Query gi|254780239|ref|YP_003064652.1| 30S ribosomal protein S13 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 122 No_of_seqs 126 out of 1448 Neff 6.1 Searched_HMMs 33803 Date Tue May 24 02:46:37 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780239.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >3bbn_M Ribosomal protein S13; 100.0 6.2E-37 1.8E-41 250.3 -2.8 100 1-112 46-145 (145) 2 >2zkq_m 40S ribosomal protein 99.8 3E-21 8.8E-26 153.0 2.1 73 1-73 12-87 (88) 3 >2vqe_M 30S ribosomal protein 99.8 4E-20 1.2E-24 146.1 1.8 64 1-64 1-64 (64) 4 >3i1m_M 30S ribosomal protein 99.7 3E-19 9E-24 140.6 1.8 62 1-62 1-62 (63) 5 >2zbk_B Type 2 DNA topoisomera 99.5 5.8E-16 1.7E-20 120.2 -1.3 68 1-72 13-80 (82) 6 >1mu5_A Type II DNA topoisomer 97.0 0.00055 1.6E-08 45.8 3.6 43 20-62 32-74 (82) 7 >1k82_A Formamidopyrimidine-DN 96.8 0.0018 5.2E-08 42.7 4.5 51 11-61 21-74 (97) 8 >1tdz_A Formamidopyrimidine-DN 96.6 0.003 8.9E-08 41.3 4.4 49 13-61 19-70 (136) 9 >3a46_A Formamidopyrimidine-DN 96.3 0.0053 1.6E-07 39.8 4.5 50 12-61 11-64 (146) 10 >3gpu_A DNA glycosylase; DNA g 96.3 0.0051 1.5E-07 39.8 4.4 51 12-62 23-76 (124) 11 >1ee8_A MUTM (FPG) protein; be 96.2 0.0059 1.7E-07 39.5 4.3 51 11-61 22-75 (99) 12 >1k3x_A Endonuclease VIII; hyd 96.2 0.0065 1.9E-07 39.2 4.3 52 11-62 25-79 (138) 13 >1tdh_A NEI endonuclease VIII- 95.0 0.004 1.2E-07 40.5 -0.4 49 14-62 5-56 (209) 14 >2i0z_A NAD(FAD)-utilizing deh 91.7 0.28 8.2E-06 29.1 4.5 49 11-61 18-66 (67) 15 >3fut_A Dimethyladenosine tran 88.8 0.73 2.2E-05 26.5 4.6 48 14-62 19-66 (68) 16 >2nrt_A Uvrabc system protein 84.8 0.54 1.6E-05 27.3 2.1 43 14-58 9-51 (64) 17 >1kft_A UVRC, excinuclease ABC 79.3 0.87 2.6E-05 26.0 1.5 44 11-56 18-61 (78) 18 >1s5l_U Photosystem II 12 kDa 79.1 2.4 7.2E-05 23.2 3.7 53 9-61 8-63 (87) 19 >2vf7_A UVRA2, excinuclease AB 76.1 2.5 7.4E-05 23.2 3.1 36 26-61 21-56 (88) 20 >2bgw_A XPF endonuclease; hydr 74.8 2.1 6.2E-05 23.6 2.4 38 15-54 12-49 (49) 21 >2a1j_A DNA repair endonucleas 74.5 2.4 7.1E-05 23.3 2.7 39 17-57 4-42 (63) 22 >1z00_A DNA excision repair pr 73.2 1.1 3.4E-05 25.3 0.8 50 14-63 16-74 (89) 23 >3fyd_A Probable dimethyladeno 71.3 0.37 1.1E-05 28.3 -2.1 51 12-62 20-80 (85) 24 >3doa_A Fibrinogen binding pro 71.2 1.4 4E-05 24.8 0.8 33 14-46 24-57 (70) 25 >1x2i_A HEF helicase/nuclease; 70.2 1.8 5.4E-05 24.0 1.2 38 14-53 11-48 (49) 26 >3ftd_A Dimethyladenosine tran 69.8 3.3 9.7E-05 22.4 2.5 38 25-62 209-246 (249) 27 >1z00_B DNA repair endonucleas 68.4 3.9 0.00012 21.9 2.6 44 12-57 13-56 (71) 28 >3c1y_A DNA integrity scanning 67.4 1.2 3.7E-05 25.0 -0.1 45 10-56 5-49 (74) 29 >3bz1_U Photosystem II 12 kDa 66.4 7.9 0.00023 20.1 3.9 50 12-61 28-80 (104) 30 >3fhf_A Mjogg, N-glycosylase/D 66.4 2.6 7.6E-05 23.1 1.4 25 16-40 87-111 (113) 31 >2ztd_A Holliday junction ATP- 64.7 2.2 6.6E-05 23.5 0.8 25 15-39 7-31 (75) 32 >2duy_A Competence protein com 63.1 7 0.00021 20.4 3.1 52 10-61 20-74 (75) 33 >2r6f_A Excinuclease ABC subun 62.6 9 0.00027 19.7 3.6 36 25-60 23-58 (82) 34 >3e1s_A Exodeoxyribonuclease V 61.3 1.3 4E-05 24.8 -0.9 30 14-43 41-70 (149) 35 >3i0w_A 8-oxoguanine-DNA-glyco 60.8 3 8.9E-05 22.7 0.9 24 13-36 29-52 (58) 36 >1cuk_A RUVA protein; DNA repa 60.6 3.6 0.00011 22.2 1.3 26 14-39 5-30 (79) 37 >1kg2_A A/G-specific adenine g 56.7 3.2 9.4E-05 22.5 0.4 21 17-37 23-43 (139) 38 >2edu_A Kinesin-like protein K 55.5 8 0.00024 20.0 2.3 44 18-61 41-91 (98) 39 >1ngn_A Methyl-CPG binding pro 54.9 5 0.00015 21.3 1.2 21 17-37 104-124 (129) 40 >1qyr_A KSGA, high level kasug 54.8 14 0.0004 18.6 3.4 35 28-62 216-250 (252) 41 >1orn_A Endonuclease III; DNA 51.9 5.2 0.00015 21.2 0.9 23 14-36 83-105 (110) 42 >1ixr_A Holliday junction DNA 51.8 1.3 3.9E-05 24.9 -2.2 28 12-39 67-94 (191) 43 >1pzn_A RAD51, DNA repair and 51.2 12 0.00037 18.8 2.7 45 13-58 31-75 (95) 44 >3fsp_A A/G-specific adenine g 50.5 5.3 0.00016 21.1 0.7 22 15-36 83-104 (110) 45 >3bzc_A TEX; helix-turn-helix, 50.4 14 0.00041 18.6 2.8 46 16-61 9-61 (70) 46 >3c65_A Uvrabc system protein 50.3 3.9 0.00011 22.0 0.0 41 14-56 170-210 (226) 47 >1dgs_A DNA ligase; AMP comple 48.4 16 0.00047 18.2 2.9 36 21-56 19-54 (116) 48 >2gqf_A Hypothetical protein H 48.2 22 0.00066 17.3 3.7 33 27-60 29-61 (61) 49 >2h56_A DNA-3-methyladenine gl 48.1 7.2 0.00021 20.3 1.1 32 17-48 61-93 (156) 50 >2ihm_A POL MU, DNA polymerase 46.8 7.2 0.00021 20.3 0.9 36 17-52 61-96 (129) 51 >2abk_A Endonuclease III; DNA- 46.8 6.4 0.00019 20.6 0.7 22 15-36 85-106 (111) 52 >2i5h_A Hypothetical protein A 45.5 4 0.00012 21.9 -0.5 43 7-49 122-164 (205) 53 >2jhn_A ALKA, 3-methyladenine 44.8 7.4 0.00022 20.2 0.7 22 13-34 27-48 (55) 54 >1m3q_A 8-oxoguanine DNA glyco 44.2 8 0.00024 20.0 0.9 20 17-36 108-127 (133) 55 >1kea_A Possible G-T mismatche 44.1 7.7 0.00023 20.1 0.7 19 17-35 87-105 (111) 56 >2aq4_A DNA repair protein REV 42.6 20 0.00059 17.6 2.7 41 18-61 3-45 (67) 57 >1a76_A Flap endonuclease-1 pr 40.3 16 0.00046 18.2 1.8 21 19-39 18-38 (65) 58 >1pu6_A 3-methyladenine DNA gl 40.3 9.6 0.00028 19.5 0.7 11 45-55 50-60 (123) 59 >3fhg_A Mjogg, N-glycosylase/D 40.2 14 0.00041 18.5 1.6 22 19-40 46-67 (69) 60 >1rxw_A Flap structure-specifi 39.4 18 0.00052 17.9 2.0 21 19-39 17-37 (68) 61 >1jx4_A DNA polymerase IV (fam 38.8 31 0.00093 16.4 3.8 34 22-56 1-34 (55) 62 >2izo_A FEN1, flap structure-s 37.8 14 0.00042 18.5 1.3 21 19-39 18-38 (82) 63 >1exn_A 5'-exonuclease, 5'-nuc 36.8 20 0.0006 17.5 1.9 20 20-39 25-44 (80) 64 >1mpg_A ALKA, 3-methyladenine 35.8 13 0.00039 18.7 0.9 17 18-34 104-120 (127) 65 >1ul1_X Flap endonuclease-1; p 32.9 25 0.00073 17.0 1.9 21 19-39 31-51 (89) 66 >2bcq_A DNA polymerase lambda; 31.9 8 0.00024 20.0 -0.8 43 17-60 57-99 (128) 67 >3i3w_A Phosphoglucosamine mut 31.5 31 0.0009 16.4 2.2 34 7-40 13-46 (104) 68 >2w9m_A Polymerase X; SAXS, DN 31.2 9.9 0.00029 19.4 -0.4 49 13-61 53-101 (118) 69 >1qyi_A ZR25, hypothetical pro 30.0 42 0.0013 15.5 2.7 25 36-60 23-47 (194) 70 >2eo2_A Adult MALE hypothalamu 29.0 37 0.0011 15.9 2.2 26 33-59 36-61 (71) 71 >1vdd_A Recombination protein 28.8 24 0.0007 17.1 1.2 34 15-48 10-43 (66) 72 >2get_A Pantothenate kinase; h 26.7 39 0.0012 15.8 2.0 82 8-89 84-183 (248) 73 >1b22_A DNA repair protein RAD 25.7 31 0.00092 16.4 1.4 40 16-56 24-63 (114) 74 >2ze6_A Isopentenyl transferas 25.5 52 0.0015 15.0 2.5 41 25-66 48-88 (128) 75 >1u5t_A Appears to BE function 25.0 33 0.00096 16.3 1.4 16 46-61 22-37 (77) 76 >2ftc_E Mitochondrial ribosoma 24.2 48 0.0014 15.2 2.1 53 7-62 9-64 (72) 77 >1szp_A DNA repair protein RAD 24.0 51 0.0015 15.0 2.2 41 18-60 13-53 (56) 78 >1b43_A Protein (FEN-1); nucle 22.3 60 0.0018 14.6 4.2 41 19-59 28-70 (77) 79 >1t94_A Polymerase (DNA direct 20.7 39 0.0012 15.8 1.1 40 17-60 12-51 (70) 80 >1i4w_A Mitochondrial replicat 20.6 65 0.0019 14.4 2.9 47 12-62 18-67 (88) 81 >1dd3_A 50S ribosomal protein 20.3 41 0.0012 15.6 1.1 55 8-62 8-63 (71) No 1 >>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa} (M:) Probab=100.00 E-value=6.2e-37 Score=250.33 Aligned_cols=100 Identities=48% Similarity=0.735 Sum_probs=93.6 Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH Q ss_conf 94551675899857666431200717689999999808882120022798999999986124564333788999999999 Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKR 80 (122) Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~r 80 (122) ||||+|+|||++|+|.+|||+|||||+++|.+||+++||||+. +++|+++|+..|.+.. +.+++||+| T Consensus 46 mvrI~gt~i~~~K~i~~ALt~IyGIG~~~A~~Ic~~lGi~~~k-~~~Lt~~qi~~l~~L~-----------r~v~~dI~R 113 (145) T 3bbn_M 46 CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDNKV-TKDLSEEEVIILRKEK-----------RFNRVAIER 113 (145) T ss_dssp -CCCSSSCCCCSSBTTTGGGGSTTCCSSTTTGGGTTTTCCSCB-TTSCCSSTTHHHHSSC-----------CCCSTTTHH T ss_pred EEEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHH-HHHCCHHHHHHHHHHH-----------HHHHHHHHH T ss_conf 8999586379997889986537550899999999986985454-6543588999989999-----------988999999 Q ss_pred HHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCC Q ss_conf 97303100123317987877077877657777 Q gi|254780239|r 81 LMDLGCYRGLRHRRGLPVRGQRTHTNARTRKK 112 (122) Q Consensus 81 l~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~ 112 (122) |++|+||||+||.+|||||||||||||||+|+ T Consensus 114 l~~I~sYRG~RH~~GLPVRGQRTrTNart~kg 145 (145) T 3bbn_M 114 LKEIRCYRGIRHKLGLPVRGQRTKNNCRTLKG 145 (145) T ss_dssp HHCCCCSCCTTTTTTCCSSSCCTTTCCCSSCC T ss_pred HHHHCCEEEHHHCCCCCCCCCCCCCCCCCCCC T ss_conf 87523101013306998787778777546788 No 2 >>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=99.81 E-value=3e-21 Score=153.03 Aligned_cols=73 Identities=23% Similarity=0.342 Sum_probs=70.1 Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHH---HHHH Q ss_conf 945516758998576664312007176899999998088821200227989999999861245643337---8899 Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGD---LRRT 73 (122) Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~---L~~~ 73 (122) ||||+|+|||++|+|.