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 23785 Date Tue May 24 00:41:44 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780239.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 2vqe_M 30S ribosomal protein S 100.0 0 0 311.5 5.6 122 1-122 1-122 (126) 2 2zkq_m 40S ribosomal protein S 100.0 1.4E-45 0 302.1 8.4 119 1-122 12-152 (152) 3 3ofp_M 30S ribosomal protein S 100.0 2.2E-43 0 289.5 -0.1 113 2-115 1-113 (113) 4 3bbn_M Ribosomal protein S13; 100.0 5.4E-38 2.3E-42 256.0 -2.0 100 1-112 46-145 (145) 5 1ee8_A MUTM (FPG) protein; bet 96.5 0.0023 9.8E-08 41.0 4.3 50 12-61 143-195 (266) 6 3gpu_A DNA glycosylase; DNA gl 96.5 0.0026 1.1E-07 40.7 4.4 50 12-61 155-207 (256) 7 1tdz_A Formamidopyrimidine-DNA 96.4 0.003 1.2E-07 40.4 4.5 49 13-61 155-206 (272) 8 3a46_A Formamidopyrimidine-DNA 96.4 0.0029 1.2E-07 40.4 4.5 48 14-61 156-207 (289) 9 1k3x_A Endonuclease VIII; hydr 96.3 0.0035 1.5E-07 39.9 4.3 52 11-62 149-203 (262) 10 1k82_A Formamidopyrimidine-DNA 96.3 0.0043 1.8E-07 39.4 4.5 48 14-61 152-202 (268) 11 1tdh_A NEI endonuclease VIII-l 89.4 0.075 3.1E-06 31.7 0.7 42 13-54 159-203 (364) 12 1mu5_A Type II DNA topoisomera 88.7 0.37 1.6E-05 27.4 3.8 43 20-62 261-303 (471) 13 1x2i_A HEF helicase/nuclease; 84.7 0.38 1.6E-05 27.3 2.1 52 15-66 12-72 (75) 14 3fut_A Dimethyladenosine trans 83.8 1.3 5.6E-05 23.9 4.6 50 12-62 220-269 (271) 15 1z00_A DNA excision repair pro 83.7 0.27 1.1E-05 28.3 1.0 50 14-65 16-76 (89) 16 2a1j_B DNA excision repair pro 81.0 0.29 1.2E-05 28.0 0.3 49 14-64 29-88 (91) 17 3ftd_A Dimethyladenosine trans 78.4 1.8 7.5E-05 23.1 3.7 34 30-63 214-247 (249) 18 1qyr_A KSGA, high level kasuga 77.2 0.67 2.8E-05 25.7 1.2 45 12-62 206-250 (252) 19 1s5l_U Photosystem II 12 kDa e 73.3 3.5 0.00015 21.3 4.0 54 9-62 55-111 (134) 20 3bz1_U Photosystem II 12 kDa e 71.3 4 0.00017 21.0 4.0 54 9-62 25-81 (104) 21 1kft_A UVRC, excinuclease ABC 70.2 0.81 3.4E-05 25.3 0.2 46 9-56 15-61 (78) 22 2a1j_A DNA repair endonuclease 69.4 2.6 0.00011 22.1 2.7 37 19-57 6-42 (63) 23 3fhg_A Mjogg, N-glycosylase/DN 67.7 4.2 0.00018 20.8 3.4 40 17-60 117-156 (207) 24 1cuk_A RUVA protein; DNA repai 61.7 1.8 7.7E-05 23.0 0.7 20 18-37 109-128 (203) 25 2nrt_A Uvrabc system protein C 59.8 5.1 0.00022 20.3 2.7 39 17-57 168-206 (220) 26 1z00_B DNA repair endonuclease 59.8 5 0.00021 20.3 2.6 39 18-58 19-57 (84) 27 1ixr_A Holliday junction DNA h 58.4 2.5 0.00011 22.2 0.9 21 18-38 108-128 (191) 28 2ztd_A Holliday junction ATP-d 57.3 2.6 0.00011 22.2 0.8 21 18-38 124-144 (212) 29 2ihm_A POL MU, DNA polymerase 55.1 7.5 0.00031 19.3 2.9 37 17-54 102-142 (360) 30 2grj_A Dephospho-COA kinase; T 54.4 10 0.00042 18.5 3.4 54 12-65 10-67 (192) 31 2w9m_A Polymerase X; SAXS, DNA 52.7 4 0.00017 20.9 1.2 23 17-40 97-119 (578) 32 3fhf_A Mjogg, N-glycosylase/DN 51.9 4.3 0.00018 20.7 1.2 39 18-60 126-164 (214) 33 1jms_A Terminal deoxynucleotid 51.7 4.1 0.00017 20.9 1.1 25 16-41 120-144 (381) 34 1vq8_Y 50S ribosomal protein L 49.8 2.8 0.00012 21.9 0.0 45 12-57 10-54 (241) 35 2duy_A Competence protein come 49.2 9.8 0.00041 18.5 2.7 49 12-60 22-73 (75) 36 1mpg_A ALKA, 3-methyladenine D 47.7 13 0.00053 17.8 3.1 35 14-48 204-239 (282) 37 3mr3_A DNA polymerase ETA; POL 47.5 16 0.00068 17.2 3.6 40 17-56 253-292 (435) 38 1pu6_A 3-methyladenine DNA gly 45.6 17 0.00072 17.0 4.3 41 16-60 120-160 (218) 39 1m3q_A 8-oxoguanine DNA glycos 45.5 5.3 0.00022 20.2 0.9 42 14-58 227-268 (317) 40 3c65_A Uvrabc system protein C 44.1 3.9 0.00016 21.0 0.0 41 14-56 170-210 (226) 41 2bgw_A XPF endonuclease; hydro 43.8 13 0.00053 17.8 2.6 22 17-38 162-183 (219) 42 3i0w_A 8-oxoguanine-DNA-glycos 43.8 5.8 0.00024 20.0 0.9 30 15-44 209-238 (290) 43 2fmp_A DNA polymerase beta; nu 43.4 7 0.00029 19.4 1.2 39 17-56 98-140 (335) 44 2hnh_A DNA polymerase III alph 41.0 12 0.00052 17.9 2.2 50 9-58 825-884 (910) 45 2h56_A DNA-3-methyladenine gly 39.6 6.1 0.00025 19.8 0.4 45 14-64 135-180 (233) 46 2eo2_A Adult MALE hypothalamus 39.4 14 0.00059 17.5 2.3 26 33-59 36-61 (71) 47 3e1s_A Exodeoxyribonuclease V, 38.6 3.6 0.00015 21.2 -0.9 28 16-43 43-70 (574) 48 1im4_A DBH; DNA polymerase PAL 38.0 13 0.00054 17.8 1.9 20 70-89 130-149 (221) 49 2edu_A Kinesin-like protein KI 37.1 23 0.00095 16.3 3.0 42 18-59 41-89 (98) 50 3f2b_A DNA-directed DNA polyme 36.5 24 0.001 16.1 4.4 60 12-90 962-1021(1041) 51 1gm5_A RECG; helicase, replica 35.1 13 0.00055 17.7 1.6 29 11-40 109-137 (780) 52 2jhn_A ALKA, 3-methyladenine D 34.2 9.7 0.00041 18.6 0.7 33 15-48 208-241 (295) 53 2bcq_A DNA polymerase lambda; 32.9 5.8 0.00024 19.9 -0.6 30 10-40 89-118 (335) 54 1kg2_A A/G-specific adenine gl 30.9 13 0.00056 17.7 1.0 28 8-38 103-130 (225) 55 2abk_A Endonuclease III; DNA-r 30.0 14 0.00057 17.7 0.9 22 16-37 108-129 (211) 56 1orn_A Endonuclease III; DNA r 29.2 15 0.00065 17.3 1.1 27 8-37 107-133 (226) 57 3fsp_A A/G-specific adenine gl 29.1 15 0.00062 17.4 1.0 28 7-37 111-138 (369) 58 3doa_A Fibrinogen binding prot 28.7 13 0.00057 17.7 0.7 36 14-49 189-225 (288) 59 3mfi_A DNA polymerase ETA; DNA 27.8 16 0.00065 17.3 0.9 40 17-56 307-352 (520) 60 1kea_A Possible G-T mismatches 27.4 17 0.00073 17.0 1.1 25 17-41 115-139 (221) 61 1zq9_A Probable dimethyladenos 25.1 37 0.0016 14.9 3.8 32 30-62 248-279 (285) 62 3lay_A Zinc resistance-associa 23.1 41 0.0017 14.7 2.9 58 5-62 21-82 (175) 63 3n5n_X A/G-specific adenine DN 23.0 22 0.00092 16.4 0.9 20 19-38 131-150 (287) 64 1vdd_A Recombination protein R 22.6 26 0.0011 16.0 1.2 80 15-95 10-108 (228) 65 2r6f_A Excinuclease ABC subuni 22.2 42 0.0018 14.6 3.6 85 27-113 336-442 (972) 66 3hdt_A Putative kinase; struct 22.0 43 0.0018 14.6 3.1 34 7-40 7-41 (223) 67 1ngn_A Methyl-CPG binding prot 21.3 28 0.0012 15.7 1.2 19 18-36 105-123 (155) No 1 >2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ... Probab=100.00 E-value=0 Score=311.47 Aligned_cols=122 Identities=59% Similarity=0.919 Sum_probs=117.9 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 1 M~RI~g~~i~~~K~v~~aLt~I~GIG~~~A~~Ic~~lGId~~~kvg~Lt~~qi~~l~~~i~~~~~i~~~L~~~~~~~i~r 80 (126) T 2vqe_M 1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKR 80 (126) T ss_dssp -CCCSTTCCCCSSBHHHHHTTSSSCCSHHHHHHTTTTTCCTTSBGGGCCHHHHHHHHHHHHTTSCCHHHHHHHHHHHHHH T ss_pred CCEECCCCCCCCCEEEEEECCEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 97265744899978787620434838999999999859796630163999999999999831451147899999998999 Q ss_pred HHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 973031001233179878770778776577776655423469 Q gi|254780239|r 81 LMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122 (122) Q Consensus 81 l~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk 122 (122) |++|+||||+||.+|||||||||||||||+|+..+++.++|| T Consensus 81 l~~i~syrG~RH~~gLpvRGQrT~tn~rt~kg~~~~~~~kk~ 122 (126) T 2vqe_M 81 LMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKK 122 (126) T ss_dssp HHHTTCHHHHHHHTTCCSSSCCCSSCCHHHHCSCCCCCCCCS T ss_pred HHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 887431212334069987777787775567888553555667 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 3jyv_M* Probab=100.00 E-value=1.4e-45 Score=302.09 Aligned_cols=119 Identities=29% Similarity=0.472 Sum_probs=114.6 Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCC----------------- Q ss_conf 945516758998576664312007176899999998088821200227989999999861245----------------- Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQD----------------- 63 (122) Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~----------------- 63 (122) ||||+|+|||++|+|.+|||+|||||+++|.+||+.