensus 21 ~L~~la~~~~~~g~~r--~~aY~kA~~sl-k~~p~pi-~s~~~l~~lpgiG~~ia~kI~e~l 78 (87) T 2kp7_A 21 WLTEWRDEAASRGRHT--RFVFQKALRSL-QRYPLPL-RSGKEAKILQHFGDRLCRMLDEKL 78 (87) T ss_dssp HHHHHHHHHHHHTCTT--HHHHHHHHHHH-HHCCSCC-CSHHHHHTCTTTCHHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCHH--HHHHHHHHHHH-HHCCCCC-CCHHHHHCCCCCCHHHHHHHHHHH T ss_conf 9999999999708468--99999999999-9789887-889998738998789999999999 No 36 >>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* (A:304-377) Probab=91.19 E-value=0.14 Score=30.89 Aligned_cols=57 Identities=21% Similarity=0.289 Sum_probs=35.7 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 1268999999997300379999997523554442001---00001456777643235888899998754 Q gi|254780383|r 85 AIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDN---KIPQTLEGLTRLPGIGRKGANVILSMAFG 150 (227) Q Consensus 85 ~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g---~vP~~~~~L~~LpGVG~ktA~~il~~~~~ 150 (227) +.+...+-.-|+.+|- ..|+. |.+.|+. -...+.++|.++||||+++|..|..+--+ T Consensus 7 ~~~~~~~L~~I~giG~--~~a~~-------L~~~fgsl~~i~~as~~~L~~v~GiG~~~A~~i~~~~~~ 66 (74) T 3c1y_A 7 SARGYRLLKTVARIPL--SIGYN-------VVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISS 66 (74) T ss_dssp CCCSHHHHHHTSCCCH--HHHHH-------HHHHHCSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHH T ss_pred CCHHHHHHHCCCCCCH--HHHHH-------HHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 7316888733999989--99999-------999853899998579988854478469999999999999 No 37 >>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} (A:96-122,A:256-317) Probab=91.12 E-value=0.3 Score=28.66 Aligned_cols=20 Identities=25% Similarity=0.449 Sum_probs=17.0 Q ss_pred HHHHHHHHCCCHHHHHHHHH Q ss_conf 75421000121046787765 Q gi|254780383|r 148 AFGIPTIGVDTHIFRISNRI 167 (227) Q Consensus 148 ~~~~p~~~VDthv~Rv~~Rl 167 (227) -|.--+|||||||.||+.|. T Consensus 23 ~~~~~AvPVDTHI~rIa~r~ 42 (89) T 1m3q_A 23 KFQGVAVPVEVHMWHIAQRD 42 (89) T ss_dssp HSTTCCCCCSHHHHHHHHHH T ss_pred HCCCCEEEEEHHHHHHHHHH T ss_conf 77897677519999999997 No 38 >>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A (A:235-295) Probab=90.35 E-value=0.73 Score=26.05 Aligned_cols=52 Identities=15% Similarity=0.239 Sum_probs=35.2 Q ss_pred HHHCCC-HHHHHHHHHHHH-CCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 000121-046787765654-07888999999962188422678999999996651 Q gi|254780383|r 153 TIGVDT-HIFRISNRIGLA-PGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYV 205 (227) Q Consensus 153 ~~~VDt-hv~Rv~~Rlgl~-~~~~~~~~~~~l~~~~p~~~~~~~~~~li~~G~~i 205 (227) +||||| +|.|++.++-.. ...+..+++....+.+- ...+.+.+.|-.++|+- T Consensus 1 vFPvDtVWIkrim~~~Y~~~~~~s~~~i~~f~r~~FG-~yaGyAQqYLF~y~R~~ 54 (61) T 2jhn_A 1 VFPADDLGVRRAVSRLYFNGEIQSAEKVREIARERFG-RFARDILFYLFLYDRFF 54 (61) T ss_dssp CCCTTCHHHHHHHHHHHSTTCCCCHHHHHHHHHHHTG-GGHHHHHHHHHHHHHHT T ss_pred CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCC-CHHHHHHHHHHHHCHHH T ss_conf 4237579999999997088889999999999987566-69999999999828332 No 39 >>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:1-118) Probab=89.66 E-value=0.2 Score=29.80 Aligned_cols=44 Identities=23% Similarity=0.323 Sum_probs=29.2 Q ss_pred HHHHHHHHHHHHHHHCCCCHH-HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999975235544420010000-145677764323588889999875 Q gi|254780383|r 105 SENIISLSHILINEFDNKIPQ-TLEGLTRLPGIGRKGANVILSMAF 149 (227) Q Consensus 105 Ak~I~~~a~~i~~~~~g~vP~-~~~~L~~LpGVG~ktA~~il~~~~ 149 (227) +..-..++..| +.++-.+.. +.++|.+|||||+++|+.|--+.- T Consensus 34 ~~aYr~Aa~~i-~~l~~~i~~~~~~~l~~lpGIG~~~a~kI~E~l~ 78 (118) T 2w9m_A 34 SRAYRSAARSL-EELNEETPELLAREFTGIPKVGKGIAAELSDFAR 78 (118) T ss_dssp HHHHHHHHHHH-HSCC----------CCSSTTCCHHHHHHHHHHHH T ss_pred HHHHHHHHHHH-HHCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHH T ss_conf 99999999999-9688236675498862599987899999999998 No 40 >>2ofk_A 3-methyladenine DNA glycosylase I, constitutive; DNA repair, base excision, helix-hairpin-helix, hydrolase; HET: PGE; 1.50A {Salmonella typhi} PDB: 2ofi_A* 1lmz_A 1nku_A 1p7m_A* (A:) Probab=89.43 E-value=1.4 Score=24.14 Aligned_cols=74 Identities=20% Similarity=0.217 Sum_probs=57.1 Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHCCC--CCHHHCCCCHHHHHHHHHHHHH--HHHHHHHHHHHHHHH---HHHHC Q ss_conf 8999999999633320356799899873176--2000101268999999997300--379999997523554---44200 Q gi|254780383|r 48 HFTLIVAVLLSAQSTDVNVNKATKHLFEIAD--TPQKMLAIGEKKLQNYIRTIGI--YRKKSENIISLSHIL---INEFD 120 (227) Q Consensus 48 p~~~LVa~iLs~qT~d~~v~~~~~~L~~~yp--t~e~l~~a~~~el~~~ir~~G~--~~~KAk~I~~~a~~i---~~~~~ 120 (227) -|+.|+-++.-+==++..|.+--+.+-+.|. +|+.++..++++++.++.--|. .+.|-..++.=|+.+ .++|| T Consensus 31 lFE~L~Le~fQaGLsW~tIL~Kr~~fr~aF~~Fd~~~VA~~~e~~ie~Ll~d~~IIRnr~KI~Avi~NA~~~~~i~~e~g 110 (183) T 2ofk_A 31 LFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPIRIAAMQEEDVERLLQNTGIIRHRGKIQAIISNARAWLAMEQNGE 110 (183) T ss_dssp HHHHHHHHHHTTTSCHHHHHHTHHHHHHHTGGGCHHHHHTCCHHHHHHHTTCTTSCCCHHHHHHHHHHHHHHHHHHHTTC T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 99999999975248799999999999999967899999708999999884433313304689999999999999987259 Q ss_pred C Q ss_conf 1 Q gi|254780383|r 121 N 121 (227) Q Consensus 121 g 121 (227) + T Consensus 111 s 111 (183) T 2ofk_A 111 S 111 (183) T ss_dssp C T ss_pred C T ss_conf 8 No 41 >>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (A:) Probab=89.22 E-value=0.26 Score=29.04 Aligned_cols=36 Identities=25% Similarity=0.475 Sum_probs=24.6 Q ss_pred HHHHHHHCC---CCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 554442001---000014567776432358888999987 Q gi|254780383|r 113 HILINEFDN---KIPQTLEGLTRLPGIGRKGANVILSMA 148 (227) Q Consensus 113 ~~i~~~~~g---~vP~~~~~L~~LpGVG~ktA~~il~~~ 148 (227) +.|.+.|++ -.-.+.++|.++||||++.|..|.-|. T Consensus 33 ~~L~~~F~s~~~i~~A~~~~L~~v~GiG~~~A~~i~~~~ 71 (89) T 1z00_A 33 QTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVL 71 (89) T ss_dssp HHHHHHTCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHH T ss_pred HHHHHHHCCCHHHHHHHHHHHCHHCCCCHHHHHHHHHHH T ss_conf 999999099478766547510000332799999999998 No 42 >>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A (A:80-154) Probab=88.90 E-value=0.21 Score=29.72 Aligned_cols=61 Identities=13% Similarity=0.154 Sum_probs=36.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHH-HHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCC Q ss_conf 145677764323588889999-87542-100012104678776565407888999999962188 Q gi|254780383|r 126 TLEGLTRLPGIGRKGANVILS-MAFGI-PTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIP 187 (227) Q Consensus 126 ~~~~L~~LpGVG~ktA~~il~-~~~~~-p~~~VDthv~Rv~~Rlgl~~~~~~~~~~~~l~~~~p 187 (227) -++.|.++.|||+|+|-.||+ +..+. -..+...++.++..==|+ ..|+.+++-.+|..-+. T Consensus 7 ~F~~L~~V~GIGpk~Al~iLs~~~~~el~~aI~~~D~~~L~~ipGI-G~KtA~rii~ELk~k~~ 69 (75) T 2ztd_A 7 LFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGI-GKRGAERMVLELRDKVG 69 (75) T ss_dssp HHHHHHTSTTCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTC-CHHHHHHHHHHHTTTCC T ss_pred HHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHCCCCC-CHHHHHHHHHHHHCCCC T ss_conf 9999854132236666232215776777788853688998508883-56889999999841112 No 43 >>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:66-144) Probab=88.42 E-value=0.21 Score=29.66 Aligned_cols=61 Identities=20% Similarity=0.163 Sum_probs=36.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHH-HHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCC Q ss_conf 145677764323588889999-87542-100012104678776565407888999999962188 Q gi|254780383|r 126 TLEGLTRLPGIGRKGANVILS-MAFGI-PTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIP 187 (227) Q Consensus 126 ~~~~L~~LpGVG~ktA~~il~-~~~~~-p~~~VDthv~Rv~~Rlgl~~~~~~~~~~~~l~~~~p 187 (227) -+..|.++.|||+|+|=.||+ +..+. -..+...++.++.+==|+ ..|+.+++--+|..-++ T Consensus 6 ~F~~L~~V~GIGpk~Al~iLs~~~~~el~~aI~~~D~~~L~~ipGI-G~KtAerii~eLk~K~~ 68 (79) T 1cuk_A 6 LFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGI-GKKTAERLIVEMKDRFK 68 (79) T ss_dssp HHHHHHHSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTC-CHHHHHHHHHHHHHHGG T ss_pred HHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHCCCC-CHHHHHHHHHHHHHHHH T ss_conf 9998734788489999999757999999999992899998419998-89999999999998887 No 44 >>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} (A:1-95) Probab=88.35 E-value=0.76 Score=25.91 Aligned_cols=27 Identities=22% Similarity=0.145 Sum_probs=18.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 001456777643235888899998754 Q gi|254780383|r 124 PQTLEGLTRLPGIGRKGANVILSMAFG 150 (227) Q Consensus 124 P~~~~~L~~LpGVG~ktA~~il~~~~~ 150 (227) ..+.++|.++||||+++|..|.-+.