+|||+|||||+++|.+||+++||||++++++||++|+++|+++|+++|.+|+| |+|. T Consensus 12 mvrI~g~~l~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~~~~k~~~Lt~~qi~~l~~~i~~~~~~e~p~w~l~R~ 87 (88) T 2zkq_m 12 ILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIMQNPRQYKIPDWFLNRQ 87 (88) T ss_dssp -CCCSTTCCCCSSBHHHHGGGSTTCCHHHHHHHHHHHTCCTTSBTTTSCHHHHHHHHHHHHTTCSCCSCCCSSCSS T ss_pred HHHCCCCCCCCCCEEEEEHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHCC T ss_conf 2421384189996873603024662899999999982999543336399999999999984000203637776151 No 3 >>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=99.78 E-value=4e-20 Score=146.06 Aligned_cols=64 Identities=48% Similarity=0.756 Sum_probs=63.1 Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCC Q ss_conf 9455167589985766643120071768999999980888212002279899999998612456 Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDY 64 (122) Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~ 64 (122) ||||+|+|||++|++.+|||+|||||+++|.+||+++||||++++++||++|+++|+++|+++| T Consensus 1 MvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~k~~~Lt~~qi~~i~~~i~~~y 64 (64) T 2vqe_M 1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTW 64 (64) T ss_dssp -CCCSTTCCCCSSBHHHHHTTSSSCCSHHHHHHTTTTTCCTTSBGGGCCHHHHHHHHHHHHTTS T ss_pred CCEECCCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCC T ss_conf 9716375589996888873306581899999999982998332215135999999999873165 No 4 >>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=99.74 E-value=3e-19 Score=140.55 Aligned_cols=62 Identities=35% Similarity=0.553 Sum_probs=61.0 Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 94551675899857666431200717689999999808882120022798999999986124 Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) ||||+|+|||++|+|.+|||+|||||+++|.+||+++||||++++++||++|+++|+++|++ T Consensus 1 MvrI~g~~i~~~K~v~~aLt~i~GIG~~~A~~Ic~~~gi~~~~k~~~Lt~~qi~~l~~~i~~ 62 (63) T 3i1m_M 1 MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAK 62 (63) T ss_dssp -CCCSSSCCCCSSCHHHHGGGSTTCCHHHHHHHHTTTTCCSSCCSTTCCHHHHHHHHTTSSS T ss_pred CCEECCCCCCCCCEEEEEEECEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 97364632799968888753445738999999999919896423463569999999988752 No 5 >>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=99.52 E-value=5.8e-16 Score=120.21 Aligned_cols=68 Identities=15% Similarity=0.221 Sum_probs=62.4 Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHH Q ss_conf 945516758998576664312007176899999998088821200227989999999861245643337889 Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRR 72 (122) Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~ 72 (122) |+||+++|++++|++.+||++|||||+++|.+||+.+||||++++++||++|+++|.+.+. +|+||++ T Consensus 13 ~~ri~~~~~~~~k~i~~aLt~i~GIG~~~A~~I~~~~gi~~~~~~~~Lt~~qi~~L~~~~~----~e~~lrr 80 (82) T 2zbk_B 13 IKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFK----KDEDFRS 80 (82) T ss_dssp HHHHHTTCSSCCBHHHHHHTTSTTCCHHHHHHHHHHTTCCSSCBSSCCCHHHHHHHHHHHH----HCCCCCC T ss_pred HHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHCCCC----CEEEECC T ss_conf 7887750232101334551576467608777666552366334723336788876411010----1111023 No 6 >>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} (A:230-311) Probab=97.03 E-value=0.00055 Score=45.84 Aligned_cols=43 Identities=19% Similarity=0.404 Sum_probs=39.5 Q ss_pred EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 1200717689999999808882120022798999999986124 Q gi|254780239|r 20 CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 20 t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) +.+-|||..+|..||..+||+|++++++|+++|+..|-+.+.+ T Consensus 32 ~~~~GiGn~~a~EiL~~agi~P~~~~~~Ls~~e~~~L~~~~~~ 74 (82) T 1mu5_A 32 NEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK 74 (82) T ss_dssp TSSSSCCHHHHHHHHHHTTCCTTSBGGGCCTTHHHHHHHHHHH T ss_pred HHHCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 6515557689999999718996667565999999999999986 No 7 >>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} (A:129-225) Probab=96.79 E-value=0.0018 Score=42.72 Aligned_cols=51 Identities=18% Similarity=0.224 Sum_probs=42.9 Q ss_pred CCCEEEEEEE---EEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 9857666431---20071768999999980888212002279899999998612 Q gi|254780239|r 11 RAKRVVRALC---YIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 11 ~~K~i~~aLt---~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) .+++|.-+|- .|-|||...|..||..++|+|+.++++||++|+..|-..+. T Consensus 21 ~~~~ik~~LlDQ~~iaGiGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~ 74 (97) T 1k82_A 21 KKTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIK 74 (97) T ss_dssp CCSBHHHHHTCTTTCSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHH T ss_pred CCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHH T ss_conf 555541378517612667588999999873789778120199999999999999 No 8 >>1tdz_A Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis} (A:137-272) Probab=96.57 E-value=0.003 Score=41.28 Aligned_cols=49 Identities=24% Similarity=0.382 Sum_probs=41.7 Q ss_pred CEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 5766643---120071768999999980888212002279899999998612 Q gi|254780239|r 13 KRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 13 K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) .+|.-+| +.|-|||...+..||..++|+|..++++|+++|+..|-+.+- T Consensus 19 ~~Ik~~LlDQ~~iaGIGNiy~~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~~~ 70 (136) T 1tdz_A 19 KKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSII 70 (136) T ss_dssp SBHHHHHHTSSSSSCCCHHHHHHHHHHTTCCTTCBGGGCCHHHHHHHHHHHH T ss_pred CCCEEEEEECCEECCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 1100167505255056767255576564432533222020100466787763 No 9 >>3a46_A Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_A (A:144-289) Probab=96.33 E-value=0.0053 Score=39.78 Aligned_cols=50 Identities=22% Similarity=0.284 Sum_probs=42.1 Q ss_pred CCEEEEEE--EE-E-ECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 85766643--12-0-071768999999980888212002279899999998612 Q gi|254780239|r 12 AKRVVRAL--CY-I-HGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 12 ~K~i~~aL--t~-I-~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) +.+|.-+| +. | -|||.-.+..||..++|+|..++.+|+++|+..|-+.+. T Consensus 11 ~~~Ik~~LlDQ~~i~AGIGNiy~dEiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~ 64 (146) T 3a46_A 11 KQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIK 64 (146) T ss_dssp CSBHHHHHHCSSSSCBCCCHHHHHHHHHHTTBCTTCBGGGCCHHHHHHHHHHHH T ss_pred HHHHHHHHHCCCCEECCCCHHHHHHHHHHHHCCCCCHHCCCCHHHHHHHHHHHH T ss_conf 022346644367366485389999999975048334011099999999999999 No 10 >>3gpu_A DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* 3jr5_A* ... (A:133-256) Probab=96.32 E-value=0.0051 Score=39.84 Aligned_cols=51 Identities=18% Similarity=0.251 Sum_probs=42.6 Q ss_pred CCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 85766643---1200717689999999808882120022798999999986124 Q gi|254780239|r 12 AKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 12 ~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) +++|.-+| +-|-|||.-.|..||..++|+|..++.+|+++|+..|-+.+.+ T Consensus 23 ~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~ihP~~~~~~Ls~~~~~~L~~~i~~ 76 (124) T 3gpu_A 23 KRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVA 76 (124) T ss_dssp CSBHHHHHHCTTTSTTCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHH T ss_pred CCCHHHHEECCCEEEECCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 755678501075263034125788998816884775655546667678999999 No 11 >>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8} (A:121-219) Probab=96.24 E-value=0.0059 Score=39.49 Aligned_cols=51 Identities=20% Similarity=0.277 Sum_probs=42.7 Q ss_pred CCCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 985766643---120071768999999980888212002279899999998612 Q gi|254780239|r 11 RAKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 11 ~~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) .+.+|.-+| +-|-|||.-+|..||..++|+|..++.+|+++|+..|-+.+. T Consensus 22 ~~~~Ik~~LlDQ~viaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~ 75 (99) T 1ee8_A 22 SARPLKALLLDQRLAAGVGNIYADEALFRARLSPFRPARSLTEEEARRLYRALR 75 (99) T ss_dssp CCSBHHHHHHHSSSSTTCCHHHHHHHHHHTTCCSSSBGGGCCHHHHHHHHHHHH T ss_pred CCCCHHHHHHCCCEECCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH T ss_conf 875288986158813156698999999974899778822189999999999999 No 12 >>1k3x_A Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli} (A:125-262) Probab=96.19 E-value=0.0065 Score=39.20 Aligned_cols=52 Identities=13% Similarity=0.307 Sum_probs=44.9 Q ss_pred CCCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 985766643---1200717689999999808882120022798999999986124 Q gi|254780239|r 11 RAKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 11 ~~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) .