Query 537021.9.peg.817_1 Match_columns 148 No_of_seqs 127 out of 965 Neff 6.6 Searched_HMMs 33803 Date Wed May 25 01:25:21 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_817.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >3c1y_A DNA integrity scanning 97.7 7.2E-05 2.1E-09 51.8 5.5 50 51-101 17-66 (74) 2 >1kft_A UVRC, excinuclease ABC 97.6 5.9E-05 1.7E-09 52.4 4.1 40 59-98 36-75 (78) 3 >1z00_A DNA excision repair pr 97.6 0.00011 3.3E-09 50.6 5.5 50 49-99 22-71 (89) 4 >1pzn_A RAD51, DNA repair and 97.2 0.00055 1.6E-08 46.1 4.7 50 49-99 38-88 (95) 5 >2nrt_A Uvrabc system protein 96.7 0.00075 2.2E-08 45.3 2.1 41 50-91 16-56 (64) 6 >3c65_A Uvrabc system protein 96.3 0.00073 2.2E-08 45.3 0.0 49 49-99 176-224 (226) 7 >1ixr_A Holliday junction DNA 96.0 0.01 3.1E-07 37.9 4.6 97 38-140 66-166 (191) 8 >2a1j_A DNA repair endonucleas 95.8 0.013 3.9E-07 37.2 4.5 48 50-99 8-55 (63) 9 >1z00_B DNA repair endonucleas 95.6 0.0074 2.2E-07 38.9 2.5 40 50-90 22-61 (71) 10 >1pu6_A 3-methyladenine DNA gl 95.0 0.046 1.4E-06 33.7 5.0 63 35-97 51-117 (123) 11 >1m3q_A 8-oxoguanine DNA glyco 94.3 0.083 2.5E-06 32.1 4.9 58 40-97 62-126 (133) 12 >1kg2_A A/G-specific adenine g 94.1 0.084 2.5E-06 32.0 4.7 59 40-98 9-69 (86) 13 >1wcn_A Transcription elongati 93.7 0.16 4.7E-06 30.2 5.5 41 58-98 18-59 (70) 14 >2ztd_A Holliday junction ATP- 92.3 0.25 7.3E-06 29.0 4.8 40 58-97 20-62 (75) 15 >1cuk_A RUVA protein; DNA repa 91.9 0.29 8.7E-06 28.5 4.8 46 58-105 19-67 (79) 16 >1x2i_A HEF helicase/nuclease; 91.3 0.13 3.9E-06 30.8 2.5 32 50-82 18-49 (49) 17 >1kea_A Possible G-T mismatche 91.2 0.68 2E-05 26.2 6.0 64 41-104 10-76 (111) 18 >3fhf_A Mjogg, N-glycosylase/D 91.0 0.013 4E-07 37.2 -2.8 69 26-97 29-106 (113) 19 >2bgw_A XPF endonuclease; hydr 90.7 0.18 5.2E-06 30.0 2.6 31 51-82 19-49 (49) 20 >1orn_A Endonuclease III; DNA 90.6 0.26 7.7E-06 28.9 3.5 60 42-101 10-72 (110) 21 >1szp_A DNA repair protein RAD 90.6 0.3 8.9E-06 28.4 3.7 30 69-98 2-31 (56) 22 >3fsp_A A/G-specific adenine g 90.0 1.5 4.5E-05 23.9 7.2 65 41-105 9-76 (110) 23 >1lb2_B DNA-directed RNA polym 89.9 0.85 2.5E-05 25.5 5.6 41 60-100 21-63 (84) 24 >1z3e_B DNA-directed RNA polym 89.9 0.83 2.5E-05 25.6 5.5 42 59-100 19-62 (73) 25 >3gfk_B DNA-directed RNA polym 89.8 0.57 1.7E-05 26.6 4.7 42 59-100 26-69 (79) 26 >1orn_A Endonuclease III; DNA 89.7 0.87 2.6E-05 25.5 5.5 60 35-97 42-104 (110) 27 >1ngn_A Methyl-CPG binding pro 89.2 1.1 3.4E-05 24.7 5.8 63 40-102 33-98 (129) 28 >1coo_A RNA polymerase alpha s 88.6 0.81 2.4E-05 25.7 4.7 41 60-100 35-77 (98) 29 >3bzc_A TEX; helix-turn-helix, 87.0 0.71 2.1E-05 26.0 3.7 32 73-104 4-35 (70) 30 >2edu_A Kinesin-like protein K 86.2 0.96 2.8E-05 25.2 4.0 33 70-102 31-63 (98) 31 >2a1j_B DNA excision repair pr 85.5 0.63 1.9E-05 26.4 2.7 31 52-82 37-67 (67) 32 >2duy_A Competence protein com 85.0 0.74 2.2E-05 25.9 2.9 32 70-101 18-49 (75) 33 >1kea_A Possible G-T mismatche 85.0 0.54 1.6E-05 26.8 2.2 61 34-97 42-105 (111) 34 >3bz1_U Photosystem II 12 kDa 84.9 0.52 1.5E-05 26.9 2.1 34 67-100 21-54 (104) 35 >1dgs_A DNA ligase; AMP comple 84.4 0.8 2.4E-05 25.7 2.9 37 45-82 80-116 (116) 36 >2abk_A Endonuclease III; DNA- 80.3 2 6E-05 23.1 3.7 54 40-96 48-104 (111) 37 >1s5l_U Photosystem II 12 kDa 80.3 0.57 1.7E-05 26.7 0.8 30 69-98 6-35 (87) 38 >1b22_A DNA repair protein RAD 78.3 1.8 5.3E-05 23.4 2.9 39 59-97 37-76 (114) 39 >2h56_A DNA-3-methyladenine gl 77.8 3.7 0.00011 21.4 4.4 62 41-102 5-69 (77) 40 >1u9l_A Transcription elongati 76.4 5.9 0.00017 20.1 5.2 40 58-97 17-57 (70) 41 >2a1j_A DNA repair endonucleas 76.1 0.99 2.9E-05 25.1 1.0 52 77-128 2-57 (63) 42 >1d8b_A SGS1 RECQ helicase; fi 75.2 5.6 0.00017 20.2 4.7 41 70-110 39-79 (81) 43 >2w9m_A Polymerase X; SAXS, DN 74.3 3.5 0.0001 21.6 3.5 48 53-102 33-80 (118) 44 >2kp7_A Crossover junction end 73.9 6.8 0.0002 19.7 6.1 57 41-102 24-81 (87) 45 >3i0w_A 8-oxoguanine-DNA-glyco 71.9 7.6 0.00022 19.4 6.0 33 65-97 15-51 (58) 46 >2csb_A Topoisomerase V, TOP61 70.2 8.2 0.00024 19.2 5.1 39 57-96 7-45 (48) 47 >2jhn_A ALKA, 3-methyladenine 65.5 8.3 0.00024 19.2 3.8 43 57-100 73-129 (134) 48 >2ihm_A POL MU, DNA polymerase 65.2 4.9 0.00014 20.6 2.6 25 77-101 59-83 (129) 49 >2h56_A DNA-3-methyladenine gl 64.1 5.8 0.00017 20.2 2.8 21 77-97 59-79 (156) 50 >2fmp_A DNA polymerase beta; n 62.3 5.4 0.00016 20.4 2.4 42 56-102 38-80 (119) 51 >2jhn_A ALKA, 3-methyladenine 59.8 7.7 0.00023 19.4 2.8 38 58-96 10-48 (55) 52 >1mpg_A ALKA, 3-methyladenine 59.0 13 0.00039 17.8 6.1 47 50-96 72-120 (127) 53 >2a6h_A DNA-directed RNA polym 57.9 2.4 7.2E-05 22.6 0.0 41 60-100 140-182 (190) 54 >1kg2_A A/G-specific adenine g 57.1 7.7 0.00023 19.4 2.4 25 75-99 19-43 (139) 55 >1vdd_A Recombination protein 55.1 9.4 0.00028 18.8 2.6 19 78-96 11-29 (66) 56 >2bcq_A DNA polymerase lambda; 52.9 16 0.00047 17.4 3.5 50 48-102 29-80 (128) 57 >1exn_A 5'-exonuclease, 5'-nuc 51.9 3.3 9.7E-05 21.8 -0.2 37 70-106 13-49 (80) 58 >1jms_A Terminal deoxynucleoti 51.9 11 0.00034 18.3 2.6 41 57-102 62-103 (154) 59 >1a76_A Flap endonuclease-1 pr 51.0 8.6 0.00025 19.1 1.9 22 81-102 18-39 (65) 60 >1rxw_A Flap structure-specifi 48.6 9.9 0.00029 18.7 1.9 24 82-105 18-41 (68) 61 >1r4t_A Exoenzyme S; EXOS, GAP 47.3 20 0.0006 16.6 4.9 72 47-126 63-151 (153) 62 >3i1m_M 30S ribosomal protein 46.1 12 0.00037 18.0 2.1 23 79-101 17-39 (63) 63 >2zkq_m 40S ribosomal protein 45.1 10 0.00031 18.5 1.5 24 79-102 28-51 (88) 64 >2izo_A FEN1, flap structure-s 44.3 13 0.00039 17.8 2.0 19 81-99 18-36 (82) 65 >3e1s_A Exodeoxyribonuclease V 42.1 7.1 0.00021 19.6 0.3 87 41-131 9-108 (149) 66 >2i5h_A Hypothetical protein A 40.5 15 0.00046 17.4 1.8 59 72-130 125-185 (205) 67 >1b43_A Protein (FEN-1); nucle 39.8 17 0.00049 17.2 1.9 18 58-75 37-54 (77) 68 >2owo_A DNA ligase; protein/DN 39.7 27 0.00079 15.9 6.6 58 46-104 9-66 (168) 69 >2e1f_A Werner syndrome ATP-de 39.6 27 0.00079 15.9 5.4 49 71-119 49-97 (103) 70 >2vqe_M 30S ribosomal protein 39.1 14 0.00041 17.7 1.4 24 79-102 17-40 (64) 71 >2dgz_A Werner syndrome protei 39.1 21 0.00063 16.5 2.4 46 70-115 55-100 (113) 72 >2r4f_A 3-hydroxy-3-methylglut 37.3 21 0.00063 16.5 2.1 29 27-55 15-46 (85) 73 >2zbk_B Type 2 DNA topoisomera 36.4 21 0.00063 16.5 2.0 23 79-101 29-51 (82) 74 >3bq0_A POL IV, DBH, DNA polym 35.1 21 0.00063 16.5 1.8 34 62-97 9-44 (51) 75 >1jei_A Emerin; membrane prote 35.0 13 0.00039 17.9 0.7 33 34-66 3-35 (53) 76 >2dla_A 397AA long hypothetica 33.4 14 0.00041 17.7 0.7 18 59-76 11-28 (134) 77 >2ziu_A MUS81 protein; helix-h 32.1 33 0.00098 15.3 2.4 20 79-98 8-27 (82) 78 >2rhf_A DNA helicase RECQ; HRD 29.7 38 0.0011 14.9 4.7 35 71-105 39-74 (77) 79 >2w9m_A Polymerase X; SAXS, DN 26.2 44 0.0013 14.5 2.3 56 77-137 11-66 (123) 80 >5csm_A Chorismate mutase; cho 25.9 30 0.0009 15.5 1.3 37 85-121 138-175 (256) 81 >1t6c_A Exopolyphosphatase; al 25.5 34 0.001 15.2 1.5 94 23-116 35-159 (162) 82 >3bqs_A Uncharacterized protei 24.8 23 0.00069 16.3 0.6 21 77-97 2-22 (93) 83 >2ziu_B Crossover junction end 23.5 50 0.0015 14.1 2.5 19 57-75 24-42 (100) 84 >3cer_A Possible exopolyphosph 23.0 28 0.00084 15.7 0.7 44 70-113 126-169 (185) 85 >2p6r_A Afuhel308 helicase; pr 22.8 50 0.0015 14.1 2.0 35 59-96 10-45 (68) 86 >1ul1_X Flap endonuclease-1; p 22.0 53 0.0016 13.9 2.3 26 82-107 32-57 (89) 87 >1wud_A ATP-dependent DNA heli 20.7 56 0.0017 13.8 4.3 37 70-106 46-83 (89) No 1 >>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* (A:304-377) Probab=97.70 E-value=7.2e-05 Score=51.84 Aligned_cols=50 Identities=22% Similarity=0.297 Sum_probs=41.9 Q ss_pred CCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 998988999999997379978985099789973789889999997549999 Q 537021.9.peg.8 51 IPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVA 101 (148) Q Consensus 51 ~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~El 101 (148) .|+.. ...|+.|+.+|||+..+.+||+++|.+++|||+.+|..|...+.- T Consensus 17 I~giG-~~~a~~L~~~fgsl~~i~~as~~~L~~v~GiG~~~A~~i~~~~~~ 66 (74) T 3c1y_A 17 VARIP-LSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISS 66 (74) T ss_dssp TSCCC-HHHHHHHHHHHCSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHH T ss_pred CCCCC-HHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 99998-999999999853899998579988854478469999999999999 No 2 >>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} (A:) Probab=97.62 E-value=5.9e-05 Score=52.40 Aligned_cols=40 Identities=20% Similarity=0.246 Sum_probs=37.0 Q ss_pred HHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHH Q ss_conf 9999997379978985099789973789889999997549 Q 537021.9.peg.8 59 IAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLV 98 (148) Q Consensus 59 lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~ 98 (148) .|+.|+++|||+.++.+|+.+||.+|+|||+.+|..|.-. T Consensus 36 ~a~~L~~~Fgs~~~i~~As~eeL~~v~gIG~~~A~~I~~~ 75 (78) T 1kft_A 36 RRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWS 75 (78) T ss_dssp HHHHHHHHHSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHH T ss_pred HHHHHHHHCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH T ss_conf 9999999909989998578999973899899999999999 No 3 >>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (A:) Probab=97.61 E-value=0.00011 Score=50.63 Aligned_cols=50 Identities=20% Similarity=0.181 Sum_probs=42.1 Q ss_pred CCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 379989889999999973799789850997899737898899999975499 Q 537021.9.peg.8 49 RLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVS 99 (148) Q Consensus 49 ~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~ 99 (148) +|.|+..- ..|+.|+.+|||+..+.+|++++|.+++|||+.+|..|.-.+ T Consensus 22 ~~I~gIG~-~~a~~L~~~F~s~~~i~~A~~~~L~~v~GiG~~~A~~i~~~~ 71 (89) T 1z00_A 22 TTVKSVNK-TDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVL 71 (89) T ss_dssp TTSSSCCH-HHHHHHHHHTCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHH T ss_pred CCCCCCCH-HHHHHHHHHHCCCHHHHHHHHHHHCHHCCCCHHHHHHHHHHH T ss_conf 58997699-999999999099478766547510000332799999999998 No 4 >>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} (A:1-95) Probab=97.18 E-value=0.00055 Score=46.14 Aligned_cols=50 Identities=22% Similarity=0.249 Sum_probs=41.2 Q ss_pred CCCCCCCHHHHHHHHHHH-CCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 379989889999999973-799789850997899737898899999975499 Q 537021.9.peg.8 49 RLIPRKDTKSIAKALLKR-FATLGGVFGAPLHLLQEINRIGKRVALELKLVS 99 (148) Q Consensus 49 ~g~~~~~~~~lA~~lL~~-fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~ 99 (148) .