-+ T Consensus 64 ~As~e~L~~i~Gig~~~A~~I~~~~~~ 90 (95) T 1pzn_A 64 VASPIELKEVAGISEGTALKIIQAARK 90 (95) T ss_dssp TCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_pred HCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 289999997549899999999999987 No 45 >>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} (A:1-95) Probab=88.33 E-value=0.49 Score=27.20 Aligned_cols=43 Identities=21% Similarity=0.209 Sum_probs=23.5 Q ss_pred HHHHHHC-CCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8998731-762000101268999999997300379999997523554 Q gi|254780383|r 70 TKHLFEI-ADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHIL 115 (227) Q Consensus 70 ~~~L~~~-ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i 115 (227) ..+|.++ |.|++++..|+.++|.++ -|+...+|..|++..+.. T Consensus 48 a~~L~~~~~~s~e~i~~As~e~L~~i---~Gig~~~A~~I~~~~~~~ 91 (95) T 1pzn_A 48 AEKLREAGYDTLEAIAVASPIELKEV---AGISEGTALKIIQAARKA 91 (95) T ss_dssp HHHHHTTTCCSHHHHHTCCHHHHHHH---HCCCHHHHHHHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHCCHHHHHHH---HCCCHHHHHHHHHHHHHH T ss_conf 99999859971999982899999975---498999999999999873 No 46 >>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} (A:) Probab=88.13 E-value=0.23 Score=29.46 Aligned_cols=36 Identities=19% Similarity=0.329 Sum_probs=23.8 Q ss_pred HHHHHHHCC---CCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 554442001---000014567776432358888999987 Q gi|254780383|r 113 HILINEFDN---KIPQTLEGLTRLPGIGRKGANVILSMA 148 (227) Q Consensus 113 ~~i~~~~~g---~vP~~~~~L~~LpGVG~ktA~~il~~~ 148 (227) +.|.+.||. ..-.+.++|.+++|||+++|..|.-|- T Consensus 38 ~~L~~~Fgs~~~i~~As~eeL~~v~gIG~~~A~~I~~~l 76 (78) T 1kft_A 38 QMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSL 76 (78) T ss_dssp HHHHHHHSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHH T ss_pred HHHHHHCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH T ss_conf 999999099899985789999738998999999999997 No 47 >>2jg6_A DNA-3-methyladenine glycosidase; 3-methyladenine-DNA-glycosylase-I, hydrolase; 1.70A {Staphylococcus aureus} (A:1-121) Probab=87.49 E-value=1.4 Score=24.12 Aligned_cols=74 Identities=18% Similarity=0.184 Sum_probs=57.1 Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHCCC--CCHHHCCCCHHHHHHHHHHHHH--HHHHHHHHHHHHHHH---HHHHC Q ss_conf 8999999999633320356799899873176--2000101268999999997300--379999997523554---44200 Q gi|254780383|r 48 HFTLIVAVLLSAQSTDVNVNKATKHLFEIAD--TPQKMLAIGEKKLQNYIRTIGI--YRKKSENIISLSHIL---INEFD 120 (227) Q Consensus 48 p~~~LVa~iLs~qT~d~~v~~~~~~L~~~yp--t~e~l~~a~~~el~~~ir~~G~--~~~KAk~I~~~a~~i---~~~~~ 120 (227) -|+.|+-+++-+=-++..|.+--+.+-+.|. +|+.++..+++++++++.--|. .+.|-+.++.=|+.+ .++|| T Consensus 31 lFe~L~le~fQaGLsW~~Vl~Kr~~fr~aF~~Fd~~~va~~~e~~ie~l~~d~~iIRn~~KI~avi~NA~~~l~i~~e~g 110 (121) T 2jg6_A 31 LFKLLALESQHAGLSWLTILKKKEAYEEAFYDFEPEKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLKIEQAYG 110 (121) T ss_dssp HHHHHHHHHTCTTSCHHHHHHHHHHHHHHTGGGCHHHHTTCCHHHHHHHTTCTTSCCCHHHHHHHHHHHHHHHHHHHHHS T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHCCCCEEECHHHHHHHHHHHHHHHHHHHHCC T ss_conf 99999999975258699999999999999967998999768999999885276722357889999999999999998628 Q ss_pred C Q ss_conf 1 Q gi|254780383|r 121 N 121 (227) Q Consensus 121 g 121 (227) + T Consensus 111 s 111 (121) T 2jg6_A 111 S 111 (121) T ss_dssp C T ss_pred C T ss_conf 9 No 48 >>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=86.59 E-value=1.1 Score=24.92 Aligned_cols=58 Identities=21% Similarity=0.219 Sum_probs=36.2 Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0101268999999997300379999997523554442001000014567776432358888999987 Q gi|254780383|r 82 KMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMA 148 (227) Q Consensus 82 ~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~ 148 (227) ++=.|+.++|..+ -|+...+|+.|++. ++.+|+ . .++++|..++|+|+++..-+..+. T Consensus 33 diNtAs~~eL~~l---pgig~~~A~~Ii~~----R~~~G~-f-~siedL~~v~gi~~~~~~~l~~~~ 90 (98) T 2edu_A 33 LLNEGSARDLRSL---QRIGPKKAQLIVGW----RELHGP-F-SQVEDLERVEGITGKQMESFLKAN 90 (98) T ss_dssp HHHHSCHHHHHHS---TTCCHHHHHHHHHH----HHHHCC-C-SSGGGGGGSTTCCHHHHHHHHHHH T ss_pred CCCCCCHHHHHHC---CCCCHHHHHHHHHH----HHHCCC-C-CCHHHHHCCCCCCHHHHHHHHHHC T ss_conf 1357999999757---89899999999999----998589-5-889998258898999999999828 No 49 >>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} (A:499-568) Probab=86.17 E-value=0.52 Score=27.02 Aligned_cols=56 Identities=14% Similarity=0.192 Sum_probs=35.5 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 01268999999997300379999997523554442001000014567776432358888999987 Q gi|254780383|r 84 LAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMA 148 (227) Q Consensus 84 ~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~ 148 (227) =.|+.++|+.+ -|+...+|++|++. ++++|+ + .++++|..++|+|+++.+-+..|. T Consensus 5 N~A~~~~L~~l---pgig~~~A~~Ii~~----R~~~G~-f-~s~~dL~~v~gl~~~~~~~l~~~i 60 (70) T 3bzc_A 5 NTASAALLARI---SGLNSTLAQNIVAH----RDANGA-F-RTRDELKKVSRLGEKTFEQAAGFL 60 (70) T ss_dssp TTCCHHHHHTS---TTCCHHHHHHHHHH----HHHHCC-C-SSGGGGGGSTTCCHHHHHHHGGGE T ss_pred HHHHHHHHHHC---CCCCHHHHHHHHHH----HHHCCC-C-CCHHHHHHCCCCCHHHHHHCCEEE T ss_conf 87548888660---69788999999999----996699-5-779999856788812898718089 No 50 >>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} (A:499-568) Probab=85.18 E-value=0.43 Score=27.59 Aligned_cols=24 Identities=21% Similarity=0.271 Sum_probs=21.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 014567776432358888999987 Q gi|254780383|r 125 QTLEGLTRLPGIGRKGANVILSMA 148 (227) Q Consensus 125 ~~~~~L~~LpGVG~ktA~~il~~~ 148 (227) .+.++|.+|||||++.|..|+.+- T Consensus 7 A~~~~L~~lpgig~~~A~~Ii~~R 30 (70) T 3bzc_A 7 ASAALLARISGLNSTLAQNIVAHR 30 (70) T ss_dssp CCHHHHHTSTTCCHHHHHHHHHHH T ss_pred HHHHHHHHCCCCCHHHHHHHHHHH T ss_conf 548888660697889999999999 No 51 >>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} (U:48-134) Probab=84.61 E-value=0.45 Score=27.47 Aligned_cols=22 Identities=14% Similarity=0.225 Sum_probs=12.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 1456777643235888899998 Q gi|254780383|r 126 TLEGLTRLPGIGRKGANVILSM 147 (227) Q Consensus 126 ~~~~L~~LpGVG~ktA~~il~~ 147 (227) +.++|.+|||||+++|..|+.+ T Consensus 14 ~~~~L~~ipGig~~~A~~Iv~~ 35 (87) T 1s5l_U 14 NIAAFIQYRGLYPTLAKLIVKN 35 (87) T ss_dssp CGGGGGGSTTCTHHHHHHHHHT T ss_pred CHHHHHHHHHHHHHHHHHHHHC T ss_conf 8999977103469999999982 No 52 >>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} (A:) Probab=83.81 E-value=0.42 Score=27.64 Aligned_cols=22 Identities=45% Similarity=0.557 Sum_probs=11.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 1456777643235888899998 Q gi|254780383|r 126 TLEGLTRLPGIGRKGANVILSM 147 (227) Q Consensus 126 ~~~~L~~LpGVG~ktA~~il~~ 147 (227) +.++|.++||||++.|+.|+.+ T Consensus 25 ~~~~L~~lpGig~~~A~~Ii~~ 46 (75) T 2duy_A 25 SLEELXALPGIGPVLARRIVEG 46 (75) T ss_dssp CHHHHTTSTTCCHHHHHHHHHT T ss_pred CHHHHHHCCCCCHHHHHHHHHC T ss_conf 7999977789899999999986 No 53 >>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} (A:) Probab=83.48 E-value=1.8 Score=23.47 Aligned_cols=42 Identities=14% Similarity=0.340 Sum_probs=26.3 Q ss_pred HHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9989987317620001012689999999973003799999975235 Q gi|254780383|r 68 KATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSH 113 (227) Q Consensus 68 ~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~ 113 (227) +..+.|.++|.|.+.+.+|+.+||.++ .| ....|+.|.++.+ T Consensus 15 ~~a~~Ll~~f~Si~~i~~As~eeL~~i---~g-g~~~A~~i~~~l~ 56 (63) T 2a1j_A 15 KNCRSLMHHVKNIAELAALSQDELTSI---LG-NAANAKQLYDFIH 56 (63) T ss_dssp HHHHHHHHHCSSHHHHHTCCHHHHHHH---HS-CHHHHHHHHHHHH T ss_pred HHHHHHHHHHCCHHHHHHCCHHHHHHC---CC-CHHHHHHHHHHHC T ss_conf 999999998078999986999999778---59-6899999999982 No 54 >>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; NMR {Homo sapiens} (A:) Probab=83.21 E-value=1 Score=25.00 Aligned_cols=36 Identities=25% Similarity=0.265 Sum_probs=13.2 Q ss_pred CCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 762000101268999999997300379999997523554 Q gi|254780383|r 77 ADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHIL 115 (227) Q Consensus 77 ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i 115 (227) +.|.++|+.+++++|.++ .|+...+|.+|+..++.+ T Consensus 46 i~Tv~~la~~~~~~L~~i---~G~~~~~a~~i~~~ar~~ 81 (114) T 1b22_A 46 FHTVEAVAYAPKKELINI---KGISEAKADKILAEAAKL 81 (114) T ss_dssp CSSGGGBTSSBHHHHHTT---TTCSTTHHHHHHHHHHHH T ss_pred CCHHHHHHHCCHHHHHHH---CCCCHHHHHHHHHHHHHH T ss_conf 853999985899999862---063699999999999986 No 55 >>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} (A:149-197) Probab=81.90 E-value=0.57 Score=26.77 Aligned_cols=23 Identities=52% Similarity=0.798 Sum_probs=18.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 456777643235888899998754 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILSMAFG 150 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~~~~~ 150 (227) ...|.++||||++++...