+.+|.-+| +-|-|||.-.|..|+..++|+|..++.+||++|+..|-+.+.. T Consensus 25 ~~~~ik~~LlDQ~~iaGiGNiy~dEiLf~a~ihP~~~~~~Ls~~~~~~L~~~i~~ 79 (138) T 1k3x_A 25 RNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLE 79 (138) T ss_dssp TTSCHHHHTTCTTTSBTCCHHHHHHHHHHHTCCSSCCGGGSCHHHHHHHHHHHHH T ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCEEHEHHHHHHHHHHHHHHH T ss_conf 0268999984277434656899999998600487661010027789999999999 No 13 >>1tdh_A NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens} (A:156-364) Probab=94.99 E-value=0.004 Score=40.51 Aligned_cols=49 Identities=22% Similarity=0.328 Sum_probs=41.3 Q ss_pred EEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 766643---1200717689999999808882120022798999999986124 Q gi|254780239|r 14 RVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 14 ~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) +|.-+| +.|-|||...+..||..++|+|..++.+|+++|+..|-..|.. T Consensus 5 pIk~~LLDQ~~iaGIGN~~~dEILf~A~IhP~~~~~~L~~~~~~~L~~~i~~ 56 (209) T 1tdh_A 5 PICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELT 56 (209) T ss_dssp BHHHHTTCTTTSTTCCHHHHHHHHHHHTCCTTSBHHHHHGGGC-----CCSC T ss_pred CHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCH T ss_conf 2889984477015664348999999828996663123457664134421000 No 14 >>2i0z_A NAD(FAD)-utilizing dehydrogenases; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; HET: FAD; 1.84A {Bacillus cereus} (A:302-368) Probab=91.75 E-value=0.28 Score=29.10 Aligned_cols=49 Identities=10% Similarity=0.022 Sum_probs=39.0 Q ss_pred CCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 985766643120071768999999980888212002279899999998612 Q gi|254780239|r 11 RAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 11 ~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) ++|.+.-+|. ..+-.+.+..+|..+|||+++++++||..++..|...+. T Consensus 18 ~~k~i~n~l~--~~lP~rL~~~ll~~~gI~~~~~~~~ls~~~~~~L~~~lK 66 (67) T 2i0z_A 18 PKKGIKNVLK--GYVPERYFLFLLEKNEIDGSEQAGQVSHEKIRALVKDFK 66 (67) T ss_dssp TTSBHHHHTT--TSSCHHHHHHHHHHTTCCTTSBGGGSCHHHHHHHHHHHH T ss_pred CCHHHHHHHH--HHHHHHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHHHH T ss_conf 1001222221--000245689998750332011231078999999999875 No 15 >>3fut_A Dimethyladenosine transferase; methyltransferase, dimethyltransferase, dual-specific methyltransferase, 16S rRNA methyltransferase; 1.52A {Thermus thermophilus HB8} PDB: 3fuu_A* 3fuv_A 3fuw_A* 3fux_A* (A:204-271) Probab=88.77 E-value=0.73 Score=26.49 Aligned_cols=48 Identities=21% Similarity=0.346 Sum_probs=37.2 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 7666431200717689999999808882120022798999999986124 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) .+.-+|..+ +.+...+..++..+||||+.+..+||.+|...|.+.+++ T Consensus 19 ~L~n~L~~~-~~~k~~~~~~l~~~~i~~~~R~E~Ls~~~f~~L~~~l~~ 66 (68) T 3fut_A 19 TLLNALAAA-GYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLEG 66 (68) T ss_dssp CHHHHHHHT-TCCHHHHHHHHHHTTCCTTCCGGGCCHHHHHHHHHHHC- T ss_pred HHHHHHHHH-CCCHHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHC T ss_conf 999998763-588889999999869695549254999999999999865 No 16 >>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=84.78 E-value=0.54 Score=27.29 Aligned_cols=43 Identities=12% Similarity=0.190 Sum_probs=36.3 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHH Q ss_conf 766643120071768999999980888212002279899999998 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQ 58 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~ 58 (122) .+.++|+.|.|||+.+|..+++..| .-..+.+-|.+|+.++.. T Consensus 9 ~~~~~L~~I~gIG~~~a~~L~~~F~--s~~~i~~As~eeL~~v~g 51 (64) T 2nrt_A 9 SLRSVLDNVPGIGPIRKKKLIEHFG--SLENIRSASLEEIARVIG 51 (64) T ss_dssp HHHHHHTTSTTCCHHHHHHHHHHHC--SHHHHHTSCHHHHHHHHT T ss_pred HHCCHHHCCCCCCHHHHHHHHHHCC--CHHHHHCCCHHHHHHCCC T ss_conf 2015222053107999999999868--999997099999986879 No 17 >>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} (A:) Probab=79.35 E-value=0.87 Score=26.02 Aligned_cols=44 Identities=16% Similarity=0.172 Sum_probs=31.8 Q ss_pred CCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH Q ss_conf 9857666431200717689999999808882120022798999999 Q gi|254780239|r 11 RAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQI 56 (122) Q Consensus 11 ~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l 56 (122) +...+.++|+.|.|||+.+|..++...|= -..+.+-+.+++.++ T Consensus 18 ~~~~~~~~L~~I~gIG~~~a~~L~~~Fgs--~~~i~~As~eeL~~v 61 (78) T 1kft_A 18 GSHMNTSSLETIEGVGPKRRQMLLKYMGG--LQGLRNASVEEIAKV 61 (78) T ss_dssp -----CCGGGGCTTCSSSHHHHHHHHHSC--HHHHHHCCHHHHTTS T ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHCCC--HHHHHHCCHHHHHHC T ss_conf 41203284656999479999999999099--899985789999738 No 18 >>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=79.07 E-value=2.4 Score=23.24 Aligned_cols=53 Identities=15% Similarity=0.130 Sum_probs=41.9 Q ss_pred CCCCCEEEEEEEEEECCCHHHHHHHHHHCCC---CHHHHHCCCCHHHHHHHHHHHC Q ss_conf 8998576664312007176899999998088---8212002279899999998612 Q gi|254780239|r 9 IPRAKRVVRALCYIHGIGFKSSQDICNKLAI---PPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 9 i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgI---d~~~kv~~Lt~~qi~~l~~~I~ 61 (122) ++=|.--..-|..+-|||+..|..|+..=++ +.-.++..+++..++.|..++. T Consensus 8 vdiN~A~~~~L~~ipGig~~~A~~Iv~~g~f~s~~dL~~v~gi~~~~~~~i~~~l~ 63 (87) T 1s5l_U 8 IDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLE 63 (87) T ss_dssp EETTTSCGGGGGGSTTCTHHHHHHHHHTCCCSSGGGGGGCTTCCHHHHHHHHHHHT T ss_pred EECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHHHC T ss_conf 41640789999771034699999999827848799996177579999999998653 No 19 >>2vf7_A UVRA2, excinuclease ABC, subunit A.; DNA-binding protein, nucleotide-binding, zinc-binding domain, SOS response, metal-binding; HET: ADP; 2.30A {Deinococcus radiodurans} PDB: 2vf8_A* (A:169-256) Probab=76.10 E-value=2.5 Score=23.18 Aligned_cols=36 Identities=25% Similarity=0.138 Sum_probs=29.3 Q ss_pred CHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 768999999980888212002279899999998612 Q gi|254780239|r 26 GFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 26 G~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) ....-.++|..+|+|.++...+|++++.+.|-.=-+ T Consensus 21 ~~~~l~~~a~~~g~dld~P~~dL~~~~~~~ll~G~~ 56 (88) T 2vf7_A 21 GGQNQRDILVTLGIDVDVPWRELPEETRHWILFTDE 56 (88) T ss_dssp HHHHHHHHHHHTTCCSSSBGGGSCHHHHHHHHHCCC T ss_pred CHHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHHCCC T ss_conf 089999999974998676632356998889870688 No 20 >>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} (A:149-197) Probab=74.77 E-value=2.1 Score=23.63 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=31.2 Q ss_pred EEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHH Q ss_conf 6664312007176899999998088821200227989999 Q gi|254780239|r 15 VVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVI 54 (122) Q Consensus 15 i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~ 54 (122) ....|..|-|||+.++..++...| .-..+..-|.+|+. T Consensus 12 ~~s~L~~IpGIG~k~~~~LL~~Fg--Si~~i~~As~eeLa 49 (49) T 2bgw_A 12 QLYILQSFPGIGRRTAERILERFG--SLERFFTASKAEIS 49 (49) T ss_dssp HHHHHHTSTTCCHHHHHHHHHHHS--SHHHHTTCCHHHHH T ss_pred HHHHHHCCCCCCHHHHHHHHHHCC--CHHHHHHCCHHHHH T ss_conf 888885356899789999999869--99999858999996 No 21 >>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=74.54 E-value=2.4 Score=23.28 Aligned_cols=39 Identities=15% Similarity=0.235 Sum_probs=32.3 Q ss_pred EEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHH Q ss_conf 64312007176899999998088821200227989999999 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIR 57 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~ 57 (122) ..|..|-|||+..|..++...| .=..+.+.+.+++.++. T Consensus 4 s~L~~IpgVG~~~a~~Ll~~f~--Si~~i~~As~eeL~~i~ 42 (63) T 2a1j_A 4 DFLLKMPGVNAKNCRSLMHHVK--NIAELAALSQDELTSIL 42 (63) T ss_dssp HHHHTSTTCCHHHHHHHHHHCS--SHHHHHTCCHHHHHHHH T ss_pred HHHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHHCC T ss_conf 8885199989999999999807--89999869999997785 No 22 >>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (A:) Probab=73.15 E-value=1.1 Score=25.27 Aligned_cols=50 Identities=12% Similarity=0.121 Sum_probs=33.5 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHCCCC---------HHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 766643120071768999999980888---------21200227989999999861245 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNKLAIP---------PERRVHQLVESEVIQIRQAIEQD 63 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId---------~~~kv~~Lt~~qi~~l~~~I~~~ 63 (122) .