Query gi|254780636|ref|YP_003065049.1| ribonuclease D [Candidatus Liberibacter asiaticus str. psy62] Match_columns 207 No_of_seqs 126 out of 2436 Neff 6.8 Searched_HMMs 23785 Date Tue May 31 18:21:46 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780636.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1yt3_A Ribonuclease D, RNAse D 100.0 0 0 307.9 15.6 188 2-192 1-191 (375) 2 2hbj_A Exosome complex exonucl 100.0 0 0 295.4 14.4 176 10-188 95-271 (410) 3 3cym_A Uncharacterized protein 100.0 0 0 288.9 13.5 175 10-189 26-205 (440) 4 2e6m_A Werner syndrome ATP-dep 100.0 1.1E-37 4.6E-42 237.0 11.1 167 17-183 37-207 (208) 5 2hhv_A DNA polymerase I; DNA r 100.0 1.2E-34 4.9E-39 219.4 11.7 180 20-203 17-201 (580) 6 1vk0_A Hypothetical protein; h 100.0 8.3E-34 3.5E-38 214.5 10.9 151 17-169 43-205 (206) 7 2kfn_A Klenow fragment of DNA 100.0 2E-31 8.4E-36 200.6 11.6 199 3-203 6-226 (605) 8 1x9m_A DNA polymerase; DNA plo 99.9 1E-25 4.4E-30 167.4 10.9 177 22-203 1-230 (698) 9 3m8r_A DNA polymerase I, therm 99.9 5E-24 2.1E-28 157.6 8.6 155 27-203 2-161 (540) 10 1bgx_T TAQ DNA polymerase; DNA 99.7 6.3E-18 2.6E-22 122.2 7.4 146 24-203 306-453 (832) 11 1wlj_A Interferon stimulated g 99.4 1.1E-12 4.6E-17 91.7 8.2 143 18-175 3-173 (189) 12 2p1j_A POLIII, DNA polymerase 99.1 3.1E-10 1.3E-14 77.5 6.9 142 14-177 6-182 (186) 13 2is3_A Ribonuclease T; RNAse, 99.0 9.9E-10 4.2E-14 74.5 8.2 142 18-179 15-209 (215) 14 2ioc_B Three prime repair exon 98.7 4.4E-08 1.9E-12 65.0 8.5 134 20-171 12-215 (242) 15 1y97_A Three prime repair exon 98.6 2.5E-07 1.1E-11 60.6 8.8 82 74-171 113-210 (238) 16 2f96_A Ribonuclease T; RNAse, 98.6 3.9E-07 1.6E-11 59.4 9.8 86 76-176 128-218 (224) 17 2qxf_A Exodeoxyribonuclease I; 98.4 3.6E-06 1.5E-10 53.9 10.7 134 18-170 7-200 (482) 18 3ikm_A DNA polymerase subunit 98.2 2.3E-06 9.9E-11 54.9 6.0 99 73-173 194-349 (1172) 19 2gui_A DNA polymerase III epsi 97.9 3.5E-05 1.5E-09 48.1 7.2 133 18-168 7-182 (194) 20 2d5r_A CCR4-NOT transcription 97.6 0.00033 1.4E-08 42.4 8.3 141 16-174 20-238 (252) 21 2xri_A ERI1 exoribonuclease 3; 97.6 0.00034 1.4E-08 42.4 8.2 133 22-170 33-213 (224) 22 1qht_A Protein (DNA polymerase 97.6 0.0023 9.6E-08 37.6 12.4 165 4-171 107-330 (775) 23 1uoc_A POP2; hydrolase, DEDD n 97.5 0.0014 5.8E-08 38.8 10.6 140 16-171 34-265 (289) 24 1s5j_A DNA polymerase I; repli 97.4 0.0011 4.7E-08 39.3 9.6 145 19-167 189-389 (847) 25 2py5_A DNA polymerase; protein 97.3 0.0035 1.5E-07 36.5 11.1 142 20-170 6-183 (575) 26 2p51_A SPCC18.06C protein; DED 97.3 0.00094 4E-08 39.8 7.9 140 16-173 41-258 (333) 27 3nae_A DNA polymerase, GP43; R 96.8 0.0059 2.5E-07 35.2 8.0 97 71-169 208-340 (903) 28 2gv9_A DNA polymerase; polymer 96.7 0.0046 1.9E-07 35.8 7.0 97 71-169 415-552 (1193) 29 3iay_A DNA polymerase delta ca 96.5 0.012 4.9E-07 33.4 7.9 102 66-169 320-467 (919) 30 2gbz_A Oligoribonuclease; ORN, 96.1 0.0022 9.4E-08 37.6 2.5 28 17-46 6-33 (194) 31 2igi_A Oligoribonuclease; RNAs 96.0 0.0028 1.2E-07 37.1 2.5 27 18-46 3-29 (180) 32 3k59_A POL II, DNA polymerase 95.8 0.0074 3.1E-07 34.6 4.1 142 20-168 153-350 (786) 33 1w0h_A 3'-5' exonuclease ERI1; 95.4 0.11 4.6E-06 27.8 11.1 77 78-170 109-194 (204) 34 3d45_A Poly(A)-specific ribonu 95.4 0.023 9.5E-07 31.8 5.2 99 70-173 272-394 (507) 35 1noy_A Protein (DNA polymerase 95.1 0.14 5.8E-06 27.2 10.4 95 71-167 205-335 (388) 36 3cg7_A CRN-4, cell death-relat 94.4 0.22 9.1E-06 26.1 9.5 134 21-170 20-208 (308) 37 2a1r_A Poly(A)-specific ribonu 92.9 0.18 7.8E-06 26.5 5.5 99 70-173 277-399 (430) 38 1zbu_A ERI-1 homolog, 3'-5' ex 89.0 0.97 4.1E-05 22.3 7.9 74 80-169 229-311 (349) 39 1zbh_A 3'-5' exonuclease ERI1; 73.5 4 0.00017 18.7 11.3 76 78-169 177-261 (299) 40 2hwk_A Helicase NSP2; rossman 33.6 20 0.00085 14.6 2.3 16 141-156 300-315 (320) 41 2vwa_A Putative uncharacterize 27.9 25 0.0011 14.1 3.8 25 145-169 42-66 (101) No 1 >1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5 Probab=100.00 E-value=0 Score=307.87 Aligned_cols=188 Identities=24% Similarity=0.361 Sum_probs=167.5 Q ss_pred CCEEECCC--CCCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEE Q ss_conf 72153257--888578-424898279971777898544507999984189428997465778570677677732364023 Q gi|254780636|r 2 TTIRVHEG--DIPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKI 78 (207) Q Consensus 2 ~~~~~~~~--dl~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV 78 (207) |||+++.. +|.+.+ .++.+++|||||||+++++|++++||||||++++ +|++++.... ....