|-. || T Consensus 13 ~s~L~~IpGIG~k~~~~LL~~-Fg 35 (49) T 2bgw_A 13 LYILQSFPGIGRRTAERILER-FG 35 (49) T ss_dssp HHHHHTSTTCCHHHHHHHHHH-HS T ss_pred HHHHHCCCCCCHHHHHHHHHH-CC T ss_conf 888853568997899999998-69 No 56 >>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B (A:) Probab=80.85 E-value=1.6 Score=23.83 Aligned_cols=43 Identities=16% Similarity=0.166 Sum_probs=28.3 Q ss_pred HHHHHHC-CCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8998731-762000101268999999997300379999997523554 Q gi|254780383|r 70 TKHLFEI-ADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHIL 115 (227) Q Consensus 70 ~~~L~~~-ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i 115 (227) ..+|.+. |.|.++|+.+++++|.++ -|+...+|..|+..|+.+ T Consensus 20 a~~L~~aGi~TvedLa~a~~~eL~~i---~Gi~~~~A~~ii~~Ar~~ 63 (70) T 1wcn_A 20 AFKLAARGVCTLEDLAEQGIDDLADI---EGLTDEKAGALIMAARNI 63 (70) T ss_dssp HHHHHTTTCCSHHHHHTSCHHHHHTS---SSCCHHHHHHHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHCHHHHHHH---CCCCHHHHHHHHHHHHHC T ss_conf 99999969975999987299999765---179999999999999865 No 57 >>3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3a0b_U* 3a0h_U* (U:) Probab=80.43 E-value=0.85 Score=25.61 Aligned_cols=61 Identities=11% Similarity=0.220 Sum_probs=33.5 Q ss_pred CCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 17620001012689999999973003799999975235544420010000145677764323588889999875 Q gi|254780383|r 76 IADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAF 149 (227) Q Consensus 76 ~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~ 149 (227) .....-++=.|+.++|..+ -|+...+|++|++ |++ + .++++|..++|||.++-.-+.-|.. T Consensus 20 ~~~~~vdIN~As~~~L~~i---pGig~~~A~~Iv~--------~gp-f-~s~~dL~~v~gi~~~~~~~i~~~l~ 80 (104) T 3bz1_U 20 AYGEKIDLNNTNIAAFIQY---RGLYPTLAKLIVK--------NAP-Y-ESVEDVLNIPGLTERQKQILRENLE 80 (104) T ss_dssp SBTTBEETTSSCGGGGGGS---TTTTHHHHHHHHH--------SCC-C-SSGGGGGGCTTCCHHHHHHHHHHGG T ss_pred CCCCCEECCCCCHHHHHHC---CCCCHHHHHHHHH--------CCC-C-CCHHHHHCCCCCCHHHHHHHHHHHC T ss_conf 1588567722899999777---5869999999997--------089-7-8799996179989999999998761 No 58 >>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A (A:157-220) Probab=79.10 E-value=2.4 Score=22.62 Aligned_cols=24 Identities=13% Similarity=0.170 Sum_probs=10.7 Q ss_pred HHHHHCCCCCHHHCCCCHHHHHHH Q ss_conf 998731762000101268999999 Q gi|254780383|r 71 KHLFEIADTPQKMLAIGEKKLQNY 94 (227) Q Consensus 71 ~~L~~~ypt~e~l~~a~~~el~~~ 94 (227) ..|.++|.|++++.+|+.+||.++ T Consensus 26 ~~L~~~F~s~~~i~~As~eeL~~v 49 (64) T 2nrt_A 26 KKLIEHFGSLENIRSASLEEIARV 49 (64) T ss_dssp HHHHHHHCSHHHHHTSCHHHHHHH T ss_pred HHHHHHCCCHHHHHCCCHHHHHHC T ss_conf 999998689999970999999868 No 59 >>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} (A:) Probab=78.70 E-value=0.81 Score=25.76 Aligned_cols=38 Identities=16% Similarity=0.147 Sum_probs=16.6 Q ss_pred HHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99873176200010126899999999730037999999752 Q gi|254780383|r 71 KHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISL 111 (227) Q Consensus 71 ~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~ 111 (227) ..|.+.|.|++++.+|+.+||.++ -|....+|..|+++ T Consensus 38 ~~L~~~Fgs~~~i~~As~eeL~~v---~gIG~~~A~~I~~~ 75 (78) T 1kft_A 38 QMLLKYMGGLQGLRNASVEEIAKV---PGISQGLAEKIFWS 75 (78) T ss_dssp HHHHHHHSCHHHHHHCCHHHHTTS---SSTTSHHHHHHHHH T ss_pred HHHHHHCCCHHHHHHCCHHHHHHC---CCCCHHHHHHHHHH T ss_conf 999999099899985789999738---99899999999999 No 60 >>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (B:1-71) Probab=76.95 E-value=3.4 Score=21.53 Aligned_cols=20 Identities=20% Similarity=0.501 Sum_probs=10.4 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 45677764323588889999 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILS 146 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~ 146 (227) .+.|.++||||++++..+|. T Consensus 17 ~~~L~~ipGIg~k~~~~Ll~ 36 (71) T 1z00_B 17 QDFLLKMPGVNAKNCRSLMH 36 (71) T ss_dssp HHHHHTCSSCCHHHHHHHHH T ss_pred HHHHHCCCCCCHHHHHHHHH T ss_conf 99998089988999999999 No 61 >>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix- hairpin-helix, HHH motif, three helix bundle; 2.30A {Methanopyrus kandleri} (A:181-225,A:375-471) Probab=76.93 E-value=2.9 Score=22.02 Aligned_cols=90 Identities=20% Similarity=0.327 Sum_probs=47.0 Q ss_pred CCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 20001012689999999973003799999975235544420010000145677764323588889999875421000121 Q gi|254780383|r 79 TPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDT 158 (227) Q Consensus 79 t~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~p~~~VDt 158 (227) ++..+...+.++|+.......+.. +-|...|.-...+|.+-.|||+|||.-.|- +||.|.- T Consensus 47 siagilatdleeier~yeegrlse--------------eayraaveiqlaeltkkegvgrktaerllr-afgnper---- 107 (142) T 2csb_A 47 SIAGILATDLEEIERXYEEGRLSE--------------EAYRAAVEIQLAELTKKEGVGRKTAERLLR-AFGNPER---- 107 (142) T ss_dssp SHHHHHTSCHHHHHHHHHHTSSCH--------------HHHHHHHHHHHHHHHTSTTCCHHHHHHHHH-HHSSHHH---- T ss_pred HHHHHHHCCHHHHHHHHHCCCCCH--------------HHHHHHHHHHHHHHHHHCCCCHHHHHHHHH-HHCCHHH---- T ss_conf 888898604999999987156448--------------999888987799776540645657999999-7099899---- Q ss_pred HHHHHHHHHHHHCCCCHHH-HHHHHHHCCCH Q ss_conf 0467877656540788899-99999621884 Q gi|254780383|r 159 HIFRISNRIGLAPGKTPNK-VEQSLLRIIPP 188 (227) Q Consensus 159 hv~Rv~~Rlgl~~~~~~~~-~~~~l~~~~p~ 188 (227) |..+..-+.+.+-.+.+- -++.|..++|. T Consensus 108 -vkqlarefeieklasvegvgervlrslvpg 137 (142) T 2csb_A 108 -VKQLAREFEIEKLASVEGVGERVLRSLVPG 137 (142) T ss_dssp -HHHHHHTTCHHHHHTSTTCSHHHHHHHSTT T ss_pred -HHHHHHHHHHHHHHHCCCHHHHHHHHHCCC T ss_conf -999998875888750033289999986534 No 62 >>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} (A:) Probab=76.06 E-value=0.62 Score=26.50 Aligned_cols=23 Identities=35% Similarity=0.719 Sum_probs=17.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 456777643235888899998754 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILSMAFG 150 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~~~~~ 150 (227) .--+.++||||+++|..++.. || T Consensus 172 ~~~~~~I~~IG~~~a~~Ll~~-Fg 194 (226) T 3c65_A 172 HSVLDDIPGVGEKRKKALLNY-FG 194 (226) T ss_dssp ------------------------ T ss_pred CCHHHHHHHHCHHHHHHHHHH-CC T ss_conf 176889987479999999998-58 No 63 >>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} (A:1-49) Probab=73.49 E-value=1.3 Score=24.41 Aligned_cols=23 Identities=26% Similarity=0.290 Sum_probs=16.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 456777643235888899998754 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILSMAFG 150 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~~~~~ 150 (227) .-.|..+||||+++|...+-. |+ T Consensus 13 ~~~L~~I~gVG~~~ak~Ll~~-Fg 35 (49) T 1x2i_A 13 RLIVEGLPHVSATLARRLLKH-FG 35 (49) T ss_dssp HHHHTTSTTCCHHHHHHHHHH-HC T ss_pred HHHHCCCCCCCHHHHHHHHHH-CC T ss_conf 999858999789999999997-06 No 64 >>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanococcus jannaschii} (A:210-274) Probab=70.50 E-value=1.7 Score=23.49 Aligned_cols=18 Identities=28% Similarity=0.281 Sum_probs=14.4 Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 777643235888899998 Q gi|254780383|r 130 LTRLPGIGRKGANVILSM 147 (227) Q Consensus 130 L~~LpGVG~ktA~~il~~ 147 (227) +-.+||||+|||.-++.. T Consensus 18 ipGV~GIGpKtA~~li~~ 35 (65) T 1a76_A 18 PGGVKGIGFKRAYELVRS 35 (65) T ss_dssp TTTTTTCCHHHHHHHHHH T ss_pred CCCCCCEEHHHHHHHHHH T ss_conf 555685629999999997 No 65 >>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} (A:427-542) Probab=68.76 E-value=3.2 Score=21.72 Aligned_cols=71 Identities=15% Similarity=0.160 Sum_probs=41.4 Q ss_pred HHHHHHH--CCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHH-HHHHHHHHHHHHHHHHHHHH Q ss_conf 9899873--17620001012689999999973003799999975235544420010000-14567776432358888999 Q gi|254780383|r 69 ATKHLFE--IADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQ-TLEGLTRLPGIGRKGANVIL 145 (227) Q Consensus 69 ~~~~L~~--~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~-~~~~L~~LpGVG~ktA~~il 145 (227) ....++. ...++.++..++.+++..+ -||.+.++.++...-.. +. +.|. ..=..+.+||||+++|..++ T Consensus 27 ~i~~~~~~~~i~~~~d~~~L~~~~~~~l---~~~~~~r~e~~~~ai~~----~r-~~~~~~~l~algI~giG~~~ak~L~ 98 (116) T 1dgs_A 27 LIERLLEKGLVRDVADLYHLRKEDLLGL---ERMGEKSAQNLLRQIEE----SK-HRGLERLLYALGLPGVGEVLARNLA 98 (116) T ss_dssp HHHHHHHTTSCSSGGGGGGGCCHHHHTT---SSCCSTTHHHHHHHHHH----GG-GCCHHHHHHHTTCSSCCHHHHHHHH T ss_pred HHHHHHHCCCCCCHHHHHHCCHHHHHCC---CCCCHHHHHHHHHHHHH----HC-CCCHHHHHHHCCCCCCCHHHHHHHH T ss_conf 9999997688688799871899998346---68257899999999998----62-7999999997699754568999998 Q ss_pred HH Q ss_conf 98 Q gi|254780383|r 146 SM 147 (227) Q Consensus 146 ~~ 147 (227) .+ T Consensus 99 ~~ 100 (116) T 1dgs_A 99 RR 100 (116) T ss_dssp HT T ss_pred HH T ss_conf 76 No 66 >>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} (A:182-261) Probab=64.94 E-value=2.3 Score=22.63 Aligned_cols=21 Identities=24% Similarity=0.349 Sum_probs=15.