+.|+.. ...|+.|+.+ |+++..+.+|++++|.+|+|||+.+|..|...+ T Consensus 38 l~I~gIG-~~~a~~L~~~~~~s~e~i~~As~e~L~~i~Gig~~~A~~I~~~~ 88 (95) T 1pzn_A 38 EDLPGVG-PATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAA 88 (95) T ss_dssp SCCTTCC-HHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHH T ss_pred HHCCCCC-HHHHHHHHHCCCCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 4379979-99999999859971999982899999975498999999999999 No 5 >>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=96.71 E-value=0.00075 Score=45.26 Aligned_cols=41 Identities=17% Similarity=0.223 Sum_probs=34.4 Q ss_pred CCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHH Q ss_conf 799898899999999737997898509978997378988999 Q 537021.9.peg.8 50 LIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRV 91 (148) Q Consensus 50 g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~ak 91 (148) |.|+-.. ..|+.|+++|||+..+.+||.+||++|+|||+.. T Consensus 16 ~I~gIG~-~~a~~L~~~F~s~~~i~~As~eeL~~v~gig~~A 56 (64) T 2nrt_A 16 NVPGIGP-IRKKKLIEHFGSLENIRSASLEEIARVIGSTEIA 56 (64) T ss_dssp TSTTCCH-HHHHHHHHHHCSHHHHHTSCHHHHHHHHTCHHHH T ss_pred CCCCCCH-HHHHHHHHHCCCHHHHHCCCHHHHHHCCCCHHHH T ss_conf 0531079-9999999986899999709999998687929999 No 6 >>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=96.31 E-value=0.00073 Score=45.33 Aligned_cols=49 Identities=27% Similarity=0.219 Sum_probs=39.3 Q ss_pred CCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 379989889999999973799789850997899737898899999975499 Q 537021.9.peg.8 49 RLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVS 99 (148) Q Consensus 49 ~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~ 99 (148) .+.|+- -...|+.|+++|||+..+.+||.+||++| |||+.+|..|...+ T Consensus 176 ~~I~~I-G~~~a~~Ll~~Fgsl~~i~~As~eeL~~v-giG~~~A~~I~~~f 224 (226) T 3c65_A 176 DDIPGV-GEKRKKALLNYFGSVKKMKEATVEELQRA-NIPRAVAEKIYEKL 224 (226) T ss_dssp --------------------------------------------------- T ss_pred HHHHHH-CHHHHHHHHHHCCCHHHHHHCCHHHHHHC-CCCHHHHHHHHHHH T ss_conf 899874-79999999998589999983999999877-99999999999996 No 7 >>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=95.98 E-value=0.01 Score=37.89 Aligned_cols=97 Identities=18% Similarity=0.245 Sum_probs=55.9 Q ss_pred CHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCC---HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 98999999973379989889999999973799---789850997899737898899999975499999999998764067 Q 537021.9.peg.8 38 AYYEILELILFRLIPRKDTKSIAKALLKRFAT---LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKK 114 (148) Q Consensus 38 sD~ELLallL~~g~~~~~~~~lA~~lL~~fGs---L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~ 114 (148) .+-|+-..++. .++-- --.|..+|++|+. ...+.++|+++|+++||||+..|-+|.. ||-..+......... T Consensus 66 ~er~~F~~L~~--V~GIG-pk~Al~iL~~~~~~el~~aI~~~d~~~L~~ipGIG~KtA~rIi~--eLk~k~~~~~~~~~~ 140 (191) T 1ixr_A 66 ENLALFELLLS--VSGVG-PKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIAL--ELKGKVPPHLLAGEK 140 (191) T ss_dssp HHHHHHHHHHS--SSCCC-HHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHH--HHTTTSCSCC----- T ss_pred HHHHHHHHHHC--CCCCC-HHHHHHHHHCCCHHHHHHHHHCCCHHHHCCCCCCCHHHHHHHHH--HHHHHCCCCCCCCCC T ss_conf 99999999857--58847-78899998559999999999828999851388845688999999--998642521001123 Q ss_pred CCCCH-HHHHHHHHHHHCCCCEEEEEE Q ss_conf 78898-999999999845978000252 Q 537021.9.peg.8 115 FLTPG-QPCLISVERHYPMKNANNFAY 140 (148) Q Consensus 115 ~l~s~-~~v~~yl~~~l~~~~~E~F~v 140 (148) ..+++ +++..-| ..||+.+.|.-.+ T Consensus 141 ~~~~~~~e~~~aL-~~LGy~~~ea~~a 166 (191) T 1ixr_A 141 VESEAAEEAVMAL-AALGFKEAQARAV 166 (191) T ss_dssp --------------------------- T ss_pred CCCCCHHHHHHHH-HHCCCCHHHHHHH T ss_conf 3555689999999-9869999999999 No 8 >>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} (A:) Probab=95.80 E-value=0.013 Score=37.20 Aligned_cols=48 Identities=13% Similarity=0.108 Sum_probs=36.6 Q ss_pred CCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 79989889999999973799789850997899737898899999975499 Q 537021.9.peg.8 50 LIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVS 99 (148) Q Consensus 50 g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~ 99 (148) +.|+... ..|+.|+.+|||+.++.+||.+||.+|+| |+.+|-.|.-.+ T Consensus 8 ~IpgVG~-~~a~~Ll~~f~Si~~i~~As~eeL~~i~g-g~~~A~~i~~~l 55 (63) T 2a1j_A 8 KMPGVNA-KNCRSLMHHVKNIAELAALSQDELTSILG-NAANAKQLYDFI 55 (63) T ss_dssp TSTTCCH-HHHHHHHHHCSSHHHHHTCCHHHHHHHHS-CHHHHHHHHHHH T ss_pred CCCCCCH-HHHHHHHHHHCCHHHHHHCCHHHHHHCCC-CHHHHHHHHHHH T ss_conf 1999899-99999999807899998699999977859-689999999998 No 9 >>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (B:1-71) Probab=95.58 E-value=0.0074 Score=38.87 Aligned_cols=40 Identities=13% Similarity=0.204 Sum_probs=33.2 Q ss_pred CCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHH Q ss_conf 79989889999999973799789850997899737898899 Q 537021.9.peg.8 50 LIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKR 90 (148) Q Consensus 50 g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~a 90 (148) +.|+-..+. ++.|+.+|||+.++.+||.+||.+++|++.. T Consensus 22 ~ipGIg~k~-~~~Ll~~f~si~~i~~As~eeL~~v~G~~~~ 61 (71) T 1z00_B 22 KMPGVNAKN-CRSLMHHVKNIAELAALSQDELTSILGNAAN 61 (71) T ss_dssp TCSSCCHHH-HHHHHHHSSCHHHHHHSCHHHHHHHHSCHHH T ss_pred CCCCCCHHH-HHHHHHHCCCHHHHHHCCHHHHHHCCCCHHH T ss_conf 089988999-9999999079999987899999887597899 No 10 >>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} (A:23-145) Probab=94.97 E-value=0.046 Score=33.69 Aligned_cols=63 Identities=16% Similarity=0.148 Sum_probs=50.1 Q ss_pred HHCCHHHHHHHHHHCCCC---CCCHHHHHHHHHHHCCCHHHHHC-CCHHHHHHCCCCCHHHHHHHHH Q ss_conf 218989999999733799---89889999999973799789850-9978997378988999999754 Q 537021.9.peg.8 35 NALAYYEILELILFRLIP---RKDTKSIAKALLKRFATLGGVFG-APLHLLQEINRIGKRVALELKL 97 (148) Q Consensus 35 ~~LsD~ELLallL~~g~~---~~~~~~lA~~lL~~fGsL~~ll~-as~~eL~~i~GIG~aka~~l~a 97 (148) ..+++.||.+++=..|.. -+....+|+.+.+.++++.++-. ...++|++++|||+..|-.++. T Consensus 51 ~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~~~~~~~~l~~~~~~~~~~~L~~l~GIG~~tA~~ill 117 (123) T 1pu6_A 51 AYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILC 117 (123) T ss_dssp HHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHHHSSHHHHHHHCCHHHHHTSTTCCHHHHHHHHH T ss_pred HCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHH T ss_conf 7799999999999879958999999999999998663103799467999998489966999999999 No 11 >>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=94.26 E-value=0.083 Score=32.06 Aligned_cols=58 Identities=19% Similarity=0.047 Sum_probs=42.1 Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH---CCC----HHHHHHCCCCCHHHHHHHHH Q ss_conf 99999997337998988999999997379978985---099----78997378988999999754 Q 537021.9.peg.8 40 YEILELILFRLIPRKDTKSIAKALLKRFATLGGVF---GAP----LHLLQEINRIGKRVALELKL 97 (148) Q Consensus 40 ~ELLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll---~as----~~eL~~i~GIG~aka~~l~a 97 (148) .+.+.-.-.++.+-+....+|+.+.++||+.-.+- +.+ .++|++++|||+..|-.+.. T Consensus 62 ~~~l~~~g~~~~ka~~i~~~a~~~~~~~~g~~~~~~~~~~~~~~~~~~L~~lpGIG~~tA~~ill 126 (133) T 1m3q_A 62 VEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICL 126 (133) T ss_dssp HHHHHHHTTCTTHHHHHHHHHHHHHHTSCSHHHHHHTTTSCHHHHHHHHTTSTTCCHHHHHHHHH T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 89999864747899999999999874245435799771399899999998468837999999999 No 12 >>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} (A:24-109) Probab=94.13 E-value=0.084 Score=32.02 Aligned_cols=59 Identities=17% Similarity=0.187 Sum_probs=51.4 Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHH-CCCCCHH-HHHHHHHH Q ss_conf 99999997337998988999999997379978985099789973-7898899-99997549 Q 537021.9.peg.8 40 YEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQE-INRIGKR-VALELKLV 98 (148) Q Consensus 40 ~ELLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~-i~GIG~a-ka~~l~a~ 98 (148) .-|++.+|..-++..+|.....+|.++|.+...+.+++.++|.. |+++|-- ||..|+.+ T Consensus 9 ~~Lia~iLsq~T~~~~~~~~~~~L~~~~~t~~~l~~a~~~~l~~~i~~~G~~~Ka~~i~~~ 69 (86) T 1kg2_A 9 KVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKA 69 (86) T ss_dssp HHHHHHHHHTSSCHHHHHHHHHHHHHHCSSHHHHHHSCHHHHHHHHTTSCCTHHHHHHHHH T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHH T ss_conf 9999999981184999999999999987999999860899999998846899999999999 No 13 >>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=93.72 E-value=0.16 Score=30.24 Aligned_cols=41 Identities=22% Similarity=0.211 Sum_probs=35.4 Q ss_pred HHHHHHHHH-CCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHH Q ss_conf 999999973-79978985099789973789889999997549 Q 537021.9.peg.8 58 SIAKALLKR-FATLGGVFGAPLHLLQEINRIGKRVALELKLV 98 (148) Q Consensus 58 ~lA~~lL~~-fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~ 98 (148) ..|+.|-+. |.++..|..+++++|..|+|||..+|..|... T Consensus 18 ~~a~~L~~aGi~TvedLa~a~~~eL~~i~Gi~~~~A~~ii~~ 59 (70) T 1wcn_A 18 DLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMA 59 (70) T ss_dssp HHHHHHHTTTCCSHHHHHTSCHHHHHTSSSCCHHHHHHHHHH T ss_pred HHHHHHHHCCCCCHHHHHHHCHHHHHHHCCCCHHHHHHHHHH T ss_conf 999999996997599998729999976517999999999999 No 14 >>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=0.25 Score=29.01 Aligned_cols=40 Identities=25% Similarity=0.210 Sum_probs=32.2 Q ss_pred HHHHHHHHHCCC---HHHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 999999973799---7898509978997378988999999754 Q 537021.9.peg.8 58 SIAKALLKRFAT---LGGVFGAPLHLLQEINRIGKRVALELKL 97 (148) Q Consensus 58 ~lA~~lL~~fGs---L~~ll~as~~eL~~i~GIG~aka~~l~a 97 (148) -+|-.+|..|+- ...+.+.+...|+++||||+..