|+++|+|++|+|| T Consensus 1 m~y~~I~t~~~L~~~~~~l~~~~~ia~DtE~~~~~ty~~~l~LiQi~~~~~-~~liD~l~~~-~~~~L~~ll~~~~i~kv 78 (375) T 1yt3_A 1 MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEH-LALIDPLGIT-DWSPLKAILRDPSITKF 78 (375) T ss_dssp CCCEEECSHHHHHHHHHHHTTSSEEEEEEEEECCSCSSCEEEEEEEECSSC-EEEECGGGCS-CCHHHHHHHHCTTSEEE T ss_pred CCEEEECCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEEEEEEEECCE-EEEEECCCCC-CHHHHHHHHHCCCCEEE T ss_conf 927998989999999999847990899798489888888789999876892-7999658987-78999999819886199 Q ss_pred ECCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHH Q ss_conf 01000016888654200000004578988652110000008877765420024675200365654432368999986459 Q gi|254780636|r 79 FHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVV 158 (207) Q Consensus 79 ~Hn~~~D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~ 158 (207) |||+++|+.+|.+++|+.+.|+||||+|+.+++ ++.++||+.+++++||++++|+.|+|||+.||||++|+.|||.||+ T Consensus 79 ~h~~~~D~~~L~~~~~~~~~~~fDt~ia~~~~~-~~~~~~l~~l~~~~l~~~l~K~~~~sdW~~rPLs~~ql~YAa~Dv~ 157 (375) T 1yt3_A 79 LHAGSEDLEVFLNVFGELPQPLIDTQILAAFCG-RPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVW 157 (375) T ss_dssp ESSCHHHHHHHHHHHSSCCSSEEEHHHHHHHTT-CCTTCCHHHHHHHHHCCCCCCTTTTSCTTSSSCCHHHHHHHHHHHH T ss_pred EECHHHHHHHHHHHCCCCCCCEEECHHHHHHHC-CCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHCCCE T ss_conf 725586799999964988887166388898838-7506788899999864503305545222566687899999840732 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH Q ss_conf 9999999999999974918999999964006899 Q gi|254780636|r 159 HLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAE 192 (207) Q Consensus 159 ~l~~L~~~l~~~L~~~~~~~~~~~e~~~l~~~~~ 192 (207) ||++||+.|.++|.+.|+.+|+.+||+.+..... T Consensus 158 ~l~~l~~~l~~~L~~~~~~~~~~ee~~~l~~~~~ 191 (375) T 1yt3_A 158 YLLPITAKLMVETEASGWLPAALDECRLMQMRRQ 191 (375) T ss_dssp THHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH T ss_pred EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 3799999999877630004678999999874431 No 2 >2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance, RNA processing, hydrolase, gene regulation; 2.10A {Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB: 2hbk_A 2hbl_A* 2hbm_A* Probab=100.00 E-value=0 Score=295.35 Aligned_cols=176 Identities=22% Similarity=0.204 Sum_probs=159.0 Q ss_pred CCCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHH Q ss_conf 888578-4248982799717778985445079999841894289974657785706776777323640230100001688 Q gi|254780636|r 10 DIPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAV 88 (207) Q Consensus 10 dl~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~ 88 (207) +|.+.+ .++.++.|||||||++.+++++++||||+|++++ +|++++.........|+++|+|++|+|||||+++|+.+ T Consensus 95 ~L~~~~~~L~~~~~iavDtE~~~~~t~~~~l~LiQi~t~~~-~~liD~l~l~~~l~~L~~ll~d~~I~KV~H~~~~Dl~~ 173 (410) T 2hbj_A 95 ELESMLEDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTRER-DYLVDTLKLRENLHILNEVFTNPSIVKVFHGAFMDIIW 173 (410) T ss_dssp HHHHHHHHHTTCSEEEEEEEEECSSSSSCEEEEEEEECSSC-EEEEETTTTTTTGGGGHHHHTCTTSEEEESSCHHHHHH T ss_pred HHHHHHHHHHCCCEEEEEEEECCCCCCCCCEEEEEEEECCC-CEEEEECCCCCCHHHHHHHHCCCCCEEEEECHHHHHHH T ss_conf 99999999845991999704778851677068999981897-78985014533589999997499942999557877999 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 86542000000045789886521100000088777654200246752003656544323689999864599999999999 Q gi|254780636|r 89 LFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 89 L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) |.+++|+.+.|+||||+|+++++. .++||+.|+++|||++++|+.|+|||++||||++|+.|||.||+||++||+.|. T Consensus 174 L~~~~g~~~~~~fDT~ia~~~l~~--~~~sL~~L~~~~l~~~l~K~~q~sDW~~RPL~~~qi~YAa~Dv~~Ll~ly~~L~ 251 (410) T 2hbj_A 174 LQRDLGLYVVGLFDTYHASKAIGL--PRHSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAAARADTHFLLNIYDQLR 251 (410) T ss_dssp HHHHHCCCCSSEEEHHHHHHHHTC--SCCSHHHHHHHHSCCCCCCTTTTSCTTCSSCCHHHHHHHHHHHHTHHHHHHHHH T ss_pred HHHHCCCCCCCCCCHHHHHHHCCC--CCCCHHHHHHHHHCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 998457567872026999998098--875699999987366656413342004555879999999853788999999999 Q ss_pred HHHHHCCCHHHHHHHHHHHH Q ss_conf 99997491899999996400 Q gi|254780636|r 169 EKLQRLGRSDLATSCCNFLM 188 (207) Q Consensus 169 ~~L~~~~~~~~~~~e~~~l~ 188 (207) ++|.+.|+++|+.+||+.+. T Consensus 252 ~~L~~~~~l~~~~ee~~~~~ 271 (410) T 2hbj_A 252 NKLIESNKLAGVLYESRNVA 271 (410) T ss_dssp HHHHHTTCHHHHHHHHHHHH T ss_pred HHHHHCCCHHHHHHHHHHHH T ss_conf 99997666589999999999 No 3 >3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function, ribonuclease D, exonuclease; 2.10A {Bifidobacterium adolescentis ATCC15703} Probab=100.00 E-value=0 Score=288.94 Aligned_cols=175 Identities=21% Similarity=0.307 Sum_probs=149.8 Q ss_pred CCCHHHH-C-CCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCC---CCCCCHHHHHHHHCCCCCEEECCCCH Q ss_conf 8885784-2-48982799717778985445079999841894289974657---78570677677732364023010000 Q gi|254780636|r 10 DIPAECA-A-RYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAA---GQKNAPNLVGMLVDEKREKIFHYGRF 84 (207) Q Consensus 10 dl~~~~~-l-~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~---~~~~~~~L~~ll~d~~i~KV~Hn~~~ 84 (207) +|.