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 456777643235888899998 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILSM 147 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~~ 147 (227) -+.+-.+||||+|||-.++.- T Consensus 21 sD~ipGV~GIG~ktA~~Li~~ 41 (80) T 1exn_A 21 GDNIRGVEGIGAKRGYNIIRE 41 (80) T ss_dssp GGTBCCCTTCCHHHHHHHHHH T ss_pred CCCCCCCCCCCHHHHHHHHHH T ss_conf 136899997679999999999 No 67 >>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-binding, excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} (A:219-300) Probab=60.49 E-value=3.2 Score=21.71 Aligned_cols=18 Identities=28% Similarity=0.340 Sum_probs=14.2 Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 777643235888899998 Q gi|254780383|r 130 LTRLPGIGRKGANVILSM 147 (227) Q Consensus 130 L~~LpGVG~ktA~~il~~ 147 (227) +-.+||||+|||-.++.- T Consensus 18 i~GV~GiG~ktA~~li~~ 35 (82) T 2izo_A 18 PDGIRGIGPERALKIIKK 35 (82) T ss_dssp TTCSTTCCHHHHHHHHHH T ss_pred CCCCCCCCHHHHHHHHHH T ss_conf 334799448899999998 No 68 >>2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae} (B:229-310) Probab=59.91 E-value=6.5 Score=19.67 Aligned_cols=22 Identities=27% Similarity=0.295 Sum_probs=17.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 4567776432358888999987 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILSMA 148 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~~~ 148 (227) .-.|.++.|||+++|+.|+..+ T Consensus 28 ~~aLt~i~GIG~~~A~~I~~~~ 49 (82) T 2zbk_B 28 EFLVNEFQSIGDTTADKILELA 49 (82) T ss_dssp HHHHTTSTTCCHHHHHHHHHHT T ss_pred HHHHCCCCCCCHHHHHHHHHHH T ss_conf 4551576467608777666552 No 69 >>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family DNA polymerase, translesion DNA synthesis, lesion bypass; 2.40A {Homo sapiens} (A:271-340) Probab=59.87 E-value=6.2 Score=19.79 Aligned_cols=17 Identities=18% Similarity=0.565 Sum_probs=12.8 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 77764323588889999 Q gi|254780383|r 130 LTRLPGIGRKGANVILS 146 (227) Q Consensus 130 L~~LpGVG~ktA~~il~ 146 (227) +..+||||++|+.-.-. T Consensus 14 i~~i~GIG~~~~~~L~~ 30 (70) T 1t94_A 14 IRKVSGIGKVTEKMLKA 30 (70) T ss_dssp GGGCTTSCHHHHHHHHH T ss_pred CCCCCCCCCCCHHHHHH T ss_conf 14025763110045454 No 70 >>3i1m_M 30S ribosomal protein S13; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ... (M:1-63) Probab=58.64 E-value=4.6 Score=20.67 Aligned_cols=20 Identities=30% Similarity=0.581 Sum_probs=16.5 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 45677764323588889999 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILS 146 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~ 146 (227) .-.|.++.|||+.+|..|+. T Consensus 16 ~~aLt~i~GIG~~~A~~Ic~ 35 (63) T 3i1m_M 16 VIALTSIYGVGKTRSKAILA 35 (63) T ss_dssp HHHGGGSTTCCHHHHHHHHT T ss_pred EEEEECEECCCHHHHHHHHH T ss_conf 88753445738999999999 No 71 >>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication; 2.00A {Pyrococcus furiosus} (A:212-288) Probab=58.48 E-value=3.6 Score=21.34 Aligned_cols=47 Identities=23% Similarity=0.398 Sum_probs=24.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999730037999999752355444200100001456777643235888899998754 Q gi|254780383|r 91 LQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFG 150 (227) Q Consensus 91 l~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~ 150 (227) |+++....|+.+ ..++.++-..=..|+ +-.+||||+|||-.++.. || T Consensus 1 l~~i~~~~g~~~---~q~id~~~L~G~d~n---------i~GV~GiG~ktA~kli~~-~g 47 (77) T 1b43_A 1 LEEVLKELKLTR---EKLIELAILVGTDYN---------PGGIKGIGLKKALEIVRH-SK 47 (77) T ss_dssp HHHHHHHHTCCH---HHHHHHHHHHCCTTS---------TTCSTTCCHHHHHHHHHT-CS T ss_pred HHHHHHHCCCCH---HHHHHHHHHCCCCCC---------CCCCCCCCHHHHHHHHHH-HC T ss_conf 898566329789---999999997286656---------565896249999999999-59 No 72 >>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} (B:) Probab=58.45 E-value=4.6 Score=20.64 Aligned_cols=48 Identities=17% Similarity=0.248 Sum_probs=30.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 973003799999975235544420010000145677764323588889999 Q gi|254780383|r 96 RTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILS 146 (227) Q Consensus 96 r~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~ 146 (227) ..+++. +|+.+..+-+.+. ..+.-+-.+.++|++++|+|+|+.+-|.. T Consensus 19 ~~L~Ls-~R~~n~L~~~gI~--tv~dL~~~s~~dLl~i~nlG~ksl~EI~~ 66 (79) T 3gfk_B 19 EELDLS-VRSYNCLKRAGIN--TVQELANKTEEDMMKVRNLGRKSLEEVKA 66 (79) T ss_dssp GGSCCB-HHHHHHHHHTTCC--BHHHHTTCCHHHHTTSTTCHHHHHHHHHH T ss_pred HHHCCC-HHHHHHHHHCCCC--CHHHHHHCCHHHHHHCCCCCHHHHHHHHH T ss_conf 984688-9999999891896--79999878999998578986736999999 No 73 >>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase/DNA complex; 2.00A {Archaeoglobus fulgidus} (A:221-288) Probab=57.93 E-value=3.7 Score=21.28 Aligned_cols=18 Identities=22% Similarity=0.230 Sum_probs=14.0 Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 777643235888899998 Q gi|254780383|r 130 LTRLPGIGRKGANVILSM 147 (227) Q Consensus 130 L~~LpGVG~ktA~~il~~ 147 (227) +-.+||||+|||--++.. T Consensus 17 ~pGV~GIG~ktA~~li~~ 34 (68) T 1rxw_A 17 NEGVKGVGVKKALNYIKT 34 (68) T ss_dssp BCCCTTCCHHHHHHHHHH T ss_pred CCCCCCCCHHHHHHHHHH T ss_conf 589999578999999999 No 74 >>2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M (m:1-88) Probab=57.60 E-value=4.9 Score=20.45 Aligned_cols=20 Identities=35% Similarity=0.599 Sum_probs=16.8 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 45677764323588889999 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILS 146 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~ 146 (227) .-.|.++.|||+.+|..|+. T Consensus 27 ~~ALt~I~GIG~~~A~~Ic~ 46 (88) T 2zkq_m 27 AFAITAIKGVGRRYAHVVLR 46 (88) T ss_dssp HHHGGGSTTCCHHHHHHHHH T ss_pred EEEHHCCCCCCHHHHHHHHH T ss_conf 36030246628999999999 No 75 >>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} (A:143-207) Probab=57.43 E-value=5.7 Score=20.03 Aligned_cols=31 Identities=29% Similarity=0.280 Sum_probs=22.3 Q ss_pred HCCCHHHHHHHHHHHHCCC--------CHHHHHHHHHHC Q ss_conf 0121046787765654078--------889999999621 Q gi|254780383|r 155 GVDTHIFRISNRIGLAPGK--------TPNKVEQSLLRI 185 (227) Q Consensus 155 ~VDthv~Rv~~Rlgl~~~~--------~~~~~~~~l~~~ 185 (227) .+|-||.|.+.++|+.++. .+.+.|..+.++ T Consensus 2 ILDrHILr~l~~~g~i~e~~pk~~t~k~Yle~E~~l~~~ 40 (65) T 3fhg_A 2 IIDRHIIDFMRRIGAIGETNVKQLSKSLYISFENILKSI 40 (65) T ss_dssp CCCHHHHHHHHHTTSSCCCCCSCCCHHHHHHHHHHHHHH T ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH T ss_conf 068899999999088689997731399999999999877 No 76 >>1lb2_B DNA-directed RNA polymerase alpha chain; protein-DNA complex, gene-regulatory, gene regulation/DNA complex; HET: CMP; 3.10A {Escherichia coli} (B:) Probab=57.08 E-value=5.9 Score=19.96 Aligned_cols=46 Identities=20% Similarity=0.288 Sum_probs=29.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 3003799999975235544420010000145677764323588889999 Q gi|254780383|r 98 IGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILS 146 (227) Q Consensus 98 ~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~ 146 (227) +++. +|+.+..+-+.+- ..+.-+-.+.++|++++|+|+|+.+-|.- T Consensus 15 L~Ls-~R~~n~L~~agI~--ti~dL~~~s~~dLl~i~n~G~kSl~EI~~ 60 (84) T 1lb2_B 15 LELT-VRSANCLKAEAIH--YIGDLVQRTEVELLKTPNLGKKSLTEIKD 60 (84) T ss_dssp GCCC-HHHHHHHHHTTCC--BHHHHHTCCHHHHHHSTTCCHHHHHHHHH T ss_pred HCCC-HHHHHHHHHHCCC--CHHHHHHCCHHHHHHCCCCCHHHHHHHHH T ss_conf 0788-9999999891894--69998728999997488987889999999 No 77 >>1szp_A DNA repair protein RAD51; homologous recombination, asymmetry, RAD51 filament, DNA binding protein; HET: DNA; 3.25A {Saccharomyces cerevisiae} (A:26-81) Probab=56.86 E-value=4.8 Score=20.53 Aligned_cols=37 Identities=19% Similarity=0.265 Sum_probs=30.5 Q ss_pred CCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 6200010126899999999730037999999752355444 Q gi|254780383|r 78 DTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILIN 117 (227) Q Consensus 78 pt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~ 117 (227) .|.++++.++..+|.++ -|+...||..|++.|+.++. T Consensus 1 ~Tve~ia~at~k~L~~i---kGisE~ka~KIi~aA~kl~~ 37 (56) T 1szp_A 1 HTAEAVAYAPRKDLLEI---KGISEAKADKLLNEAARLVP 37 (56) T ss_dssp CSHHHHHHSCSHHHHTS---TTCCHHHHHHHHHHHHHHSC T ss_pred CCHHHHHCCCHHHHHHH---HCCCHHHHHHHHHHHHHHHC T ss_conf 63999973899999876---39999999999999998744 No 78 >>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} (A:) Probab=49.97 E-value=7 Score=19.45 Aligned_cols=41 Identities=24% Similarity=0.329 Sum_probs=29.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 145677764323588889999875421000121046787765654 Q gi|254780383|r 126 TLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLA 170 (227) Q Consensus 126 ~~~~L~~LpGVG~ktA~~il~~~~~~p~~~VDthv~Rv~~Rlgl~ 170 (227) .