+||||++++++||++|+++|+++|+++ T Consensus 12 ivRI~g~dI~g~K~v~~aLt~I~GIG~~~A~~Ic~~lgI~~~~kvg~Lt~~ql~kl~~~I~~~~~~~ip~w~~nr~~d~~ 91 (152) T 2zkq_m 12 ILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIMQNPRQYKIPDWFLNRQKDVK 91 (152) T ss_dssp -CCCSTTCCCCSSBHHHHGGGSTTCCHHHHHHHHHHHTCCTTSBTTTSCHHHHHHHHHHHHTTCSCCSCCCSSCSSSCCC T ss_pred HHHEECCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 34132852799978876500210658999999999938995430151999999999999850001157558776566650 Q ss_pred -----CCCCHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf -----64333788999999999973031001233179878770778776577776655423469 Q gi|254780239|r 64 -----YQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122 (122) Q Consensus 64 -----~~i~~~L~~~~~~~i~rl~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk 122 (122) |++|+||++.+++||+||++|+||||+||++|||||||||||||||++++ +|.+|| T Consensus 92 ~g~~~hli~~dL~~~~~~dI~rl~~i~syRG~RH~~gLpVRGQrT~tN~R~~~~~---gv~~kK 152 (152) T 2zkq_m 92 DGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTGRRGRTV---GVSKKK 152 (152) T ss_dssp CCSSCCCSSHHHHHHHHHHHHHHHHSSCHHHHHHHHTCBSBCCCSSSSCCSSSCC---CCCCCC T ss_pred CCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC---CCCCCC T ss_conf 4531022076799999997999998605889998758987877688777778866---767789 No 3 >3ofp_M 30S ribosomal protein S13; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_M* 2wwl_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M 2qbf_M 2qbh_M* 2qbj_M* 2qou_M* 2qow_M* 2qoy_M* 2qp0_M* ... Probab=100.00 E-value=2.2e-43 Score=289.50 Aligned_cols=113 Identities=56% Similarity=0.875 Sum_probs=109.5 Q ss_pred CEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH Q ss_conf 45516758998576664312007176899999998088821200227989999999861245643337889999999999 Q gi|254780239|r 2 ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRL 81 (122) Q Consensus 2 vrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~rl 81 (122) +||+|+|||++|+|++|||+|||||+++|.+||+++||||++++++||++|++.|+++|+ +|.+|+||++.+.+||+|| T Consensus 1 aRI~g~dip~~K~v~~ALt~I~GIG~~~A~~Ic~~lgi~~~~rv~~Lt~~qi~~l~~~i~-~~~i~~~L~~~~~~~I~rl 79 (113) T 3ofp_M 1 ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA-KFVVEGDLRREISMSIKRL 79 (113) T ss_dssp CCTTSSCCCCCCCHHHHHTSSSSCCSSHHHHGGGTTTCCSSCCSSSCCTTSSTTTHHHHH-SSCCHHHHHHHTTTHHHHG T ss_pred CEECCCCCCCCCEEEEEEECEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHH T ss_conf 902686699997866550143474899999999984989874048599999999999986-1031025899999979999 Q ss_pred HHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 7303100123317987877077877657777665 Q gi|254780239|r 82 MDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGK 115 (122) Q Consensus 82 ~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~ 115 (122) ++|+||||+||.+|||||||||||||||+|+.++ T Consensus 80 ~~i~~yRG~RH~~gLpvRGQrT~tnart~k~~~k 113 (113) T 3ofp_M 80 MDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 113 (113) T ss_dssp GGSSCSTTTTTTTSSCSSSCCSSSCCSSSSCSCC T ss_pred HHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 8851042111226998887778777524588998 No 4 >3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa} Probab=100.00 E-value=5.4e-38 Score=256.01 Aligned_cols=100 Identities=48% Similarity=0.740 Sum_probs=92.9 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 ~vRI~GvnIp~nK~V~~ALT~IyGIG~~~A~~Ic~~lgId~-kkv~dLteeel~~i~~~r-----------r~~~~dIkR 113 (145) T 3bbn_M 46 CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDN-KVTKDLSEEEVIILRKEK-----------RFNRVAIER 113 (145) T ss_dssp -CCCSSSCCCCSSBTTTGGGGSTTCCSSTTTGGGTTTTCCS-CBTTSCCSSTTHHHHSSC-----------CCCSTTTHH T ss_pred EEEEECCCCCCCCEEEEHHHHHHCCCHHHHHHHHHHCCCCH-HHHHHCCHHHHHHHHHHH-----------HHHHHHHHH T ss_conf 89984874899977212355674638899999999859974-667654787999999999-----------998999999 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 Lk~I~sYRG~RH~~gLPVRGQRTrTNaRT~KG 145 (145) T 3bbn_M 114 LKEIRCYRGIRHKLGLPVRGQRTKNNCRTLKG 145 (145) T ss_dssp HHCCCCSCCTTTTTTCCSSSCCTTTCCCSSCC T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC T ss_conf 99850055445524998687778777666687 No 5 >1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 Probab=96.51 E-value=0.0023 Score=41.03 Aligned_cols=50 Identities=20% Similarity=0.284 Sum_probs=42.3 Q ss_pred CCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 85766643---120071768999999980888212002279899999998612 Q gi|254780239|r 12 AKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 12 ~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) +++|.-+| ..|-|||...+..||..++|+|..++.+|+++|+..|-+.+. T Consensus 143 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~L~~~e~~~L~~~~~ 195 (266) T 1ee8_A 143 ARPLKALLLDQRLAAGVGNIYADEALFRARLSPFRPARSLTEEEARRLYRALR 195 (266) T ss_dssp CSBHHHHHHHSSSSTTCCHHHHHHHHHHTTCCSSSBGGGCCHHHHHHHHHHHH T ss_pred CCHHHHHHCCCCEECCCCHHHHHHHHHHHCCCHHHCCCCCCHHHHHHHHHHHH T ss_conf 64065762157612246699999999985798023267289999999999999 No 6 >3gpu_A DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 3go8_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* ... Probab=96.47 E-value=0.0026 Score=40.73 Aligned_cols=50 Identities=18% Similarity=0.257 Sum_probs=42.3 Q ss_pred CCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 85766643---120071768999999980888212002279899999998612 Q gi|254780239|r 12 AKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 12 ~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) +.+|.-+| ..|-|||...|..||..++|+|..++++||++|+..|-+.+- T Consensus 155 ~~~Ik~~LlDQ~~iaGIGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~ 207 (256) T 3gpu_A 155 KRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMV 207 (256) T ss_dssp CSBHHHHHHCTTTSTTCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHH T ss_pred CCCHHHHHCCCCEECCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH T ss_conf 76455631136513343488999999973148376313389999999999999 No 7 >1tdz_A Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1pji_A* 1pm5_A* 1xc8_A* 3c58_A* 1nnj_A 1kfv_A 1pjj_A* Probab=96.45 E-value=0.003 Score=40.39 Aligned_cols=49 Identities=24% Similarity=0.382 Sum_probs=41.3 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 155 ~~Ik~~LlDQ~~iaGIGNiy~~EiLf~a~I~P~~~~~~L~~~e~~~L~~~~~ 206 (272) T 1tdz_A 155 KKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSII 206 (272) T ss_dssp SBHHHHHHTSSSSSCCCHHHHHHHHHHTTCCTTCBGGGCCHHHHHHHHHHHH T ss_pred CCCCEEEECCCEECCCCHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHH T ss_conf 3200267507635444473798998872798676752407999999999999 No 8 >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 Probab=96.44 E-value=0.0029 Score=40.40 Aligned_cols=48 Identities=23% Similarity=0.288 Sum_probs=40.3 Q ss_pred EEEEEE--EE-E-ECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 766643--12-0-071768999999980888212002279899999998612 Q gi|254780239|r 14 RVVRAL--CY-I-HGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 14 ~i~~aL--t~-I-~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) ++.-+| ++ | -|||.-.|..||..++|+|..++.+||++|+..|-+.