+.+. + +..++|||||||+++++|++++|||||++.++.+|+|++.. .......|++++. +|+|||||+++ T Consensus 26 ~l~~~~~~L~~~~~~iavDtE~~~~~~y~~~~~LvQi~~~g~~~~liDp~~~~~~~~~~~~L~~~l~--~i~kv~H~~~~ 103 (440) T 3cym_A 26 AFRDYCSELASSHGSLAADAERASGFRYGHEDWLVQFKRDGAGIGLLDPQALAAAGADWNDFNRAVG--DAVWILHDSLQ 103 (440) T ss_dssp HHHHHHHHHHSCEEEEEEEEEECTTTSSSCCEEEEEEEEETTEEEEECHHHHHHTTCCHHHHHHHHT--TCEEEESSHHH T ss_pred HHHHHHHHHHHCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEEECCCCCCCCCHHHHHHHHHC--CCEEEEECCHH T ss_conf 9999999997179918997986788806874789998678988799805555655531799999867--98199977478 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 16888654200000004578988652110000008877765420024675200365654432368999986459999999 Q gi|254780636|r 85 DIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 85 D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~ 164 (207) |+.+|.+ +|+.|.|+||||+|+++++ . .++||+.|++++||++++|+.|+|||++||||++|+.|||.||.||++|| T Consensus 104 Dl~~l~~-~g~~~~~~fDTqiAa~~lg-~-~~~gl~~l~~~~lg~~l~K~~~~sdW~~rPLs~~q~~YAa~Dv~~L~~l~ 180 (440) T 3cym_A 104 DLPGFDE-LGMEPQRLFDTEIAARLLG-L-KRFGLAAVTEHFLGLTLAKEHSAADWSYRPLPRDWRNYAALDVELLIELE 180 (440) T ss_dssp HHHHHHH-HTCCCCEEEEHHHHHHHTT-C-SSCSHHHHHHHHHCEECCCCCTTCCTTCSSCCHHHHHHHHHHHHTHHHHH T ss_pred HHHHHHH-CCCCCCCCHHHHHHHHHCC-C-CCCCHHHHHHHHHCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 9999998-7881288122999998728-8-87779999999947665638888761787788899999986067789999 Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 9999999974918999999964006 Q gi|254780636|r 165 LQFTEKLQRLGRSDLATSCCNFLMD 189 (207) Q Consensus 165 ~~l~~~L~~~~~~~~~~~e~~~l~~ 189 (207) +.|.++|.+.++.+|+++||..+-. T Consensus 181 ~~l~~~L~~~~~~~~~~ee~~~~~~ 205 (440) T 3cym_A 181 TKMRAELKRQGKMEWAQEEFDYALK 205 (440) T ss_dssp HHHHHHHHHHTCHHHHHHHHHHHHH T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHH T ss_conf 9999999871217889999999985 No 4 >2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form, hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A 2fbv_A 2fbx_A 2fbt_A 2fc0_A* Probab=100.00 E-value=1.1e-37 Score=237.01 Aligned_cols=167 Identities=18% Similarity=0.142 Sum_probs=144.5 Q ss_pred CCCCCCEEEECCCC--CCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHH Q ss_conf 24898279971777--8985445079999841894289974657785706776777323640230100001688865420 Q gi|254780636|r 17 ARYVDAIAVDTETL--GLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFG 94 (207) Q Consensus 17 l~~~~~iaiDtEt~--~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~g 94 (207) +...++|||||||+ ......+++|+||+|++++.|+++++......++.|+++|+|++|.|||||+++|+..|.+++| T Consensus 37 l~~~~vig~D~E~~~~~~~~~~~~v~liQla~~~~~~~i~~~~~~~~~~~~L~~lL~~~~i~Kvg~~~~~D~~~L~~~~~ 116 (208) T 2e6m_A 37 LSDGDVVGFDMEWPPIYKPGKRSRVAVIQLCVSESKCYLFHISSMSVFPQGLKMLLENKSIKKAGVGIEGDQWKLLRDFD 116 (208) T ss_dssp CCTTCEEEEEEECCC---CCSCCCCCEEEEECSSSEEEEECGGGCSSCCHHHHHHHTCTTSEEEESSHHHHHHHHHHHHC T ss_pred HCCCCEEEEECEECCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCC T ss_conf 54899899977017887888548678999986898789993676663439999997699823034337518999843022 Q ss_pred CCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC--CCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 000000457898865211000000887776542002467--520036565443236899998645999999999999999 Q gi|254780636|r 95 VRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISK--AQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQ 172 (207) Q Consensus 95 i~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK--~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~ 172 (207) +.+.|++|++.++........++||+.+++++||.+++| +.|+|||++||||++|+.|||.||++++.||++|.+..+ T Consensus 117 ~~~~~~~d~~~~~~~~~~~~~~~~l~~l~~~~l~~~~~k~k~~q~s~W~~rpLt~~qi~YAA~Da~~~~~l~~~L~~~~~ 196 (208) T 2e6m_A 117 VKLESFVELTDVANEKLKCAETWSLNGLVKHVLGKQLLKDKSIRCSNWSNFPLTEDQKLYAATDAYAGLIIYQKLGNLGD 196 (208) T ss_dssp CCCCSEEEHHHHHHHHTTCCCCCCHHHHHHHHHSCBCCCCHHHHTSCTTSSSCCHHHHHHHHHHHHHHHHHHHHHHTCC- T ss_pred CCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHCCEECCCHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 34573121538999981587653599999998293214207553477765889999999999999999999999986115 Q ss_pred HCCCHHHHHHH Q ss_conf 74918999999 Q gi|254780636|r 173 RLGRSDLATSC 183 (207) Q Consensus 173 ~~~~~~~~~~e 183 (207) +....