+..|..|||||+++|..|+-.--+.|.--++ -+..|.++. T Consensus 130 i~~~L~~I~GiG~~~a~~Iie~Re~g~F~S~e----Dl~~Rv~~~ 170 (205) T 2i5h_A 130 RMHQLELLPGVGKKMMWAIIEERKKRPFESFE----DIAQRVKGI 170 (205) T ss_dssp SSBGGGGSTTCCHHHHHHHHHHHHHSCCCSHH----HHHHHSTTC T ss_pred HHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHH----HHHHHHCCC T ss_conf 78988744451589999999997548988999----999885467 No 79 >>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family, transferase/DNA complex; HET: DNA MSE ADI; 1.70A {Sulfolobus solfataricus} (A:183-237) Probab=48.98 E-value=8.1 Score=19.00 Aligned_cols=33 Identities=27% Similarity=0.280 Sum_probs=20.5 Q ss_pred CCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 62000101268999999997300379999997523554 Q gi|254780383|r 78 DTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHIL 115 (227) Q Consensus 78 pt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i 115 (227) -|.++|++++++.|.+.+- ...+.+|+++|+-+ T Consensus 18 ~ti~dl~~~~~~~L~~~~G-----~~~g~~l~~~a~Gi 50 (55) T 1jx4_A 18 NKLVDTLSIEFDKLKGXIG-----EAKAKYLISLARDE 50 (55) T ss_dssp CBGGGGGSSCHHHHHHHHC-----HHHHHHHHHHHTTC T ss_pred CCCHHCCCCCHHHHHHHHC-----CHHHHHHHHHHCCC T ss_conf 6823121379999998968-----07789999985898 No 80 >>3bqs_A Uncharacterized protein; 10114F, NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.42A {Listeria monocytogenes str} PDB: 3bqt_A (A:) Probab=48.73 E-value=6.8 Score=19.53 Aligned_cols=41 Identities=24% Similarity=0.259 Sum_probs=23.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH Q ss_conf 45677764323588889999875421000121046787765 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRI 167 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~~~~~~p~~~VDthv~Rv~~Rl 167 (227) ...|..|||||+.|+...-..+...+.=...........|+ T Consensus 3 ~~~l~~LPNiG~~~e~~L~~iGI~tv~~L~~~ga~~~~~~l 43 (93) T 3bqs_A 3 LANLSELPNIGKVLEQDLIKAGIKTPVELKDVGSKEAFLRI 43 (93) T ss_dssp CSCGGGSTTCCHHHHHHHHHTTCCSHHHHHHHHHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHH T ss_conf 57785689999999999998399989999877999999999 No 81 >>1t57_A Conserved protein MTH1675; structural genomics, FMN, methanobacterium thermoautotrophicum, PSI; HET: FMN; 2.30A {Methanothermobacterthermautotrophicus} (A:) Probab=48.09 E-value=18 Score=16.72 Aligned_cols=106 Identities=15% Similarity=0.120 Sum_probs=65.1 Q ss_pred HHHHCCCHHHHHHHHHHHHHC---------CCCCHHHCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHCCCCHH Q ss_conf 996333203567998998731---------76200010126899999999730037-99999975235544420010000 Q gi|254780383|r 56 LLSAQSTDVNVNKATKHLFEI---------ADTPQKMLAIGEKKLQNYIRTIGIYR-KKSENIISLSHILINEFDNKIPQ 125 (227) Q Consensus 56 iLs~qT~d~~v~~~~~~L~~~---------ypt~e~l~~a~~~el~~~ir~~G~~~-~KAk~I~~~a~~i~~~~~g~vP~ 125 (227) |+.+-|+.+...++.+.+-.. |..| ...+++ +|..+.++..|.-- .-.--+-.+-+.|..+|||.-|. T Consensus 55 iVVASssG~TA~k~~e~~~~~iVvVTh~~GF~~p-g~~e~~-~e~~~~L~~~Gv~V~t~TH~lSg~eR~is~kfgG~~p~ 132 (206) T 1t57_A 55 FVVASVSGETALRLSEXVEGNIVSVTHHAGFREK-GQLELE-DEARDALLERGVNVYAGSHALSGVGRGISNRFGGVTPV 132 (206) T ss_dssp EEEECSSSHHHHHHHTTCCSEEEEECCCTTSSST-TCCSSC-HHHHHHHHHHTCEEECCSCTTTTHHHHHHHHHCSCCHH T ss_pred EEEEECCCHHHHHHHHHCCCCEEEEECCCCCCCC-CCCCCC-HHHHHHHHHCCCEEEEECCCCCCCHHHHHHHCCCCCHH T ss_conf 9998078679999998638979999465787899-966469-99999999769889995130344155522322798989 Q ss_pred H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH Q ss_conf 1-4567776432358888999987542100012104678 Q gi|254780383|r 126 T-LEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRI 163 (227) Q Consensus 126 ~-~~~L~~LpGVG~ktA~~il~~~~~~p~~~VDthv~Rv 163 (227) . +.+-+++=|.|-|.|--|-+.+.+.-.+++|.-|.=+ T Consensus 133 EiIA~tLR~fgqG~KVavEi~iMAaDaGlIp~~eeVIAi 171 (206) T 1t57_A 133 EIXAETLRXVSQGFKVCVEIAIXAADAGLIPVDEEVIAI 171 (206) T ss_dssp HHHHHHHTTTCHHHHHHHHHHHHHHHTTSSCSSSCEEEE T ss_pred HHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCCEEEEE T ss_conf 999999997378757999999986067877789849997 No 82 >>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, hydrolase; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A* (A:1-149) Probab=47.37 E-value=3.8 Score=21.20 Aligned_cols=113 Identities=18% Similarity=0.199 Sum_probs=61.5 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHH----HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHCCCH Q ss_conf 689999999973003799999975235544420010000----14567776432358888999987542---10001210 Q gi|254780383|r 87 GEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQ----TLEGLTRLPGIGRKGANVILSMAFGI---PTIGVDTH 159 (227) Q Consensus 87 ~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~----~~~~L~~LpGVG~ktA~~il~~~~~~---p~~~VDth 159 (227) ...++...+.+.|+.... +..|.+.||..... +-=.|..++|||=++||.|... +|. .-.=+..- T Consensus 6 ~~~~~~~~L~~~Gi~~~~-------a~ki~~~yg~~a~~~i~~nPY~L~~i~gigF~~aD~iA~~-~gi~~dd~~Ri~a~ 77 (149) T 3e1s_A 6 LERRLLAGLQGLGLTINQ-------AQRAVKHFGADALDRLEKDLFTLTEVEGIGFLTADKLWQA-RGGALDDPRRLTAA 77 (149) T ss_dssp ---------------------------------------------CGGGTSSSCCHHHHHTTC--------CCHHHHHHH T ss_pred HHHHHHHHHHHCCCCHHH-------HHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHH-CCCCCCCHHHHHHH T ss_conf 999999999877999999-------9999999849999999949935541589995999999997-69898999999999 Q ss_pred HHHHHHHHHHHCCCC---HHHHHHHHHHC--CCHHHHHHHHHHHHHHHHHHCC Q ss_conf 467877656540788---89999999621--8842267899999999665164 Q gi|254780383|r 160 IFRISNRIGLAPGKT---PNKVEQSLLRI--IPPKHQYNAHYWLVLHGRYVCK 207 (227) Q Consensus 160 v~Rv~~Rlgl~~~~~---~~~~~~~l~~~--~p~~~~~~~~~~li~~G~~iC~ 207 (227) +.-+++......+.+ .+.......++ ++.+.....-..++..|+.+.. T Consensus 78 i~~~L~~~~~~~Ght~l~~~~L~~~~~~lL~~~~~~i~~~l~~l~~~~~iv~~ 130 (149) T 3e1s_A 78 AVYALQLAGTQAGHSFLPRSRAEKGVVHYTRVTPGQARLAVETAVELGRLSED 130 (149) T ss_dssp HHHHHHHHHHHTCCSCEEHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTSSEEE T ss_pred HHHHHHHHHHCCCCEEEEHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 99999997334898721499999999998679967899999999885246654 No 83 >>3gzu_A Inner capsid protein VP2; 7RP, DLP, metal- binding, virion, zinc, core protein, RNA-binding, icosaderal virus; 3.80A {Rotavirus A} (A:1-37,A:228-511) Probab=47.32 E-value=10 Score=18.40 Aligned_cols=53 Identities=15% Similarity=0.203 Sum_probs=28.7 Q ss_pred CCHHHHHHHHHHHHCCCH-HHHHHHHHH------HHHCCCC----CHHHCCCCHHHHHHHHHHH Q ss_conf 868999999999633320-356799899------8731762----0001012689999999973 Q gi|254780383|r 46 VNHFTLIVAVLLSAQSTD-VNVNKATKH------LFEIADT----PQKMLAIGEKKLQNYIRTI 98 (227) Q Consensus 46 ~~p~~~LVa~iLs~qT~d-~~v~~~~~~------L~~~ypt----~e~l~~a~~~el~~~ir~~ 98 (227) .|.|+.+|+++|||||-. +-|-.-+-. |+..-|+ -|++...-..-+..+|.|+ T Consensus 106 ndaFK~iI~~~LsqRT~s~~FvTsnymSL~S~M~LmtivP~~mFiResLvA~QLAiiNTiiYPa 169 (321) T 3gzu_A 106 NDCFKTLIAAMLSQRTMSLDFVTTNYMSLISGMWLLTVVPNDMFIRESLVACQLAIVNTIIYPA 169 (321) T ss_dssp HHHHHHHHHHHHHTCCEEEECCSSCHHHHHHHHHHHHSSCGGGBCHHHHHHHHHHHHHHTTSTT T ss_pred HHHHHHHHHHHHHHHEEEEEEECCCHHHHHHHHHHHEECCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7899999999986313578864234276886515320263678888889999999988766332 No 84 >>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} (B:) Probab=46.65 E-value=9.2 Score=18.64 Aligned_cols=49 Identities=18% Similarity=0.270 Sum_probs=31.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9973003799999975235544420010000145677764323588889999 Q gi|254780383|r 95 IRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILS 146 (227) Q Consensus 95 ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~ 146 (227) |..+++. +||.+...-+.+- ..+.-+-.+.++|++++|+|+|+..-|.- T Consensus 11 I~~L~Ls-~R~~N~L~~~gI~--ti~dL~~~s~~dLl~i~n~G~kSl~EI~~ 59 (73) T 1z3e_B 11 IEELDLS-VRSYNCLKRAGIN--TVQELANKTEEDMMKVRNLGRKSLEEVKA 59 (73) T ss_dssp GGGSCCB-HHHHHHHHHTTCC--BHHHHHTSCHHHHHTSTTCCHHHHHHHHH T ss_pred HHHHCCC-HHHHHHHHHCCCC--CHHHHHHCCHHHHHHCCCCCHHHHHHHHH T ss_conf 9883588-9999999883894--79999877999997588976605999999 No 85 >>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (M:1-64) Probab=46.50 E-value=5.5 Score=20.14 Aligned_cols=20 Identities=35% Similarity=0.371 Sum_probs=16.2 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 45677764323588889999 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILS 146 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~ 146 (227) .-.|.++.|||+.+|..|+. T Consensus 16 ~~aLt~I~GIG~~~A~~Ic~ 35 (64) T 2vqe_M 16 DVALTYIYGIGKARAKEALE 35 (64) T ss_dssp HHHHTTSSSCCSHHHHHHTT T ss_pred EEEEEEEECCCHHHHHHHHH T ss_conf 88733065818999999999 No 86 >>1d8b_A SGS1 RECQ helicase; five helices, three-helical bundle flanked by two helices, DNA binding protein; NMR {Saccharomyces cerevisiae} (A:) Probab=45.21 E-value=8.8 Score=18.77 Aligned_cols=21 Identities=14% Similarity=0.146 Sum_probs=17.9 Q ss_pred CCHHHHHHHHHHHHHHHHHHH Q ss_conf 000014567776432358888 Q gi|254780383|r 122 KIPQTLEGLTRLPGIGRKGAN 142 (227) Q Consensus 122 ~vP~~~~~L~~LpGVG~ktA~ 142 (227) ..