|-+|.. T Consensus 20 k~Al~iLs~~~~~el~~aI~~~D~~~L~~ipGIG~KtA~rii~ 62 (75) T 2ztd_A 20 RLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVL 62 (75) T ss_dssp HHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHH T ss_pred HHHHHHHCCCCHHHHHHHHHCCCHHHHHCCCCCCHHHHHHHHH T ss_conf 6662322157767777888536889985088835688999999 No 15 >>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:66-144) Probab=91.91 E-value=0.29 Score=28.53 Aligned_cols=46 Identities=24% Similarity=0.297 Sum_probs=35.2 Q ss_pred HHHHHHHHHCCC---HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 999999973799---789850997899737898899999975499999999 Q 537021.9.peg.8 58 SIAKALLKRFAT---LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRI 105 (148) Q Consensus 58 ~lA~~lL~~fGs---L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~ 105 (148) -+|-.+|..|+- ...+.+.+.+.|+++||||+..|-+|. .||-.++ T Consensus 19 k~Al~iLs~~~~~el~~aI~~~D~~~L~~ipGIG~KtAerii--~eLk~K~ 67 (79) T 1cuk_A 19 KLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLI--VEMKDRF 67 (79) T ss_dssp HHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHH--HHHHHHG T ss_pred HHHHHHHCCCCHHHHHHHHHHCCHHHHHHCCCCCHHHHHHHH--HHHHHHH T ss_conf 999999757999999999992899998419998899999999--9999888 No 16 >>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} (A:1-49) Probab=91.31 E-value=0.13 Score=30.76 Aligned_cols=32 Identities=31% Similarity=0.510 Sum_probs=25.5 Q ss_pred CCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHH Q ss_conf 799898899999999737997898509978997 Q 537021.9.peg.8 50 LIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQ 82 (148) Q Consensus 50 g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~ 82 (148) |.|+-.. ..|+.|+++|||+.++.+||.+||+ T Consensus 18 ~I~gVG~-~~ak~Ll~~Fgsi~~i~~As~eeL~ 49 (49) T 1x2i_A 18 GLPHVSA-TLARRLLKHFGSVERVFTASVAELM 49 (49) T ss_dssp TSTTCCH-HHHHHHHHHHCSHHHHHHCCHHHHT T ss_pred CCCCCCH-HHHHHHHHHCCHHHHHHHCCHHHHH T ss_conf 8999789-9999999970628888626798886 No 17 >>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=91.20 E-value=0.68 Score=26.16 Aligned_cols=64 Identities=14% Similarity=0.196 Sum_probs=50.5 Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHC---CCCCHHHHHHHHHHHHHHHH Q ss_conf 99999973379989889999999973799789850997899737---89889999997549999999 Q 537021.9.peg.8 41 EILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEI---NRIGKRVALELKLVSVASQR 104 (148) Q Consensus 41 ELLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i---~GIG~aka~~l~a~~El~rR 104 (148) -|++.+|...+....+..+..++.+.||+...+..++.+++... -|....||..|..+.+.-.. T Consensus 10 ~Lv~~Il~qq~s~~~a~~~~~~l~~~~~~~~~l~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~~~~ 76 (111) T 1kea_A 10 ILITEILLRRTTAGHVKKIYDKFFVKYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVIN 76 (111) T ss_dssp HHHHHHHTTTSCHHHHHHHHHHHHHHCCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 9999999831969999999999999788999998399889999989768899999999999998887 No 18 >>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=91.04 E-value=0.013 Score=37.19 Aligned_cols=69 Identities=13% Similarity=-0.070 Sum_probs=44.1 Q ss_pred HHHHHHCCHHHCCHHHHHHHHHHCCCC-----CCCHHHHHHHHHHHCCCHHHHHCCC----HHHHHHCCCCCHHHHHHHH Q ss_conf 999982392218989999999733799-----8988999999997379978985099----7899737898899999975 Q 537021.9.peg.8 26 RDRFLQKGENALAYYEILELILFRLIP-----RKDTKSIAKALLKRFATLGGVFGAP----LHLLQEINRIGKRVALELK 96 (148) Q Consensus 26 RErll~~G~~~LsD~ELLallL~~g~~-----~~~~~~lA~~lL~~fGsL~~ll~as----~~eL~~i~GIG~aka~~l~ 96 (148) -.||.+. ....+..++.+++-..|.. -+....+|+.+.++++ ..+.+.+ .++|+++||||+..|-.++ T Consensus 29 ~~~l~~~-~~~~~~~~~~~~~~~~g~~~~~~ka~~l~~~a~~~~~~~~--~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l 105 (113) T 3fhf_A 29 QKEIGDG-FLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDI--VESFENEKVAREFLVRNIKGIGYKEASHFL 105 (113) T ss_dssp HHHHTTH-HHHSCHHHHHHHHHHTTCTTHHHHHHHHHHHGGGCCHHHH--HHHSSSHHHHHHHHHHHSTTCCHHHHHHHH T ss_pred HHHHHHH-HHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH--HHHCCCCCCCHHHHHHHCCCCCHHHHHHHH T ss_conf 9999999-8718976799999994524667889999999999988767--776068897639999878583299999999 Q ss_pred H Q ss_conf 4 Q 537021.9.peg.8 97 L 97 (148) Q Consensus 97 a 97 (148) . T Consensus 106 ~ 106 (113) T 3fhf_A 106 R 106 (113) T ss_dssp H T ss_pred H T ss_conf 9 No 19 >>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} (A:149-197) Probab=90.71 E-value=0.18 Score=29.97 Aligned_cols=31 Identities=26% Similarity=0.405 Sum_probs=23.9 Q ss_pred CCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHH Q ss_conf 99898899999999737997898509978997 Q 537021.9.peg.8 51 IPRKDTKSIAKALLKRFATLGGVFGAPLHLLQ 82 (148) Q Consensus 51 ~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~ 82 (148) .|+..- .-++.||.+|||+.++..||.+||. T Consensus 19 IpGIG~-k~~~~LL~~FgSi~~i~~As~eeLa 49 (49) T 2bgw_A 19 FPGIGR-RTAERILERFGSLERFFTASKAEIS 49 (49) T ss_dssp STTCCH-HHHHHHHHHHSSHHHHTTCCHHHHH T ss_pred CCCCCH-HHHHHHHHHCCCHHHHHHCCHHHHH T ss_conf 568997-8999999986999999858999996 No 20 >>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} (A:28-137) Probab=90.62 E-value=0.26 Score=28.86 Aligned_cols=60 Identities=18% Similarity=0.319 Sum_probs=30.0 Q ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHH-CCCCCH--HHHHHHHHHHHH Q ss_conf 999997337998988999999997379978985099789973-789889--999997549999 Q 537021.9.peg.8 42 ILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQE-INRIGK--RVALELKLVSVA 101 (148) Q Consensus 42 LLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~-i~GIG~--aka~~l~a~~El 101 (148) |++.+|...++...+..+-.+|.++||+...+..++.+++.. ++++|- .|+..|..+.+. T Consensus 10 Li~~Il~Qqt~~~~a~~~~~~l~~~~~~~~~~~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~ 72 (110) T 1orn_A 10 LIAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAM 72 (110) T ss_dssp HHHHHHHTTSCHHHHHHHHHHHHHHCCSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHHH T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHCCCCHHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHH T ss_conf 999999810869999999999986049989986078999999999732499999999998789 No 21 >>1szp_A DNA repair protein RAD51; homologous recombination, asymmetry, RAD51 filament, DNA binding protein; HET: DNA; 3.25A {Saccharomyces cerevisiae} (A:26-81) Probab=90.56 E-value=0.3 Score=28.44 Aligned_cols=30 Identities=33% Similarity=0.138 Sum_probs=26.6 Q ss_pred CHHHHHCCCHHHHHHCCCCCHHHHHHHHHH Q ss_conf 978985099789973789889999997549 Q 537021.9.peg.8 69 TLGGVFGAPLHLLQEINRIGKRVALELKLV 98 (148) Q Consensus 69 sL~~ll~as~~eL~~i~GIG~aka~~l~a~ 98 (148) ++.++..+++.+|+.|+||+++|+..|..+ T Consensus 2 Tve~ia~at~k~L~~ikGisE~ka~KIi~a 31 (56) T 1szp_A 2 TAEAVAYAPRKDLLEIKGISEAKADKLLNE 31 (56) T ss_dssp SHHHHHHSCSHHHHTSTTCCHHHHHHHHHH T ss_pred CHHHHHCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 399997389999987639999999999999 No 22 >>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=89.95 E-value=1.5 Score=23.88 Aligned_cols=65 Identities=14% Similarity=0.063 Sum_probs=51.2 Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHH-C--CCCCHHHHHHHHHHHHHHHHH Q ss_conf 9999997337998988999999997379978985099789973-7--898899999975499999999 Q 537021.9.peg.8 41 EILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQE-I--NRIGKRVALELKLVSVASQRI 105 (148) Q Consensus 41 ELLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~-i--~GIG~aka~~l~a~~El~rR~ 105 (148) -|+..+|...+....+..+-.+|.++||+...+..++..+|.. + -|....|+..+.++.++.... T Consensus 9 ~Li~~Il~q~~s~~~a~~~~~rl~~~~~t~~~~~~~~~~~l~~~l~~~g~~~~k~~~i~~~~~~~~~~ 76 (110) T 3fsp_A 9 VWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRY 76 (110) T ss_dssp HHHHHHHTTTSCHHHHHHHHHHHHHHCCSHHHHHTSCHHHHHHTTTTSSCTHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH T ss_conf 99999986108788999999999997799999977899999999872671999999999899986863 No 23 >>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=89.88 E-value=0.85 Score=25.53 Aligned_cols=41 Identities=22% Similarity=0.184 Sum_probs=34.3 Q ss_pred HHHHHHHC--CCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 99999737--997898509978997378988999999754999 Q 537021.9.peg.8 60 AKALLKRF--ATLGGVFGAPLHLLQEINRIGKRVALELKLVSV 100 (148) Q Consensus 60 A~~lL~~f--GsL~~ll~as~~eL~~i~GIG~aka~~l~a~~E 100 (148) +.+.|.+. ..++.|...+.++|.+++|+|+...-+|....+ T Consensus 21 ~~n~L~~agI~ti~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~ 63 (84) T 1lb2_B 21 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 63 (84) T ss_dssp HHHHHHHTTCCBHHHHHTCCHHHHHHSTTCCHHHHHHHHHHHH T ss_pred HHHHHHHHCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 9999989189469998728999997488987889999999999 No 24 >>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} (B:) Probab=89.86 E-value=0.83 Score=25.61 Aligned_cols=42 Identities=17% Similarity=0.145 Sum_probs=35.5 Q ss_pred HHHHHHHHC--CCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 999999737--997898509978997378988999999754999 Q 537021.9.peg.8 59 IAKALLKRF--ATLGGVFGAPLHLLQEINRIGKRVALELKLVSV 100 (148) Q Consensus 59 lA~~lL~~f--GsL~~ll~as~~eL~~i~GIG~aka~~l~a~~E 100 (148) -|.+.|.+. .+++.|...+.+||.+|+|+|+...-+|..+.+ T Consensus 19 R~~N~L~~~gI~ti~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~ 62 (73) T 1z3e_B 19 RSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLE 62 (73) T ss_dssp HHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHH T ss_pred HHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 99999988389479999877999997588976605999999999 No 25 >>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} (B:) Probab=89.80 E-value=0.57 Score=26.65 Aligned_cols=42 Identities=17% Similarity=0.145 Sum_probs=35.3 Q ss_pred HHHHHHHHC--CCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 999999737--997898509978997378988999999754999 Q 537021.9.peg.8 59 IAKALLKRF--ATLGGVFGAPLHLLQEINRIGKRVALELKLVSV 100 (148) Q Consensus 59 lA~~lL~~f--GsL~~ll~as~~eL~~i~GIG~aka~~l~a~~E 100 (148) -+.+.|.+. .+++.|...+.++|.+|+|+|+...-+|+...