+.++|+.|.|||+..|..++...|=- .=..+..+.+....+|.+++..+ T Consensus 16 ~~l~~L~~I~gIG~~~a~~L~~~F~s~~~i~~A~~~~L~~v~GiG~~~A~~i~~~~~~~ 74 (89) T 1z00_A 16 RVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEP 74 (89) T ss_dssp HHHHHHTTSSSCCHHHHHHHHHHTCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSC T ss_pred HHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCHHCCCCHHHHHHHHHHHHCH T ss_conf 99998658997699999999999099478766547510000332799999999998183 No 23 >>3fyd_A Probable dimethyladenosine transferase; rossman fold, rRNA methylase, ribosomal assembly, methyltransferase, RNA-binding; 1.75A {Methanocaldococcus jannaschii} PDB: 3fyc_A* (A:179-263) Probab=71.30 E-value=0.37 Score=28.32 Aligned_cols=51 Identities=12% Similarity=0.118 Sum_probs=37.6 Q ss_pred CCEEEEEEEEEECCC----------HHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 857666431200717----------689999999808882120022798999999986124 Q gi|254780239|r 12 AKRVVRALCYIHGIG----------FKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 12 ~K~i~~aLt~I~GIG----------~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) .|.+.-+|...++.. .......+..+||||+.+..+||.+|+..|.+.+.+ T Consensus 20 RKtLrn~L~~~~~~~~~~~~~~~~~~~~~~~~l~~~gid~~~R~E~Ls~~ef~~La~~l~~ 80 (85) T 3fyd_A 20 NKSVRKALIDSSKELNYNKDEMKKILEDFLNTNSEIKNLINEKVFKLSVKDIVNLSNEFYR 80 (85) T ss_dssp TSBHHHHHHHTGGGGTCCHHHHHHHHHHHHTSCHHHHHHHHSBGGGSCHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHH T ss_conf 1679999886644406788999999985358544565553016554999999999999999 No 24 >>3doa_A Fibrinogen binding protein; structural genomics, MCSG., PSI-2, protein structure initiative, midwest center for structural genomics; 2.81A {Staphylococcus aureus subsp} (A:166-235) Probab=71.24 E-value=1.4 Score=24.80 Aligned_cols=33 Identities=9% Similarity=0.179 Sum_probs=26.2 Q ss_pred EEEEEE-EEEECCCHHHHHHHHHHCCCCHHHHHC Q ss_conf 766643-120071768999999980888212002 Q gi|254780239|r 14 RVVRAL-CYIHGIGFKSSQDICNKLAIPPERRVH 46 (122) Q Consensus 14 ~i~~aL-t~I~GIG~~~A~~Ic~~lgId~~~kv~ 46 (122) ++.-|| +.+-||++-.|..||..+|+|.+..+- T Consensus 24 ~i~Kal~~~f~GiSPliA~EI~~RAgld~~~~L~ 57 (70) T 3doa_A 24 NIAKQLLNQFEGFSPLITNEIVSRRQFMTSSTLP 57 (70) T ss_dssp CHHHHHHHHBTTCCHHHHHHHHTTSSSCSTTHHH T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCHHH T ss_conf 1999999873898989999999973999622499 No 25 >>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} (A:1-49) Probab=70.20 E-value=1.8 Score=24.04 Aligned_cols=38 Identities=11% Similarity=0.065 Sum_probs=28.9 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHH Q ss_conf 7666431200717689999999808882120022798999 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEV 53 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi 53 (122) .+.++|..|-|||+.+|..++...|= -..+..-+.+|+ T Consensus 11 ~~~~~L~~I~gVG~~~ak~Ll~~Fgs--i~~i~~As~eeL 48 (49) T 1x2i_A 11 RQRLIVEGLPHVSATLARRLLKHFGS--VERVFTASVAEL 48 (49) T ss_dssp HHHHHHTTSTTCCHHHHHHHHHHHCS--HHHHHHCCHHHH T ss_pred HHHHHHCCCCCCCHHHHHHHHHHCCH--HHHHHHCCHHHH T ss_conf 99999858999789999999997062--888862679888 No 26 >>3ftd_A Dimethyladenosine transferase; KSGA, rossmann-like fold, RNA methyltransferase, mtase, antibiotic resistance, methyltransferase; 1.44A {Aquifex aeolicus VF5} PDB: 3ftc_A 3fte_A 3ftf_A* (A:) Probab=69.82 E-value=3.3 Score=22.43 Aligned_cols=38 Identities=24% Similarity=0.412 Sum_probs=32.3 Q ss_pred CCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 17689999999808882120022798999999986124 Q gi|254780239|r 25 IGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 25 IG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) +-......++..+||+++.++.+||.+|+-.|-+.+.+ T Consensus 209 l~~~l~~~~~~~~~i~~~~R~~~l~~~~~~~L~~~~~~ 246 (249) T 3ftd_A 209 LRKKIPEELLKEAGINPDARVEQLSLEDFFKLYRLIED 246 (249) T ss_dssp GGGTSCHHHHHHTTCCTTCCGGGCCHHHHHHHHHHHHC T ss_pred HHHHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHH T ss_conf 77878999999869598789367999999999999997 No 27 >>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (B:1-71) Probab=68.35 E-value=3.9 Score=21.94 Aligned_cols=44 Identities=14% Similarity=0.169 Sum_probs=33.9 Q ss_pred CCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHH Q ss_conf 8576664312007176899999998088821200227989999999 Q gi|254780239|r 12 AKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIR 57 (122) Q Consensus 12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~ 57 (122) +......|..|-|||+..+..++...| .-..+.+.|.+|+..+. T Consensus 13 ~~~~~~~L~~ipGIg~k~~~~Ll~~f~--si~~i~~As~eeL~~v~ 56 (71) T 1z00_B 13 NPGPQDFLLKMPGVNAKNCRSLMHHVK--NIAELAALSQDELTSIL 56 (71) T ss_dssp CHHHHHHHHTCSSCCHHHHHHHHHHSS--CHHHHHHSCHHHHHHHH T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHHCC--CHHHHHHCCHHHHHHCC T ss_conf 204999998089988999999999907--99999878999998875 No 28 >>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=67.36 E-value=1.2 Score=25.05 Aligned_cols=45 Identities=9% Similarity=0.101 Sum_probs=32.0 Q ss_pred CCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH Q ss_conf 99857666431200717689999999808882120022798999999 Q gi|254780239|r 10 PRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQI 56 (122) Q Consensus 10 ~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l 56 (122) ..+......|+.|.|||+..|..++...|= -..+-+-+.+++..+ T Consensus 5 ~k~~~~~~~L~~I~giG~~~a~~L~~~fgs--l~~i~~as~~~L~~v 49 (74) T 3c1y_A 5 LVSARGYRLLKTVARIPLSIGYNVVRMFKT--LDQISKASVEDLKKV 49 (74) T ss_dssp BCCCCSHHHHHHTSCCCHHHHHHHHHHHCS--HHHHTTCCHHHHTTS T ss_pred CCCCHHHHHHHCCCCCCHHHHHHHHHHHCC--HHHHHHCCHHHHHHC T ss_conf 557316888733999989999999998538--999985799888544 No 29 >>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=66.42 E-value=7.9 Score=20.06 Aligned_cols=50 Identities=14% Similarity=0.137 Sum_probs=40.3 Q ss_pred CCEEEEEEEEEECCCHHHHHHHHHHCCCCHH---HHHCCCCHHHHHHHHHHHC Q ss_conf 8576664312007176899999998088821---2002279899999998612 Q gi|254780239|r 12 AKRVVRALCYIHGIGFKSSQDICNKLAIPPE---RRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~---~kv~~Lt~~qi~~l~~~I~ 61 (122) |.--.--|..+-|||+..|..|++.=++..- ..+..+++..++.|..++. T Consensus 28 N~As~~~L~~ipGig~~~A~~Iv~~gpf~s~~dL~~v~gi~~~~~~~i~~~l~ 80 (104) T 3bz1_U 28 NNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLE 80 (104) T ss_dssp TSSCGGGGGGSTTTTHHHHHHHHHSCCCSSGGGGGGCTTCCHHHHHHHHHHGG T ss_pred CCCCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHHHC T ss_conf 22899999777586999999999708978799996179989999999998761 No 30 >>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=66.35 E-value=2.6 Score=23.09 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=18.5 Q ss_pred EEEEEEEECCCHHHHHHHHHHCCCC Q ss_conf 6643120071768999999980888 Q gi|254780239|r 16 VRALCYIHGIGFKSSQDICNKLAIP 40 (122) Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~lgId 40 (122) .-.|++|.|||+.+|..++.-+|.+ T Consensus 87 ~~~L~~l~GIG~~tA~~~l~f~~~~ 111 (113) T 3fhf_A 87 EFLVRNIKGIGYKEASHFLRNVGYD 111 (113) T ss_dssp HHHHHHSTTCCHHHHHHHHHHTTCC T ss_pred HHHHHHCCCCCHHHHHHHHHHHCCC T ss_conf 9999878583299999999996799 No 31 >>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=64.71 E-value=2.2 Score=23.45 Aligned_cols=25 Identities=12% Similarity=0.127 Sum_probs=19.6 Q ss_pred EEEEEEEEECCCHHHHHHHHHHCCC Q ss_conf 6664312007176899999998088 Q gi|254780239|r 15 VVRALCYIHGIGFKSSQDICNKLAI 39 (122) Q Consensus 15 i~~aLt~I~GIG~~~A~~Ic~~lgI 39 (122) ++.-|..|.|||+++|..|+..++. T Consensus 7 ~F~~L~~V~GIGpk~Al~iLs~~~~ 31 (75) T 2ztd_A 7 LFLTLLSVSGVGPRLAMAALAVHDA 31 (75) T ss_dssp HHHHHHTSTTCCHHHHHHHHHHSCH T ss_pred HHHHHHCCCCCCHHHHHHHHCCCCH T ss_conf 9999854132236666232215776 No 32 >>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} (A:) Probab=63.08 E-value=7 Score=20.38 Aligned_cols=52 Identities=13% Similarity=0.165 Sum_probs=40.2 Q ss_pred CCCCEEEEEEEEEECCCHHHHHHHHHHCCCC---HHHHHCCCCHHHHHHHHHHHC Q ss_conf 9985766643120071768999999980888---212002279899999998612 Q gi|254780239|r 10 PRAKRVVRALCYIHGIGFKSSQDICNKLAIP---PERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 10 ~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId---~~~kv~~Lt~~qi~~l~~~I~ 61 (122) +=|.--.-.|..+.|||+..|..|.+.=-+. .-..+..|++..+++|..+|. T Consensus 20 diNtA~~~~L~~lpGig~~~A~~Ii~~R~f~s~~dL~~v~gl~~~~~~~l~~~ir 74 (75) T 2duy_A 20 SLNEASLEELXALPGIGPVLARRIVEGRPYARVEDLLKVKGIGPATLERLRPYLR 74 (75) T ss_dssp ETTTCCHHHHTTSTTCCHHHHHHHHHTCCCSSGGGGGGSTTCCHHHHHHHGGGEE T ss_pred ECCCCCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHHCCCCCHHHHHHHHHHCC T ss_conf 0612879999777898999999999868989899996188989999999986618 No 33 >>2r6f_A Excinuclease ABC subunit A; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, ATP-binding cassette, cytoplasm; HET: ADP; 3.20A {Geobacillus stearothermophilus 10} (A:312-393) Probab=62.65 E-value=9 Score=19.71 Aligned_cols=36 Identities=17% Similarity=0.243 Sum_probs=29.2 Q ss_pred CCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH Q ss_conf 176899999998088821200227989999999861 Q gi|254780239|r 25 IGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 (122) Q Consensus 25 IG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I 60 (122) --...