+. T Consensus 156 ~ik~~LLdq~~i~aGIGNiya~EiLf~a~I~P~~~~~~Ls~~e~~~L~~~i~ 207 (289) T 3a46_A 156 PIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIK 207 (289) T ss_dssp BHHHHHHCSSSSCBCCCHHHHHHHHHHTTBCTTCBGGGCCHHHHHHHHHHHH T ss_pred HHHHHHHCCCCEECCCCHHHHHHHHHHHHCCHHHHHHHCCHHHHHHHHHHHH T ss_conf 2457752466267064089999999985068546667499999999999999 No 9 >1k3x_A Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A* Probab=96.32 E-value=0.0035 Score=39.91 Aligned_cols=52 Identities=13% Similarity=0.307 Sum_probs=44.0 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 149 ~~~~Ik~~LlDQ~~iaGIGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~ 203 (262) T 1k3x_A 149 RNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLE 203 (262) T ss_dssp TTSCHHHHTTCTTTSBTCCHHHHHHHHHHHTCCSSCCGGGSCHHHHHHHHHHHHH T ss_pred CCHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 0068999984177445656999999998720685450134447789999999999 No 10 >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} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 Probab=96.27 E-value=0.0043 Score=39.40 Aligned_cols=48 Identities=19% Similarity=0.208 Sum_probs=40.7 Q ss_pred EEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC Q ss_conf 766643---120071768999999980888212002279899999998612 Q gi|254780239|r 14 RVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122) Q Consensus 14 ~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122) .|.-+| ..|-|||...+..||..++|+|..++++|+++|+..|-+.+. T Consensus 152 ~ik~~LlDQ~~iaGIGN~y~~EiLf~a~IhP~~~~~~L~~~e~~~L~~~~~ 202 (268) T 1k82_A 152 AIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIK 202 (268) T ss_dssp BHHHHHTCTTTCSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHH T ss_pred CCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHH T ss_conf 541488617604667588999999872798668632399999999999999 No 11 >1tdh_A NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 Probab=89.44 E-value=0.075 Score=31.67 Aligned_cols=42 Identities=26% Similarity=0.460 Sum_probs=34.3 Q ss_pred CEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHH Q ss_conf 5766643---12007176899999998088821200227989999 Q gi|254780239|r 13 KRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVI 54 (122) Q Consensus 13 K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~ 54 (122) ++|.-+| +.|-|||.-+|..||..++|+|..++.+|++++.. T Consensus 159 ~~IK~~LLDQ~iiaGIGNIYadEiLf~A~IhP~r~a~~ls~~~~~ 203 (364) T 1tdh_A 159 RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQ 203 (364) T ss_dssp SBHHHHTTCTTTSTTCCHHHHHHHHHHHTCCTTSBHHHHHGGGC- T ss_pred CCHHHHHHCCCEECCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHC T ss_conf 608998724770225428899999998489966741234576641 No 12 >1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} SCOP: a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A* 1z5a_A* 1z59_A* 1z5c_A* 2hkj_A* Probab=88.66 E-value=0.37 Score=27.38 Aligned_cols=43 Identities=19% Similarity=0.404 Sum_probs=38.8 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 261 ~~Fs~V~~~~a~~i~~~~g~~~~~~p~~l~~~e~~~l~~a~~~ 303 (471) T 1mu5_A 261 NEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK 303 (471) T ss_dssp TSSSSCCHHHHHHHHHHTTCCTTSBGGGCCTTHHHHHHHHHHH T ss_pred HHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 7547769899999999749997777144999999999999985 No 13 >1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Probab=84.66 E-value=0.38 Score=27.31 Aligned_cols=52 Identities=12% Similarity=0.109 Sum_probs=36.0 Q ss_pred EEEEEEEEECCCHHHHHHHHHHCC---------CCHHHHHCCCCHHHHHHHHHHHCCCCCC Q ss_conf 666431200717689999999808---------8821200227989999999861245643 Q gi|254780239|r 15 VVRALCYIHGIGFKSSQDICNKLA---------IPPERRVHQLVESEVIQIRQAIEQDYQV 66 (122) Q Consensus 15 i~~aLt~I~GIG~~~A~~Ic~~lg---------Id~~~kv~~Lt~~qi~~l~~~I~~~~~i 66 (122) ..+.|+.|-|||+..|..|+...| .+.-..+..+.+.-..+|.+++..+|.- T Consensus 12 ~~~~L~~IpgIG~~~a~~L~~~F~s~~~i~~As~eeL~~v~GIG~~~a~~i~~~~~~~~~~ 72 (75) T 1x2i_A 12 QRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYIE 72 (75) T ss_dssp HHHHHTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSCCCC T ss_pred HHHHHCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCHHHC T ss_conf 9999848999429999999999688898999789999855897999999999998576320 No 14 >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* Probab=83.79 E-value=1.3 Score=23.89 Aligned_cols=50 Identities=22% Similarity=0.349 Sum_probs=39.6 Q ss_pred CCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 857666431200717689999999808882120022798999999986124 Q gi|254780239|r 12 AKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) .|.+.-+|..+ +........++..+||+|+.+..+||.+|+..|-+.+++ T Consensus 220 RK~l~n~L~~~-~~~~~~~~~~l~~~~i~~~~R~e~Ls~~~~~~L~~~l~~ 269 (271) T 3fut_A 220 RKTLLNALAAA-GYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLEG 269 (271) T ss_dssp TSCHHHHHHHT-TCCHHHHHHHHHHTTCCTTCCGGGCCHHHHHHHHHHHC- T ss_pred HHHHHHHHHHH-CCCHHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHC T ss_conf 57999998763-688889999999869796639154999999999999865 No 15 >1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Probab=83.74 E-value=0.27 Score=28.26 Aligned_cols=50 Identities=10% Similarity=0.207 Sum_probs=32.9 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCH-----------HHHHHHHHHHCCCCC Q ss_conf 7666431200717689999999808882120022798-----------999999986124564 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVE-----------SEVIQIRQAIEQDYQ 65 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~-----------~qi~~l~~~I~~~~~ 65 (122) ++..+|+.|.|||...|..++...| .-..+-.-+. ....+|.+++.++|. T Consensus 16 ~~~~~L~~I~gIG~~~a~~L~~~Fg--sl~~i~~As~eeL~~i~GiG~~~A~~I~~~f~~pf~ 76 (89) T 1z00_A 16 RVTECLTTVKSVNKTDSQTLLTTFG--SLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFL 76 (89) T ss_dssp HHHHHHTTSSSCCHHHHHHHHHHTC--BHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSCSS T ss_pred HHHHHHCCCCCCCHHHHHHHHHHHC--CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCHHC T ss_conf 9999875899759999999999948--889999987877726899699999999999808420 No 16 >2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Probab=81.01 E-value=0.29 Score=28.03 Aligned_cols=49 Identities=10% Similarity=0.244 Sum_probs=32.2 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHH-----------HHHHHHHCCCC Q ss_conf 7666431200717689999999808882120022798999-----------99998612456 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEV-----------IQIRQAIEQDY 64 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi-----------~~l~~~I~~~~ 64 (122) ++..+|+.|.|||...|..++...| + -..+..-+.+++ .+|.+++.++| T Consensus 29 ~~~~~L~~I~gIGk~~A~~L~~~F~-S-i~~l~~As~eeL~~i~GIG~~~A~~I~~~f~~pf 88 (91) T 2a1j_B 29 RVTECLTTVKSVNKTDSQTLLTTFG-S-LEQLIAASREDLALCPGLGPQKARRLFDVLHEPF 88 (91) T ss_dssp HHHHHHTTSTTCCHHHHHHHHHHHS-S-HHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHSCS T ss_pred HHHHHHCCCCCCCHHHHHHHHHHHC-C-CHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCH T ss_conf 9999864688859999999999958-8-2989998999755779969999999999984814 No 17 >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* Probab=78.45 E-value=1.8 Score=23.13 Aligned_cols=34 Identities=24% Similarity=0.466 Sum_probs=30.1 Q ss_pred HHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 9999998088821200227989999999861245 Q gi|254780239|r 30 SQDICNKLAIPPERRVHQLVESEVIQIRQAIEQD 63 (122) Q Consensus 30 A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~ 63 (122) ...++..+||+|+.++.+|+.+|+..|-+.++++ T Consensus 214 ~~~~l~~~~i~~~~R~e~Ls~~~~~~L~~~l~~~ 247 (249) T 3ftd_A 214 PEELLKEAGINPDARVEQLSLEDFFKLYRLIEDS 247 (249) T ss_dssp CHHHHHHTTCCTTCCGGGCCHHHHHHHHHHHHCC T ss_pred HHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHHC T ss_conf 9999998795988894779999999999999971 No 18 >1qyr_A KSGA, high level kasugamycin resistance protein, S-; adenosine dimethyltransferase, rRNA modification, transferase, translation; 2.10A {Escherichia coli} SCOP: c.66.1.24 Probab=77.19 E-value=0.67 Score=25.75 Aligned_cols=45 Identities=13% Similarity=0.278 Sum_probs=34.4 Q ss_pred CCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 857666431200717689999999808882120022798999999986124 Q gi|254780239|r 12 AKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) .