|.+.++|.+++|||.+-+. T Consensus 42 ~~P~t~~eL~~i~G~~~~k~~ 62 (81) T 1d8b_A 42 ILPMNDSAFATLGTVEDKYRR 62 (81) T ss_dssp HCCCSHHHHGGGSCCCHHHHH T ss_pred HCCCCHHHHHCCCCCCHHHHH T ss_conf 789999998179999999999 No 87 >>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} (X:1-14,X:218-292) Probab=43.16 E-value=5.5 Score=20.16 Aligned_cols=30 Identities=27% Similarity=0.338 Sum_probs=19.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH Q ss_conf 777643235888899998754210001210467877656 Q gi|254780383|r 130 LTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIG 168 (227) Q Consensus 130 L~~LpGVG~ktA~~il~~~~~~p~~~VDthv~Rv~~Rlg 168 (227) +-.+||||+|||-.++.- |+ ++..|+..+. T Consensus 31 ~pGV~GIG~KtA~kLI~~-yg--------sle~ii~~l~ 60 (89) T 1ul1_X 31 CESIRGIGPKRAVDLIQK-HK--------SIEEIVRRLD 60 (89) T ss_dssp SCCCTTCCHHHHHHHHHH-SS--------SHHHHHTTCC T ss_pred CCCCCCCCHHHHHHHHHH-CC--------CHHHHHHHHH T ss_conf 355788569999999998-09--------9999999998 No 88 >>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A* (A:240-306) Probab=42.64 E-value=10 Score=18.31 Aligned_cols=18 Identities=33% Similarity=0.565 Sum_probs=12.7 Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 777643235888899998 Q gi|254780383|r 130 LTRLPGIGRKGANVILSM 147 (227) Q Consensus 130 L~~LpGVG~ktA~~il~~ 147 (227) +.+|||||++|+.-+-.. T Consensus 4 i~~i~GVG~~t~~kL~~~ 21 (67) T 2aq4_A 4 LDDLPGVGHSTLSRLEST 21 (67) T ss_dssp GGGSTTCCHHHHHHHHHH T ss_pred CCCHHCCCHHHHHHHHHH T ss_conf 230120278999999987 No 89 >>1f6f_A Placental lactogen; 4-helical bundle, alpha helical bundle, ternary complex, FN III domains, beta sheet domains, cytokine-receptor complex; 2.30A {Ovis aries} (A:) Probab=38.31 E-value=27 Score=15.52 Aligned_cols=63 Identities=10% Similarity=0.006 Sum_probs=37.4 Q ss_pred HHHHHHHHHHHHHHHHCCCCH----HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHCCCHHHHHHHH Q ss_conf 999997523554442001000----014567776432358---888999987542100012104678776 Q gi|254780383|r 104 KSENIISLSHILINEFDNKIP----QTLEGLTRLPGIGRK---GANVILSMAFGIPTIGVDTHIFRISNR 166 (227) Q Consensus 104 KAk~I~~~a~~i~~~~~g~vP----~~~~~L~~LpGVG~k---tA~~il~~~~~~p~~~VDthv~Rv~~R 166 (227) |.+.|.+-.+.|..+..+.-. -.+..|-+|.+-... .|..-|++.|.+..--||||..=+==| T Consensus 124 ~~~~L~egi~~i~~~~~~~~~~~~~~~~s~l~~l~s~d~~~~~~~~y~Ll~Clr~D~~KV~tyLk~LkCR 193 (199) T 1f6f_A 124 KAKVLVDGVEVIQKRIHPGEKNEPYPVWSEQSSLTSQDENVRRVAFYRLFHCLHRDSSKIYTYLRILKCR 193 (199) T ss_dssp HHHHHHHHHHHHHHHHSTTCCCCCCCCCGGGGGGGCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 9999999999999982765335788775543113588588898850765776604158999999999545 No 90 >>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} (A:) Probab=38.30 E-value=13 Score=17.54 Aligned_cols=39 Identities=10% Similarity=0.031 Sum_probs=30.1 Q ss_pred HHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99899873176200010126899999999730037999999752 Q gi|254780383|r 68 KATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISL 111 (227) Q Consensus 68 ~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~ 111 (227) .-++.|...||+|-.=. ++|.++||.+. ...|+.++..+ T Consensus 36 ~n~p~lK~efP~W~~R~----KQI~KlWR~ls-se~r~py~qkA 74 (90) T 2yuk_A 36 INFPNLKEEFPDWTTRV----KQIAKLWRKAS-SQERAPYVQKA 74 (90) T ss_dssp HHCTTHHHHCCSHHHHH----HHHHHHHHHSC-HHHHHHHHHHH T ss_pred CCCHHHHHHCCCHHHHH----HHHHHHHHHCC-HHHHCHHHHHH T ss_conf 47778887785658999----99999998577-76404499998 No 91 >>2fj0_A JuvenIle hormone esterase; manduca sexta, alpha-beta hydrolase; HET: TFC; 2.70A {Trichoplusia NI} (A:237-300) Probab=36.88 E-value=28 Score=15.38 Aligned_cols=41 Identities=22% Similarity=0.463 Sum_probs=29.8 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH Q ss_conf 787765654078889999999621884226789999999-9665 Q gi|254780383|r 162 RISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVL-HGRY 204 (227) Q Consensus 162 Rv~~Rlgl~~~~~~~~~~~~l~~~~p~~~~~~~~~~li~-~G~~ 204 (227) +++.-+|+ ++.+++++++.|-+ +|.+...+.|.-+++ +|=. T Consensus 15 ~fl~~lGI-nsTDpeeIH~~LI~-~P~ekl~eAn~~l~~~~Glt 56 (64) T 2fj0_A 15 LFVTNIGI-TATDPEEIHQKLIE-MPAEKLNEANRFLLEQFGLT 56 (64) T ss_dssp HHHHHTTC-CCCSHHHHHHHHHT-SCHHHHHHHHHHHHHHHSSC T ss_pred HHHHHCCC-CCCHHHHHHHHHHH-CCHHHHHHHHHHHHHHCCCC T ss_conf 99984276-42027889998862-88999999999876531663 No 92 >>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged helix, DNA binding; 2.60A {Pyrococcus furiosus} (A:155-202) Probab=36.31 E-value=23 Score=15.99 Aligned_cols=40 Identities=15% Similarity=0.247 Sum_probs=26.9 Q ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHH Q ss_conf 1210467877656540788899999996218842267899 Q gi|254780383|r 156 VDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAH 195 (227) Q Consensus 156 VDthv~Rv~~Rlgl~~~~~~~~~~~~l~~~~p~~~~~~~~ 195 (227) |.|++.-++.|+.=.+....+++-+++++++|++.....- T Consensus 1 vetyien~mrr~seenrqi~ekifkdie~ilpp~yar~ik 40 (48) T 2p4w_A 1 IETYIENTMRRLAEENRQIIEEIFRDIEKILPPGYARSLK 40 (48) T ss_dssp HHHHHHHHHHHHHHHCHHHHHHHHHHHTTTSCHHHHHHHH T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 9999988999987503889999999878753522318999 No 93 >>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} (A:1-37,A:151-214) Probab=36.29 E-value=25 Score=15.68 Aligned_cols=38 Identities=24% Similarity=0.163 Sum_probs=26.1 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHCC--C-----CHHHHHHHHHHC Q ss_conf 7542100012104678776565407--8-----889999999621 Q gi|254780383|r 148 AFGIPTIGVDTHIFRISNRIGLAPG--K-----TPNKVEQSLLRI 185 (227) Q Consensus 148 ~~~~p~~~VDthv~Rv~~Rlgl~~~--~-----~~~~~~~~l~~~ 185 (227) -|..--..+|-||.|.+.++|+.+. + .+.+.|..+.++ T Consensus 32 ~~~~~~AILDRHILR~L~~~Gii~EipKtlTkk~YLelE~~l~ei 76 (101) T 3fhf_A 32 EFKSFKAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDI 76 (101) T ss_dssp HHHGGGCCCCHHHHHHHHHTTSSSSCCSSCCHHHHHHHHHHHHHH T ss_pred HHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHH T ss_conf 716567776279999999848866777633387899999999987 No 94 >>2b1e_A Exocyst complex component EXO70; tethering complex, endocytosis/exocytosis complex; 2.00A {Saccharomyces cerevisiae} PDB: 2b7m_A 2pfv_A (A:459-564) Probab=35.93 E-value=29 Score=15.28 Aligned_cols=72 Identities=10% Similarity=0.050 Sum_probs=45.2 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCC----CCHHHCCCCHHHHHHHHHH Q ss_conf 899999999999976799987777868999999999633320356799899873176----2000101268999999997 Q gi|254780383|r 22 PKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIAD----TPQKMLAIGEKKLQNYIRT 97 (227) Q Consensus 22 ~~~~~~I~~~L~~~yp~~~~~l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~yp----t~e~l~~a~~~el~~~ir~ 97 (227) ++++......+++.|..-..+...+.-.+. .+- +.-...|.++|.+++.+|+ +++....-++++|+..|.. T Consensus 29 Kerf~~Fn~~fee~~~~q~~w~VpD~~LR~---~Lr--~~i~~~VvpaY~~Fl~r~~~~~k~~~kyikytpe~le~~l~~ 103 (106) T 2b1e_A 29 KEKFRKFNEGFEDLVSKTKQYKLSDPSLKV---TLK--SEIISLVMPMYERFYSRYKDSFKNPRKHIKYTPDELTTVLNQ 103 (106) T ss_dssp HHHHHHHHHHHHHHHHHHTTCCCCCHHHHH---HHH--HHHHHHHHHHHHHHHHHHGGGSSSGGGTCSCCHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHH---HHH--HHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCHHHHHHHHHH T ss_conf 999999999999999982861286899999---999--999999999999999984645789875461389999999998 Q ss_pred H Q ss_conf 3 Q gi|254780383|r 98 I 98 (227) Q Consensus 98 ~ 98 (227) + T Consensus 104 L 104 (106) T 2b1e_A 104 L 104 (106) T ss_dssp H T ss_pred H T ss_conf 6 No 95 >>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} (A:1-28,A:102-142) Probab=33.97 E-value=31 Score=15.07 Aligned_cols=22 Identities=32% Similarity=0.409 Sum_probs=18.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0145677764323588889999 Q gi|254780383|r 125 QTLEGLTRLPGIGRKGANVILS 146 (227) Q Consensus 125 ~~~~~L~~LpGVG~ktA~~il~ 146 (227) ..+++|..+.|+|-|-|+-.|- T Consensus 41 eaRe~LvniKGiGyKEASHFLR 62 (69) T 3fhg_A 41 LARERLLNIKGIGMQEASHFLR 62 (69) T ss_dssp HHHHHHTTSTTCCHHHHHHHHH T ss_pred HHHHHHHHCCCCHHHHHHHHHH T ss_conf 9999999675853999999999 No 96 >>2rhf_A DNA helicase RECQ; HRDC, D. radiodurans, ATP-binding, hydrolase, nucleotide-binding; HET: DNA; 1.10A {Deinococcus radiodurans R1} (A:) Probab=33.21 E-value=15 Score=17.26 Aligned_cols=21 Identities=38% Similarity=0.773 Sum_probs=17.6 Q ss_pred CCHHHHHHHHHHHHHHHHHHH Q ss_conf 000014567776432358888 Q gi|254780383|r 122 KIPQTLEGLTRLPGIGRKGAN 142 (227) Q Consensus 122 ~vP~~~~~L~~LpGVG~ktA~ 142 (227) ..|.+.++|.+++|||+.