+ T Consensus 26 R~~n~L~~~gI~tv~dL~~~s~~dLl~i~nlG~ksl~EI~~~L~ 69 (79) T 3gfk_B 26 RSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLE 69 (79) T ss_dssp HHHHHHHHTTCCBHHHHTTCCHHHHTTSTTCHHHHHHHHHHHHH T ss_pred HHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 99999989189679999878999998578986736999999999 No 26 >>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} (A:28-137) Probab=89.74 E-value=0.87 Score=25.49 Aligned_cols=60 Identities=12% Similarity=0.112 Sum_probs=46.7 Q ss_pred HHCCHHHHHHHHHHCCCC---CCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 218989999999733799---898899999999737997898509978997378988999999754 Q 537021.9.peg.8 35 NALAYYEILELILFRLIP---RKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKL 97 (148) Q Consensus 35 ~~LsD~ELLallL~~g~~---~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a 97 (148) ...+..|+.+.+-..|.+ -....++|+.+.+.+++ -.....++|++++|||+..|..++. T Consensus 42 ~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~~~~~~~~---~~~~~~~~L~~l~GIG~~ta~~~ll 104 (110) T 1orn_A 42 IAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNG---EVPRDRDELMKLPGVGRKTANVVVS 104 (110) T ss_dssp HSSCHHHHHHHTGGGSSHHHHHHHHHHHHHHHHHHSTT---SCCSCHHHHTTSTTCCHHHHHHHHH T ss_pred HCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCC---CCCCCHHHHHHCCCCCHHHHHHHHH T ss_conf 60789999999997324999999999987899999399---8988899997587975258999999 No 27 >>1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} (A:1-129) Probab=89.20 E-value=1.1 Score=24.70 Aligned_cols=63 Identities=13% Similarity=0.101 Sum_probs=51.9 Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHH-CCCCC--HHHHHHHHHHHHHH Q ss_conf 99999997337998988999999997379978985099789973-78988--99999975499999 Q 537021.9.peg.8 40 YEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQE-INRIG--KRVALELKLVSVAS 102 (148) Q Consensus 40 ~ELLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~-i~GIG--~aka~~l~a~~El~ 102 (148) .-|+..+|...+....+..+-++|..+||+...+..++..++.. ++.+| ..|+..|..+.+.. T Consensus 33 e~Li~~Il~Qq~s~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~G~~~~Ka~~i~~~a~~~ 98 (129) T 1ngn_A 33 KLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEY 98 (129) T ss_dssp HHHHHHHHHTTSCHHHHHHHHHHHHHHSCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 999999998618699999999999998879999971675868989812447999999999998246 No 28 >>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} (A:) Probab=88.64 E-value=0.81 Score=25.67 Aligned_cols=41 Identities=24% Similarity=0.210 Sum_probs=34.6 Q ss_pred HHHHHHHCC--CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 999997379--97898509978997378988999999754999 Q 537021.9.peg.8 60 AKALLKRFA--TLGGVFGAPLHLLQEINRIGKRVALELKLVSV 100 (148) Q Consensus 60 A~~lL~~fG--sL~~ll~as~~eL~~i~GIG~aka~~l~a~~E 100 (148) |.+.|.+.| .++.|...+.++|++|+|+|+...-.|....+ T Consensus 35 s~N~Lk~~gI~ti~dL~~~s~~dLl~i~n~G~kSl~Ei~~~L~ 77 (98) T 1coo_A 35 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 77 (98) T ss_dssp THHHHHTTTCCBHHHHHTSCHHHHTTSTTCCHHHHHHHHHHHH T ss_pred HHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 9989999399759999858999998677987878999999999 No 29 >>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=87.04 E-value=0.71 Score=26.04 Aligned_cols=32 Identities=22% Similarity=0.160 Sum_probs=25.5 Q ss_pred HHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHH Q ss_conf 85099789973789889999997549999999 Q 537021.9.peg.8 73 VFGAPLHLLQEINRIGKRVALELKLVSVASQR 104 (148) Q Consensus 73 ll~as~~eL~~i~GIG~aka~~l~a~~El~rR 104 (148) +-.|+.++|+.++|||+.+|..|....+-.-+ T Consensus 4 iN~A~~~~L~~lpgig~~~A~~Ii~~R~~~G~ 35 (70) T 3bzc_A 4 VNTASAALLARISGLNSTLAQNIVAHRDANGA 35 (70) T ss_dssp TTTCCHHHHHTSTTCCHHHHHHHHHHHHHHCC T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCC T ss_conf 68754888866069788999999999996699 No 30 >>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=86.21 E-value=0.96 Score=25.20 Aligned_cols=33 Identities=18% Similarity=0.077 Sum_probs=26.2 Q ss_pred HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 789850997899737898899999975499999 Q 537021.9.peg.8 70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVAS 102 (148) Q Consensus 70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~ 102 (148) .-++-.|+.++|++++|||+.+|..|..-.+.. T Consensus 31 ~idiNtAs~~eL~~lpgig~~~A~~Ii~~R~~~ 63 (98) T 2edu_A 31 LDLLNEGSARDLRSLQRIGPKKAQLIVGWRELH 63 (98) T ss_dssp HHHHHHSCHHHHHHSTTCCHHHHHHHHHHHHHH T ss_pred CCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHC T ss_conf 441357999999757898999999999999985 No 31 >>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} (B:1-67) Probab=85.48 E-value=0.63 Score=26.37 Aligned_cols=31 Identities=23% Similarity=0.280 Sum_probs=24.5 Q ss_pred CCCCHHHHHHHHHHHCCCHHHHHCCCHHHHH Q ss_conf 9898899999999737997898509978997 Q 537021.9.peg.8 52 PRKDTKSIAKALLKRFATLGGVFGAPLHLLQ 82 (148) Q Consensus 52 ~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~ 82 (148) .+.=-+.=|-.|+..||||.++++|+.++|. T Consensus 37 ir~VNKTDa~tLls~FgSl~~ii~As~e~Ls 67 (67) T 2a1j_B 37 VKSVNKTDSQTLLTTFGSLEQLIAASREDLA 67 (67) T ss_dssp STTCCHHHHHHHHHHHSSHHHHHSCCHHHHH T ss_pred CCCCCHHHHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 9985999999999991893465553043787 No 32 >>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} (A:) Probab=85.04 E-value=0.74 Score=25.92 Aligned_cols=32 Identities=19% Similarity=0.036 Sum_probs=24.7 Q ss_pred HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 78985099789973789889999997549999 Q 537021.9.peg.8 70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVA 101 (148) Q Consensus 70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El 101 (148) .-++-.|+.++|++++|||+..|..|..-.++ T Consensus 18 ~idiNtA~~~~L~~lpGig~~~A~~Ii~~R~f 49 (75) T 2duy_A 18 PVSLNEASLEELXALPGIGPVLARRIVEGRPY 49 (75) T ss_dssp SEETTTCCHHHHTTSTTCCHHHHHHHHHTCCC T ss_pred CEECCCCCHHHHHHCCCCCHHHHHHHHHCCCC T ss_conf 70061287999977789899999999986898 No 33 >>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=85.03 E-value=0.54 Score=26.80 Aligned_cols=61 Identities=11% Similarity=0.087 Sum_probs=43.5 Q ss_pred HHHCCHHHHHHHHHHCCCCCC---CHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 221898999999973379989---8899999999737997898509978997378988999999754 Q 537021.9.peg.8 34 ENALAYYEILELILFRLIPRK---DTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKL 97 (148) Q Consensus 34 ~~~LsD~ELLallL~~g~~~~---~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a 97 (148) ...++..||.+++-..|..+. ....+|+.+.+.+++ =.....++|++++|||+..|-.++. T Consensus 42 l~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~~~~~~~~---~~~~~~~~L~~l~GIG~~tA~~~ll 105 (111) T 1kea_A 42 ILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGG---RVPRNRKAILDLPGVGKYTCAAVMC 105 (111) T ss_dssp HHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHHHTT---SCCSCHHHHHTSTTCCHHHHHHHHH T ss_pred HHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHHCCCCCCHHHHHHHHH T ss_conf 983998899999897688999999999999988875159---9973046765089876168999999 No 34 >>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=84.87 E-value=0.52 Score=26.93 Aligned_cols=34 Identities=3% Similarity=-0.072 Sum_probs=25.4 Q ss_pred CCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 7997898509978997378988999999754999 Q 537021.9.peg.8 67 FATLGGVFGAPLHLLQEINRIGKRVALELKLVSV 100 (148) Q Consensus 67 fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~E 100 (148) .+..-++-.|+.++|++++|||+.+|..|..-.. T Consensus 21 ~~~~vdIN~As~~~L~~ipGig~~~A~~Iv~~gp 54 (104) T 3bz1_U 21 YGEKIDLNNTNIAAFIQYRGLYPTLAKLIVKNAP 54 (104) T ss_dssp BTTBEETTSSCGGGGGGSTTTTHHHHHHHHHSCC T ss_pred CCCCEECCCCCHHHHHHCCCCCHHHHHHHHHCCC T ss_conf 5885677228999997775869999999997089 No 35 >>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} (A:427-542) Probab=84.42 E-value=0.8 Score=25.71 Aligned_cols=37 Identities=27% Similarity=0.389 Sum_probs=27.8 Q ss_pred HHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHH Q ss_conf 99733799898899999999737997898509978997 Q 537021.9.peg.8 45 LILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQ 82 (148) Q Consensus 45 llL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~ 82 (148) ++...|.|+---. -|+.|+++|||+.++.+||.+||+ T Consensus 80 ~l~algI~giG~~-~ak~L~~~f~s~~~i~~As~eeL~ 116 (116) T 1dgs_A 80 LLYALGLPGVGEV-LARNLARRFGTMDRLLEASLEELI 116 (116) T ss_dssp HHHHTTCSSCCHH-HHHHHHHTTSBHHHHTTCCHHHHH T ss_pred HHHHCCCCCCCHH-HHHHHHHHCCCHHHHHCCCHHHHH T ss_conf 9997699754568-999998766899999728999995 No 36 >>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} (A:23-133) Probab=80.34 E-value=2 Score=23.11 Aligned_cols=54 Identities=11% Similarity=0.081 Sum_probs=23.3 Q ss_pred HHHHHHHHHCCCCC---CCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHH Q ss_conf 99999997337998---9889999999973799789850997899737898899999975 Q 537021.9.peg.8 40 YEILELILFRLIPR---KDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELK 96 (148) Q Consensus 40 ~ELLallL~~g~~~---~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~ 96 (148) .++.+.+=+.|..+ .....+|+.+++.+|+ -.....++|++++|||+..|..++ T Consensus 48 ~~~~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~---~~~~~~~~L~~l~GIG~~tA~~vl 104 (111) T 2abk_A 48 EGVKTYIKTIGLYNSKAENIIKTCRILLEQHNG---EVPEDRAALEALPGVGRKTANVVL 104 (111) T ss_dssp HHHHHHHTTSTTHHHHHHHHHHHHHHHHHHTTT---SCCSCHHHHHHSTTCCHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CHHHHHHHHHHHHHCCCHHHHHHH T ss_conf 667777674115677888999999999986041---136779999989860635999999 No 37 >>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=80.32 E-value=0.57 Score=26.66 Aligned_cols=30 Identities=3% Similarity=-0.136 Sum_probs=20.7 Q ss_pred CHHHHHCCCHHHHHHCCCCCHHHHHHHHHH Q ss_conf 978985099789973789889999997549 Q 537021.9.peg.8 69 TLGGVFGAPLHLLQEINRIGKRVALELKLV 98 (148) Q Consensus 69 sL~~ll~as~~eL~~i~GIG~aka~~l~a~ 98 (148) ..-++-.|+.++|++++|||+..|..|..