|.+.-+|..++. ..+...+||+|+.+..+|+.+|+.+|-+.+++ T Consensus 206 RK~l~n~L~~~~~------~~~l~~~~i~~~~R~e~Ls~~~~~~L~~~l~~ 250 (252) T 1qyr_A 206 RKTIRNSLGNLFS------VEVLTGMGIDPAMRAENISVAQYCQMANYLAE 250 (252) T ss_dssp TSBHHHHTTTTCC------HHHHHHTTCCTTSBGGGSCHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHCC------HHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHH T ss_conf 2889998740441------99999779882339333999999999999984 No 19 >1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} Probab=73.27 E-value=3.5 Score=21.31 Aligned_cols=54 Identities=15% Similarity=0.158 Sum_probs=40.0 Q ss_pred CCCCCEEEEEEEEEECCCHHHHHHHHHHCC---CCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 899857666431200717689999999808---882120022798999999986124 Q gi|254780239|r 9 IPRAKRVVRALCYIHGIGFKSSQDICNKLA---IPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 9 i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lg---Id~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) ++=|.--.-.|+.+.|||+..|..|...-. ++.=..+.-+++.+++.|+++++. T Consensus 55 idlN~A~~~eL~~lpGig~~~A~~Iv~~gpf~svedl~~v~Gig~~~~e~l~~~l~~ 111 (134) T 1s5l_U 55 IDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEH 111 (134) T ss_dssp EETTTSCGGGGGGSTTCTHHHHHHHHHTCCCSSGGGGGGCTTCCHHHHHHHHHHHTT T ss_pred EECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHHHCC T ss_conf 416407899997710346999999998278487999961775799999999986535 No 20 >3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3kzi_U* 3a0b_U* 3a0h_U* Probab=71.27 E-value=4 Score=20.96 Aligned_cols=54 Identities=15% Similarity=0.158 Sum_probs=39.9 Q ss_pred CCCCCEEEEEEEEEECCCHHHHHHHHHHCC---CCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 899857666431200717689999999808---882120022798999999986124 Q gi|254780239|r 9 IPRAKRVVRALCYIHGIGFKSSQDICNKLA---IPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 9 i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lg---Id~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) ++=|.--...|+.+-|||+..|..|+..=. ++.-.++..+++..++.|..+++. T Consensus 25 idlN~As~~eL~~lpGig~~~A~~Iv~~gpf~s~~dL~~V~Gig~~~~e~ik~yl~~ 81 (104) T 3bz1_U 25 IDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEH 81 (104) T ss_dssp EETTSSCGGGGGGSTTTTHHHHHHHHHSCCCSSGGGGGGCTTCCHHHHHHHHHHGGG T ss_pred EECCCCCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHHHCC T ss_conf 578408999996589979999999997499798999963899899999999986545 No 21 >1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Probab=70.20 E-value=0.81 Score=25.26 Aligned_cols=46 Identities=20% Similarity=0.324 Sum_probs=32.6 Q ss_pred CCCCCEEE-EEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH Q ss_conf 89985766-6431200717689999999808882120022798999999 Q gi|254780239|r 9 IPRAKRVV-RALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQI 56 (122) Q Consensus 9 i~~~K~i~-~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l 56 (122) ++-.|.+. -.|..|.|||+.++..++...+ .-..+.+.+.+|+.++ T Consensus 15 ~~R~K~~~~S~L~~IpGIG~k~ak~Ll~~F~--si~~i~~As~eeL~~v 61 (78) T 1kft_A 15 VPRGSHMNTSSLETIEGVGPKRRQMLLKYMG--GLQGLRNASVEEIAKV 61 (78) T ss_dssp --------CCGGGGCTTCSSSHHHHHHHHHS--CHHHHHHCCHHHHTTS T ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHC--CHHHHHHHCHHHHHCC T ss_conf 6675442338265699932999999999929--9499988379999807 No 22 >2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A* Probab=69.37 E-value=2.6 Score=22.10 Aligned_cols=37 Identities=16% Similarity=0.271 Sum_probs=31.6 Q ss_pred EEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHH Q ss_conf 312007176899999998088821200227989999999 Q gi|254780239|r 19 LCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIR 57 (122) Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~ 57 (122) |..|-|||...+..++...| .=..+.+.|.+|+.++. T Consensus 6 L~~IPGIg~~~~~~Ll~~fg--Si~~l~~as~eeL~~v~ 42 (63) T 2a1j_A 6 LLKMPGVNAKNCRSLMHHVK--NIAELAALSQDELTSIL 42 (63) T ss_dssp HHTSTTCCHHHHHHHHHHCS--SHHHHHTCCHHHHHHHH T ss_pred HHCCCCCCHHHHHHHHHHCC--CHHHHHHCCHHHHHHCC T ss_conf 85299988999999999867--99999879999998786 No 23 >3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} Probab=67.65 E-value=4.2 Score=20.84 Aligned_cols=40 Identities=18% Similarity=0.360 Sum_probs=27.6 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 117 ~~L~~l~GIG~ktA~~~L~~~~~~~~~----~vD~hv~Ri~~r~ 156 (207) T 3fhg_A 117 ERLLNIKGIGMQEASHFLRNVGYFDLA----IIDRHIIDFMRRI 156 (207) T ss_dssp HHHTTSTTCCHHHHHHHHHHTTCCSSC----CCCHHHHHHHHHT T ss_pred HHHHHCCCCCHHHHHHHHHHHCCCCCC----CCCHHHHHHHHHH T ss_conf 999987887299999999997688766----7847999999992 No 24 >1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A Probab=61.68 E-value=1.8 Score=23.05 Aligned_cols=20 Identities=30% Similarity=0.511 Sum_probs=9.7 Q ss_pred EEEEEECCCHHHHHHHHHHC Q ss_conf 43120071768999999980 Q gi|254780239|r 18 ALCYIHGIGFKSSQDICNKL 37 (122) Q Consensus 18 aLt~I~GIG~~~A~~Ic~~l 37 (122) +|+++-|||.++|..|+-.| T Consensus 109 ~L~~vpGIGkKtA~rIilEL 128 (203) T 1cuk_A 109 ALVKLPGIGKKTAERLIVEM 128 (203) T ss_dssp HHHTSTTCCHHHHHHHHHHH T ss_pred HHHCCCCCCHHHHHHHHHHH T ss_conf 86069987799999999999 No 25 >2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Probab=59.76 E-value=5.1 Score=20.27 Aligned_cols=39 Identities=13% Similarity=0.221 Sum_probs=33.8 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 168 S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~I~~As~eeL~~v~ 206 (220) T 2nrt_A 168 SVLDNVPGIGPIRKKKLIEHFG--SLENIRSASLEEIARVI 206 (220) T ss_dssp HHHTTSTTCCHHHHHHHHHHHC--SHHHHHTSCHHHHHHHH T ss_pred CCCHHCCCCCHHHHHHHHHHCC--CHHHHHHCCHHHHHHCC T ss_conf 6410037969999999999818--99999718999998686 No 26 >1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Probab=59.76 E-value=5 Score=20.34 Aligned_cols=39 Identities=15% Similarity=0.229 Sum_probs=31.0 Q ss_pred EEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHH Q ss_conf 43120071768999999980888212002279899999998 Q gi|254780239|r 18 ALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQ 58 (122) Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~ 58 (122) -|..|-|||+..+..|+...| .=..+.+.+.+++..+.- T Consensus 19 ~L~~iPGIg~k~~~~Ll~~f~--sl~~i~~AS~eeL~~v~G 57 (84) T 1z00_B 19 FLLKMPGVNAKNCRSLMHHVK--NIAELAALSQDELTSILG 57 (84) T ss_dssp HHHTCSSCCHHHHHHHHHHSS--CHHHHHHSCHHHHHHHHS T ss_pred HHHCCCCCCHHHHHHHHHHCC--CHHHHHHCCHHHHHHCCC T ss_conf 998389999999999999966--999998599999988759 No 27 >1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2 Probab=58.38 E-value=2.5 Score=22.21 Aligned_cols=21 Identities=24% Similarity=0.349 Sum_probs=10.6 Q ss_pred EEEEEECCCHHHHHHHHHHCC Q ss_conf 431200717689999999808 Q gi|254780239|r 18 ALCYIHGIGFKSSQDICNKLA 38 (122) Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lg 38 (122) +|+++-|||.++|..|+-.|. T Consensus 108 ~L~~vpGIGkKtAerIilELk 128 (191) T 1ixr_A 108 LLTSASGVGRRLAERIALELK 128 (191) T ss_dssp HHTTSTTCCHHHHHHHHHHHT T ss_pred HHHCCCCCCHHHHHHHHHHHH T ss_conf 950188846889999999998 No 28 >2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Probab=57.30 E-value=2.6 Score=22.15 Aligned_cols=21 Identities=29% Similarity=0.472 Sum_probs=13.7 Q ss_pred EEEEEECCCHHHHHHHHHHCC Q ss_conf 431200717689999999808 Q gi|254780239|r 18 ALCYIHGIGFKSSQDICNKLA 38 (122) Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lg 38 (122) +|+++-|||.++|..|+-.