-.. T Consensus 41 ~~P~t~~eL~~i~gi~~~~~~ 61 (77) T 2rhf_A 41 RQPRTLAELAEVPGLGEKRIE 61 (77) T ss_dssp HCCCSHHHHTTSTTTCHHHHH T ss_pred CCCCCHHHHCCCCCCCHHHHH T ss_conf 093499997379998999999 No 97 >>2pft_A Exocytosis protein; helix-turn-helix, endocytosis/exocytosis complex; 2.25A {Mus musculus} (A:470-571) Probab=32.93 E-value=32 Score=14.96 Aligned_cols=72 Identities=8% Similarity=-0.025 Sum_probs=45.2 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCC------CCHHHCCCCHHHHHHHH Q ss_conf 899999999999976799987777868999999999633320356799899873176------20001012689999999 Q gi|254780383|r 22 PKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIAD------TPQKMLAIGEKKLQNYI 95 (227) Q Consensus 22 ~~~~~~I~~~L~~~yp~~~~~l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~yp------t~e~l~~a~~~el~~~i 95 (227) ++++......+++.|..-..|...+.-.+.-+. +.-...|.++|..++.+|. +++....-++++|+..| T Consensus 20 Kerf~~Fn~~Fee~~~~q~~w~VpD~~LR~~Lr-----~~i~~~Vip~Y~~F~~ry~~~~~~k~~~Kyikytpe~le~~l 94 (102) T 2pft_A 20 KERFKGFNDGLEELCKIQKVWAIPDTEQRDKIR-----QAQKDIVKETYGAFLHRYGSVPFTKNPEKYIKYRVEQVGDMI 94 (102) T ss_dssp HHHHHHHHHHHHHHHHHHTTCCCCCHHHHHHHH-----HHHHHHHHHHHHHHHHHHHSSCCCSCHHHHCCCCHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH-----HHHHHHHHHHHHHHHHHHCCCCCCCCCCCEECCCHHHHHHHH T ss_conf 999999999999999973970595899999999-----999999999999999983776556897551047899999999 Q ss_pred HHH Q ss_conf 973 Q gi|254780383|r 96 RTI 98 (227) Q Consensus 96 r~~ 98 (227) ..+ T Consensus 95 ~~L 97 (102) T 2pft_A 95 DRL 97 (102) T ss_dssp HTS T ss_pred HHH T ss_conf 998 No 98 >>1huw_A Human growth hormone; 2.00A {Homo sapiens} (A:) Probab=32.01 E-value=33 Score=14.86 Aligned_cols=105 Identities=12% Similarity=-0.026 Sum_probs=50.9 Q ss_pred HCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-C-----CCH--HHHHHH Q ss_conf 33320356799899873176200010126899999999730037999999752355444200-1-----000--014567 Q gi|254780383|r 59 AQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFD-N-----KIP--QTLEGL 130 (227) Q Consensus 59 ~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~-g-----~vP--~~~~~L 130 (227) ||+.++.-.+..-.|..-|.+|-.........-..++...-.-..|-+.|.+-.+.|..+-. | ..| .....| T Consensus 68 qq~s~~~LL~~~l~ll~sW~~PL~~L~~~~~~~~~i~s~a~~I~~kl~~L~egi~~l~~~~~~~~~~~~~~~~w~~l~~l 147 (191) T 1huw_A 68 QQKSNLELLRISLLLIQSWLEPVQFLRSVFANSLVYGASDSNVYDLLKDLEEGIQTLMGRLEDGSPRTGQIFKQTYSKFD 147 (191) T ss_dssp HTSCHHHHHHHHHHHHHTTTTGGGGGHHHHHHCCSTTTTTCCHHHHHHHHHHHHHHHHHHHC------------------ T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCC T ss_conf 65312589999999999987199999999864011156634099999989999999975502699871278998885406 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH Q ss_conf 776432358888999987542100012104678 Q gi|254780383|r 131 TRLPGIGRKGANVILSMAFGIPTIGVDTHIFRI 163 (227) Q Consensus 131 ~~LpGVG~ktA~~il~~~~~~p~~~VDthv~Rv 163 (227) .+...-.+-.|..-|++.|.+..--||+|..=+ T Consensus 148 ~s~~~~~~~~~~y~Ll~Clr~D~~Kv~tyLkvL 180 (191) T 1huw_A 148 TNSHNDDALLKNYGLLYCFNKDMSKVSTYLRTV 180 (191) T ss_dssp -------CHHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred CCCCCCHHHHHHCCEEEEECCCHHHHHHHHHHE T ss_conf 777670889873775567445378898887640 No 99 >>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} (A:) Probab=31.37 E-value=11 Score=18.03 Aligned_cols=49 Identities=18% Similarity=0.289 Sum_probs=29.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9973003799999975235544420010000145677764323588889999 Q gi|254780383|r 95 IRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILS 146 (227) Q Consensus 95 ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~ 146 (227) |.-+++. +||.+..+-+.+- ..+.-+-.+.++|++++|+|+|+..-|-- T Consensus 26 I~~L~Ls-~Rs~N~Lk~~gI~--ti~dL~~~s~~dLl~i~n~G~kSl~Ei~~ 74 (98) T 1coo_A 26 VDDLELT-VRSANCLKAEAIH--YIGDLVQRTEVELLKTPNLGKKSLTEIKD 74 (98) T ss_dssp GGGGTCC-TTTHHHHHTTTCC--BHHHHHTSCHHHHTTSTTCCHHHHHHHHH T ss_pred HHHHCCC-HHHHHHHHHCCCC--CHHHHHHCCHHHHHHCCCCCHHHHHHHHH T ss_conf 9982688-9999899993997--59999858999998677987878999999 No 100 >>2ziu_B Crossover junction endonuclease EME1; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Homo sapiens} PDB: 2ziw_B 2zix_B 2ziv_B (B:242-341) Probab=28.55 E-value=17 Score=16.89 Aligned_cols=29 Identities=17% Similarity=0.196 Sum_probs=16.9 Q ss_pred HHHCCCHHHHHHHHHHHHHCCCCCHHHCCC Q ss_conf 963332035679989987317620001012 Q gi|254780383|r 57 LSAQSTDVNVNKATKHLFEIADTPQKMLAI 86 (227) Q Consensus 57 Ls~qT~d~~v~~~~~~L~~~ypt~e~l~~a 86 (227) +++|...-...+| ....++||||.+|.++ T Consensus 15 ~L~qI~gvs~~kA-~aI~~~YPTp~~L~~a 43 (100) T 2ziu_B 15 QIQQLNRVSLEMA-SAVVNAYPSPQLLVQA 43 (100) T ss_dssp HHTTSTTCCHHHH-HHHHHHSCSHHHHHHH T ss_pred HHHHCCCCCHHHH-HHHHHHCCCHHHHHHH T ss_conf 9986579999999-9999978999999999 No 101 >>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (A:1-47,A:173-315) Probab=27.62 E-value=35 Score=14.72 Aligned_cols=49 Identities=18% Similarity=0.334 Sum_probs=30.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9997300379999997523554442001000014567776432358888999 Q gi|254780383|r 94 YIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVIL 145 (227) Q Consensus 94 ~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il 145 (227) -|.-+++. +|+.+..+-+.+- .-+.-+-.+.++|++++|+|.|+.+-|. T Consensus 130 ~IeeL~Ls-~R~~n~Lk~a~I~--ti~dL~~~s~~dL~~i~n~G~ksl~EI~ 178 (190) T 2a6h_A 130 PLEELGLS-TRVLHSLKEEGIE--SVRALLALNLKDLKNIPGIGERSLEEIK 178 (190) T ss_dssp ---------------------------------------------------- T ss_pred CHHHHCCC-HHHHHHHHHCCCC--CHHHHHHCCHHHHHCCCCCCCCCHHHHH T ss_conf 59990587-8888678775894--7999884999998459997605599999 No 102 >>1c7v_A CAVP, calcium vector protein; EF-hand family, calcium binding protein,; NMR {Branchiostoma lanceolatum} (A:) Probab=27.48 E-value=36 Score=14.68 Aligned_cols=59 Identities=7% Similarity=0.025 Sum_probs=35.6 Q ss_pred HHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH Q ss_conf 89987317620001012689999999973003799999975235544420010000145677 Q gi|254780383|r 70 TKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLT 131 (227) Q Consensus 70 ~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~ 131 (227) +..+|+.| +...=-..+.+|+..+++.+|+.......+..+.+.+-...+|.| ++++.+ T Consensus 10 l~~~F~~~-D~d~~G~I~~~el~~~l~~~~~~~~~~~~~~~~~~~~D~d~dg~I--~~~EF~ 68 (81) T 1c7v_A 10 ILRAFKVF-DANGDGVIDFDEFKFIMQKVGEEPLTDAEVEEAMKEADEDGNGVI--DIPEFM 68 (81) T ss_dssp HHHHHHHH-SCSGGGEECHHHHHHHSSTTTTCCCCHHHHHHHHHHHCSSGGGSE--EHHHHH T ss_pred HHHHHHHH-CCCCCCEECHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCE--EHHHHH T ss_conf 99999988-589749074999999999838887879999999998789989949--299999 No 103 >>1l2l_A ADP-dependent glucokinase; ADP glucokinase APO, transferase; 2.00A {Pyrococcus horikoshii} (A:33-116,A:172-217) Probab=26.78 E-value=41 Score=14.27 Aligned_cols=74 Identities=12% Similarity=0.209 Sum_probs=49.7 Q ss_pred CCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHC Q ss_conf 2000101268999999997300379999997523554442001000014567776432358888999987542--10001 Q gi|254780383|r 79 TPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGI--PTIGV 156 (227) Q Consensus 79 t~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~--p~~~V 156 (227) ++.++..++.++|+.+|...|=-. |+ .-+++|-++ ..+... -.|..+.+.-.|+ .++.+ T Consensus 3 NIDAIkyL~~edie~LI~~fg~ee-----V~----~rieeyPr~----I~sp~D------fvArLl~amK~GK~aEvpv~ 63 (130) T 1l2l_A 3 NIDAIKYLKREDLEKRIEKVGKEE-----VL----RYSEELPKE----IETIPQ------LLGSILWSIKRGKAAELLVV 63 (130) T ss_dssp EEEEECBCCHHHHHHHHHHHCHHH-----HH----HHHHSCCSS----BCSHHH------HHHHHHHHHHHTCCEEEEBC T ss_pred CEEEEEECCHHHHHHHHHHCCCHH-----HH----HHHHCCCCC----CCCHHH------HHHHHHHHHHCCCCEEEEEC T ss_conf 413799648899999998608413-----32----455439845----699999------99999998418952487615 Q ss_pred CCHHHHHHHHHHHHC Q ss_conf 210467877656540 Q gi|254780383|r 157 DTHIFRISNRIGLAP 171 (227) Q Consensus 157 Dthv~Rv~~Rlgl~~ 171 (227) +.-|+..+++|||.. T Consensus 64 ~~ev~~w~~~~~~de 78 (130) T 1l2l_A 64 SREVREYMRKWGWDE 78 (130) T ss_dssp CHHHHHHHHHHCCSE T ss_pred CHHHHHHHHHCCCCE T ss_conf 878999998655525 No 104 >>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} (T:1-19,T:58-205) Probab=26.36 E-value=8.7 Score=18.79 Aligned_cols=16 Identities=38% Similarity=0.578 Sum_probs=12.0 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 4567776432358888 Q gi|254780383|r 127 LEGLTRLPGIGRKGAN 142 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~ 142 (227) -+.+-.+||||++||. T Consensus 152 ~D~~~GIpGiG~ktA~ 167 (167) T 1bgx_T 152 SDNLPGVKGIGEKTAR 167 (167) T ss_dssp SSCCCCCCCSSSCTTT T ss_pred CCCCCCCCCCCCCCHH T ss_conf 0367778887742213 No 105 >>1wud_A ATP-dependent DNA helicase RECQ; DNA-binding domain, HRDC, hydrolase; 2.20A {Escherichia coli} (A:) Probab=25.53 E-value=25 Score=15.69 Aligned_cols=22 Identities=18% Similarity=0.348 Sum_probs=17.8 Q ss_pred CCHHHHHHHHHHHHHHHHHHHH Q ss_conf 0000145677764323588889 Q gi|254780383|r 122 KIPQTLEGLTRLPGIGRKGANV 143 (227) Q Consensus 122 ~vP~~~~~L~~LpGVG~ktA~~ 143 (227) ..|.+.++|.+++|||..-+.