+++++| T Consensus 197 ~~~~~~~~~~~ 207 (208) T 2e6m_A 197 TVQVFALNKAE 207 (208) T ss_dssp ----------- T ss_pred HHHHHHHHHHC T ss_conf 18899988741 No 5 >2hhv_A DNA polymerase I; DNA replication, klenow fragment, protein- DNA complex, O6-methyl-guanine, transferase/DNA complex; HET: DNA 6OG SUC; 1.55A {Geobacillus stearothermophilus} SCOP: c.55.3.5 e.8.1.1 PDB: 2hhs_A* 2hht_A* 2hhu_A* 2hhq_A* 2hhx_A* 2hw3_A* 1nk4_A* 1l3t_A* 1l3u_A* 1l3v_A* 1l5u_A* 1njw_A* 1l3s_A* 1njy_A* 1njz_A* 1nk0_A* 1njx_A* 1nk5_A* 1nk6_A* 1nk7_A* ... Probab=100.00 E-value=1.2e-34 Score=219.40 Aligned_cols=180 Identities=16% Similarity=0.100 Sum_probs=153.0 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCC Q ss_conf 98279971777898544507999984189428997465778570677677732364023010000168886542000000 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRP 99 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~ 99 (207) ++.+||||||+|++++.+++++|++|.+++.+|+++.... ..+.|+++|+|+++.||+||++||+.+|.++ |+.+++ T Consensus 17 ~~~~a~~~e~~~~~~~~~~ivGis~~~~~~~~~y~p~~~~--~~~~l~~~l~d~~~~ki~hN~k~D~~~L~~~-Gi~l~g 93 (580) T 2hhv_A 17 ADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETAL--ADPQFVAWLGDETKKKSMFDSKRAAVALKWK-GIELCG 93 (580) T ss_dssp CSEEEEEEECCSSSCTTCCCCEEEEEETTEEEEECHHHHT--TCHHHHHHHHCTTSEEEESSHHHHHHHHHTT-TCCCCC T ss_pred CCCCEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCC--CHHHHHHHHCCCCCCEEEEEHHHHHHHHHHC-CCCCCC T ss_conf 7884799976999735072899999966977999453546--6489999966999865885279999999978-882799 Q ss_pred H-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECC---CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 0-457898865211000000887776542002467520036---565443236899998645999999999999999749 Q gi|254780636|r 100 V-FCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSD---WSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLG 175 (207) Q Consensus 100 i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~Sd---W~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~ 175 (207) + ||||||++++++....++|+.+++++++..+.+...... +...|-.+....|||.||.++++||+.|.++|.+.+ T Consensus 94 ~~~DTmiaa~ll~~~~~~~~L~~l~~~~~~~~~~~~~~~~gk~~~~~~~~~~~~~~Ya~~Da~~t~~L~~~l~~~l~~~~ 173 (580) T 2hhv_A 94 VSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNE 173 (580) T ss_dssp EEEEHHHHHHHHCGGGCCCSHHHHHHTTTCCSSCCHHHHHCSGGGCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT T ss_pred CEEHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 73289999997599999888999999867998784887518771002632799999999999999999999999975434 Q ss_pred CHHHHH-HHHHHHHHHHHHHHCCCCCCCC Q ss_conf 189999-9996400689998667988884 Q gi|254780636|r 176 RSDLAT-SCCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 176 ~~~~~~-~e~~~l~~~~~me~~g~~~~~~ 203 (207) +..+|. .|++++|++++||.+|++ +|. T Consensus 174 l~~~~~~iE~pl~~vL~~ME~~Gi~-vD~ 201 (580) T 2hhv_A 174 QDRLLVELEQPLSSILAEMEFAGVK-VDT 201 (580) T ss_dssp CHHHHHTTHHHHHHHHHHHHHHCEE-ECH T ss_pred HHHHHHHHHHHHHHHHHHHHHCCEE-EEH T ss_conf 3314888997789999999745988-708 No 6 >1vk0_A Hypothetical protein; homohexamer, AT5G06450, structural genomics, protein structure initiative, center for eukaryotic structural genomics; 2.10A {Arabidopsis thaliana} SCOP: c.55.3.5 PDB: 2q3s_A Probab=100.00 E-value=8.3e-34 Score=214.46 Aligned_cols=151 Identities=15% Similarity=0.074 Sum_probs=124.9 Q ss_pred CCCCCCEEEECCCCCC--------CCCCCEEEEEEEEECCCCEEEECCCC-CCCCCHHHHHHHHCCCCCEEECCCCHHHH Q ss_conf 2489827997177789--------85445079999841894289974657-78570677677732364023010000168 Q gi|254780636|r 17 ARYVDAIAVDTETLGL--------MPRRDRLCIVQLSPGDGTVDIIRIAA-GQKNAPNLVGMLVDEKREKIFHYGRFDIA 87 (207) Q Consensus 17 l~~~~~iaiDtEt~~l--------~~~~~~l~LiQl~~~~~~~~l~~~~~-~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~ 87 (207) +....+|||||||... .....++|+||||+++ .|+++++.+ ....++.|+++|+|++|+||||++++|+. T Consensus 43 ~~~~~~ig~D~EW~~~~~~~~~~~~~~~~~valiQl~t~~-~~~li~l~~~~~~~~~~L~~~L~~~~i~KVG~~i~~D~~ 121 (206) T 1vk0_A 43 LNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRN-LCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLD 121 (206) T ss_dssp HHSTTEEEEEEEEECCC------CGGGGCEEEEEEEECSS-EEEEEECCSSCCGGGHHHHHHHTCSSSEEEESSCHHHHH T ss_pred HCCCCEEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEECC-CEEEEECCCCCCHHHHHHHHHHCCCCEEEEEECHHHHHH T ss_conf 2379669998004787766776553357615999998689-389998882111107999999659981599962698899 Q ss_pred HHHHHHHCCCCCHHHHHHHH-HHHH-HHCCCHHHHHHHHHHHCCCCCCCCE-ECCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 88654200000004578988-6521-1000000887776542002467520-0365654432368999986459999999 Q gi|254780636|r 88 VLFYTFGVRVRPVFCTKIAS-RLTR-TYTNQHGLKDNLKELLGINISKAQQ-SSDWSADDLSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 88 ~L~~~~gi~~~~i~DT~ias-~l~~-~~~~~~~L~~L~~~~lg~~ldK~~q-~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~ 164 (207) .