|. T Consensus 124 ~L~~vpGIGkKtAeRIilELk 144 (212) T 2ztd_A 124 ALTRVPGIGKRGAERMVLELR 144 (212) T ss_dssp HHHTSTTCCHHHHHHHHHHHT T ss_pred HHHHCCCCCHHHHHHHHHHHH T ss_conf 985177824888999999997 No 29 >2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Probab=55.06 E-value=7.5 Score=19.26 Aligned_cols=37 Identities=11% Similarity=0.302 Sum_probs=24.6 Q ss_pred EEEEEEECCCHHHHHHHHHHCCCCHHH----HHCCCCHHHHH Q ss_conf 643120071768999999980888212----00227989999 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLAIPPER----RVHQLVESEVI 54 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~----kv~~Lt~~qi~ 54 (122) ..|+.|+|||+.+|..+-.. ||..-. ....|+..|.- T Consensus 102 ~~l~~i~GvGpk~a~~l~~~-Gi~si~dL~~~~~~l~~~q~~ 142 (360) T 2ihm_A 102 KLFTQVFGVGVKTANRWYQE-GLRTLDELREQPQRLTQQQKA 142 (360) T ss_dssp HHHHTSTTCCHHHHHHHHHT-TCCSHHHHHTCCTTCCHHHHH T ss_pred HHHHHCCCCCHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHH T ss_conf 99975778789999999983-988799998778750154653 No 30 >2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme A kinase, structural genomics, joint center for structural genomics, JCSG; HET: ADP COD; 2.60A {Thermotoga maritima} Probab=54.41 E-value=10 Score=18.49 Aligned_cols=54 Identities=15% Similarity=0.129 Sum_probs=37.0 Q ss_pred CCEEEEEEEEEECCCHHHHHHHHH-HCCC---CHHHHHCCCCHHHHHHHHHHHCCCCC Q ss_conf 857666431200717689999999-8088---82120022798999999986124564 Q gi|254780239|r 12 AKRVVRALCYIHGIGFKSSQDICN-KLAI---PPERRVHQLVESEVIQIRQAIEQDYQ 65 (122) Q Consensus 12 ~K~i~~aLt~I~GIG~~~A~~Ic~-~lgI---d~~~kv~~Lt~~qi~~l~~~I~~~~~ 65 (122) .-++.+|||.--|-|.++...++. ++|+ |.+.-+++|-++-...|.+....+.. T Consensus 10 ~~~mIIgiTG~igSGKStv~~~l~~~~g~~vidaD~i~~~l~~~~~~~i~~~fg~~i~ 67 (192) T 2grj_A 10 HHHMVIGVTGKIGTGKSTVCEILKNKYGAHVVNVDRIGHEVLEEVKEKLVELFGGSVL 67 (192) T ss_dssp CCEEEEEEECSTTSSHHHHHHHHHHHHCCEEEEHHHHHHHHHHHTHHHHHHHHCGGGB T ss_pred CCCEEEEEECCCCCCHHHHHHHHHHHCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 5777999878987889999999988539989970699999866458899887097222 No 31 >2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Probab=52.67 E-value=4 Score=20.94 Aligned_cols=23 Identities=22% Similarity=0.245 Sum_probs=17.4 Q ss_pred EEEEEEECCCHHHHHHHHHHCCCC Q ss_conf 643120071768999999980888 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLAIP 40 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgId 40 (122) ..|+.|+|||+++|.++.+ .||. T Consensus 97 ~~l~~I~GvGpk~A~~l~~-~Gi~ 119 (578) T 2w9m_A 97 LDLLGVRGLGPKKIRSLWL-AGID 119 (578) T ss_dssp HHHTTSTTCCHHHHHHHHH-TTCC T ss_pred HHHHCCCCCCHHHHHHHHH-HCCC T ss_conf 9984789868999999998-0998 No 32 >3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} PDB: 3knt_A* Probab=51.85 E-value=4.3 Score=20.73 Aligned_cols=39 Identities=13% Similarity=0.249 Sum_probs=29.1 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 126 ~L~~l~GIG~ktA~~~L~~~~~~~~~i----vD~hv~Ri~~rl 164 (214) T 3fhf_A 126 LVRNIKGIGYKEASHFLRNVGYDDVAI----IDRHILRELYEN 164 (214) T ss_dssp HHHHSTTCCHHHHHHHHHHTTCCSCCC----CCHHHHHHHHHT T ss_pred HHHHCCCCCHHHHHHHHHHHCCCCCCC----CCHHHHHHHHHH T ss_conf 997488876999999999976998631----327999999993 No 33 >1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A* Probab=51.65 E-value=4.1 Score=20.86 Aligned_cols=25 Identities=12% Similarity=0.424 Sum_probs=19.6 Q ss_pred EEEEEEEECCCHHHHHHHHHHCCCCH Q ss_conf 66431200717689999999808882 Q gi|254780239|r 16 VRALCYIHGIGFKSSQDICNKLAIPP 41 (122) Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~lgId~ 41 (122) ...|+.|+|||+.+|..+.+ +||.. T Consensus 120 l~~l~~I~GiGpk~a~~l~~-~Gi~t 144 (381) T 1jms_A 120 FKLFTSVFGVGLKTAEKWFR-MGFRT 144 (381) T ss_dssp HHHHHTSTTCCHHHHHHHHH-TTCCS T ss_pred HHHHHHCCCCCHHHHHHHHH-CCCCC T ss_conf 89987377878999999998-69777 No 34 >1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Probab=49.83 E-value=2.8 Score=21.92 Aligned_cols=45 Identities=16% Similarity=0.215 Sum_probs=32.0 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 10 ~~~~~~~l~~i~gvG~~~~~~l~~-~g~~~~~~i~~~~~~~L~~~~ 54 (241) T 1vq8_Y 10 AEEEYTELTDISGVGPSKAESLRE-AGFESVEDVRGADQSALADVS 54 (241) T ss_dssp ---------------------------------------------- T ss_pred HHHHHHHHCCCCCCCHHHHHHHHH-CCCCCHHHHHHCCHHHHHHCC T ss_conf 688674325889989999999997-689999999869999997468 No 35 >2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} SCOP: a.60.2.7 Probab=49.15 E-value=9.8 Score=18.53 Aligned_cols=49 Identities=14% Similarity=0.199 Sum_probs=33.9 Q ss_pred CCEEEEEEEEEECCCHHHHHHHHHHCC---CCHHHHHCCCCHHHHHHHHHHH Q ss_conf 857666431200717689999999808---8821200227989999999861 Q gi|254780239|r 12 AKRVVRALCYIHGIGFKSSQDICNKLA---IPPERRVHQLVESEVIQIRQAI 60 (122) Q Consensus 12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lg---Id~~~kv~~Lt~~qi~~l~~~I 60 (122) |.--.-.|..+-|||+..|..|.+.=. ++.-..+..+++..+++|..+| T Consensus 22 N~As~~eL~~lpGig~~~A~~Iv~~R~f~s~~dL~~v~gi~~~~~~~i~~~l 73 (75) T 2duy_A 22 NEASLEELMALPGIGPVLARRIVEGRPYARVEDLLKVKGIGPATLERLRPYL 73 (75) T ss_dssp TTCCHHHHTTSTTCCHHHHHHHHHTCCCSSGGGGGGSTTCCHHHHHHHGGGE T ss_pred CCCCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHHCCCCCHHHHHHHHHHC T ss_conf 1287999977789899999999985898989999757898999999999772 No 36 >1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A* 3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A* 3d4v_A* Probab=47.70 E-value=13 Score=17.84 Aligned_cols=35 Identities=11% Similarity=0.061 Sum_probs=23.7 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHCCCCHHH-HHCCC Q ss_conf 766643120071768999999980888212-00227 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNKLAIPPER-RVHQL 48 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~-kv~~L 48 (122) .+.-.|+.|.|||+.+|..++-..-=+|+. .++|+ T Consensus 204 e~~~~L~~l~GIGpWTA~~vll~~lg~~D~fp~~Dl 239 (282) T 1mpg_A 204 QAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDY 239 (282) T ss_dssp HHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCCTTCH T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCHHH T ss_conf 999999976798869999999997699883874349 No 37 >3mr3_A DNA polymerase ETA; POL ETA, polymerase, thymine dimer, CPD, XPV, xeroderma PIGM variant, DNA damage; HET: DNA TTD DZ4; 1.75A {Homo sapiens} PDB: 3mr2_A* 3mr5_A* 3mr6_A* Probab=47.50 E-value=16 Score=17.19 Aligned_cols=40 Identities=20% Similarity=0.192 Sum_probs=29.6 Q ss_pred EEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH Q ss_conf 6431200717689999999808882120022798999999 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQI 56 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l 56 (122) ..+..+.|||.++...++..+||..-.-+..++.+++... T Consensus 253 lpi~~l~GiG~k~~~~~L~~~gi~ti~dl~~~~~~~L~~~ 292 (435) T 3mr3_A 253 MPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSH 292 (435) T ss_dssp CBGGGSTTCSSHHHHHHHHHHTCCBGGGGGGSCHHHHHHH T ss_pred CCCCEECCCCHHHHHHHHHHHCCCCHHHHHHCCHHHHHHH T ss_conf 7677607767578999999958947899873999899999 No 38 >1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A* Probab=45.63 E-value=17 Score=17.01 Aligned_cols=41 Identities=17% Similarity=0.078 Sum_probs=27.4 Q ss_pred EEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH Q ss_conf 664312007176899999998088821200227989999999861 Q gi|254780239|r 16 VRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 (122) Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I 60 (122) .-.|..+.|||+.+|..|+..+.=.|.. .-+..+..+-.