- T Consensus 6 ~~vdiN~A~~~~L~~ipGig~~~A~~Iv~~ 35 (87) T 1s5l_U 6 EKIDLNNTNIAAFIQYRGLYPTLAKLIVKN 35 (87) T ss_dssp TSEETTTSCGGGGGGSTTCTHHHHHHHHHT T ss_pred CEEECCCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 704164078999977103469999999982 No 38 >>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; NMR {Homo sapiens} (A:) Probab=78.29 E-value=1.8 Score=23.43 Aligned_cols=39 Identities=28% Similarity=0.196 Sum_probs=31.3 Q ss_pred HHHHHHH-HCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 9999997-37997898509978997378988999999754 Q 537021.9.peg.8 59 IAKALLK-RFATLGGVFGAPLHLLQEINRIGKRVALELKL 97 (148) Q Consensus 59 lA~~lL~-~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a 97 (148) .|+.|-. .+-++..|..+++++|.++.|+|..+|..|.. T Consensus 37 ~~~~L~~~Gi~Tv~~la~~~~~~L~~i~G~~~~~a~~i~~ 76 (114) T 1b22_A 37 DVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILA 76 (114) T ss_dssp HHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHH T ss_pred HHHHHHHCCCCHHHHHHHCCHHHHHHHCCCCHHHHHHHHH T ss_conf 9999999698539999858999998620636999999999 No 39 >>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=77.81 E-value=3.7 Score=21.40 Aligned_cols=62 Identities=10% Similarity=-0.038 Sum_probs=47.3 Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH---HHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 9999997337998988999999997379978---9850997899737898899999975499999 Q 537021.9.peg.8 41 EILELILFRLIPRKDTKSIAKALLKRFATLG---GVFGAPLHLLQEINRIGKRVALELKLVSVAS 102 (148) Q Consensus 41 ELLallL~~g~~~~~~~~lA~~lL~~fGsL~---~ll~as~~eL~~i~GIG~aka~~l~a~~El~ 102 (148) -|+..+|..-+....+..+..+|.++||+.. ........++.+--|....||-.|+.+.+.. T Consensus 5 ~Li~~Ilsqqts~~~a~~~~~rl~~~~~~~~~~~~~~~~~~~~~ir~~G~~~~Ka~~i~~~a~~i 69 (77) T 2h56_A 5 SLVSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHV 69 (77) T ss_dssp HHHHHHHHTTSCHHHHHHHHHHHHHHHTSCCCCTHHHHTSCHHHHHHTTCCHHHHHHHHHHHHHH T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHHHCHHHHHHHHHHHH T ss_conf 99999981700399999999999998600236889986379999877764100016899999999 No 40 >>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} (A:) Probab=76.36 E-value=5.9 Score=20.11 Aligned_cols=40 Identities=25% Similarity=0.345 Sum_probs=33.8 Q ss_pred HHHHHHHH-HCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 99999997-37997898509978997378988999999754 Q 537021.9.peg.8 58 SIAKALLK-RFATLGGVFGAPLHLLQEINRIGKRVALELKL 97 (148) Q Consensus 58 ~lA~~lL~-~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a 97 (148) .+|+-|.. .|.|+-.+...+.++|..|.|...-.+..|+. T Consensus 17 ~iA~lLV~EGFtslEEiAyvp~~El~~IegfDee~a~eL~~ 57 (70) T 1u9l_A 17 DFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRE 57 (70) T ss_dssp HHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHH T ss_pred HHHHHHHHHCCCCHHHHHCCCHHHHHHHCCCCHHHHHHHHH T ss_conf 99999998465879998658999997600447999999999 No 41 >>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=76.05 E-value=0.99 Score=25.10 Aligned_cols=52 Identities=6% Similarity=-0.017 Sum_probs=37.8 Q ss_pred CHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC----HHHHHHHHHH Q ss_conf 978997378988999999754999999999987640677889----8999999999 Q 537021.9.peg.8 77 PLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTP----GQPCLISVER 128 (148) Q Consensus 77 s~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~l~s----~~~v~~yl~~ 128 (148) ....|..|||||++.+..|..-+.-..++..+...+-..+.- .+.+++|+.. T Consensus 2 ~~s~L~~IpgVG~~~a~~Ll~~f~Si~~i~~As~eeL~~i~gg~~~A~~i~~~l~~ 57 (63) T 2a1j_A 2 PQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHT 57 (63) T ss_dssp CCHHHHTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHHHSCHHHHHHHHHHHHC T ss_pred CHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCHHHHHHHHHHHCC T ss_conf 68888519998999999999980789999869999997785968999999999822 No 42 >>1d8b_A SGS1 RECQ helicase; five helices, three-helical bundle flanked by two helices, DNA binding protein; NMR {Saccharomyces cerevisiae} (A:) Probab=75.16 E-value=5.6 Score=20.25 Aligned_cols=41 Identities=5% Similarity=0.094 Sum_probs=32.5 Q ss_pred HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 78985099789973789889999997549999999999876 Q 537021.9.peg.8 70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANW 110 (148) Q Consensus 70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~ 110 (148) +....=.+.++|.+|+|+|+.++...-...+...++..++. T Consensus 39 ia~~~P~t~~eL~~i~G~~~~k~~~yG~~l~~I~~~~~e~~ 79 (81) T 1d8b_A 39 MAAILPMNDSAFATLGTVEDKYRRRFKYFKATIADLSKKRS 79 (81) T ss_dssp HHHHCCCSHHHHGGGSCCCHHHHHHGGGTHHHHHHHHHHTT T ss_pred HHHHCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99978999999817999999999999999999999999856 No 43 >>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:1-118) Probab=74.32 E-value=3.5 Score=21.59 Aligned_cols=48 Identities=17% Similarity=0.142 Sum_probs=37.0 Q ss_pred CCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 89889999999973799789850997899737898899999975499999 Q 537021.9.peg.8 53 RKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS 102 (148) Q Consensus 53 ~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~ 102 (148) +.-+..-|-..+..++ ..+-.++.+++.+++|||+..|..|.-..+-+ T Consensus 33 r~~aYr~Aa~~i~~l~--~~i~~~~~~~l~~lpGIG~~~a~kI~E~l~tG 80 (118) T 2w9m_A 33 KSRAYRSAARSLEELN--EETPELLAREFTGIPKVGKGIAAELSDFARSG 80 (118) T ss_dssp SHHHHHHHHHHHHSCC------------CCSSTTCCHHHHHHHHHHHHHS T ss_pred HHHHHHHHHHHHHHCC--CHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHC T ss_conf 8999999999999688--23667549886259998789999999999849 No 44 >>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} (A:) Probab=73.86 E-value=6.8 Score=19.70 Aligned_cols=57 Identities=16% Similarity=0.021 Sum_probs=44.2 Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHCC-CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 9999997337998988999999997379-9789850997899737898899999975499999 Q 537021.9.peg.8 41 EILELILFRLIPRKDTKSIAKALLKRFA-TLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS 102 (148) Q Consensus 41 ELLallL~~g~~~~~~~~lA~~lL~~fG-sL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~ 102 (148) |+....-..|..+..+..-|-+.|..++ -+ .+..++..++|||+.-+..|.=..+=+ T Consensus 24 ~la~~~~~~g~~r~~aY~kA~~slk~~p~pi-----~s~~~l~~lpgiG~~ia~kI~e~l~tg 81 (87) T 2kp7_A 24 EWRDEAASRGRHTRFVFQKALRSLQRYPLPL-----RSGKEAKILQHFGDRLCRMLDEKLKQH 81 (87) T ss_dssp HHHHHHHHHTCTTHHHHHHHHHHHHHCCSCC-----CSHHHHHTCTTTCHHHHHHHHHHHHHH T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHCCCCC-----CCHHHHHCCCCCCHHHHHHHHHHHHHH T ss_conf 9999999708468999999999999789887-----889998738998789999999999999 No 45 >>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=71.85 E-value=7.6 Score=19.40 Aligned_cols=33 Identities=18% Similarity=0.070 Sum_probs=24.2 Q ss_pred HHCCCHHHHHCCCHHH----HHHCCCCCHHHHHHHHH Q ss_conf 7379978985099789----97378988999999754 Q 537021.9.peg.8 65 KRFATLGGVFGAPLHL----LQEINRIGKRVALELKL 97 (148) Q Consensus 65 ~~fGsL~~ll~as~~e----L~~i~GIG~aka~~l~a 97 (148) ..-=++..+...+.+| |++++|||+..|-.+.. T Consensus 15 ~~~Ldl~~L~~l~~eea~~~L~~i~GIGpwTAdciLL 51 (58) T 3i0w_A 15 SANLNLEYIKSLNDNECHEELKKFMGVGPQVADCIML 51 (58) T ss_dssp HTTSCHHHHHHSCHHHHHHHHTTSTTCCHHHHHHHHH T ss_pred HHHCCHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 7457989973135446789998268812999999999 No 46 >>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix- hairpin-helix, HHH motif, three helix bundle; 2.30A {Methanopyrus kandleri} (A:472-519) Probab=70.19 E-value=8.2 Score=19.17 Aligned_cols=39 Identities=28% Similarity=0.335 Sum_probs=33.5 Q ss_pred HHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHH Q ss_conf 9999999973799789850997899737898899999975 Q 537021.9.peg.8 57 KSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELK 96 (148) Q Consensus 57 ~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~ 96 (148) .+-|.+||+.||+.+.+-.|..++|.. .|+.++....++ T Consensus 7 reraerllkkyggyskvreagveelre-dgltdaqirelk 45 (48) T 2csb_A 7 RERAERLLKKYGGYSKVREAGVEELRE-DGLTDAQIRELK 45 (48) T ss_dssp HHHHHHHHHHHTSHHHHHTSCHHHHHH-TTCCHHHHHHHH T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHH-CCCCHHHHHHHC T ss_conf 899999999837805888850899987-577488888750 No 47 >>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=65.51 E-value=8.3 Score=19.16 Aligned_cols=43 Identities=21% Similarity=0.297 Sum_probs=32.5 Q ss_pred HHHHHHHHHHCC--------------CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 999999997379--------------97898509978997378988999999754999 Q 537021.9.peg.8 57 KSIAKALLKRFA--------------TLGGVFGAPLHLLQEINRIGKRVALELKLVSV 100 (148) Q Consensus 57 ~~lA~~lL~~fG--------------sL~~ll~as~~eL~~i~GIG~aka~~l~a~~E 100 (148) ..+..+|.++|| +...|..+++++|..+ |+|-.||..|..+.+ T Consensus 73 ~sIi~RLve~yGe~Ie~~g~~~yaFPTPEqLA~as~EeLRac-GlsyRKA~YI~~lAq 129 (134) T 2jhn_A 73 EKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEGLREC-GLSRRKAELIVEIAK 129 (134) T ss_dssp HHHHHHHHHHHSCEEEETTEEEECCCCHHHHHHHHHHHHHHT-TCCHHHHHHHHHHHT T ss_pred HHHHHHHHHHHCCCCCCCCHHHCCCCCHHHHHCCCHHHHHHH-CCCCHHHHHHHHCCC T ss_conf 999999999855755666213215589999974999998541-023004566552011 No 48 >>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} (A:1-129) Probab=65.23 E-value=4.9 Score=20.63 Aligned_cols=25 Identities=12% Similarity=0.142 Sum_probs=14.7 Q ss_pred CHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 9789973789889999997549999 Q 537021.9.peg.8 77 PLHLLQEINRIGKRVALELKLVSVA 101 (148) Q Consensus 77 s~~eL~~i~GIG~aka~~l~a~~El 101 (148) +.+++..++|||+.-+..|.-..+- T Consensus 59 s~~~~~~lpgIG~~ia~~I~E~l~t 83 (129) T 2ihm_A 59 SLSQLHGLPYFGEHSTRVIQELLEH 83 (129) T ss_dssp SGGGGTTCTTCCHHHHHHHHHHHHH T ss_pred CHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 9999835999778999999999970 No 49 >>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=64.12 E-value=5.8 Score=20.17 Aligned_cols=21 Identities=24% Similarity=0.306 Sum_probs=17.2 Q ss_pred CHHHHHHCCCCCHHHHHHHHH Q ss_conf 978997378988999999754 Q 537021.9.peg.8 77 PLHLLQEINRIGKRVALELKL 97 (148) Q Consensus 77 s~~eL~~i~GIG~aka~~l~a 97 (148) ..++|++++|||+..|..