|.+++|+.+++++|++..+ .... +...++||+.|++++||+.++|..+ +|+|. ||||++|+.|||.||+++++|| T Consensus 122 ~L~~~~gi~~~~~vDl~~~a~~~~~~~~~~~~~l~~L~~~~lg~~l~K~~~~~s~W~-~pLs~~Qi~YAA~DA~~~~~iy 200 (206) T 1vk0_A 122 LLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWE-KAGPEEQLEAAAIEGWLIVNVW 200 (206) T ss_dssp HHHHHHCCCCSSEEEHHHHHHHHHTCGGGGGCCHHHHHHHHHCCCCHHHHHHHHTGG-GSCHHHHHHHHHHHHHHHHHHH T ss_pred HHHHHCCCCCCCEEECHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCEECCCCC-CCCCHHHHHHHHHHHHHHHHHH T ss_conf 985124976553552569999873254413100999999976986786765214876-8899999999999899999999 Q ss_pred HHHHH Q ss_conf 99999 Q gi|254780636|r 165 LQFTE 169 (207) Q Consensus 165 ~~l~~ 169 (207) ++|.+ T Consensus 201 ~~L~~ 205 (206) T 1vk0_A 201 DQLSD 205 (206) T ss_dssp HHHHH T ss_pred HHHHC T ss_conf 99852 No 7 >2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A* Probab=99.97 E-value=2e-31 Score=200.64 Aligned_cols=199 Identities=20% Similarity=0.167 Sum_probs=156.8 Q ss_pred CEEECCC--CCCHHHH-CCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCC----------CHHHHHH Q ss_conf 2153257--8885784-2489827997177789854450799998418942899746577857----------0677677 Q gi|254780636|r 3 TIRVHEG--DIPAECA-ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN----------APNLVGM 69 (207) Q Consensus 3 ~~~~~~~--dl~~~~~-l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~----------~~~L~~l 69 (207) ||+.+.+ +|...+. +...+.+||||||+|++++.+++++||+|..++.++++|+.+.... ...|+++ T Consensus 6 ~y~~i~~~~~l~~~~~~l~~~~~~a~D~ETt~ld~~~~~ivgis~s~~~~~~~yipi~h~~~~~~~~~~~~~vl~~Lk~~ 85 (605) T 2kfn_A 6 NYVTILDEETLKAWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPL 85 (605) T ss_dssp SSEECCSHHHHHHHHHHHHTSSSEEEEEEESCSCTTTCCEEEEEEEEETTEEEEEECCCCSTTCCCCCCHHHHHHHHHHH T ss_pred CCEEECCHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCEEEEEEEECCCCEEEEEEECCCCCCCCCCCCHHHHHHHHHHH T ss_conf 65288989999999999852994999831799983657499999982498599998226667775558999999999999 Q ss_pred HHCCCCCEEECCCCHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCC-- Q ss_conf 732364023010000168886542000000-04578988652110000008877765420024675200365654432-- Q gi|254780636|r 70 LVDEKREKIFHYGRFDIAVLFYTFGVRVRP-VFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLS-- 146 (207) Q Consensus 70 l~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~-i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs-- 146 (207) |+|+++.||+||++||+.+|.++ |+.+.+ ++|||+|+++++.....+++..+++++++..+++.....+|++..++ T Consensus 86 l~~~~i~kV~HNakFD~~~L~~~-Gi~l~~~~~DTmiaa~ll~~~~~~~~l~~~~~~~l~~~~~~~~~~~g~~k~~~~~~ 164 (605) T 2kfn_A 86 LEDEKALKVGQNLKYDRGILANY-GIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFN 164 (605) T ss_dssp HTCTTSCEEESSHHHHHHHHHTT-TCCCCCEEEEHHHHHHHHCTTSSCCSHHHHHHHHSCCCCCCHHHHHCSSTTCCCGG T ss_pred HHCCCCCEEEECHHHHHHHHHHC-CCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCHHHHHCCCCCCCCHH T ss_conf 81899979997269999999977-99889840207778777256555565899999863877675898705774438801 Q ss_pred ----HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHH-HHHHHHHHHHHHHHCCCCCCCC Q ss_conf ----368999986459999999999999997491-89999-9996400689998667988884 Q gi|254780636|r 147 ----DEQLQYAASDVVHLHALRLQFTEKLQRLGR-SDLAT-SCCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 147 ----~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~-~~~~~-~e~~~l~~~~~me~~g~~~~~~ 203 (207) .....|++.|+..+..++..+...+.+... ..++. .|+++.+++++|+..|+. +|. T Consensus 165 ~~~~~~~~~y~~~d~~~~~~~~~~l~~~~~~~~~~~~~~~~lE~pl~~vla~Me~~Gi~-vD~ 226 (605) T 2kfn_A 165 QIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVK-IDP 226 (605) T ss_dssp GSCHHHHHHHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHTHHHHHHHHHHHHHHCBC-BCH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH-HHH T ss_conf 22377899999999999999999999999986899999999981738999988440176-529 No 8 >1x9m_A DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene, replication block, mutagenesis, transferase/electron transport/DNA complex; HET: DNA 2DT 8FG; 2.10A {Enterobacteria phage T7} SCOP: c.55.3.5 e.8.1.1 PDB: 1skr_A* 1skw_A* 1sl0_A* 1sks_A* 1sl2_A* 1t7p_A* 1t8e_A* 1tk0_A* 1tk5_A* 1tk8_A* 1tkd_A* 1sl1_A* 1x9s_A* 1x9w_A* 1zyq_A* 2ajq_A* Probab=99.93 E-value=1e-25 Score=167.38 Aligned_cols=177 Identities=16% Similarity=0.127 Sum_probs=130.7 Q ss_pred CEEEECCCCCCCCCCCEEEEEEEEECCC-CEEEECCCCCCCCCHHHHHHHHCCCCCEEECCC-CHHHHHHHHHHHCCC-- Q ss_conf 2799717778985445079999841894-289974657785706776777323640230100-001688865420000-- Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLCIVQLSPGDG-TVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYG-RFDIAVLFYTFGVRV-- 97 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~LiQl~~~~~-~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~-~~D~~~L~~~~gi~~-- 97 (207) +|+||+||+||.