-+ T Consensus 120 ~~~L~~lpGIG~kTA~~il~~~~~~~~~----~vD~~v~Rv~~Rl 160 (218) T 1pu6_A 120 REWLLDQKGIGKESADAILCYACAKEVM----VVDKYSYLFLKKL 160 (218) T ss_dssp HHHHHTSTTCCHHHHHHHHHHTTCCSCC----CCCHHHHHHHHHT T ss_pred HHHHHCCCCCCHHHHHHHHHHHCCCCCC----CCCHHHHHHHHHH T ss_conf 9999848996699999999998799806----2042599999990 No 39 >1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} SCOP: a.96.1.3 d.129.1.2 PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A* 2nol_A* 3ktu_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* ... Probab=45.51 E-value=5.3 Score=20.22 Aligned_cols=42 Identities=29% Similarity=0.448 Sum_probs=25.3 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 227 e~~~~L~~l~GIG~wtAd~ilLf~lg~~dafP--v-D~~v~r~~~ 268 (317) T 1m3q_A 227 EAHKALCILPGVGTKVADCICLMALDKPQAVP--V-EVHMWHIAQ 268 (317) T ss_dssp HHHHHHTTSTTCCHHHHHHHHHHHSCCTTCCC--C-SHHHHHHHH T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHCCCCCEEE--E-EHHHHHHHH T ss_conf 99999985489488999999998579998677--5-299999999 No 40 >3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Probab=44.07 E-value=3.9 Score=21.03 Aligned_cols=41 Identities=17% Similarity=0.233 Sum_probs=30.7 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 ~~~S~Ld~I~GIG~~~~~~Ll~~Fg--s~~~i~~As~eeL~~v 210 (226) T 3c65_A 170 MFHSVLDDIPGVGEKRKKALLNYFG--SVKKMKEATVEELQRA 210 (226) T ss_dssp ------------------------------------------- T ss_pred HCCCCCCCCCCCCHHHHHHHHHHCC--CHHHHHHCCHHHHHHC T ss_conf 2037110268869999999999818--9999973899999876 No 41 >2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Probab=43.81 E-value=13 Score=17.83 Aligned_cols=22 Identities=23% Similarity=0.400 Sum_probs=18.7 Q ss_pred EEEEEEECCCHHHHHHHHHHCC Q ss_conf 6431200717689999999808 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLA 38 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lg 38 (122) ..|+.|.|||...|..|+...+ T Consensus 162 ~~L~~Ipgi~~~~A~~Ll~~f~ 183 (219) T 2bgw_A 162 YILQSFPGIGRRTAERILERFG 183 (219) T ss_dssp HHHHTSTTCCHHHHHHHHHHHS T ss_pred HHHHCCCCCCHHHHHHHHHHCC T ss_conf 9984079989999999999869 No 42 >3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A Probab=43.80 E-value=5.8 Score=19.95 Aligned_cols=30 Identities=13% Similarity=-0.066 Sum_probs=21.3 Q ss_pred EEEEEEEEECCCHHHHHHHHHHCCCCHHHH Q ss_conf 666431200717689999999808882120 Q gi|254780239|r 15 VVRALCYIHGIGFKSSQDICNKLAIPPERR 44 (122) Q Consensus 15 i~~aLt~I~GIG~~~A~~Ic~~lgId~~~k 44 (122) +.-.|+.|.|||+.+|..||-..-=.++.- T Consensus 209 ~~~~L~~i~GIG~wtAd~ilLf~lg~~d~f 238 (290) T 3i0w_A 209 CHEELKKFMGVGPQVADCIMLFSMQKYSAF 238 (290) T ss_dssp HHHHHTTSTTCCHHHHHHHHHHHHCCTTCC T ss_pred HHHHHHHCCCCCHHHHHHHHHHHCCCCCEE T ss_conf 999998679948899999999967999967 No 43 >2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ... Probab=43.36 E-value=7 Score=19.44 Aligned_cols=39 Identities=18% Similarity=0.239 Sum_probs=24.7 Q ss_pred EEEEEEECCCHHHHHHHHHHCCCCHHHH----HCCCCHHHHHHH Q ss_conf 6431200717689999999808882120----022798999999 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLAIPPERR----VHQLVESEVIQI 56 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~k----v~~Lt~~qi~~l 56 (122) ..|+.|+|||+++|..+- .+||..-.- ...|++.|..-| T Consensus 98 ~~l~~I~GvGpk~a~~l~-~~Gi~ti~dL~~~~~kl~~~q~~gl 140 (335) T 2fmp_A 98 NFLTRVSGIGPSAARKFV-DEGIKTLEDLRKNEDKLNHHQRIGL 140 (335) T ss_dssp HHHTTSTTCCHHHHHHHH-HTTCCSHHHHHTCGGGSCHHHHHHH T ss_pred HHHHHCCCCCHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 998745687989999999-8188759999877887688999889 No 44 >2hnh_A DNA polymerase III alpha subunit; DNA replication, nucleotidyltransferase, POL beta, PHP; HET: DNA; 2.30A {Escherichia coli} PDB: 2hqa_A* Probab=40.95 E-value=12 Score=17.93 Aligned_cols=50 Identities=14% Similarity=0.148 Sum_probs=32.2 Q ss_pred CCCCCEEEEEEEEEECCCHHHHHHHHHHC---CC-----CHHHHH--CCCCHHHHHHHHH Q ss_conf 89985766643120071768999999980---88-----821200--2279899999998 Q gi|254780239|r 9 IPRAKRVVRALCYIHGIGFKSSQDICNKL---AI-----PPERRV--HQLVESEVIQIRQ 58 (122) Q Consensus 9 i~~~K~i~~aLt~I~GIG~~~A~~Ic~~l---gI-----d~~~kv--~~Lt~~qi~~l~~ 58 (122) +.++..|.++|+.|.|||...|..|...= |. |-..++ +.++..+++.|.+ T Consensus 825 ~~~~~~i~~gl~~ikgig~~~a~~Iv~~R~~~~~f~s~~Df~~r~~~~~~~~~~~~~Li~ 884 (910) T 2hnh_A 825 VNDDGEIVYGIGAIKGVGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLEKLIM 884 (910) T ss_dssp ECTTSCEECBGGGSTTCCHHHHHHHHHHHHTTCCCSSHHHHTTSSCSSSSCHHHHHHHHH T ss_pred ECCCCEEEECHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHH T ss_conf 768995983254359989999999999897479989999999870646799999999987 No 45 >2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} Probab=39.59 E-value=6.1 Score=19.83 Aligned_cols=45 Identities=18% Similarity=0.152 Sum_probs=28.8 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHCCCCHHH-HHCCCCHHHHHHHHHHHCCCC Q ss_conf 766643120071768999999980888212-002279899999998612456 Q gi|254780239|r 14 RVVRALCYIHGIGFKSSQDICNKLAIPPER-RVHQLVESEVIQIRQAIEQDY 64 (122) Q Consensus 14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~-kv~~Lt~~qi~~l~~~I~~~~ 64 (122) .+.-.|+.|.|||+.+|..++-..-=+|+. .++|+ .|.+.++.-| T Consensus 135 e~~~~L~~ikGIGpWTA~~illf~lgr~DvfP~~Dl------~l~ra~~~ly 180 (233) T 2h56_A 135 TVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVGDV------GLQRGAKWLY 180 (233) T ss_dssp HHHHHHHTSTTCCHHHHHHHHHHTTCCSCCCCTTCH------HHHHHHHHHH T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCH------HHHHHHHHHH T ss_conf 999998806884878999999996899978986379------9999999982 No 46 >2eo2_A Adult MALE hypothalamus cDNA, riken FULL-length enriched library, clone:A230045M11...; FTHFSDC1, structural genomics, NPPSFA; NMR {Mus musculus} Probab=39.40 E-value=14 Score=17.55 Aligned_cols=26 Identities=27% Similarity=0.247 Sum_probs=20.5 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~kt-dP~~LT~EE~~~F~RL 61 (71) T 2eo2_A 36 RLKKLGIHKT-DPSTLTEEEVRKFARL 61 (71) T ss_dssp HHHHHTCCCC-STTTCCHHHHHHHHHT T ss_pred HHHHCCCCCC-CCCCCCHHHHHHHHEE T ss_conf 9998398989-9021899998440131 No 47 >3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, hydrolase; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A* Probab=38.64 E-value=3.6 Score=21.23 Aligned_cols=28 Identities=18% Similarity=0.310 Sum_probs=24.4 Q ss_pred EEEEEEEECCCHHHHHHHHHHCCCCHHH Q ss_conf 6643120071768999999980888212 Q gi|254780239|r 16 VRALCYIHGIGFKSSQDICNKLAIPPER 43 (122) Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~lgId~~~ 43 (122) .|.|..|.|||+..|..|...+|++++. T Consensus 43 Py~l~~i~gi~f~~aD~ia~~~g~~~~d 70 (574) T 3e1s_A 43 LFTLTEVEGIGFLTADKLWQARGGALDD 70 (574) T ss_dssp -CGGGTSSSCCHHHHHTTC-------CC T ss_pred CCEEEECCCCCHHHHHHHHHHCCCCCCC T ss_conf 9123125889958999999976999899 No 48 >1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix, fidelity, processivity, transferase; 2.30A {Sulfolobus solfataricus} SCOP: e.8.1.7 Probab=37.95 E-value=13 Score=17.83 Aligned_cols=20 Identities=20% Similarity=0.233 Sum_probs=7.0 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 130 ~a~~ir~~I~~~~gl~~siG 149 (221) T 1im4_A 130 LARKIKQEILEKEKITVTVG 149 (221) T ss_dssp HHHHHHHHHHHHHCCCEEEE T ss_pred HHHHHHHHHHHHHCCCEEEE T ss_conf 99999999999869876653 No 49 >2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7 Probab=37.12 E-value=23 Score=16.28 Aligned_cols=42 Identities=21% Similarity=0.189 Sum_probs=27.2 Q ss_pred EEEEEECCCHHHHHHHHHHC-------CCCHHHHHCCCCHHHHHHHHHH Q ss_conf 43120071768999999980-------8882120022798999999986 Q gi|254780239|r 18 ALCYIHGIGFKSSQDICNKL-------AIPPERRVHQLVESEVIQIRQA 59 (122) Q Consensus 18 aLt~I~GIG~~~A~~Ic~~l-------gId~~~kv~~Lt~~qi~~l~~~ 59 (122) -|..+.|||+..|..|...- .++.=.++.-+++..+++|.