-.++|+..|+|.++...+|++++.+.|-.=- T Consensus 23 ~~~~~l~~~a~~~g~~l~~P~~~L~~~~~~~iLyG~ 58 (82) T 2r6f_A 23 YYPQLLEAVCRHYGIPXDVPVKDLPKEQLDKILYGS 58 (82) T ss_dssp CHHHHHHHHHHHHCCCSSCBGGGSCHHHHHHHHHCC T ss_pred HHHHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHCCC T ss_conf 577889999998599867762337699999997089 No 34 >>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=61.28 E-value=1.3 Score=24.83 Aligned_cols=30 Identities=17% Similarity=0.287 Sum_probs=26.1 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHCCCCHHH Q ss_conf 766643120071768999999980888212 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNKLAIPPER 43 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~ 43 (122) .=+|-|..|.|||+.+|..|..++|++++. T Consensus 41 ~nPY~L~~i~gigF~~aD~iA~~~gi~~dd 70 (149) T 3e1s_A 41 KDLFTLTEVEGIGFLTADKLWQARGGALDD 70 (149) T ss_dssp ---CGGGTSSSCCHHHHHTTC-------CC T ss_pred HCCCEEEECCCCCHHHHHHHHHHCCCCCCC T ss_conf 499355415899959999999976989899 No 35 >>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=60.83 E-value=3 Score=22.68 Aligned_cols=24 Identities=17% Similarity=0.099 Sum_probs=18.5 Q ss_pred CEEEEEEEEEECCCHHHHHHHHHH Q ss_conf 576664312007176899999998 Q gi|254780239|r 13 KRVVRALCYIHGIGFKSSQDICNK 36 (122) Q Consensus 13 K~i~~aLt~I~GIG~~~A~~Ic~~ 36 (122) ..+.-.|+.|.|||+.+|..+|-- T Consensus 29 eea~~~L~~i~GIGpwTAdciLLF 52 (58) T 3i0w_A 29 NECHEELKKFMGVGPQVADCIMLF 52 (58) T ss_dssp HHHHHHHTTSTTCCHHHHHHHHHH T ss_pred HHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 467899982688129999999998 No 36 >>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:66-144) Probab=60.57 E-value=3.6 Score=22.15 Aligned_cols=26 Identities=19% Similarity=0.309 Sum_probs=20.5 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHCCC Q ss_conf 76664312007176899999998088 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNKLAI 39 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~lgI 39 (122) .++.-|..|.|||+++|..|+..++. T Consensus 5 ~~F~~L~~V~GIGpk~Al~iLs~~~~ 30 (79) T 1cuk_A 5 TLFKELIKTNGVGPKLALAILSGMSA 30 (79) T ss_dssp HHHHHHHHSSSCCHHHHHHHHHHSCH T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCCH T ss_conf 99998734788489999999757999 No 37 >>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} (A:1-23,A:110-225) Probab=56.69 E-value=3.2 Score=22.51 Aligned_cols=21 Identities=14% Similarity=0.233 Sum_probs=18.6 Q ss_pred EEEEEEECCCHHHHHHHHHHC Q ss_conf 643120071768999999980 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKL 37 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~l 37 (122) -+|..+.|||+.+|..||.-. T Consensus 23 ~eL~~LpGIG~ktAd~Illfa 43 (139) T 1kg2_A 23 PEVAALPGVGRSTAGAILSLS 43 (139) T ss_dssp GHHHTSTTCCHHHHHHHHHHH T ss_pred CHHHCCCCCCHHHHHHHHHHH T ss_conf 998628987278999999984 No 38 >>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=55.47 E-value=8 Score=20.04 Aligned_cols=44 Identities=20% Similarity=0.139 Sum_probs=35.0 Q ss_pred EEEEEECCCHHHHHHHHHHC-------CCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 43120071768999999980-------888212002279899999998612 Q gi|254780239|r 18 ALCYIHGIGFKSSQDICNKL-------AIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 18 aLt~I~GIG~~~A~~Ic~~l-------gId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) .|..+.|||+..|..|...= .++.-..+..+++..++.|..++. T Consensus 41 eL~~lpgig~~~A~~Ii~~R~~~G~f~siedL~~v~gi~~~~~~~l~~~~~ 91 (98) T 2edu_A 41 DLRSLQRIGPKKAQLIVGWRELHGPFSQVEDLERVEGITGKQMESFLKANI 91 (98) T ss_dssp HHHHSTTCCHHHHHHHHHHHHHHCCCSSGGGGGGSTTCCHHHHHHHHHHHH T ss_pred HHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHHCC T ss_conf 997578989999999999999858958899982588989999999998283 No 39 >>1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} (A:1-129) Probab=54.86 E-value=5 Score=21.29 Aligned_cols=21 Identities=24% Similarity=0.148 Sum_probs=15.8 Q ss_pred EEEEEEECCCHHHHHHHHHHC Q ss_conf 643120071768999999980 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKL 37 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~l 37 (122) -.|+.+.|||+.+|..|+-.. T Consensus 104 ~~L~~l~GIG~~tA~~vll~~ 124 (129) T 1ngn_A 104 RYPIELHGIGKYGNDSYRIFC 124 (129) T ss_dssp SSGGGSTTCCHHHHHHHHHHT T ss_pred HHHHHCCCCCHHHHHHHHHHH T ss_conf 665627996689999999997 No 40 >>1qyr_A KSGA, high level kasugamycin resistance protein, S-; adenosine dimethyltransferase, rRNA modification, transferase, translation; 2.10A {Escherichia coli} (A:) Probab=54.75 E-value=14 Score=18.59 Aligned_cols=35 Identities=14% Similarity=0.249 Sum_probs=28.7 Q ss_pred HHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 89999999808882120022798999999986124 Q gi|254780239|r 28 KSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 28 ~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) .....+...+||+|+.++++|+.+|..+|-+.+.+ T Consensus 216 ~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~~~~ 250 (252) T 1qyr_A 216 LFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAE 250 (252) T ss_dssp TCCHHHHHHTTCCTTSBGGGSCHHHHHHHHHHHHH T ss_pred HCCHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHH T ss_conf 44099999779883349322999999999999984 No 41 >>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=51.85 E-value=5.2 Score=21.20 Aligned_cols=23 Identities=22% Similarity=0.309 Sum_probs=17.3 Q ss_pred EEEEEEEEEECCCHHHHHHHHHH Q ss_conf 76664312007176899999998 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNK 36 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~ 36 (122) .+.-.|++|.|||+.+|..++-. T Consensus 83 ~~~~~L~~l~GIG~~ta~~~llf 105 (110) T 1orn_A 83 RDRDELMKLPGVGRKTANVVVSV 105 (110) T ss_dssp SCHHHHTTSTTCCHHHHHHHHHH T ss_pred CCHHHHHHCCCCCHHHHHHHHHH T ss_conf 88999975879752589999999 No 42 >>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=51.78 E-value=1.3 Score=24.90 Aligned_cols=28 Identities=18% Similarity=0.228 Sum_probs=19.1 Q ss_pred CCEEEEEEEEEECCCHHHHHHHHHHCCC Q ss_conf 8576664312007176899999998088 Q gi|254780239|r 12 AKRVVRALCYIHGIGFKSSQDICNKLAI 39 (122) Q Consensus 12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lgI 39 (122) .+.++.-|..|.|||+++|..|+..++. T Consensus 67 er~~F~~L~~V~GIGpk~Al~iL~~~~~ 94 (191) T 1ixr_A 67 NLALFELLLSVSGVGPKVALALLSALPP 94 (191) T ss_dssp HHHHHHHHHSSSCCCHHHHHHHHHHSCH T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHCCCH T ss_conf 9999999857588477889999855999 No 43 >>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=51.22 E-value=12 Score=18.84 Aligned_cols=45 Identities=9% Similarity=0.236 Sum_probs=33.6 Q ss_pred CEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHH Q ss_conf 5766643120071768999999980888212002279899999998 Q gi|254780239|r 13 KRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQ 58 (122) Q Consensus 13 K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~ 58 (122) ......|..|.|||..+|..++.. +++.-..+-+-+.+++.++.. T Consensus 31 ~~~~~~ll~I~gIG~~~a~~L~~~-~~~s~e~i~~As~e~L~~i~G 75 (95) T 1pzn_A 31 EKIIRSIEDLPGVGPATAEKLREA-GYDTLEAIAVASPIELKEVAG 75 (95) T ss_dssp ----CCSSCCTTCCHHHHHHHHTT-TCCSHHHHHTCCHHHHHHHHC T ss_pred HHHHCCHHHCCCCCHHHHHHHHHC-CCCCHHHHHHCCHHHHHHHHC T ss_conf 233214643799799999999985-997199998289999997549 No 44 >>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=50.54 E-value=5.3 Score=21.12 Aligned_cols=22 Identities=9% Similarity=0.134 Sum_probs=15.9 Q ss_pred EEEEEEEEECCCHHHHHHHHHH Q ss_conf 6664312007176899999998 Q gi|254780239|r 15 VVRALCYIHGIGFKSSQDICNK 36 (122) Q Consensus 15 i~~aLt~I~GIG~~~A~~Ic~~ 36 (122) ..-.|+++.|||+.+|..++-. T Consensus 83 ~~~~L~~lpGIG~~tA~~vll~ 104 (110) T 3fsp_A 83 DPDEFSRLKGVGPYTVGAVLSL 104 (110) T ss_dssp SHHHHHTSTTCCHHHHHHHHHH T ss_pred CHHHHHHHHHHHHHHHHHHHHH T ss_conf 8999951112689999999999 No 45 >>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=50.37 E-value=14 Score=18.55 Aligned_cols=46 Identities=22% Similarity=0.197 Sum_probs=35.1 Q ss_pred EEEEEEEECCCHHHHHHHHHHC----C---CCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 6643120071768999999980----8---88212002279899999998612 Q gi|254780239|r 16 VRALCYIHGIGFKSSQDICNKL----A---IPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~l----g---Id~~~kv~~Lt~~qi~~l~~~I~ 61 (122) .-.|..+.|||+..|..|.+.- + ++.=.++..+++..++.+..