+..+++..|.+...+. .++.+.........+.++.++++.+.+ ||||+ +||+.+|.+.+|+.+ T Consensus 1 ~~v~DiET~gL~~~~~~i~~i~~~d~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~l-VgHN~~~FD~~~L~k~~g~~~~~ 79 (698) T 1x9m_A 1 MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLI-VFHNGHKYDVPALTKLAKLQLNR 79 (698) T ss_dssp CEEEEEEESSCGGGCCCEEEEEEEETTTTEEEEECGGGHHHHHHHHHHHHHTTCCE-EESSTTTTHHHHHHHHHHHHHCC T ss_pred CEEEECCCCCCCCCCCEEEEEEEEECCCCEEEEECCCCHHHHHHHHHHHHHCCCEE-EECCCHHCCHHHHHHHHCCCCCC T ss_conf 98999168997756787999999978997289847654057999999998559969-97572320899998873874233 Q ss_pred ------CCHHHHHHHHHHHHHH------------CCCHHHHHHHHHHHCCC---------------CCCCCEECCCCCCC Q ss_conf ------0004578988652110------------00000887776542002---------------46752003656544 Q gi|254780636|r 98 ------RPVFCTKIASRLTRTY------------TNQHGLKDNLKELLGIN---------------ISKAQQSSDWSADD 144 (207) Q Consensus 98 ------~~i~DT~ias~l~~~~------------~~~~~L~~L~~~~lg~~---------------ldK~~q~SdW~~rp 144 (207) ..++||||+|+++++. ...|||+++..+ ||.. ..+....++|.. T Consensus 80 ~~~~~~~~v~DTmi~s~ll~p~~~~~~~~~~~~~~~~hsL~a~g~r-lg~~K~~~~~~~~~~~~~~~~~~~~~~~~~~-- 156 (698) T 1x9m_A 80 EFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGALEAWGYR-LGEMKGEYKDDFKRMLEEQGEEYVDGMEWWN-- 156 (698) T ss_dssp CCCCCGGGEEEHHHHHHHHTTTSCCCTTTTSCGGGSCSCCCHHHHH-HHHHHHHHHHHHHHHHHHTTCCCCTTGGGTS-- T ss_pred CCCCCCCCEEEHHHHHHHHCCCCCCCCCHHHHCCCCCCCHHHHHHH-HCCCCCCHHHHHHHHHHHCCCCCCCHHHHHH-- T ss_conf 4566778750277887663998644431122026678788999998-5865431377764322210223344133433-- Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH----------------HHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 323689999864599999999999999974918----------------99999996400689998667988884 Q gi|254780636|r 145 LSDEQLQYAASDVVHLHALRLQFTEKLQRLGRS----------------DLATSCCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 145 Ls~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~----------------~~~~~e~~~l~~~~~me~~g~~~~~~ 203 (207) +|++|+.||+.||.++++||+.|.+.+...+.. +....|+++.+++++||.+||+ +|+ T Consensus 157 ~s~em~~Ya~~Dv~iT~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~lE~~~~~~l~~mE~nG~~-vD~ 230 (698) T 1x9m_A 157 FNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFP-FDT 230 (698) T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHTCTTTSCTTSCTTSSCHHHHHHHSCHHHHHHHHHHHHHHHHHHHCEE-BCH T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCEE-ECH T ss_conf 48999999998999999999999998643010012333210001012478999988999999998853989-729 No 9 >3m8r_A DNA polymerase I, thermostable; DNA polymerase, DNA replication, nucleotides, modified nucleotide, artificial nucleotide; HET: DNA DOC HXZ 15P; 2.00A {Thermus aquaticus} PDB: 1jxe_A* 3ktq_A* 3lwl_A* 3lwm_A* 3m8s_A* 1ktq_A* 5ktq_A* 4ktq_A* 1qtm_A* 2ktq_A* 1qss_A* 1qsy_A* Probab=99.90 E-value=5e-24 Score=157.65 Aligned_cols=155 Identities=14% Similarity=-0.002 Sum_probs=121.8 Q ss_pred CCCCCCCCCCCEEEEEEEEECC-CCEEEECCCCC--CCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCCHHHH Q ss_conf 1777898544507999984189-42899746577--85706776777323640230100001688865420000000457 Q gi|254780636|r 27 TETLGLMPRRDRLCIVQLSPGD-GTVDIIRIAAG--QKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCT 103 (207) Q Consensus 27 tEt~~l~~~~~~l~LiQl~~~~-~~~~l~~~~~~--~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i~DT 103 (207) .||+++.|..+.++++.+|.++ ..++++++... .........+.....+.|++||.++|+.+|..+.||.+.++||| T Consensus 2 ~e~~~~~p~~~~~vG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~l~~~~Gi~~~~~~Dt 81 (540) T 3m8r_A 2 LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDP 81 (540) T ss_dssp CEEECSSCCTTCEEEEEESSSCTTTCCEEEEEEEETTEEEECSSHHHHGGGCSCBCSTTHHHHHHHHHHTTCCCCBCCCH T ss_pred CCCCCCCCCCCEEEEEEEEECCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHH T ss_conf 88789998884189999985588737864012234453222257998634346777568887999999679988997718 Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHH- Q ss_conf 89886521100000088777654200246752003656544323689999864599999999999999974-9189999- Q gi|254780636|r 104 KIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRL-GRSDLAT- 181 (207) Q Consensus 104 ~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~-~~~~~~~- 181 (207) ||||+++++ .+|||..++++|+|.. ..|||.||.++++||+.|.++|.++ ++.