- T Consensus 49 ~~P~t~~eL~~i~g~~~~~~~~ 70 (89) T 1wud_A 49 QXPITASEXLSVNGVGXRKLER 70 (89) T ss_dssp HCCCSHHHHHTSTTCCHHHHHH T ss_pred HCCCCHHHHHCCCCCCHHHHHH T ss_conf 7889999980799989999999 No 106 >>2cw6_A Hydroxymethylglutaryl-COA lyase, mitochondrial; HMG-COA lyase, ketogenic enzyme; HET: 3HG; 2.10A {Homo sapiens} (A:) Probab=25.49 E-value=11 Score=18.00 Aligned_cols=20 Identities=5% Similarity=-0.059 Sum_probs=13.8 Q ss_pred CHHCCCHHHHHHHHHHHHHH Q ss_conf 00239989999999999997 Q gi|254780383|r 16 LGCLYTPKELEEIFYLFSLK 35 (227) Q Consensus 16 ~~~~~~~~~~~~I~~~L~~~ 35 (227) .+...+.+...+|+..|.+. T Consensus 20 ~~~~~~~~~k~~i~~~L~~~ 39 (298) T 2cw6_A 20 EKNIVSTPVKIKLIDMLSEA 39 (298) T ss_dssp CSSCCCHHHHHHHHHHHHHT T ss_pred CCCCCCHHHHHHHHHHHHHH T ss_conf 89998999999999999986 No 107 >>2ggm_A Centrin-2; EF-hand superfamily, DNA repair complex, cell cycle; 2.35A {Homo sapiens} (A:86-172) Probab=25.08 E-value=44 Score=14.07 Aligned_cols=62 Identities=13% Similarity=0.146 Sum_probs=35.1 Q ss_pred HHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 799899873176200010126899999999730037999999752355444200100001456777 Q gi|254780383|r 67 NKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTR 132 (227) Q Consensus 67 ~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~ 132 (227) ...++..|+.| +.+.=-..+.+|+..+++..|..- -...+..+.+.+-..-+|.| +++++.. T Consensus 18 ~~~~~~~F~~f-D~~~~G~I~~~el~~~l~~~~~~~-~~~~~~~~~~~~D~d~~G~I--~~~eF~~ 79 (87) T 2ggm_A 18 KEEILKAFKLF-DDDETGKISFKNLKRVAKELGENL-TDEELQEXIDEADRDGDGEV--SEQEFLR 79 (87) T ss_dssp HHHHHHHHHHH-CTTCCSSBCHHHHHHHHHHTTCCC-CHHHHHHHHHHHCSSSSSSB--CHHHHHH T ss_pred HHHHHHHHHHH-HHCCCCCCCHHHHHHHHHHCCCCC-CHHHHHHHHHHHCCCCCCCE--EHHHHHH T ss_conf 99999999987-107789936999988898718978-69999999999688999979--7999999 No 108 >>2aja_A Ankyrin repeat family protein; NESG, Q5ZSV0, structural genomics, PSI, protein structure initiative; 2.80A {Legionella pneumophila} (A:221-376) Probab=24.80 E-value=44 Score=14.03 Aligned_cols=46 Identities=22% Similarity=0.387 Sum_probs=30.2 Q ss_pred CCCHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH Q ss_conf 620001012-689999999973003799999975235544420010000145677764323 Q gi|254780383|r 78 DTPQKMLAI-GEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIG 137 (227) Q Consensus 78 pt~e~l~~a-~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG 137 (227) ++++++-+. +++|-. .|||= .+.++.+-+-.+-+++..|+++|+|- T Consensus 41 ~n~~~VFDl~~~eEa~-----~~FYm---------lRNLIRRND~~l~DdiRfLLsIPsvk 87 (156) T 2aja_A 41 SNPDGVFDLVTKSECL-----QGFYX---------LRNLIRRNDEVLLDDIRFLLSIPGIK 87 (156) T ss_dssp TSSSSCCCCSSHHHHH-----HHHHH---------HHHHHHHCCGGGHHHHHHHHTSTTTG T ss_pred CCHHHHHHHHHCCCCC-----CCCCC---------HHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 8999999998465421-----37763---------16999850578699999998646775 No 109 >>1rq6_A 30S ribosomal protein S17E; alpha protein, structural genomics, protein structure initiative, PSI, NESG; NMR {Methanothermobacterthermautotrophicus} (A:) Probab=23.99 E-value=16 Score=17.06 Aligned_cols=28 Identities=7% Similarity=0.217 Sum_probs=20.8 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHH Q ss_conf 7999999752355444200100001456 Q gi|254780383|r 102 RKKSENIISLSHILINEFDNKIPQTLEG 129 (227) Q Consensus 102 ~~KAk~I~~~a~~i~~~~~g~vP~~~~~ 129 (227) +.+.+.|+.+|+.|+|+|...+-.|++. T Consensus 3 ~ir~k~iKr~a~~lieky~~~~t~DF~~ 30 (62) T 1rq6_A 3 NIRTSFVKRIAKEMIETHPGKFTDDFDT 30 (62) T ss_dssp CCCCHHHHHHHHHHHTTSCCCCCCCHHH T ss_pred CCCHHHHHHHHHHHHHHCHHHHCCCHHH T ss_conf 8440699999999999864464568888 No 110 >>1ua4_A Glucokinase, ADP-dependent glucokinase; transferase; HET: GLC BGC AMP; 1.90A {Pyrococcus furiosus} (A:29-113,A:169-215) Probab=23.41 E-value=47 Score=13.86 Aligned_cols=73 Identities=16% Similarity=0.185 Sum_probs=49.2 Q ss_pred CCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHC Q ss_conf 2000101268999999997300379999997523554442001000014567776432358888999987542--10001 Q gi|254780383|r 79 TPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGI--PTIGV 156 (227) Q Consensus 79 t~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~--p~~~V 156 (227) ++.++..++.++|+++|...|=-. -+ .-+++| |...++...+ .|..+-+...|+ .++.. T Consensus 4 NIDAIkyL~~edie~LI~~f~~~e----V~-----~rieey----Pr~I~sp~Df------vArLihsmk~GK~aEvpv~ 64 (132) T 1ua4_A 4 NIDAIKYLDSKDLEERIIKAGKEE----VI-----KYSEEL----PDKINTVSQL------LGSILWSIRRGKAAELFVE 64 (132) T ss_dssp EEEEEEECCHHHHHHHHHHHCHHH----HH-----HHHHSC----CSSBCSHHHH------HHHHHHHHHHTCCEEEEBC T ss_pred CEEEEEECCHHHHHHHHHHHCCHH----HH-----HHHHCC----CCCCCCHHHH------HHHHHHHHHCCCCEEEECC T ss_conf 266899668999999998738154----43-----442238----6023999999------9999999746971477437 Q ss_pred CCHHHHHHHHHHHH Q ss_conf 21046787765654 Q gi|254780383|r 157 DTHIFRISNRIGLA 170 (227) Q Consensus 157 Dthv~Rv~~Rlgl~ 170 (227) |.-++.-+++|||. T Consensus 65 ~eev~~wl~~~~~D 78 (132) T 1ua4_A 65 SCPVRFYMKRWGWN 78 (132) T ss_dssp CHHHHHHHHHHCCS T ss_pred CHHHHHHHHHCCCC T ss_conf 77799999855663 No 111 >>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A (A:230-311) Probab=23.03 E-value=9.4 Score=18.57 Aligned_cols=27 Identities=26% Similarity=0.245 Sum_probs=13.4 Q ss_pred HCCCHHHHHHHHHHHHHCCCCCHHHCCC Q ss_conf 3332035679989987317620001012 Q gi|254780383|r 59 AQSTDVNVNKATKHLFEIADTPQKMLAI 86 (227) Q Consensus 59 ~qT~d~~v~~~~~~L~~~ypt~e~l~~a 86 (227) +|-..-...+| ...-++||||..|.+| T Consensus 11 ~qi~gvs~~~A-~aI~~~yPTp~~L~~a 37 (82) T 2ziu_A 11 MQISGVSGDKA-AAVLEHYSTVSSLLQA 37 (82) T ss_dssp TTBTTCCHHHH-HHHHHHCSSHHHHHHH T ss_pred HCCCCCCHHHH-HHHHHHCCCHHHHHHH T ss_conf 80899999999-9999976999999999 No 112 >>1fpw_A Yeast frequenin, calcium-binding protein NCS-1; EF-hand, metal binding protein; NMR {Saccharomyces cerevisiae} (A:22-95) Probab=22.24 E-value=37 Score=14.58 Aligned_cols=59 Identities=5% Similarity=-0.026 Sum_probs=28.9 Q ss_pred HHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH Q ss_conf 9987317620001012689999999973003799999975235544420010000145677 Q gi|254780383|r 71 KHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLT 131 (227) Q Consensus 71 ~~L~~~ypt~e~l~~a~~~el~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~ 131 (227) ..+|+.|-....=-..+.+|+..+++..|........+..+.+.+-..-+|.| +++|.. T Consensus 7 ~~~f~~fd~~d~~G~I~~~el~~~l~~~~~~~~~~~~~~~l~~~~D~d~dg~I--~f~EF~ 65 (74) T 1fpw_A 7 QQWHKGFLRDCPSGQLAREDFVKIYKQFFPFGSPEDFANHLFTVFDKDNNGFI--HFEEFI 65 (74) T ss_dssp HHHHHHHHHHCTTCCEEHHHHHHHHHHHCTTSCCSHHHHHHHHTCCSSCSSEE--CHHHHH T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCE--EHHHHH T ss_conf 99999996558999736999999999976899849999999999769996966--099999 No 113 >>3d48_P Prolactin, PRL; cytokine-cytokine receptor complex, four-helix bundle, glycoprotein, hormone, lactation, secreted, alternative splicing; 2.50A {Homo sapiens} PDB: 2q98_A 1n9d_A 1rw5_A 3ew3_A (P:) Probab=21.12 E-value=52 Score=13.56 Aligned_cols=40 Identities=18% Similarity=0.066 Sum_probs=28.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH Q ss_conf 4567776432358888999987542100012104678776 Q gi|254780383|r 127 LEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNR 166 (227) Q Consensus 127 ~~~L~~LpGVG~ktA~~il~~~~~~p~~~VDthv~Rv~~R 166 (227) ...|.+...-.+-.|..-|++.|.+..--||+|..=+==| T Consensus 142 l~~l~s~~~~~~l~~~y~Ll~ClrrD~hKV~tyLkvLkCR 181 (188) T 3d48_P 142 LPSLQMADEESRLSAYYNLLHCLRRDSHKIDNYLKLLKCR 181 (188) T ss_dssp HHHHSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC T ss_conf 4101467638999972712777625069999999998422 No 114 >>2h7a_A Hypothetical protein YCGL; mixed alpha/beta/alpha sandwich structure, 3-layer (alpha/beta/alpha) sandwich; NMR {Escherichia coli CFT073} (A:) Probab=20.89 E-value=48 Score=13.82 Aligned_cols=21 Identities=19% Similarity=0.415 Sum_probs=16.5 Q ss_pred HHHCCCCHHHHHHHHHHHHHH Q ss_conf 001012689999999973003 Q gi|254780383|r 81 QKMLAIGEKKLQNYIRTIGIY 101 (227) Q Consensus 81 e~l~~a~~~el~~~ir~~G~~ 101 (227) ..|+.++.+++.+.|..-||| T Consensus 63 kkLA~ad~~~V~~~L~~qGfy 83 (110) T 2h7a_A 63 KKLVNADIEKVKQALTEQGYY 83 (110) T ss_dssp CCCSSSCHHHHHHHHHHTSEE T ss_pred CHHHCCCHHHHHHHHHHCCEE T ss_conf 612119899999999868878 No 115 >>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C; HET: DGT; 2.39A {Geobacillus kaustophilus} PDB: 3f2c_A* 3f2d_A* (A:973-1041) Probab=20.00 E-value=55 Score=13.41 Aligned_cols=32 Identities=22% Similarity=0.206 Sum_probs=16.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 432358888999987542100012104678776565 Q gi|254780383|r 134 PGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGL 169 (227) Q Consensus 134 pGVG~ktA~~il~~~~~~p~~~VDthv~Rv~~Rlgl 169 (227) ||||...|..|.-.--+.|.- .+.-++.|.++ T Consensus 1 pGig~~~a~~Iv~~R~~g~F~----s~~Df~~R~~i 32 (69) T 3f2b_A 1 PGLGTNVAQAIVRAREEGEFL----SKEDLQQRGKL 32 (69) T ss_dssp TTCCHHHHHHHHHHHHTSCCC----SHHHHHHHHTC T ss_pred CCCCHHHHHHHHHHHCCCCCC----CHHHHHHHHCC T ss_conf 898999999999986579999----99999975289 Done!