+.. T Consensus 59 ~~~~LlsLPGIGpkTA~~ILl 79 (156) T 2h56_A 59 VIEKLTAIKGIGQWTAEXFXX 79 (156) T ss_dssp HHHHHHTSTTCCHHHHHHHHH T ss_pred HHHHHHHCCCCCHHHHHHHHH T ss_conf 888888738978789999998 No 50 >>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} (A:1-119) Probab=62.34 E-value=5.4 Score=20.35 Aligned_cols=42 Identities=7% Similarity=0.199 Sum_probs=26.2 Q ss_pred HHHHHHHHHHHCC-CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 8999999997379-9789850997899737898899999975499999 Q 537021.9.peg.8 56 TKSIAKALLKRFA-TLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS 102 (148) Q Consensus 56 ~~~lA~~lL~~fG-sL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~ 102 (148) +..-|-..|..+. .+ .+.+++.+++|||+.-+..|.-..+-+ T Consensus 38 aY~rAa~~l~~~p~~i-----~s~~~~~~lpgiG~~ia~~I~e~l~tG 80 (119) T 2fmp_A 38 AYRKAASVIAKYPHKI-----KSGAEAKKLPGVGTKIAEKIDEFLATG 80 (119) T ss_dssp HHHHHHHHHHHCSSCC-----CCHHHHHTSTTCCHHHHHHHHHHHHHS T ss_pred HHHHHHHHHHHCCCCC-----CCHHHHHCCCCCCHHHHHHHHHHHHCC T ss_conf 9999999998599554-----789998479996489999999999648 No 51 >>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=59.85 E-value=7.7 Score=19.38 Aligned_cols=38 Identities=24% Similarity=0.227 Sum_probs=24.1 Q ss_pred HHHHHHHHHCCCHHHHHCC-CHHHHHHCCCCCHHHHHHHH Q ss_conf 9999999737997898509-97899737898899999975 Q 537021.9.peg.8 58 SIAKALLKRFATLGGVFGA-PLHLLQEINRIGKRVALELK 96 (148) Q Consensus 58 ~lA~~lL~~fGsL~~ll~a-s~~eL~~i~GIG~aka~~l~ 96 (148) .+|+.+++.- .|..+-+. =.++|.+++|||+..|-... T Consensus 10 ~~~~~~~~~~-~L~~m~Deevi~~Lt~IkGIG~WTAem~L 48 (55) T 2jhn_A 10 GIAKAIIQQQ-ELKEWGEEEAYEYLTSFKGIGRWTAELVL 48 (55) T ss_dssp HHHHHHHTTT-GGGGSCHHHHHHHHHTSTTCCHHHHHHHH T ss_pred HHHHHHHHCC-HHHHCCCHHHHHHHHHCCCCCHHHHHHHH T ss_conf 9999999751-31202431678898753782899999999 No 52 >>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} (A:105-231) Probab=58.98 E-value=13 Score=17.82 Aligned_cols=47 Identities=21% Similarity=0.203 Sum_probs=23.6 Q ss_pred CCCCCCHHHHHHHHHHHCCCHH--HHHCCCHHHHHHCCCCCHHHHHHHH Q ss_conf 7998988999999997379978--9850997899737898899999975 Q 537021.9.peg.8 50 LIPRKDTKSIAKALLKRFATLG--GVFGAPLHLLQEINRIGKRVALELK 96 (148) Q Consensus 50 g~~~~~~~~lA~~lL~~fGsL~--~ll~as~~eL~~i~GIG~aka~~l~ 96 (148) +.+-+....+|+.+++..-++. +=.....++|++++|||+..|-.+. T Consensus 72 ~~ka~~i~~~a~~~~~~~l~~~~~~~~~~~~~~L~~lpGIG~~tA~~vl 120 (127) T 1mpg_A 72 LKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFA 120 (127) T ss_dssp HHHHHHHHHHHHHHHHTCSCSSCCSCHHHHHHHHTTSTTCCHHHHHHHH T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHH T ss_conf 6589999999999982994213446789999999865897899999999 No 53 >>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=57.95 E-value=2.4 Score=22.57 Aligned_cols=41 Identities=24% Similarity=0.224 Sum_probs=32.7 Q ss_pred HHHHHHHC--CCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 99999737--997898509978997378988999999754999 Q 537021.9.peg.8 60 AKALLKRF--ATLGGVFGAPLHLLQEINRIGKRVALELKLVSV 100 (148) Q Consensus 60 A~~lL~~f--GsL~~ll~as~~eL~~i~GIG~aka~~l~a~~E 100 (148) +.+.|++- ..++.|+..+.+||.+++|+|....-+|+-..+ T Consensus 140 ~~n~Lk~a~I~ti~dL~~~s~~dL~~i~n~G~ksl~EI~~~L~ 182 (190) T 2a6h_A 140 VLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALE 182 (190) T ss_dssp ------------------------------------------- T ss_pred HHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHH T ss_conf 8867877589479998849999984599976055999999999 No 54 >>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} (A:1-23,A:110-225) Probab=57.14 E-value=7.7 Score=19.37 Aligned_cols=25 Identities=16% Similarity=0.190 Sum_probs=20.0 Q ss_pred CCCHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 0997899737898899999975499 Q 537021.9.peg.8 75 GAPLHLLQEINRIGKRVALELKLVS 99 (148) Q Consensus 75 ~as~~eL~~i~GIG~aka~~l~a~~ 99 (148) .-+..+|++++|||+..|.-|.+-. T Consensus 19 ~~~~~eL~~LpGIG~ktAd~Illfa 43 (139) T 1kg2_A 19 RKTLPEVAALPGVGRSTAGAILSLS 43 (139) T ss_dssp CCCSGHHHTSTTCCHHHHHHHHHHH T ss_pred CCCCCHHHCCCCCCHHHHHHHHHHH T ss_conf 9879998628987278999999984 No 55 >>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} (A:1-66) Probab=55.10 E-value=9.4 Score=18.80 Aligned_cols=19 Identities=26% Similarity=0.398 Sum_probs=15.8 Q ss_pred HHHHHHCCCCCHHHHHHHH Q ss_conf 7899737898899999975 Q 537021.9.peg.8 78 LHLLQEINRIGKRVALELK 96 (148) Q Consensus 78 ~~eL~~i~GIG~aka~~l~ 96 (148) +++|.++||||+..|..+. T Consensus 11 I~~l~~LPGIG~KsA~Rla 29 (66) T 1vdd_A 11 IRELSRLPGIGPKSAQRLA 29 (66) T ss_dssp HHHHHTSTTCCHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHH T ss_conf 9999678998899999999 No 56 >>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=52.95 E-value=16 Score=17.35 Aligned_cols=50 Identities=20% Similarity=0.116 Sum_probs=27.9 Q ss_pred HCCCCCC-CHHHHHHHHHHHCC-CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 3379989-88999999997379-9789850997899737898899999975499999 Q 537021.9.peg.8 48 FRLIPRK-DTKSIAKALLKRFA-TLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS 102 (148) Q Consensus 48 ~~g~~~~-~~~~lA~~lL~~fG-sL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~ 102 (148) ..|.+.+ .+..-|-..|..++ .+ .+.+++.+++|||+.-+..|.-..+-+ T Consensus 29 ~~g~~~r~~aY~kAa~~i~~lp~~I-----~s~~~~~~lpgIG~~ia~~I~E~l~tG 80 (128) T 2bcq_A 29 VQGDKWRALGYAKAINALKSFHKPV-----TSYQEACSIPGIGKRMAEKIIEILESG 80 (128) T ss_dssp HTTCHHHHHHHHHHHHHHHSCCSCC-----CCHHHHHTSTTCCHHHHHHHHHHHHSS T ss_pred HCCCCHHHHHHHHHHHHHHHCCCCC-----CCHHHHHCCCCCCHHHHHHHHHHHHCC T ss_conf 8499589999999999998598665-----899998279996489999999999739 No 57 >>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} (A:182-261) Probab=51.92 E-value=3.3 Score=21.76 Aligned_cols=37 Identities=14% Similarity=0.150 Sum_probs=19.1 Q ss_pred HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 7898509978997378988999999754999999999 Q 537021.9.peg.8 70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRIL 106 (148) Q Consensus 70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~ 106 (148) +..|..-+.+-.-.|+|||+.+|..|..-..--..+. T Consensus 13 ~~~L~GD~sD~ipGV~GIG~ktA~~Li~~~gsle~i~ 49 (80) T 1exn_A 13 LKAIXGDLGDNIRGVEGIGAKRGYNIIREFGNVLDII 49 (80) T ss_dssp HHHHHCBGGGTBCCCTTCCHHHHHHHHHHHCSHHHHH T ss_pred HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHH T ss_conf 9997198313689999767999999999959999999 No 58 >>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} (A:1-154) Probab=51.87 E-value=11 Score=18.26 Aligned_cols=41 Identities=15% Similarity=0.175 Sum_probs=27.7 Q ss_pred HHHHHHHHHHCC-CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 999999997379-9789850997899737898899999975499999 Q 537021.9.peg.8 57 KSIAKALLKRFA-TLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS 102 (148) Q Consensus 57 ~~lA~~lL~~fG-sL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~ 102 (148) ..-|-..|..++ .+ .+.+++.+++|||+.-+..|.-..+-+ T Consensus 62 Yr~Aa~~l~~~p~~I-----~s~~~l~~lpgIG~~ia~~I~E~l~tG 103 (154) T 1jms_A 62 FMRASSVLKSLPFPI-----TSMKDTEGIPCLGDKVKSIIEGIIEDG 103 (154) T ss_dssp HHHHHHHHHTCSSCC-----CSGGGGTTCSSCCHHHHHHHHHHHHHS T ss_pred HHHHHHHHHHCCCCC-----CCHHHHHCCCCCCHHHHHHHHHHHHHC T ss_conf 999999998599777-----999998379996499999999999969 No 59 >>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=50.98 E-value=8.6 Score=19.05 Aligned_cols=22 Identities=32% Similarity=0.277 Sum_probs=14.7 Q ss_pred HHHCCCCCHHHHHHHHHHHHHH Q ss_conf 9737898899999975499999 Q 537021.9.peg.8 81 LQEINRIGKRVALELKLVSVAS 102 (148) Q Consensus 81 L~~i~GIG~aka~~l~a~~El~ 102 (148) +..|+|||+.+|..|..-..-- T Consensus 18 ipGV~GIGpKtA~~li~~~~~l 39 (65) T 1a76_A 18 PGGVKGIGFKRAYELVRSGVAK 39 (65) T ss_dssp TTTTTTCCHHHHHHHHHHTCHH T ss_pred CCCCCCEEHHHHHHHHHHCCCH T ss_conf 5556856299999999972999 No 60 >>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=48.58 E-value=9.9 Score=18.65 Aligned_cols=24 Identities=17% Similarity=0.140 Sum_probs=14.3 Q ss_pred HHCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 737898899999975499999999 Q 537021.9.peg.8 82 QEINRIGKRVALELKLVSVASQRI 105 (148) Q Consensus 82 ~~i~GIG~aka~~l~a~~El~rR~ 105 (148) -.|+|||+.+|..|..-..-...+ T Consensus 18 pGV~GIG~ktA~~li~~~~sle~i 41 (68) T 1rxw_A 18 EGVKGVGVKKALNYIKTYGDIFRA 41 (68) T ss_dssp CCCTTCCHHHHHHHHHHHSSHHHH T ss_pred CCCCCCCHHHHHHHHHHHCCHHHH T ss_conf 899995789999999994999999 No 61 >>1r4t_A Exoenzyme S; EXOS, GAP, toxin, virulence factor, signal transduction; NMR {Pseudomonas aeruginosa} (A:) Probab=47.29 E-value=20 Score=16.63 Aligned_cols=72 Identities=19% Similarity=0.124 Sum_probs=48.1 Q ss_pred HHCCCCCCCHHHHHHHHHH---------HCCCHHH-----HHCCCHHHHHHCCCCCHHHHHHHHHH---HHHHHHHHHHH Q ss_conf 7337998988999999997---------3799789-----85099789973789889999997549---99999999987 Q 537021.9.peg.8 47 LFRLIPRKDTKSIAKALLK---------RFATLGG-----VFGAPLHLLQEINRIGKRVALELKLV---SVASQRILKAN 109 (148) Q Consensus 47 L~~g~~~~~~~~lA~~lL~---------~fGsL~~-----ll~as~~eL~~i~GIG~aka~~l~a~---~El~rR~~~~~ 109 (148) ++-+...+.....|..||+ .||+-++ |.+||+++|..+ +.+|..+ .+.-+|...+. T Consensus 63 i~~~s~~~~~~~~A~~LL~~~VggipfqQWGT~GG~as~~v~~AS~e~L~~a-------~~~l~~v~~eva~L~~~V~aE 135 (153) T 1r4t_A 63 IRAGSQVEESRIQAGRLLERSIGGIALQQWGTTGGAASQLVLDASPELRREI-------TDQLHQVMSEVALLRQAVESE 135 (153) T ss_dssp HHTTCSSHHHHHHHHHHHTSEETTEEGGGTTSSSSHHHHHHHHCSHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH T ss_pred HHCCCHHHHHHHHHHHHHHCCCCCCCHHHHHCCCHHHHHHHHHCCHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH T ss_conf 7404168889999999874643563198731333589999985599999999-------999999999999999999998 Q ss_pred HHHCCCCCCHHHHHHHH Q ss_conf 64067788989999999 Q 537021.9.peg.8 110 WSIKKFLTPGQPCLISV 126 (148) Q Consensus 110 ~~~~~~l~s~~~v~~yl 126 (148) +.. ..-..|.++.||- T Consensus 136 v~~-~~a~~~~~~~~~~ 151 (153) T 1r4t_A 136 VSR-VSADYPYDVPDYA 151 (153) T ss_dssp HHH-TC----------- T ss_pred HCC-CCCCCCCCCCCCC T ss_conf 718-8788987753332 No 62 >>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=46.10 E-value=12 Score=18.02 Aligned_cols=23 Identities=17% Similarity=0.128 Sum_probs=18.2 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 89973789889999997549999 Q 537021.9.peg.8 79 HLLQEINRIGKRVALELKLVSVA 101 (148) Q Consensus 79 ~eL~~i~GIG~aka~~l~a~~El 101 (148) -.|..|.|||+..|.+|.....