++. T Consensus 9 ~~~L~~lpgig~~~A~~Ii~~R~~~G~f~s~~dL~~v~gl~~~~~~~l~~~i~ 61 (70) T 3bzc_A 9 AALLARISGLNSTLAQNIVAHRDANGAFRTRDELKKVSRLGEKTFEQAAGFLR 61 (70) T ss_dssp HHHHHTSTTCCHHHHHHHHHHHHHHCCCSSGGGGGGSTTCCHHHHHHHGGGEE T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCHHHHHHCCEEEE T ss_conf 88886606978899999999999669957799998567888128987180898 No 46 >>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=50.34 E-value=3.9 Score=22.00 Aligned_cols=41 Identities=17% Similarity=0.233 Sum_probs=26.1 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH Q ss_conf 7666431200717689999999808882120022798999999 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQI 56 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l 56 (122) ...+.+..|.|||+.+|..++...| .-..+...|.+++.++ T Consensus 170 ~~~~~~~~I~~IG~~~a~~Ll~~Fg--sl~~i~~As~eeL~~v 210 (226) T 3c65_A 170 MFHSVLDDIPGVGEKRKKALLNYFG--SVKKMKEATVEELQRA 210 (226) T ss_dssp ------------------------------------------- T ss_pred HHCCHHHHHHHHCHHHHHHHHHHCC--CHHHHHHCCHHHHHHC T ss_conf 4117688998747999999999858--9999983999999877 No 47 >>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} (A:427-542) Probab=48.45 E-value=16 Score=18.16 Aligned_cols=36 Identities=17% Similarity=0.244 Sum_probs=25.3 Q ss_pred EEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH Q ss_conf 200717689999999808882120022798999999 Q gi|254780239|r 21 YIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQI 56 (122) Q Consensus 21 ~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l 56 (122) .|.|+|.....+....--|......-.|+.+++..+ T Consensus 19 ~i~glg~~~i~~~~~~~~i~~~~d~~~L~~~~~~~l 54 (116) T 1dgs_A 19 DIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGL 54 (116) T ss_dssp CCTTCCHHHHHHHHHTTSCSSGGGGGGGCCHHHHTT T ss_pred CCCCCCHHHHHHHHHCCCCCCHHHHHHCCHHHHHCC T ss_conf 856659999999997688688799871899998346 No 48 >>2gqf_A Hypothetical protein HI0933; structural genomics, FAD-utilizing protein, flavoprotein, PSI, protein structure initiative; HET: FAD; 2.70A {Haemophilus influenzae} (A:265-325) Probab=48.25 E-value=22 Score=17.27 Aligned_cols=33 Identities=9% Similarity=0.039 Sum_probs=27.8 Q ss_pred HHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH Q ss_conf 6899999998088821200227989999999861 Q gi|254780239|r 27 FKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 (122) Q Consensus 27 ~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I 60 (122) .+.|..+|...++ ++..++++|+.++..|.+.+ T Consensus 29 kRLa~~l~~~~~l-~~~pl~q~s~~~L~~la~~L 61 (61) T 2gqf_A 29 KKLVELWIEQGIV-QDEVIANISKVRVKNLVDFI 61 (61) T ss_dssp HHHHHHHHHTTSS-CCCBGGGCCHHHHHHHHHHH T ss_pred CCHHHHHHHHCCC-CCCHHHHCCHHHHHHHHHHH T ss_conf 1011455554136-31000011466778899897 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=48.13 E-value=7.2 Score=20.31 Aligned_cols=32 Identities=19% Similarity=0.139 Sum_probs=23.6 Q ss_pred EEEEEEECCCHHHHHHHHHHCCCCHHH-HHCCC Q ss_conf 643120071768999999980888212-00227 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLAIPPER-RVHQL 48 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~-kv~~L 48 (122) -.|+.+.|||+.+|..|+...-=.|+. -+.+. T Consensus 61 ~~LlsLPGIGpkTA~~ILlfalgrpdvfpVdD~ 93 (156) T 2h56_A 61 EKLTAIKGIGQWTAEXFXXFSLGRLDVLSVGDV 93 (156) T ss_dssp HHHHTSTTCCHHHHHHHHHHTTCCSCCCCTTCH T ss_pred HHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCH T ss_conf 888873897878999999851689977864579 No 50 >>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} (A:1-129) Probab=46.76 E-value=7.2 Score=20.33 Aligned_cols=36 Identities=25% Similarity=0.099 Sum_probs=22.8 Q ss_pred EEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHH Q ss_conf 643120071768999999980888212002279899 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESE 52 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~q 52 (122) -.++.+.|||.+.|..|-..+.=..-..+.+|-.++ T Consensus 61 ~~~~~lpgIG~~ia~~I~E~l~tG~~~~le~l~~~~ 96 (129) T 2ihm_A 61 SQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCSE 96 (129) T ss_dssp GGGTTCTTCCHHHHHHHHHHHHHSCCHHHHHHHHSH T ss_pred HHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHH T ss_conf 998359997789999999999709889999886320 No 51 >>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} (A:23-133) Probab=46.75 E-value=6.4 Score=20.62 Aligned_cols=22 Identities=27% Similarity=0.298 Sum_probs=16.4 Q ss_pred EEEEEEEEECCCHHHHHHHHHH Q ss_conf 6664312007176899999998 Q gi|254780239|r 15 VVRALCYIHGIGFKSSQDICNK 36 (122) Q Consensus 15 i~~aLt~I~GIG~~~A~~Ic~~ 36 (122) ..-.|+.+.|||+.+|..++-. T Consensus 85 ~~~~L~~l~GIG~~tA~~vll~ 106 (111) T 2abk_A 85 DRAALEALPGVGRKTANVVLNT 106 (111) T ss_dssp CHHHHHHSTTCCHHHHHHHHHH T ss_pred HHHHHHHHHHCCCHHHHHHHHH T ss_conf 7999998986063599999999 No 52 >>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} (A:) Probab=45.55 E-value=4 Score=21.89 Aligned_cols=43 Identities=14% Similarity=0.132 Sum_probs=32.0 Q ss_pred CCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCC Q ss_conf 7589985766643120071768999999980888212002279 Q gi|254780239|r 7 VNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLV 49 (122) Q Consensus 7 ~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt 49 (122) ..+..+..+..+|..|.|||...|..|...-.-.|...+.||. T Consensus 122 ~~~~~n~~i~~~L~~I~GiG~~~a~~Iie~Re~g~F~S~eDl~ 164 (205) T 2i5h_A 122 NKADSITTRMHQLELLPGVGKKMMWAIIEERKKRPFESFEDIA 164 (205) T ss_dssp C--CCBCSSSBGGGGSTTCCHHHHHHHHHHHHHSCCCSHHHHH T ss_pred CCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHHHHH T ss_conf 4678761878988744451589999999997548988999999 No 53 >>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=44.84 E-value=7.4 Score=20.24 Aligned_cols=22 Identities=18% Similarity=0.220 Sum_probs=16.6 Q ss_pred CEEEEEEEEEECCCHHHHHHHH Q ss_conf 5766643120071768999999 Q gi|254780239|r 13 KRVVRALCYIHGIGFKSSQDIC 34 (122) Q Consensus 13 K~i~~aLt~I~GIG~~~A~~Ic 34 (122) ..+.-.|+.|.|||+.+|...+ T Consensus 27 eevi~~Lt~IkGIG~WTAem~L 48 (55) T 2jhn_A 27 EEAYEYLTSFKGIGRWTAELVL 48 (55) T ss_dssp HHHHHHHHTSTTCCHHHHHHHH T ss_pred HHHHHHHHHCCCCCHHHHHHHH T ss_conf 1678898753782899999999 No 54 >>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=44.22 E-value=8 Score=20.02 Aligned_cols=20 Identities=40% Similarity=0.796 Sum_probs=11.2 Q ss_pred EEEEEEECCCHHHHHHHHHH Q ss_conf 64312007176899999998 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNK 36 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~ 36 (122) -.|+.+.|||+.+|..||-. T Consensus 108 ~~L~~lpGIG~~tA~~ill~ 127 (133) T 1m3q_A 108 KALCILPGVGTKVADCICLM 127 (133) T ss_dssp HHHTTSTTCCHHHHHHHHHH T ss_pred HHHHHCCCCCHHHHHHHHHH T ss_conf 99984688379999999999 No 55 >>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=44.09 E-value=7.7 Score=20.12 Aligned_cols=19 Identities=16% Similarity=0.312 Sum_probs=11.0 Q ss_pred EEEEEEECCCHHHHHHHHH Q ss_conf 6431200717689999999 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICN 35 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~ 35 (122) -.|+.|.|||+.+|..++- T Consensus 87 ~~L~~l~GIG~~tA~~~ll 105 (111) T 1kea_A 87 KAILDLPGVGKYTCAAVMC 105 (111) T ss_dssp HHHHTSTTCCHHHHHHHHH T ss_pred HHHHCCCCCCHHHHHHHHH T ss_conf 6765089876168999999 No 56 >>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=42.60 E-value=20 Score=17.56 Aligned_cols=41 Identities=10% Similarity=0.173 Sum_probs=29.2 Q ss_pred EEEEEECCCHHHHHHHHHH-CCCCHHHHHCCCCH-HHHHHHHHHHC Q ss_conf 4312007176899999998-08882120022798-99999998612 Q gi|254780239|r 18 ALCYIHGIGFKSSQDICNK-LAIPPERRVHQLVE-SEVIQIRQAIE 61 (122) Q Consensus 18 aLt~I~GIG~~~A~~Ic~~-lgId~~~kv~~Lt~-~qi~~l~~~I~ 61 (122) .+..|.|||.+++..+... .||.. ++||.+ ...+.|.+.+. T Consensus 3 pi~~i~GVG~~t~~kL~~~~~Gi~t---i~dL~~~~~~~~L~~~~G 45 (67) T 2aq4_A 3 KLDDLPGVGHSTLSRLESTFDSPHS---LNDLRKRYTLDALKASVG 45 (67) T ss_dssp CGGGSTTCCHHHHHHHHHHTTCCCS---HHHHHHHCCHHHHHHHHC T ss_pred CCCCHHCCCHHHHHHHHHHHHCCCC---HHHHHHHHHHHHHHHHHC T ss_conf 4230120278999999987743576---999998877778887502 No 57 >>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=40.33 E-value=16 Score=18.22 Aligned_cols=21 Identities=24% Similarity=0.363 Sum_probs=17.7 Q ss_pred EEEEECCCHHHHHHHHHHCCC Q ss_conf 312007176899999998088 Q gi|254780239|r 19 LCYIHGIGFKSSQDICNKLAI 39 (122) Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lgI 39 (122) +..|-|||+.+|..+..+.+= T Consensus 18 ipGV~GIGpKtA~~li~~~~~ 38 (65) T 1a76_A 18 PGGVKGIGFKRAYELVRSGVA 38 (65) T ss_dssp TTTTTTCCHHHHHHHHHHTCH T ss_pred CCCCCCEEHHHHHHHHHHCCC T ss_conf 555685629999999997299 No 58 >>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} (A:23-145) Probab=40.30 E-value=9.6 Score=19.54 Aligned_cols=11 Identities=9% Similarity=0.114 Sum_probs=3.9 Q ss_pred HCCCCHHHHHH Q ss_conf 02279899999 Q gi|254780239|r 45 VHQLVESEVIQ 55 (122) Q Consensus 45 v~~Lt~~qi~~ 55 (122) +-+++++++.. T Consensus 50 l~~~~~~~l~~ 60 (123) T 1pu6_A 50 IAYIEFSKLAE 60 (123) T ss_dssp HHHSCHHHHHH T ss_pred HHCCCHHHHHH T ss_conf 97799999999 No 59 >>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=40.20 E-value=14 Score=18.53 Aligned_cols=22 Identities=23% Similarity=0.400 Sum_probs=17.2 Q ss_pred EEEEECCCHHHHHHHHHHCCCC Q ss_conf 3120071768999999980888 Q gi|254780239|r 19 LCYIHGIGFKSSQDICNKLAIP 40 (122) Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lgId 40 (122) |-.