++|. T Consensus 82 mlaa~ll~~--~~~~l~~la~~~l~~~-------------------~~YA~~Da~~t~~L~~~l~~~L~~~~~l~~ly~~ 140 (540) T 3m8r_A 82 MLLAYLLDP--SNTTPEGVARRYGGEW-------------------TEEAGERAALSERLFANLWGRLEGEERLLWLYRE 140 (540) T ss_dssp HHHHHHHCT--TCCCHHHHHHHHTCCC-------------------CSCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHH T ss_pred HHHHHHHCC--CCCCHHHHHHHHCCCC-------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999998399--8998699999977521-------------------5889999999999999999998602558999999 Q ss_pred HHHHHHHHHHHHHHCCCCCCCC Q ss_conf 9996400689998667988884 Q gi|254780636|r 182 SCCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 182 ~e~~~l~~~~~me~~g~~~~~~ 203 (207) .|++++|++++||.+|++ +|. T Consensus 141 iE~pl~~vLa~ME~~Gi~-vD~ 161 (540) T 3m8r_A 141 VERPLSAVLAHMEATGVR-LDV 161 (540) T ss_dssp THHHHHHHHHHHHHHCBE-ECH T ss_pred HHHHHHHHHHHHHHCCEE-EEH T ss_conf 986899999999974999-829 No 10 >1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Probab=99.73 E-value=6.3e-18 Score=122.19 Aligned_cols=146 Identities=14% Similarity=0.013 Sum_probs=114.5 Q ss_pred EEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCCHHHH Q ss_conf 99717778985445079999841894289974657785706776777323640230100001688865420000000457 Q gi|254780636|r 24 AVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCT 103 (207) Q Consensus 24 aiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i~DT 103 (207) .+++++.+.++....+..+.++.+ +.++.++.. ++. + .++.|+.|+.++|+.+|..+.|+...++||| T Consensus 306 ~~~~~~~~~~~~~a~~vg~~~~~~-~~~~~~p~~--------~~~-l--~~l~k~~~~lk~d~~vl~~~~gi~~~~~~Dt 373 (832) T 1bgx_T 306 FVGFVLSRKEPMWADLLALAAARG-GRVHRAPEP--------YKA-L--RDLKEARGLLAKDLSVLALREGLGLPPGDDP 373 (832) T ss_dssp CBEEECSSSCTTTCCCCEEECBSS-SEEECCSCH--------HHH-H--HHCSSBCBTTHHHHHHHHHHHTCCCCBCCCH T ss_pred EEEEEECCCCCCHHHHHHHHHCCC-CEEEECCHH--------HHH-H--HHHHHHHCCCCCCHHHHHHHHHHCCCHHHHH T ss_conf 578885267641215776654048-848975404--------666-6--7688862443003999864101124400259 Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHH Q ss_conf 89886521100000088777654200246752003656544323689999864599999999999999974-91899999 Q gi|254780636|r 104 KIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRL-GRSDLATS 182 (207) Q Consensus 104 ~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~-~~~~~~~~ 182 (207) |+|++++++ .++++..+++++++.. ..||+.||.++++||..|.++|.++ ++..+|.. T Consensus 374 miaayLl~p--~~~~~~~l~~~~~~e~-------------------~eYa~~Da~~t~~L~~~L~~~L~~e~~l~~l~~~ 432 (832) T 1bgx_T 374 MLLAYLLDP--SNTTPEGVARRYGGEW-------------------TEEAGERAALSERLFANLWGRLEGEERLLWLYRE 432 (832) T ss_dssp HHHHHHHCT--TCCSTTHHHHHHSCCC-------------------CSSHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHT T ss_pred HHHHHHHCC--CCCCHHHHHHHHCCCC-------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999998647--7868067777625441-------------------5779999999999999999998877889999999 Q ss_pred -HHHHHHHHHHHHHCCCCCCCC Q ss_conf -996400689998667988884 Q gi|254780636|r 183 -CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 183 -e~~~l~~~~~me~~g~~~~~~ 203 (207) |+++++++++||.+|++ +|. T Consensus 433 IE~pl~~vLa~ME~~Gi~-vD~ 453 (832) T 1bgx_T 433 VERPLSAVLAHMEATGVR-LDV 453 (832) T ss_dssp THHHHHHHHHHHHHHCBC-BCT T ss_pred HHHHHHHHHHHHHHCCCC-CCH T ss_conf 987887888999871554-329 No 11 >1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5 Probab=99.38 E-value=1.1e-12 Score=91.72 Aligned_cols=143 Identities=17% Similarity=0.103 Sum_probs=91.6 Q ss_pred CCCCCEEEECCCCCCCCCCCE-EEEEEEEECCCCEEE---ECCCC-CCCC---------------------CHHHHHHHH Q ss_conf 489827997177789854450-799998418942899---74657-7857---------------------067767773 Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRRDR-LCIVQLSPGDGTVDI---IRIAA-GQKN---------------------APNLVGMLV 71 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~~~-l~LiQl~~~~~~~~l---~~~~~-~~~~---------------------~~~L~~ll~ 71 (207) ...++|++||||+|+++.++. ++.+.+...++...+ +.+.. .... .+.+.+++. T Consensus 3 ~~~~~V~iD~ETtGl~~~~~~~i~~~aiv~~~g~~v~~~~v~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~~~ 82 (189) T 1wlj_A 3 GSREVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHMVGATPFAVARLEILQLLK 82 (189) T ss_dssp ---CEEEEEEEEEEETTTTEEEEEEEEEECTTCCEEEEEEEECSSCEEECCHHHHCCCHHHHTTCEEHHHHHHHHHHHHT T ss_pred CCCCEEEEEEECCCCCCCCCCEEEEEEEEEECCCEEEEEEECCCCCCCHHHCCCCCCCHHHHHCCCCHHHHHHHHHHHHC T ss_conf 99989999768088899998679999999837959999986699989830024889997896227847888999987631 Q ss_pred CCCCCEEECCCCHHHHHHHHHHHC-CC-CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHH Q ss_conf 236402301000016888654200-00-0004578988652110000008877765420024675200365654432368 Q gi|254780636|r 72 DEKREKIFHYGRFDIAVLFYTFGV-RV-RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQ 149 (207) Q Consensus 72 d~~i~KV~Hn~~~D~~~L~~~~gi-~~-~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Q 149 (207) +...|+||++||..+|...+.- .. .+..||+..++...+...++||..|++.++|..+....