+. T Consensus 41 eL~~lpgIg~~~A~~Iv~~R~~~G~f~sledL~~v~Gi~~k~~eki~k~ 89 (98) T 2edu_A 41 DLRSLQRIGPKKAQLIVGWRELHGPFSQVEDLERVEGITGKQMESFLKA 89 (98) T ss_dssp HHHHSTTCCHHHHHHHHHHHHHHCCCSSGGGGGGSTTCCHHHHHHHHHH T ss_pred HHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHC T ss_conf 9964799899999999999998599288999844899899999999983 No 50 >3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C; HET: DGT; 2.39A {Geobacillus kaustophilus} PDB: 3f2c_A* 3f2d_A* Probab=36.54 E-value=24 Score=16.14 Aligned_cols=60 Identities=20% Similarity=0.284 Sum_probs=36.9 Q ss_pred CCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCH Q ss_conf 8576664312007176899999998088821200227989999999861245643337889999999999730310012 Q gi|254780239|r 12 AKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGL 90 (122) Q Consensus 12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~rl~~i~syrG~ 90 (122) +..|.++|..|.|+|...|..|...-.=.|. .|-+++.. +.- + -+..++.|+..++..++ T Consensus 962 ~~~I~~gl~aIkGlG~~~a~~Iv~~R~~g~F-----~s~~Df~~-R~~------~-------~k~~le~Li~~Gafd~l 1021 (1041) T 3f2b_A 962 GNSLIPPFNAIPGLGTNVAQAIVRAREEGEF-----LSKEDLQQ-RGK------L-------SKTLLEYLESRGCLDSL 1021 (1041) T ss_dssp TTEEECCGGGSTTCCHHHHHHHHHHHHTSCC-----CSHHHHHH-HHT------C-------CHHHHHHHHHTTTTTTS T ss_pred CCEEEECHHHCCCCCHHHHHHHHHHHCCCCC-----CCHHHHHH-HHC------C-------CHHHHHHHHHCCCCCCC T ss_conf 9949951564389799999999998667999-----99999997-328------9-------99999999977997789 No 51 >1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19 Probab=35.10 E-value=13 Score=17.74 Aligned_cols=29 Identities=21% Similarity=0.423 Sum_probs=21.3 Q ss_pred CCCEEEEEEEEEECCCHHHHHHHHHHCCCC Q ss_conf 985766643120071768999999980888 Q gi|254780239|r 11 RAKRVVRALCYIHGIGFKSSQDICNKLAIP 40 (122) Q Consensus 11 ~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId 40 (122) ..+.+.-.+++++|||+++|..+ +++||. T Consensus 109 ~~~~l~~~i~~lkGVGpk~a~~L-~klGI~ 137 (780) T 1gm5_A 109 EEVDLSTDIQYAKGVGPNRKKKL-KKLGIE 137 (780) T ss_dssp CCCCSCCCSSSSSSCCHHHHHHH-HTTTCC T ss_pred CCCCCCCCCCCCCCCCHHHHHHH-HHCCCC T ss_conf 77899998601788159999999-976999 No 52 >2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A Probab=34.15 E-value=9.7 Score=18.57 Aligned_cols=33 Identities=18% Similarity=0.184 Sum_probs=21.2 Q ss_pred EEEEEEEEECCCHHHHHHHHHHCCCCHHH-HHCCC Q ss_conf 66643120071768999999980888212-00227 Q gi|254780239|r 15 VVRALCYIHGIGFKSSQDICNKLAIPPER-RVHQL 48 (122) Q Consensus 15 i~~aLt~I~GIG~~~A~~Ic~~lgId~~~-kv~~L 48 (122) +.-.|+.|.|||+.+|..|+-. +++++. .++|+ T Consensus 208 ~~~~L~~i~GIGpWTA~~ill~-~lg~d~fP~~D~ 241 (295) T 2jhn_A 208 AYEYLTSFKGIGRWTAELVLSI-ALGKNVFPADDL 241 (295) T ss_dssp HHHHHHTSTTCCHHHHHHHHHH-TTCCCCCCTTCH T ss_pred HHHHHHHCCCCCHHHHHHHHHH-HCCCCCCCCCCH T ss_conf 8889984599488999999998-169895227459 No 53 >2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ... Probab=32.85 E-value=5.8 Score=19.95 Aligned_cols=30 Identities=20% Similarity=0.241 Sum_probs=21.0 Q ss_pred CCCCEEEEEEEEEECCCHHHHHHHHHHCCCC Q ss_conf 9985766643120071768999999980888 Q gi|254780239|r 10 PRAKRVVRALCYIHGIGFKSSQDICNKLAIP 40 (122) Q Consensus 10 ~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId 40 (122) ...-++...|+.|+|||+++|..+- .+||. T Consensus 89 ~~~~p~~~~l~~I~GvGpk~a~~l~-~~Gi~ 118 (335) T 2bcq_A 89 SESVPVLELFSNIWGAGTKTAQMWY-QQGFR 118 (335) T ss_dssp CTTHHHHHHHHTSTTCCHHHHHHHH-HTTCC T ss_pred HHHCCHHHHHHCCCCCCHHHHHHHH-HCCCC T ss_conf 6334015665118876889999999-81925 No 54 >1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A Probab=30.93 E-value=13 Score=17.73 Aligned_cols=28 Identities=14% Similarity=0.301 Sum_probs=20.5 Q ss_pred CCCCCCEEEEEEEEEECCCHHHHHHHHHHCC Q ss_conf 5899857666431200717689999999808 Q gi|254780239|r 8 NIPRAKRVVRALCYIHGIGFKSSQDICNKLA 38 (122) Q Consensus 8 ~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lg 38 (122) ++|.+ .-.|.++-|||+.+|..|+..+- T Consensus 103 ~~p~~---~~~L~~LpGVG~kTA~~il~~a~ 130 (225) T 1kg2_A 103 KFPET---FEEVAALPGVGRSTAGAILSLSL 130 (225) T ss_dssp SCCCS---HHHHHTSTTCCHHHHHHHHHHHH T ss_pred CCCCH---HHHHHHCCCCCHHHHHHHHHHHC T ss_conf 99742---99997589874789999999852 No 55 >2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Probab=29.96 E-value=14 Score=17.65 Aligned_cols=22 Identities=27% Similarity=0.324 Sum_probs=17.8 Q ss_pred EEEEEEEECCCHHHHHHHHHHC Q ss_conf 6643120071768999999980 Q gi|254780239|r 16 VRALCYIHGIGFKSSQDICNKL 37 (122) Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~l 37 (122) .-.|..+-|||+.+|..|+..+ T Consensus 108 ~~~L~~LpGVG~kTA~~il~~a 129 (211) T 2abk_A 108 RAALEALPGVGRKTANVVLNTA 129 (211) T ss_dssp HHHHHHSTTCCHHHHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHHHHH T ss_conf 9998717887369999999987 No 56 >1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A* Probab=29.20 E-value=15 Score=17.31 Aligned_cols=27 Identities=22% Similarity=0.423 Sum_probs=20.9 Q ss_pred CCCCCCEEEEEEEEEECCCHHHHHHHHHHC Q ss_conf 589985766643120071768999999980 Q gi|254780239|r 8 NIPRAKRVVRALCYIHGIGFKSSQDICNKL 37 (122) Q Consensus 8 ~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~l 37 (122) .+|.+ .-.|.++-|||+.+|..|+..+ T Consensus 107 ~vP~~---~~~L~~LpGVG~kTA~~il~~a 133 (226) T 1orn_A 107 EVPRD---RDELMKLPGVGRKTANVVVSVA 133 (226) T ss_dssp SCCSC---HHHHTTSTTCCHHHHHHHHHHH T ss_pred CCCCC---HHHHHHCCCCCHHHHHHHHHHH T ss_conf 79878---9999748775367999999998 No 57 >3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A* Probab=29.10 E-value=15 Score=17.42 Aligned_cols=28 Identities=11% Similarity=0.230 Sum_probs=21.5 Q ss_pred CCCCCCCEEEEEEEEEECCCHHHHHHHHHHC Q ss_conf 7589985766643120071768999999980 Q gi|254780239|r 7 VNIPRAKRVVRALCYIHGIGFKSSQDICNKL 37 (122) Q Consensus 7 ~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~l 37 (122) -.+|.+. -.|..+-|||+.+|.+|+..+ T Consensus 111 g~~P~~~---~~L~~LpGVG~~TA~ail~~a 138 (369) T 3fsp_A 111 GKVPDDP---DEFSRLKGVGPYTVGAVLSLA 138 (369) T ss_dssp TCCCCSH---HHHHTSTTCCHHHHHHHHHHH T ss_pred CCCCCCH---HHHHHCCCHHHHHHHHHHHHH T ss_conf 9999879---998524225889999999986 No 58 >3doa_A Fibrinogen binding protein; structural genomics, MCSG., PSI-2, protein structure initiative, midwest center for structural genomics; 2.81A {Staphylococcus aureus subsp} Probab=28.75 E-value=13 Score=17.68 Aligned_cols=36 Identities=8% Similarity=0.148 Sum_probs=26.8 Q ss_pred EEEEEEEEE-ECCCHHHHHHHHHHCCCCHHHHHCCCC Q ss_conf 766643120-071768999999980888212002279 Q gi|254780239|r 14 RVVRALCYI-HGIGFKSSQDICNKLAIPPERRVHQLV 49 (122) Q Consensus 14 ~i~~aLt~I-~GIG~~~A~~Ic~~lgId~~~kv~~Lt 49 (122) .+.-+|..- -|+|+..|..+|..+|+++...+.+.- T Consensus 189 ~l~k~L~~~~~g~~~~l~~ei~~ra~~~~~~~~~~~~ 225 (288) T 3doa_A 189 NIAKQLLNQFEGFSPLITNEIVSRRQFMTSSTLPEAF 225 (288) T ss_dssp CHHHHHHHHBTTCCHHHHHHHHTTSSSCSTTHHHHHH T ss_pred CHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCHHHHH T ss_conf 1999999863899989999999974999755689999 No 59 >3mfi_A DNA polymerase ETA; DNA damage, DNA repair, DNA replication, DNA synthesis, NUCL binding, magnesium; HET: DNA DOC TTD DTP; 1.76A {Saccharomyces cerevisiae} PDB: 3mfh_A* 2r8j_A* 2r8k_A* 2wtf_A* 1jih_A* Probab=27.80 E-value=16 Score=17.29 Aligned_cols=40 Identities=8% Similarity=0.198 Sum_probs=27.3 Q ss_pred EEEEEEECCCHHHHHHHHHHCCCCH---HHHHCCC---CHHHHHHH Q ss_conf 6431200717689999999808882---1200227---98999999 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLAIPP---ERRVHQL---VESEVIQI 56 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgId~---~~kv~~L---t~~qi~~l 56 (122) ..++.|.|||..++..++..+++.. =..+++| +..++.