|+|||++-|...+...|+. T Consensus 46 LvniKGiGyKEASHFLRNvG~~ 67 (69) T 3fhg_A 46 LLNIKGIGMQEASHFLRNVGYF 67 (69) T ss_dssp HTTSTTCCHHHHHHHHHHTTCC T ss_pred HHHCCCCHHHHHHHHHHHHCCC T ss_conf 9967585399999999986699 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=39.37 E-value=18 Score=17.91 Aligned_cols=21 Identities=14% Similarity=0.175 Sum_probs=18.0 Q ss_pred EEEEECCCHHHHHHHHHHCCC Q ss_conf 312007176899999998088 Q gi|254780239|r 19 LCYIHGIGFKSSQDICNKLAI 39 (122) Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lgI 39 (122) +..|-|||+.+|..+..+.|= T Consensus 17 ~pGV~GIG~ktA~~li~~~~s 37 (68) T 1rxw_A 17 NEGVKGVGVKKALNYIKTYGD 37 (68) T ss_dssp BCCCTTCCHHHHHHHHHHHSS T ss_pred CCCCCCCCHHHHHHHHHHHCC T ss_conf 589999578999999999499 No 61 >>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=38.76 E-value=31 Score=16.35 Aligned_cols=34 Identities=18% Similarity=0.229 Sum_probs=23.9 Q ss_pred EECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH Q ss_conf 00717689999999808882120022798999999 Q gi|254780239|r 22 IHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQI 56 (122) Q Consensus 22 I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l 56 (122) |.|||+.++..+ ..+||..-.-+..++++.+.+. T Consensus 1 i~GIG~~t~~kL-~~~GI~ti~dl~~~~~~~L~~~ 34 (55) T 1jx4_A 1 VPGIGNITAEKL-KKLGINKLVDTLSIEFDKLKGX 34 (55) T ss_dssp STTCCHHHHHHH-HTTTCCBGGGGGSSCHHHHHHH T ss_pred CCCCCHHHHHHH-HHHCCCCCHHCCCCCHHHHHHH T ss_conf 259966799999-9848968231213799999989 No 62 >>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=37.85 E-value=14 Score=18.51 Aligned_cols=21 Identities=29% Similarity=0.237 Sum_probs=18.1 Q ss_pred EEEEECCCHHHHHHHHHHCCC Q ss_conf 312007176899999998088 Q gi|254780239|r 19 LCYIHGIGFKSSQDICNKLAI 39 (122) Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lgI 39 (122) +..|-|||+.+|..+..+.|= T Consensus 18 i~GV~GiG~ktA~~li~~~g~ 38 (82) T 2izo_A 18 PDGIRGIGPERALKIIKKYGK 38 (82) T ss_dssp TTCSTTCCHHHHHHHHHHSSC T ss_pred CCCCCCCCHHHHHHHHHHCCC T ss_conf 334799448899999998399 No 63 >>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} (A:182-261) Probab=36.81 E-value=20 Score=17.54 Aligned_cols=20 Identities=25% Similarity=0.338 Sum_probs=16.9 Q ss_pred EEEECCCHHHHHHHHHHCCC Q ss_conf 12007176899999998088 Q gi|254780239|r 20 CYIHGIGFKSSQDICNKLAI 39 (122) Q Consensus 20 t~I~GIG~~~A~~Ic~~lgI 39 (122) -.|.|||+.+|..+..+.|= T Consensus 25 pGV~GIG~ktA~~Li~~~gs 44 (80) T 1exn_A 25 RGVEGIGAKRGYNIIREFGN 44 (80) T ss_dssp CCCTTCCHHHHHHHHHHHCS T ss_pred CCCCCCCHHHHHHHHHHHCC T ss_conf 99997679999999999599 No 64 >>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} (A:105-231) Probab=35.76 E-value=13 Score=18.70 Aligned_cols=17 Identities=24% Similarity=0.251 Sum_probs=7.3 Q ss_pred EEEEEECCCHHHHHHHH Q ss_conf 43120071768999999 Q gi|254780239|r 18 ALCYIHGIGFKSSQDIC 34 (122) Q Consensus 18 aLt~I~GIG~~~A~~Ic 34 (122) .|+.+.|||+.+|..++ T Consensus 104 ~L~~lpGIG~~tA~~vl 120 (127) T 1mpg_A 104 TLQTFPGIGRWTANYFA 120 (127) T ss_dssp HHTTSTTCCHHHHHHHH T ss_pred HHHHCCCCCHHHHHHHH T ss_conf 99865897899999999 No 65 >>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=32.89 E-value=25 Score=16.98 Aligned_cols=21 Identities=33% Similarity=0.325 Sum_probs=17.7 Q ss_pred EEEEECCCHHHHHHHHHHCCC Q ss_conf 312007176899999998088 Q gi|254780239|r 19 LCYIHGIGFKSSQDICNKLAI 39 (122) Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lgI 39 (122) +..|.|||+.+|..+..+.|= T Consensus 31 ~pGV~GIG~KtA~kLI~~ygs 51 (89) T 1ul1_X 31 CESIRGIGPKRAVDLIQKHKS 51 (89) T ss_dssp SCCCTTCCHHHHHHHHHHSSS T ss_pred CCCCCCCCHHHHHHHHHHCCC T ss_conf 355788569999999998099 No 66 >>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=31.86 E-value=8 Score=20.01 Aligned_cols=43 Identities=23% Similarity=0.315 Sum_probs=29.8 Q ss_pred EEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH Q ss_conf 64312007176899999998088821200227989999999861 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I 60 (122) -.+..|.|||.+.|..|-..+.=..-..+.++.++.- .+..+. T Consensus 57 ~~~~~lpgIG~~ia~~I~E~l~tG~~~~le~l~~~~~-~~~~~~ 99 (128) T 2bcq_A 57 QEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVP-VLELFS 99 (128) T ss_dssp HHHHTSTTCCHHHHHHHHHHHHSSSCGGGGGCCTTHH-HHHHHH T ss_pred HHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHHCCCCC-HHHCCC T ss_conf 9982799964899999999997397888874303366-133144 No 67 >>3i3w_A Phosphoglucosamine mutase; csgid, IDP02164, isomerase, magnesium, metal-binding, phosphoprotein, structural genomics; HET: SEP; 2.30A {Francisella tularensis subsp} (A:153-256) Probab=31.50 E-value=31 Score=16.42 Aligned_cols=34 Identities=12% Similarity=0.046 Sum_probs=30.9 Q ss_pred CCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCC Q ss_conf 7589985766643120071768999999980888 Q gi|254780239|r 7 VNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIP 40 (122) Q Consensus 7 ~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId 40 (122) +|+..-+.+.+.+...+|.|......|+..+|++ T Consensus 13 id~~~~~~~kiv~d~~~G~~~~~~~~ll~~lg~~ 46 (104) T 3i3w_A 13 FAKFVNYKGKVVVDCAHGAASHNFEALLDKFGIN 46 (104) T ss_dssp HTTTCCCCSEEEEECTTSTTTTHHHHHHHHTTCE T ss_pred CCHHCCCCCEEEEECCCCCCCHHHHHHHHHCCCC T ss_conf 2011046864999768885100124455303654 No 68 >>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:1-118) Probab=31.21 E-value=9.9 Score=19.44 Aligned_cols=49 Identities=6% Similarity=-0.013 Sum_probs=31.6 Q ss_pred CEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 5766643120071768999999980888212002279899999998612 Q gi|254780239|r 13 KRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 13 K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) .-..-.|+.+-|||.++|..|-.-+.=..-.++.+|..+-...|..+.+ T Consensus 53 ~~~~~~l~~lpGIG~~~a~kI~E~l~tG~~~~le~l~~~~~~~l~~l~~ 101 (118) T 2w9m_A 53 ELLAREFTGIPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLG 101 (118) T ss_dssp ------CCSSTTCCHHHHHHHHHHHHHSSCHHHHHHHHHSCHHHHHHTT T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHC T ss_conf 7549886259998789999999999849828899987025178999857 No 69 >>1qyi_A ZR25, hypothetical protein; structural genomics, PSI, protein structure initiative, northeast structural genomics consortium, NESG; 2.50A {Staphylococcus aureus subsp} (A:13-206) Probab=30.04 E-value=42 Score=15.54 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=23.0 Q ss_pred HCCCCHHHHHCCCCHHHHHHHHHHH Q ss_conf 8088821200227989999999861 Q gi|254780239|r 36 KLAIPPERRVHQLVESEVIQIRQAI 60 (122) Q Consensus 36 ~lgId~~~kv~~Lt~~qi~~l~~~I 60 (122) -+|+++......|++++|..|+..+ T Consensus 23 yLGL~~~~~~~~l~d~~I~~IR~~V 47 (194) T 1qyi_A 23 YLGLHSHIDWETLTDNDIQDIRNRI 47 (194) T ss_dssp TTCCSCCCCGGGCCHHHHHHHHHHH T ss_pred CCCCCCCCCCCCCCHHHHHHHHHCC T ss_conf 0365534443442276899998435 No 70 >>2eo2_A Adult MALE hypothalamus cDNA, riken FULL-length enriched library, clone:A230045M11...; FTHFSDC1, structural genomics, NPPSFA; NMR {Mus musculus} (A:) Probab=28.96 E-value=37 Score=15.89 Aligned_cols=26 Identities=27% Similarity=0.247 Sum_probs=17.9 Q ss_pred HHHHCCCCHHHHHCCCCHHHHHHHHHH Q ss_conf 999808882120022798999999986 Q gi|254780239|r 33 ICNKLAIPPERRVHQLVESEVIQIRQA 59 (122) Q Consensus 33 Ic~~lgId~~~kv~~Lt~~qi~~l~~~ 59 (122) =+.+|||++.- ..+||++|+.+..-. T Consensus 36 RL~kLGI~Ktd-P~~LT~EEi~~F~RL 61 (71) T 2eo2_A 36 RLKKLGIHKTD-PSTLTEEEVRKFARL 61 (71) T ss_dssp HHHHHTCCCCS-TTTCCHHHHHHHHHT T ss_pred HHHHCCCCCCC-HHHCCHHHHHHHHEE T ss_conf 99992999999-145899998543310 No 71 >>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} (A:1-66) Probab=28.81 E-value=24 Score=17.09 Aligned_cols=34 Identities=32% Similarity=0.516 Sum_probs=25.0 Q ss_pred EEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCC Q ss_conf 6664312007176899999998088821200227 Q gi|254780239|r 15 VVRALCYIHGIGFKSSQDICNKLAIPPERRVHQL 48 (122) Q Consensus 15 i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~L 48 (122) +.-+|.++=|||+++|..+...+=-.|...+.+| T Consensus 10 LI~~l~~LPGIG~KsA~Rla~~lL~~~~~~~~~l 43 (66) T 1vdd_A 10 LIRELSRLPGIGPKSAQRLAFHLFEQPREDIERL 43 (66) T ss_dssp HHHHHHTSTTCCHHHHHHHHHHHSSSCHHHHHHH T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHH T ss_conf 9999967899889999999999972999999999 No 72 >>2get_A Pantothenate kinase; homodimer, COA biosynthesis, nucleotide binding, transferase; HET: CME COK; 2.35A {Mycobacterium tuberculosis H37RV} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* (A:1-131,A:196-312) Probab=26.72 E-value=39 Score=15.76 Aligned_cols=82 Identities=11% Similarity=0.099 Sum_probs=55.1 Q ss_pred CCCCCCEEEEEEEEEECCCHHHHHH-HHHHCC-CCHHHHHCCCCHHHHHH----------------HHHHHCCCCCCCHH Q ss_conf 5899857666431200717689999-999808-88212002279899999----------------99861245643337 Q gi|254780239|r 8 NIPRAKRVVRALCYIHGIGFKSSQD-ICNKLA-IPPERRVHQLVESEVIQ----------------IRQAIEQDYQVEGD 69 (122) Q Consensus 8 ~i~~~K~i~~aLt~I~GIG~~~A~~-Ic~~lg-Id~~~kv~~Lt~~qi~~----------------l~~~I~~~~~i~~~ 69 (122) ..