+ T Consensus 17 ~aLt~i~GIG~~~A~~Ic~~~gi 39 (63) T 3i1m_M 17 IALTSIYGVGKTRSKAILAAAGI 39 (63) T ss_dssp HHGGGSTTCCHHHHHHHHTTTTC T ss_pred EEEECEECCCHHHHHHHHHHCCC T ss_conf 87534457389999999999198 No 63 >>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=45.14 E-value=10 Score=18.54 Aligned_cols=24 Identities=17% Similarity=0.191 Sum_probs=19.7 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 899737898899999975499999 Q 537021.9.peg.8 79 HLLQEINRIGKRVALELKLVSVAS 102 (148) Q Consensus 79 ~eL~~i~GIG~aka~~l~a~~El~ 102 (148) -.|..|.|||+..|.+|.....+. T Consensus 28 ~ALt~I~GIG~~~A~~Ic~~lgi~ 51 (88) T 2zkq_m 28 FAITAIKGVGRRYAHVVLRKADID 51 (88) T ss_dssp HHGGGSTTCCHHHHHHHHHHHTCC T ss_pred EEHHCCCCCCHHHHHHHHHHCCCC T ss_conf 603024662899999999982999 No 64 >>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=44.26 E-value=13 Score=17.82 Aligned_cols=19 Identities=26% Similarity=0.214 Sum_probs=12.4 Q ss_pred HHHCCCCCHHHHHHHHHHH Q ss_conf 9737898899999975499 Q 537021.9.peg.8 81 LQEINRIGKRVALELKLVS 99 (148) Q Consensus 81 L~~i~GIG~aka~~l~a~~ 99 (148) +..|+|||+.+|..|..-. T Consensus 18 i~GV~GiG~ktA~~li~~~ 36 (82) T 2izo_A 18 PDGIRGIGPERALKIIKKY 36 (82) T ss_dssp TTCSTTCCHHHHHHHHHHS T ss_pred CCCCCCCCHHHHHHHHHHC T ss_conf 3347994488999999983 No 65 >>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=42.09 E-value=7.1 Score=19.60 Aligned_cols=87 Identities=16% Similarity=0.029 Sum_probs=54.7 Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHCC-CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH-----------HHHHHH Q ss_conf 9999997337998988999999997379-9789850997899737898899999975499999-----------999998 Q 537021.9.peg.8 41 EILELILFRLIPRKDTKSIAKALLKRFA-TLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS-----------QRILKA 108 (148) Q Consensus 41 ELLallL~~g~~~~~~~~lA~~lL~~fG-sL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~-----------rR~~~~ 108 (148) ++.+.+-..|.+ ..+|..+.+.|| .--.++..+|-.|+.+.|||-.+|-.|..-..+. ...+.+ T Consensus 9 ~~~~~L~~~Gi~----~~~a~ki~~~yg~~a~~~i~~nPY~L~~i~gigF~~aD~iA~~~gi~~dd~~Ri~a~i~~~L~~ 84 (149) T 3e1s_A 9 RLLAGLQGLGLT----INQAQRAVKHFGADALDRLEKDLFTLTEVEGIGFLTADKLWQARGGALDDPRRLTAAAVYALQL 84 (149) T ss_dssp ---------------------------------------CGGGTSSSCCHHHHHTTC-------CCHHHHHHHHHHHHHH T ss_pred HHHHHHHHCCCC----HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH T ss_conf 999999877999----9999999999849999999949935541589995999999997698989999999999999999 Q ss_pred H-HHHCCCCCCHHHHHHHHHHHHC Q ss_conf 7-6406778898999999999845 Q 537021.9.peg.8 109 N-WSIKKFLTPGQPCLISVERHYP 131 (148) Q Consensus 109 ~-~~~~~~l~s~~~v~~yl~~~l~ 131 (148) . .......-..+.+..-+...++ T Consensus 85 ~~~~~Ght~l~~~~L~~~~~~lL~ 108 (149) T 3e1s_A 85 AGTQAGHSFLPRSRAEKGVVHYTR 108 (149) T ss_dssp HHHHTCCSCEEHHHHHHHHHHHHC T ss_pred HHHCCCCEEEEHHHHHHHHHHHHC T ss_conf 733489872149999999999867 No 66 >>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} (A:) Probab=40.52 E-value=15 Score=17.40 Aligned_cols=59 Identities=7% Similarity=-0.026 Sum_probs=36.4 Q ss_pred HHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHH Q ss_conf 98509978997378988999999754999999999987640677889--899999999984 Q 537021.9.peg.8 72 GVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTP--GQPCLISVERHY 130 (148) Q Consensus 72 ~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~l~s--~~~v~~yl~~~l 130 (148) ..-++....|..|+|||+.+|-.|....+-+.=...+...++..+.. .+.+.+=+...| T Consensus 125 ~~n~~i~~~L~~I~GiG~~~a~~Iie~Re~g~F~S~eDl~~Rv~~~~~~~~~l~~~~le~L 185 (205) T 2i5h_A 125 DSITTRMHQLELLPGVGKKMMWAIIEERKKRPFESFEDIAQRVKGIQRPEKLIVSRIIYEI 185 (205) T ss_dssp CCBCSSSBGGGGSTTCCHHHHHHHHHHHHHSCCCSHHHHHHHSTTCCCHHHHHHHHHHHHH T ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 8761878988744451589999999997548988999999885467789999999999996 No 67 >>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication; 2.00A {Pyrococcus furiosus} (A:212-288) Probab=39.83 E-value=17 Score=17.22 Aligned_cols=18 Identities=11% Similarity=0.023 Sum_probs=10.2 Q ss_pred HHHHHHHHHCCCHHHHHC Q ss_conf 999999973799789850 Q 537021.9.peg.8 58 SIAKALLKRFATLGGVFG 75 (148) Q Consensus 58 ~lA~~lL~~fGsL~~ll~ 75 (148) ..|-+|+++|||+.+++. T Consensus 37 ktA~kli~~~gsle~i~~ 54 (77) T 1b43_A 37 KKALEIVRHSKDPLAKFQ 54 (77) T ss_dssp HHHHHHHHTCSSGGGGTG T ss_pred HHHHHHHHHHCCHHHHHC T ss_conf 999999999599999752 No 68 >>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} (A:504-671) Probab=39.75 E-value=27 Score=15.88 Aligned_cols=58 Identities=21% Similarity=0.184 Sum_probs=44.7 Q ss_pred HHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHH Q ss_conf 97337998988999999997379978985099789973789889999997549999999 Q 537021.9.peg.8 46 ILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQR 104 (148) Q Consensus 46 lL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR 104 (148) |-..|.++. ....|+.|.+++++...+..++.+++..+.++++..+..+......... T Consensus 9 l~~l~i~~~-g~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 66 (168) T 2owo_A 9 LYALGIREV-GEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAEESN 66 (168) T ss_dssp HHHTTCTTC-CHHHHHHHHHHHCSHHHHHTCCHHHHTTSTTCCHHHHHHHHHHHTCHHH T ss_pred HHHHHCCCC-CCCHHHHHHCCCCCHHHHHCCCHHHHHCCCCHHHHHHHHHHHHHCCHHH T ss_conf 998631454-4320234310348899997089999867598019999999999759899 No 69 >>2e1f_A Werner syndrome ATP-dependent helicase; HRDC domain, hydrolase; 2.00A {Homo sapiens} (A:) Probab=39.62 E-value=27 Score=15.87 Aligned_cols=49 Identities=8% Similarity=0.072 Sum_probs=37.2 Q ss_pred HHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH Q ss_conf 8985099789973789889999997549999999999876406778898 Q 537021.9.peg.8 71 GGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTPG 119 (148) Q Consensus 71 ~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~l~s~ 119 (148) ....=.+.++|.+|+|+|+.+....-.......++........+.+..+ T Consensus 49 A~~~P~~~~~L~~i~g~~~~~~~~~g~~l~~i~~~~~~~~~~~~~~p~~ 97 (103) T 2e1f_A 49 AKMRPTTVENVKRIDGVSEGKAAMLAPLLEVIKHFCQTNSVQTDLFSST 97 (103) T ss_dssp HHHCCCSHHHHTTSTTCCHHHHHHTHHHHHHHHHHHHHTTCCCCCCCC- T ss_pred HHHCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 9809999999837899999999999999999999998759988766777 No 70 >>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=39.06 E-value=14 Score=17.72 Aligned_cols=24 Identities=29% Similarity=0.076 Sum_probs=19.3 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 899737898899999975499999 Q 537021.9.peg.8 79 HLLQEINRIGKRVALELKLVSVAS 102 (148) Q Consensus 79 ~eL~~i~GIG~aka~~l~a~~El~ 102 (148) -.|..|.|||+..|.+|.....+. T Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgi~ 40 (64) T 2vqe_M 17 VALTYIYGIGKARAKEALEKTGIN 40 (64) T ss_dssp HHHTTSSSCCSHHHHHHTTTTTCC T ss_pred EEEEEEECCCHHHHHHHHHHCCCC T ss_conf 873306581899999999982998 No 71 >>2dgz_A Werner syndrome protein variant; HRDC domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Probab=39.06 E-value=21 Score=16.49 Aligned_cols=46 Identities=9% Similarity=0.068 Sum_probs=35.4 Q ss_pred HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 7898509978997378988999999754999999999987640677 Q 537021.9.peg.8 70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKF 115 (148) Q Consensus 70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~ 115 (148) +....=.+.++|.+|+|||+.+....-....+..+.........+. T Consensus 55 iA~~~P~t~~~L~~i~g~~~~~~~~~g~~l~~I~~~~~~~~~~~p~ 100 (113) T 2dgz_A 55 MAKMRPTTVENVKRIDGVSEGKAAMLAPLWEVIKHFCQTNSVQTDL 100 (113) T ss_dssp HHHHCCCSHHHHHHSSSCCTTGGGGGHHHHHHHHHHHHTTTCCCCC T ss_pred HHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 9983249999994689989999999999999999999983998665 No 72 >>2r4f_A 3-hydroxy-3-methylglutaryl-coenzyme A reductase; oxidoreductase, cholesterol, biocynthesis, HMG-COA, NADPH, statin, alternative splicing; HET: RIE; 1.70A {Homo sapiens} PDB: 2q1l_A* 2q6c_A* 2q6b_A* 3bgl_A* 3cct_A* 3ccw_A* 3ccz_A* 3cd0_A* 3cd5_A* 3cd7_A* 3cda_A* 3cdb_A* 1dqa_A* 1dq9_A* 1dq8_A* 1hw8_A* 1hw9_A* 1hwi_A* 1hwj_A* 1hwk_A* ... (A:1-85) Probab=37.28 E-value=21 Score=16.50 Aligned_cols=29 Identities=31% Similarity=0.392 Sum_probs=22.7 Q ss_pred HHHHH---CCHHHCCHHHHHHHHHHCCCCCCC Q ss_conf 99982---392218989999999733799898 Q 537021.9.peg.8 27 DRFLQ---KGENALAYYEILELILFRLIPRKD 55 (148) Q Consensus 27 Erll~---~G~~~LsD~ELLallL~~g~~~~~ 55 (148) ..+++ .|+.+|+|.|++.++...-.|.+. T Consensus 15 ~~i~~~~~~~~~~lsDeEIi~lv~~g~Ip~Y~ 46 (85) T 2r4f_A 15 LQILGNAEKGAKFLSDAEIIQLVNAKHIPAYK 46 (85) T ss_dssp HHHHHSTTTGGGSSCHHHHHHHHHTTSSCGGG T ss_pred HHHHHCCCCCCCCCCHHHHHHHHHCCCCCHHH T ss_conf 99872633477779989999999759976066 No 73 >>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=36.37 E-value=21 Score=16.51 Aligned_cols=23 Identities=22% Similarity=0.267 Sum_probs=17.9 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 89973789889999997549999 Q 537021.9.peg.8 79 HLLQEINRIGKRVALELKLVSVA 101 (148) Q Consensus 79 ~eL~~i~GIG~aka~~l~a~~El 101 (148) -.|..|.|||...|.+|.....+ T Consensus 29 ~aLt~i~GIG~~~A~~I~~~~gi 51 (82) T 2zbk_B 29 FLVNEFQSIGDTTADKILELAGL 51 (82) T ss_dssp HHHTTSTTCCHHHHHHHHHHTTC T ss_pred HHHCCCCCCCHHHHHHHHHHHCC T ss_conf 55157646760877766655236 No 74 >>3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} (A:185-235) Probab=35.15 E-value=21 Score=16.52 Aligned_cols=34 Identities=26% Similarity=0.315 Sum_probs=26.6 Q ss_pred HHHHHCC--CHHHHHCCCHHHHHHCCCCCHHHHHHHHH Q ss_conf 9997379--97898509978997378988999999754 Q 537021.9.peg.8 62 ALLKRFA--TLGGVFGAPLHLLQEINRIGKRVALELKL 97 (148) Q Consensus 62 ~lL~~fG--sL~~ll~as~~eL~~i~GIG~aka~~l~a 97 (148) +-|++.| -|..+++.+..+|.++ ||.+||.-|.- T Consensus 9 ~kL~~lGInkL~Dil~~~f~klk~i--iG~aKa~YL~~ 44 (51) T 3bq0_A 9 RRLNELGIQKLRDILSKNYNELEKI--TGKAKALYLLK 44 (51) T ss_dssp HHHTTTTCCBGGGGGGSCHHHHHHH--HCHHHHHHHHH T ss_pred HHHHHCCCCCHHHHHHHHHHHHHHH--HCCCHHHHHHH T ss_conf 5545327874788876426678876--06403578897 No 75 >>1jei_A Emerin; membrane protein; NMR {Synthetic} (A:) Probab=34.96 E-value=13 Score=17.88 Aligned_cols=33 Identities=18% Similarity=0.170 Sum_probs=27.7 Q ss_pred HHHCCHHHHHHHHHHCCCCCCCHHHHHHHHHHH Q ss_conf 221898999999973379989889999999973 Q 537021.9.peg.8 34 ENALAYYEILELILFRLIPRKDTKSIAKALLKR 66 (148) Q Consensus 34 ~~~LsD~ELLallL~~g~~~~~~~~lA~~lL~~ 66 (148) ...