++ T Consensus 307 lpI~~i~GIG~~~~~kL~~~L~~~~~~gI~~i~dl~~~~~~~L~~~ 352 (520) T 3mfi_A 307 FEITSFWTLGGVLGKELIDVLDLPHENSIKHIRETWPDNAGQLKEF 352 (520) T ss_dssp CCGGGSTTCSSHHHHHHHHHTTCCSSSHHHHHHHHSCSCHHHHHHH T ss_pred CCCCEECCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH T ss_conf 9801006747899999999856556685746997743899999988 No 60 >1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} SCOP: a.96.1.2 Probab=27.43 E-value=17 Score=17.00 Aligned_cols=25 Identities=12% Similarity=0.087 Sum_probs=19.7 Q ss_pred EEEEEEECCCHHHHHHHHHHCCCCH Q ss_conf 6431200717689999999808882 Q gi|254780239|r 17 RALCYIHGIGFKSSQDICNKLAIPP 41 (122) Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lgId~ 41 (122) -.|..+-|||+.+|..|+..+-=.| T Consensus 115 ~eL~~LPGVG~ktA~~vl~~a~~~~ 139 (221) T 1kea_A 115 KAILDLPGVGKYTCAAVMCLAFGKK 139 (221) T ss_dssp HHHHTSTTCCHHHHHHHHHHTTCCC T ss_pred HHHHCCCCCCHHHHHHHHHHHCCCC T ss_conf 8874489876567999999853887 No 61 >1zq9_A Probable dimethyladenosine transferase; SGC, structural genomics, structural genomics consortium; HET: SAM; 1.90A {Homo sapiens} SCOP: c.66.1.24 Probab=25.12 E-value=37 Score=14.93 Aligned_cols=32 Identities=13% Similarity=0.242 Sum_probs=25.1 Q ss_pred HHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 999999808882120022798999999986124 Q gi|254780239|r 30 SQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 30 A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122) ...++..+|+++ .+..+||.+|+.+|.+.+++ T Consensus 248 i~~~l~~~g~~~-~R~E~Ls~~~f~~L~~~l~~ 279 (285) T 1zq9_A 248 IQQILTSTGFSD-KRARSMDIDDFIRLLHGFNA 279 (285) T ss_dssp HHHHHHHHTCTT-CBGGGCCHHHHHHHHHHHHT T ss_pred HHHHHHHCCCCC-CCHHHCCHHHHHHHHHHHHH T ss_conf 999998569977-88044999999999999997 No 62 >3lay_A Zinc resistance-associated protein; salmonella typhimurium LT2, ZRAP, periplasm, structural genomics; 2.70A {Salmonella enterica subsp} Probab=23.07 E-value=41 Score=14.69 Aligned_cols=58 Identities=9% Similarity=0.062 Sum_probs=35.6 Q ss_pred ECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHC-CCCHHH---HHCCCCHHHHHHHHHHHCC Q ss_conf 167589985766643120071768999999980-888212---0022798999999986124 Q gi|254780239|r 5 AGVNIPRAKRVVRALCYIHGIGFKSSQDICNKL-AIPPER---RVHQLVESEVIQIRQAIEQ 62 (122) Q Consensus 5 ~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~l-gId~~~---kv~~Lt~~qi~~l~~~I~~ 62 (122) -++...-++.+.++|-.+-+++...+..++... |-...+ -..+||++|..++.++.++ T Consensus 21 ~~~~mk~~~~~~~~l~a~~~~~~~s~~a~a~~~~G~g~g~~~~~~~~LT~EQq~~~~~I~~~ 82 (175) T 3lay_A 21 QSNAMKRNNKSAIALIALSLLALSSGAAFAGHHWGNNDGMWQQGGSPLTTEQQATAQKIYDD 82 (175) T ss_dssp -----------------------------------------------CCHHHHHHHHHHHHH T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 55426689999999999999996123888654679889988877888999999999999999 No 63 >3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices, helix-hairpin-helix motif, iron-sulfur cluste hydrolase; 2.30A {Homo sapiens} Probab=22.96 E-value=22 Score=16.38 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=16.0 Q ss_pred EEEEECCCHHHHHHHHHHCC Q ss_conf 31200717689999999808 Q gi|254780239|r 19 LCYIHGIGFKSSQDICNKLA 38 (122) Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lg 38 (122) |..+-|||+++|..|+..+- T Consensus 131 l~~LPGVG~kTA~aIl~~af 150 (287) T 3n5n_X 131 QQLLPGVGRYTAGAIASIAF 150 (287) T ss_dssp HHHSTTCCHHHHHHHHHHHS T ss_pred CCCCCCCCHHHHHHHHHHHH T ss_conf 04688756899999999883 No 64 >1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A Probab=22.65 E-value=26 Score=15.95 Aligned_cols=80 Identities=25% Similarity=0.333 Sum_probs=45.9 Q ss_pred EEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC----CCCCCH-------HHHH--------HHH Q ss_conf 666431200717689999999808882120022798999999986124----564333-------7889--------999 Q gi|254780239|r 15 VVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ----DYQVEG-------DLRR--------TVA 75 (122) Q Consensus 15 i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~----~~~i~~-------~L~~--------~~~ 75 (122) +.-+|+++=|||+++|..+...+=-.+...+.+|.+.=.+ +.+-|.. ....+. |-.| +.. T Consensus 10 LI~~l~kLPGIG~KsA~RlA~~LL~~~~~~~~~La~~i~~-~k~~i~~C~~C~~lse~~~C~IC~D~~Rd~~~iCVVE~~ 88 (228) T 1vdd_A 10 LIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLE-AKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEP 88 (228) T ss_dssp HHHHHHTSTTCCHHHHHHHHHHHSSSCHHHHHHHHHHHHH-HHHHCEECSSSCCEESSSSCHHHHCSSSCTTEEEEESSH T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCH T ss_conf 9999966899988999999999981999999999999999-998188386788716777766435777765458997789 Q ss_pred HHHHHHHHCCCCCCHHHHCC Q ss_conf 99999973031001233179 Q gi|254780239|r 76 MNIKRLMDLGCYRGLRHRRG 95 (122) Q Consensus 76 ~~i~rl~~i~syrG~RH~~g 95 (122) .|+.-+=+.+.|+|.=|..| T Consensus 89 ~Dl~aIE~tg~y~G~YhVLg 108 (228) T 1vdd_A 89 GDVIALERSGEYRGLYHVLH 108 (228) T ss_dssp HHHHHTTTTSSCCSEEEECS T ss_pred HHHHHHHHCCCCCEEEEECC T ss_conf 99999986081126998668 No 65 >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} Probab=22.22 E-value=42 Score=14.58 Aligned_cols=85 Identities=14% Similarity=0.086 Sum_probs=47.7 Q ss_pred HHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC-----------------CCCCCHH---HHHHHHHH--HHHHHHC Q ss_conf 689999999808882120022798999999986124-----------------5643337---88999999--9999730 Q gi|254780239|r 27 FKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ-----------------DYQVEGD---LRRTVAMN--IKRLMDL 84 (122) Q Consensus 27 ~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~-----------------~~~i~~~---L~~~~~~~--i~rl~~i 84 (122) ...-..+|+..|||+++...+|++++.+.|-.=-+. .+..++- |.+...+. ...-..+ T Consensus 336 ~~~l~~~a~~~~~~~~~P~~~L~~~~~~~ll~G~~~~~~~~~~~~~~~~~~~~~~~~eGvi~~l~r~~~~~~s~~~r~~l 415 (972) T 2r6f_A 336 PQLLEAVCRHYGIPMDVPVKDLPKEQLDKILYGSGGEPIYFRYTNDFGQVREQYIAFEGVIPNVERRYRETSSDYIREQM 415 (972) T ss_dssp HHHHHHHHHHHCCCSSCBGGGSCHHHHHHHHHCCTTCCCCBCCBCSSSCBCCBCCCCCCHHHHHHHHHHHCCCTTHHHHH T ss_pred HHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCCEEEEEECCCCCEEECCCCCCCHHHHHHHHHHHCCCHHHHHHH T ss_conf 99999999985999888846668999999853899751467642367833211456432578999999864278899999 Q ss_pred CCCCCHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 31001233179878770778776577776 Q gi|254780239|r 85 GCYRGLRHRRGLPVRGQRTHTNARTRKKF 113 (122) Q Consensus 85 ~syrG~RH~~gLpvRGQRT~tn~rt~k~~ 113 (122) ..|++... =--|.|.|-+..|+..+=. T Consensus 416 ~~y~~~~~--Cp~C~G~RL~~~al~v~i~ 442 (972) T 2r6f_A 416 EKYMAEQP--CPTCQGYRLKKESLAVLVG 442 (972) T ss_dssp GGGEEEEE--CTTTTTSCBCTTTTTEESS T ss_pred HHHCCCCC--CCCCCCCCCCHHHHCCCCC T ss_conf 98536877--6665465577787506117 No 66 >3hdt_A Putative kinase; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940} Probab=22.03 E-value=43 Score=14.56 Aligned_cols=34 Identities=15% Similarity=0.162 Sum_probs=26.7 Q ss_pred CCCCCCCEEEEEEEEEECCCHHH-HHHHHHHCCCC Q ss_conf 75899857666431200717689-99999980888 Q gi|254780239|r 7 VNIPRAKRVVRALCYIHGIGFKS-SQDICNKLAIP 40 (122) Q Consensus 7 ~~i~~~K~i~~aLt~I~GIG~~~-A~~Ic~~lgId 40 (122) --+-.++++.++++.-+|-|.++ |..+++.+|+. T Consensus 7 ~~~m~~~~~iItI~g~~GsGKsTia~~LA~~Lg~~ 41 (223) T 3hdt_A 7 GRFMGNKNLIITIEREYGSGGRIVGKKLAEELGIH 41 (223) T ss_dssp -----CCCEEEEEEECTTSCHHHHHHHHHHHHTCE T ss_pred CCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCC T ss_conf 75246899799857999899799999999994986 No 67 >1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} SCOP: a.96.1.2 PDB: 3iho_A Probab=21.29 E-value=28 Score=15.74 Aligned_cols=19 Identities=21% Similarity=0.107 Sum_probs=12.8 Q ss_pred EEEEEECCCHHHHHHHHHH Q ss_conf 4312007176899999998 Q gi|254780239|r 18 ALCYIHGIGFKSSQDICNK 36 (122) Q Consensus 18 aLt~I~GIG~~~A~~Ic~~ 36 (122) .|+.+.|||+.+|..+.-- T Consensus 105 ~l~~LpGVG~ytad~~~if 123 (155) T 1ngn_A 105 YPIELHGIGKYGNDSYRIF 123 (155) T ss_dssp SGGGSTTCCHHHHHHHHHH T ss_pred CCCCCCCCCHHHHHHHHHH T ss_conf 1675898219999999999 Done!