+..++-.+++...-|+|.++... ++..+. .+...++.-.+-|..+- +++.++-..-++.| T Consensus 84 ~~~~~~p~VI~lvGptGVGKTTTiaKLA~~l~~~~~g~kV~Lit~DTFdiiiveGi~~l~~~~~~~l~~~~D~~ifvd~~ 163 (248) T 2get_A 84 NPDRPVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTDGFDILILEGLNVLQTGPTLMVSDLFDFSLYVDAR 163 (248) T ss_dssp TTTCCCCEEEEEEECTTSSHHHHHHHHHHHHHCSTTCCCEEEEEGGGGSEEEEECSSTTCCCSSCCGGGGCSEEEEEECC T ss_pred CCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEECCCCHHHCCCCCCEEEEEECC T ss_conf 36889988999727988873899999999985207999659996556587999420132154011000006569999799 Q ss_pred HHHHHHHHHHHHHHCCCCCC Q ss_conf 88999999999973031001 Q gi|254780239|r 70 LRRTVAMNIKRLMDLGCYRG 89 (122) Q Consensus 70 L~~~~~~~i~rl~~i~syrG 89 (122) ......--|+|...-..++| T Consensus 164 ~~~~~~~~i~R~~~~r~~~~ 183 (248) T 2get_A 164 IEDIEQWYVSRFLAMRTTAF 183 (248) T ss_dssp HHHHHHHHHHHHHHHHTTTT T ss_pred HHHHHHHHHHHHHHHHHHHC T ss_conf 89999999999999888723 No 73 >>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; NMR {Homo sapiens} (A:) Probab=25.70 E-value=31 Score=16.38 Aligned_cols=40 Identities=15% Similarity=0.081 Sum_probs=29.0 Q ss_pred EEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH Q ss_conf 66431200717689999999808882120022798999999 Q gi|254780239|r 16 VRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQI 56 (122) Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l 56 (122) ...|..|.|||+.++.. +..+||..-.-+-+.+.+++..+ T Consensus 24 ~~~l~~i~GVG~~~~~~-L~~~Gi~Tv~~la~~~~~~L~~i 63 (114) T 1b22_A 24 PISRLEQCGINANDVKK-LEEAGFHTVEAVAYAPKKELINI 63 (114) T ss_dssp CHHHHHHTTCSHHHHHH-HHTTCCSSGGGBTSSBHHHHHTT T ss_pred CHHHHHHCCCCHHHHHH-HHHCCCCHHHHHHHCCHHHHHHH T ss_conf 48999768999899999-99969853999985899999862 No 74 >>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis, plasmid; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A (A:126-253) Probab=25.49 E-value=52 Score=14.97 Aligned_cols=41 Identities=12% Similarity=0.292 Sum_probs=30.3 Q ss_pred CCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCC Q ss_conf 176899999998088821200227989999999861245643 Q gi|254780239|r 25 IGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQV 66 (122) Q Consensus 25 IG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i 66 (122) -|+..+...|.+-+|.|+. +-+++.+....|...|-+.|.. T Consensus 48 dGYR~~i~fa~~~~i~~d~-L~~ld~~~~~~Li~gIA~EY~~ 88 (128) T 2ze6_A 48 DGYRCAIRFARKHDLAISQ-LPNIDAGRHVELIEAIANEYLE 88 (128) T ss_dssp TTHHHHHHHHHHHTCCGGG-GGGCCTTHHHHHHHHHHHHHHH T ss_pred CCHHHHHHHHHHHCCCHHH-HHHHHHHHHHHHHHHHHHHHHH T ss_conf 2226899999871688778-8877657899999889999999 No 75 >>1u5t_A Appears to BE functionally related to SNF7; SNF8P; ESCRT, endosomal, trafficking, protein complex, transport protein; 3.60A {Saccharomyces cerevisiae} (A:1-77) Probab=24.97 E-value=33 Score=16.25 Aligned_cols=16 Identities=13% Similarity=0.489 Sum_probs=7.7 Q ss_pred CCCCHHHHHHHHHHHC Q ss_conf 2279899999998612 Q gi|254780239|r 46 HQLVESEVIQIRQAIE 61 (122) Q Consensus 46 ~~Lt~~qi~~l~~~I~ 61 (122) .+|.+.+++.+...++ T Consensus 22 ~~l~~~~~~~l~~QL~ 37 (77) T 1u5t_A 22 KTILEKQSVELRDQLM 37 (77) T ss_dssp SHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHH T ss_conf 7689999999999999 No 76 >>2ftc_E Mitochondrial ribosomal protein L7/12, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} (E:66-137) Probab=24.21 E-value=48 Score=15.17 Aligned_cols=53 Identities=17% Similarity=0.372 Sum_probs=41.2 Q ss_pred CCCCCCCEEE--EEEEE-EECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 7589985766--64312-00717689999999808882120022798999999986124 Q gi|254780239|r 7 VNIPRAKRVV--RALCY-IHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 7 ~~i~~~K~i~--~aLt~-I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) +.+|..+++. -++.. +-|+|..-|..++..+ |..--..++.++-+.+.+.++. T Consensus 9 ~~~~~~kKi~vIK~vr~~~tglgL~eAK~lVe~~---P~~ike~v~keeAE~ik~~Le~ 64 (72) T 2ftc_E 9 TEAKPVDKVKLIKEIKNYVQGINLVQAKKLVESL---PQEIKANVAKAEAEKIKAALEA 64 (72) T ss_pred CCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHC---CHHHHCCCCHHHHHHHHHHHHH T ss_conf 2477411457999999871799879999998708---8888708999999999999998 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=24.01 E-value=51 Score=15.04 Aligned_cols=41 Identities=17% Similarity=0.162 Sum_probs=25.2 Q ss_pred EEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH Q ss_conf 4312007176899999998088821200227989999999861 Q gi|254780239|r 18 ALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 (122) Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I 60 (122) .|..|.||+-.+|..|...+. .-..+|..|-.++..-++.+ T Consensus 13 ~L~~ikGisE~ka~KIi~aA~--kl~~~gF~Ta~e~~~~R~~v 53 (56) T 1szp_A 13 DLLEIKGISEAKADKLLNEAA--RLVPMGFVTAADFHMRRSEL 53 (56) T ss_dssp HHHTSTTCCHHHHHHHHHHHH--HHSCCSCCCHHHHHHHHHSS T ss_pred HHHHHHCCCHHHHHHHHHHHH--HHHCCCCCCHHHHHHHCCCC T ss_conf 998763999999999999999--87447996399999844798 No 78 >>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication; 2.00A {Pyrococcus furiosus} (A:212-288) Probab=22.26 E-value=60 Score=14.59 Aligned_cols=41 Identities=17% Similarity=0.142 Sum_probs=26.4 Q ss_pred EEEEECCCHHHHHHHHHHCCCCH--HHHHCCCCHHHHHHHHHH Q ss_conf 31200717689999999808882--120022798999999986 Q gi|254780239|r 19 LCYIHGIGFKSSQDICNKLAIPP--ERRVHQLVESEVIQIRQA 59 (122) Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lgId~--~~kv~~Lt~~qi~~l~~~ 59 (122) +..|-|||+.+|..+.++.|==. -..+.+++.....++.+. T Consensus 28 i~GV~GiG~ktA~kli~~~gsle~i~~~~~~~~~~~~~~~~~~ 70 (77) T 1b43_A 28 PGGIKGIGLKKALEIVRHSKDPLAKFQKQSDVDLYAIKEFFLN 70 (77) T ss_dssp TTCSTTCCHHHHHHHHHTCSSGGGGTGGGCSSCHHHHHHHHHS T ss_pred CCCCCCCCHHHHHHHHHHHCCHHHHHCCCCCCCHHHHHHHHCC T ss_conf 5658962499999999995999997522100168999998438 No 79 >>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=20.69 E-value=39 Score=15.75 Aligned_cols=40 Identities=15% Similarity=0.127 Sum_probs=26.1 Q ss_pred EEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH Q ss_conf 64312007176899999998088821200227989999999861 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I 60 (122) ..++.|.|||+.++.. +..+||.. ++||.......+.... T Consensus 12 lpi~~i~GIG~~~~~~-L~~~gI~t---i~dl~~~~~~~~~~~~ 51 (70) T 1t94_A 12 LPIRKVSGIGKVTEKM-LKALGIIT---CTELYQQRALLSLLFS 51 (70) T ss_dssp CBGGGCTTSCHHHHHH-HHHTTCCB---HHHHHHTHHHHHHHSC T ss_pred CCCCCCCCCCCCCHHH-HHHHCCCC---HHHHHHHHHHHHHHHH T ss_conf 9714025763110045-45413586---9999986777888851 No 80 >>1i4w_A Mitochondrial replication protein MTF1; mitochondrial transcription factor, transcription initiation; 2.60A {Saccharomyces cerevisiae} (A:266-353) Probab=20.59 E-value=65 Score=14.37 Aligned_cols=47 Identities=13% Similarity=0.142 Sum_probs=30.5 Q ss_pred CCEEEEEEEEEECCCHHHHHHHHHHCCCC---HHHHHCCCCHHHHHHHHHHHCC Q ss_conf 85766643120071768999999980888---2120022798999999986124 Q gi|254780239|r 12 AKRVVRALCYIHGIGFKSSQDICNKLAIP---PERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lgId---~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) .|++.-+|. ++++- |......++++ ++++..+||.+|+..|.+..++ T Consensus 18 RK~L~nsL~---~L~pg-a~~~l~~~~~~~~~~~kRpe~Ltveef~~La~~~~~ 67 (88) T 1i4w_A 18 RTPLNTVMD---SLGHG-GQQYFNSRITDKDLLKKCPIDLTNDEFIYLTKLFME 67 (88) T ss_dssp TSCTTTGGG---GSSTT-HHHHHTTTCCCCTTTSSCGGGCCHHHHHHHHHHHHT T ss_pred CCCHHHHHH---HHCCC-HHHHHHCCCCCHHHHHCCCCCCCCCHHHHHHHHHHH T ss_conf 375277776---52355-166652336527688609966666235678899860 No 81 >>1dd3_A 50S ribosomal protein L7/L12; dimer formation, flexibility, hinge region, four-helix- bundle, five-helix- bundle, alpha-beta structure; 2.00A {Thermotoga maritima} (A:58-128) Probab=20.26 E-value=41 Score=15.64 Aligned_cols=55 Identities=22% Similarity=0.423 Sum_probs=42.5 Q ss_pred CCCCCC-EEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 589985-7666431200717689999999808882120022798999999986124 Q gi|254780239|r 8 NIPRAK-RVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 8 ~i~~~K-~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) ++|++| .|.-++..+-|+|..-|..++..+.=.|..--..++.++.+.|.+.++. T Consensus 8 ~~~~~Ki~vIK~Vr~itglgLkEAK~lVe~~P~~~~~ike~vskeeAE~iK~~Le~ 63 (71) T 1dd3_A 8 SFGQNKIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVSKEEAEEIKKKLEE 63 (71) T ss_dssp ECTTCHHHHHHHHHHHHCCCHHHHHHHHTTTTSTTCEEEEEECHHHHHHHHHHHHH T ss_pred CCCCCCHHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHCCCCHHHHHHHHHHHHH T ss_conf 17764058999998855998899999997157872678538899999999999998 Done!