|||.||.+-+..+|.+.-.+.+.-+.+..+ T Consensus 3 ~~~LSd~ELr~~L~~~G~~~GPIt~tTR~vy~k 35 (53) T 1jei_A 3 YADLSDTELTTLLRRYNIPHGPVVGSTRRLYEK 35 (53) T ss_dssp TTTCCHHHHHHHHSSSCCSCCCCCSGGGHHHHH T ss_pred HHHHCHHHHHHHHHHHCCCCCCCCCCHHHHHHH T ss_conf 656168999999999299988800613999999 No 76 >>2dla_A 397AA long hypothetical protein; helix bundle, twisted beta-sheet, replication; 2.90A {Pyrococcus horikoshii OT3} (A:1-105,A:194-222) Probab=33.40 E-value=14 Score=17.70 Aligned_cols=18 Identities=39% Similarity=0.560 Sum_probs=14.6 Q ss_pred HHHHHHHHCCCHHHHHCC Q ss_conf 999999737997898509 Q 537021.9.peg.8 59 IAKALLKRFATLGGVFGA 76 (148) Q Consensus 59 lA~~lL~~fGsL~~ll~a 76 (148) -|++|++.|||+..++++ T Consensus 11 kAk~LlkeFG~in~fLe~ 28 (134) T 2dla_A 11 KAKELLKGFGSINDFMDA 28 (134) T ss_dssp HHHHHTTTTSSHHHHHHH T ss_pred HHHHHHHHHCCHHHHHHH T ss_conf 999999985059999987 No 77 >>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=32.14 E-value=33 Score=15.28 Aligned_cols=20 Identities=15% Similarity=0.071 Sum_probs=10.9 Q ss_pred HHHHHCCCCCHHHHHHHHHH Q ss_conf 89973789889999997549 Q 537021.9.peg.8 79 HLLQEINRIGKRVALELKLV 98 (148) Q Consensus 79 ~eL~~i~GIG~aka~~l~a~ 98 (148) ..|++|+||++.+|..|... T Consensus 8 ~~L~qi~gvs~~~A~aI~~~ 27 (82) T 2ziu_A 8 RQLMQISGVSGDKAAAVLEH 27 (82) T ss_dssp HHHTTBTTCCHHHHHHHHHH T ss_pred HHHHCCCCCCHHHHHHHHHH T ss_conf 99980899999999999997 No 78 >>2rhf_A DNA helicase RECQ; HRDC, D. radiodurans, ATP-binding, hydrolase, nucleotide-binding; HET: DNA; 1.10A {Deinococcus radiodurans R1} (A:) Probab=29.72 E-value=38 Score=14.85 Aligned_cols=35 Identities=14% Similarity=0.078 Sum_probs=23.5 Q ss_pred HHHHCCCHHHHHHCCCCCHHHHHH-HHHHHHHHHHH Q ss_conf 898509978997378988999999-75499999999 Q 537021.9.peg.8 71 GGVFGAPLHLLQEINRIGKRVALE-LKLVSVASQRI 105 (148) Q Consensus 71 ~~ll~as~~eL~~i~GIG~aka~~-l~a~~El~rR~ 105 (148) ....-.+.++|.+|+|||+.++.. -..+.++.+.+ T Consensus 39 A~~~P~t~~eL~~i~gi~~~~~~~~G~~il~~i~~~ 74 (77) T 2rhf_A 39 AARQPRTLAELAEVPGLGEKRIEAYGERILDAINTV 74 (77) T ss_dssp HHHCCCSHHHHTTSTTTCHHHHHHHHHHHHHHHHHH T ss_pred HHCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 860934999973799989999999999999999998 No 79 >>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:119-241) Probab=26.20 E-value=44 Score=14.46 Aligned_cols=56 Identities=11% Similarity=-0.017 Sum_probs=41.8 Q ss_pred CHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEEE Q ss_conf 9789973789889999997549999999999876406778898999999999845978000 Q 537021.9.peg.8 77 PLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTPGQPCLISVERHYPMKNANN 137 (148) Q Consensus 77 s~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~l~s~~~v~~yl~~~l~~~~~E~ 137 (148) ..+.+.+++|+|+.....|+...+.... ...+..+.....+.+.+...+...+.|. T Consensus 11 ~~~~i~~l~gfG~K~~~~il~gl~~~~~-----~~~ri~~~ea~~~a~~i~~~l~~~~~~~ 66 (123) T 2w9m_A 11 ESGELAGLKGFGAKSAATILENVVFLFE-----ARQRQSLRAGLAVAEELAGALTDLSPAP 66 (123) T ss_dssp HHTTTTTSTTCCHHHHHHHHHHHHHHHH-----HCSSEEHHHHHHHHHHHHHHTGGGCCEE T ss_pred HCCCHHHHHCCCHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHCCCCEEEE T ss_conf 6088012110138899999987878887-----5356699999999999997544766997 No 80 >>5csm_A Chorismate mutase; chorismate pyruvatemutase, allosteric protein, complex (isomerase/peptide), transition state analog; HET: TRP; 2.00A {Saccharomyces cerevisiae} (A:) Probab=25.89 E-value=30 Score=15.52 Aligned_cols=37 Identities=14% Similarity=0.122 Sum_probs=28.1 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCHHH Q ss_conf 8988999999754999999999987640677-889899 Q 537021.9.peg.8 85 NRIGKRVALELKLVSVASQRILKANWSIKKF-LTPGQP 121 (148) Q Consensus 85 ~GIG~aka~~l~a~~El~rR~~~~~~~~~~~-l~s~~~ 121 (148) ..-|.+.++-+.|...|+||++..+..-... -++|+. T Consensus 138 ~NyGSta~cDi~cLQALSrRIHyGKFVAEaKF~~~p~~ 175 (256) T 5csm_A 138 NNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPL 175 (256) T ss_dssp TCHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHTCHHH T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH T ss_conf 31178999999999999988764346768776419999 No 81 >>1t6c_A Exopolyphosphatase; alpha/beta protein, actin-like fold, hydrolase; 1.53A {Aquifex aeolicus VF5} (A:137-298) Probab=25.52 E-value=34 Score=15.20 Aligned_cols=94 Identities=9% Similarity=-0.017 Sum_probs=55.8 Q ss_pred HHHHHHHHHCCHHHCCHHHHHHHHHHCCC----C--------CCCHHHHHHHHHHHC-----------------CC-HHH Q ss_conf 01999998239221898999999973379----9--------898899999999737-----------------99-789 Q 537021.9.peg.8 23 NRLRDRFLQKGENALAYYEILELILFRLI----P--------RKDTKSIAKALLKRF-----------------AT-LGG 72 (148) Q Consensus 23 ~R~RErll~~G~~~LsD~ELLallL~~g~----~--------~~~~~~lA~~lL~~f-----------------Gs-L~~ 72 (148) -|++|+|...++..-.+++.+.-.+.... . +-.+..+|+-..... -. ... T Consensus 35 vrl~e~f~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~ig~gGt~r~la~l~~~~~~~~~~~~~g~~i~~~~l~~~~~~ 114 (162) T 1t6c_A 35 VNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDT 114 (162) T ss_dssp HHHHHHHCCSSSCCHHHHHHHHHHHHHHHTTTCCCCSEEEEESHHHHHHHHHHTTCCSCCHHHHTTCEEEHHHHHHHHHH T ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHH T ss_conf 88999844689976789999999999997542033366999537446588887541347843342200126889999999 Q ss_pred HHCCCHHHH-HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 850997899-73789889999997549999999999876406778 Q 537021.9.peg.8 73 VFGAPLHLL-QEINRIGKRVALELKLVSVASQRILKANWSIKKFL 116 (148) Q Consensus 73 ll~as~~eL-~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~l 116 (148) +...+.++. .+++|+++..+-.|.+...+...+++.--.+...+ T Consensus 115 l~~~~~~e~~~~~~gl~~~Ra~~i~~g~~il~~l~~~~~~~~i~v 159 (162) T 1t6c_A 115 FKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDCLIV 159 (162) T ss_dssp HTTSCHHHHHHHSTTSCGGGTTTHHHHHHHHHHHHHHHTCSEEEE T ss_pred HHCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEE T ss_conf 972999999875589996899859999999999999719898999 No 82 >>3bqs_A Uncharacterized protein; 10114F, NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.42A {Listeria monocytogenes str} PDB: 3bqt_A (A:) Probab=24.79 E-value=23 Score=16.25 Aligned_cols=21 Identities=33% Similarity=0.400 Sum_probs=15.0 Q ss_pred CHHHHHHCCCCCHHHHHHHHH Q ss_conf 978997378988999999754 Q 537021.9.peg.8 77 PLHLLQEINRIGKRVALELKL 97 (148) Q Consensus 77 s~~eL~~i~GIG~aka~~l~a 97 (148) +..+|..+||||++.+..|.. T Consensus 2 a~~~l~~LPNiG~~~e~~L~~ 22 (93) T 3bqs_A 2 SLANLSELPNIGKVLEQDLIK 22 (93) T ss_dssp CCSCGGGSTTCCHHHHHHHHH T ss_pred CHHHHHHCCCCCHHHHHHHHH T ss_conf 757785689999999999998 No 83 >>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=23.53 E-value=50 Score=14.14 Aligned_cols=19 Identities=11% Similarity=0.167 Sum_probs=9.7 Q ss_pred HHHHHHHHHHCCCHHHHHC Q ss_conf 9999999973799789850 Q 537021.9.peg.8 57 KSIAKALLKRFATLGGVFG 75 (148) Q Consensus 57 ~~lA~~lL~~fGsL~~ll~ 75 (148) .+.|..+.++|.+...|+. T Consensus 24 ~~kA~aI~~~YPTp~~L~~ 42 (100) T 2ziu_B 24 LEMASAVVNAYPSPQLLVQ 42 (100) T ss_dssp HHHHHHHHHHSCSHHHHHH T ss_pred HHHHHHHHHHCCCHHHHHH T ss_conf 9999999997899999999 No 84 >>3cer_A Possible exopolyphosphatase-like protein; NESG, BLR13, Q8G5J2, X-RAY, structure, structural genomics, PSI-2; 2.40A {Bifidobacterium longum NCC2705} (A:142-326) Probab=23.04 E-value=28 Score=15.71 Aligned_cols=44 Identities=11% Similarity=-0.116 Sum_probs=34.6 Q ss_pred HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 78985099789973789889999997549999999999876406 Q 537021.9.peg.8 70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIK 113 (148) Q Consensus 70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~ 113 (148) +..+...+.++..+++|+.+..+-.|.+..-+...+.+.--.++ T Consensus 126 ~~~l~~~~~~~r~~~~gl~~~Rad~i~~g~~il~~l~~~~~~~~ 169 (185) T 3cer_A 126 DDKFLRXTRAERREYKTIHPGRIDVVGGGAVVWSRVLARVSEAA 169 (185) T ss_dssp HHHHHSSCHHHHHTCTTSCTTTTTTHHHHHHHHHHHHHHHHHHH T ss_pred HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99997799999975579897799989999999999999876520 No 85 >>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} (A:635-702) Probab=22.76 E-value=50 Score=14.11 Aligned_cols=35 Identities=14% Similarity=0.230 Sum_probs=21.9 Q ss_pred HHHHHHH-HCCCHHHHHCCCHHHHHHCCCCCHHHHHHHH Q ss_conf 9999997-3799789850997899737898899999975 Q 537021.9.peg.8 59 IAKALLK-RFATLGGVFGAPLHLLQEINRIGKRVALELK 96 (148) Q Consensus 59 lA~~lL~-~fGsL~~ll~as~~eL~~i~GIG~aka~~l~ 96 (148) -|+.|.+ .|.|+..+..++ +.+.++ ||+..|.+|. T Consensus 10 RAR~Ly~aGiks~~dla~ap-~~l~~~--iG~k~A~~I~ 45 (68) T 2p6r_A 10 RARKLYNAGIRNAEDIVRHR-EKVASL--IGRGIAERVV 45 (68) T ss_dssp HHHHHHTTTCCSHHHHHHTH-HHHHHH--HCHHHHHHHH T ss_pred HHHHHHHCCCCCHHHHHCCC-HHHHHH--HCCCHHHHHH T ss_conf 99999987999999997498-878977--6346389999 No 86 >>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=22.03 E-value=53 Score=13.95 Aligned_cols=26 Identities=23% Similarity=0.378 Sum_probs=14.0 Q ss_pred HHCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 73789889999997549999999999 Q 537021.9.peg.8 82 QEINRIGKRVALELKLVSVASQRILK 107 (148) Q Consensus 82 ~~i~GIG~aka~~l~a~~El~rR~~~ 107 (148) ..|+|||+.+|..|..-..=...+.. T Consensus 32 pGV~GIG~KtA~kLI~~ygsle~ii~ 57 (89) T 1ul1_X 32 ESIRGIGPKRAVDLIQKHKSIEEIVR 57 (89) T ss_dssp CCCTTCCHHHHHHHHHHSSSHHHHHT T ss_pred CCCCCCCHHHHHHHHHHCCCHHHHHH T ss_conf 55788569999999998099999999 No 87 >>1wud_A ATP-dependent DNA helicase RECQ; DNA-binding domain, HRDC, hydrolase; 2.20A {Escherichia coli} (A:) Probab=20.68 E-value=56 Score=13.77 Aligned_cols=37 Identities=11% Similarity=0.055 Sum_probs=26.1 Q ss_pred HHHHHCCCHHHHHHCCCCCHHHHHHH-HHHHHHHHHHH Q ss_conf 78985099789973789889999997-54999999999 Q 537021.9.peg.8 70 LGGVFGAPLHLLQEINRIGKRVALEL-KLVSVASQRIL 106 (148) Q Consensus 70 L~~ll~as~~eL~~i~GIG~aka~~l-~a~~El~rR~~ 106 (148) +....=.+.++|.+|.|+|+.++..- ..+.++..++. T Consensus 46 iA~~~P~t~~eL~~i~g~~~~~~~~yG~~il~~i~~~~ 83 (89) T 1wud_A 46 XAEQXPITASEXLSVNGVGXRKLERFGKPFXALIRAHV 83 (89) T ss_dssp HHHHCCCSHHHHHTSTTCCHHHHHHHHHHHHHHHHHHH T ss_pred HHHHCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 99978899999807999899999999999999999998 Done!