+ T Consensus 83 --~~~lV~hn~~fD~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~~~~l~~~i~~~~~------------- 147 (189) T 1wlj_A 83 --GKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDHCRRVSLRVLSERLLHKSIQNSLL------------- 147 (189) T ss_dssp --TSEEEESSHHHHHHHTTCCCTTCEEEEGGGCHHHHHHHTC-----CCHHHHHHHHTCCCCSCCTT------------- T ss_pred --CCEEEEECHHHHHHHHHHHCHHCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCC------------- T ss_conf --34589735687899999867032665841216999998736677889999999980987789998------------- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 99998645999999999999999749 Q gi|254780636|r 150 LQYAASDVVHLHALRLQFTEKLQRLG 175 (207) Q Consensus 150 i~YAA~Dv~~l~~L~~~l~~~L~~~~ 175 (207) -.-|..||..+.+||..+.+.-.+.+ T Consensus 148 ~H~Al~DA~at~~l~~~~~~~~~~~~ 173 (189) T 1wlj_A 148 GHSSVEDARATMELYQISQRIRARRG 173 (189) T ss_dssp CCCHHHHHHHHHHHHHHHHHHHHHTT T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 88819999999999999999997469 No 12 >2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8} Probab=99.05 E-value=3.1e-10 Score=77.45 Aligned_cols=142 Identities=20% Similarity=0.300 Sum_probs=87.5 Q ss_pred HHHCCCCCCEEEECCCCCCCCCCCEEEEEEEEE---CCCC----E-EEECCCCCCCC----------------------C Q ss_conf 784248982799717778985445079999841---8942----8-99746577857----------------------0 Q gi|254780636|r 14 ECAARYVDAIAVDTETLGLMPRRDRLCIVQLSP---GDGT----V-DIIRIAAGQKN----------------------A 63 (207) Q Consensus 14 ~~~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~---~~~~----~-~l~~~~~~~~~----------------------~ 63 (207) +--+.....|.+|+||||++|.++++ ||++. .++. + .++........ . T Consensus 6 ~~~~~~~~yvviD~ETTGl~~~~~~I--ieig~v~~~~~~i~~~~~~~v~p~~~~~~~~~~i~gi~~~~~~~~~~~~~~~ 83 (186) T 2p1j_A 6 DSTFGDATFVVLDFETTGLDPQVDEI--IEIGAVKIQGGQIVDEYHTLIKPSREISRKSSEITGITQEMLENKRSIEEVL 83 (186) T ss_dssp -------CEEEEEEEESCSCTTTCCE--EEEEEEEEETTEEEEEEEEECBCSSCCCHHHHHHHCCCHHHHTTCCBHHHHH T ss_pred CCCCCCCCEEEEEEECCCCCCCCCEE--EEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHCCCCHHHCCCCCHHHHHH T ss_conf 98178884999998728999999868--9999999989968778899866887689899987098756500212199999 Q ss_pred HHHHHHHHCCCCCEEECCCCHHHHHHHHHHH----CC-CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEEC Q ss_conf 6776777323640230100001688865420----00-000045789886521100000088777654200246752003 Q gi|254780636|r 64 PNLVGMLVDEKREKIFHYGRFDIAVLFYTFG----VR-VRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSS 138 (207) Q Consensus 64 ~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~g----i~-~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~S 138 (207) +.+.+++.+ ..-|+||+.||..+|.+.+. .. +.+++||+-.++.... ..+++|.+++++ +|+...+. T Consensus 84 ~~~~~~~~~--~~~v~hn~~fD~~~L~~~~~~~~~~~~~~~~id~~~~~~~~~~-~~~~~L~~l~~~-~gi~~~~~---- 155 (186) T 2p1j_A 84 PEFLGFLED--SIIVAHNANFDYRFLRLWIKKVMGLDWERPYIDTLALAKSLLK-LRSYSLDSVVEK-LGLGPFRH---- 155 (186) T ss_dssp HHHHHHSSS--CEEEETTHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHTC-CSCCSHHHHHHH-TTCCSTTC---- T ss_pred HHHHHHCCC--CEEEEECHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCC-CCCCCHHHHHHH-CCCCCCCC---- T ss_conf 999974699--9899977898799999999984498766762020999998656-789889999998-69998989---- Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH Q ss_conf 656544323689999864599999999999999974918 Q gi|254780636|r 139 DWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRS 177 (207) Q Consensus 139 dW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~ 177 (207) .=|..||..+.++|.++.++++++|.. T Consensus 156 ------------H~Al~Da~~t~~l~~~l~~~~k~~G~~ 182 (186) T 2p1j_A 156 ------------HRALDDARVTAQVFLRFVEMMKKEGHH 182 (186) T ss_dssp ------------CHHHHHHHHHHHHHHHHTTCC------ T ss_pred ------------CCHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf ------------788999999999999999999824997 No 13 >2is3_A Ribonuclease T; RNAse, exoribonuclease, exonuclease, hydrolase, stable RNA maturation, tRNA END-turnover; 3.10A {Escherichia coli K12} Probab=99.01 E-value=9.9e-10 Score=74.53 Aligned_cols=142 Identities=18% Similarity=0.242 Sum_probs=85.1 Q ss_pred CCCCCEEEECCCCCCCCCCCEEEEEEEEE------CCCC-----E---EEECCCCCCC---------------------C Q ss_conf 48982799717778985445079999841------8942-----8---9974657785---------------------7 Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRRDRLCIVQLSP------GDGT-----V---DIIRIAAGQK---------------------N 62 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~~~l~LiQl~~------~~~~-----~---~l~~~~~~~~---------------------~ 62 (207) ++..+|.||+||||++|.++++ ||+|. +++. . ++.+...... . T Consensus 15 ~~~~~Vv~D~ETTGl~p~~d~I--IeIgav~i~~~~~~~~~~~~~~~~~~~p~~~~~i~~~~~~i~gi~~~~~~~~~~~~ 92 (215) T 2is3_A 15 RGFYPVVIDVETAGFNAKTDAL--LEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSE 92 (215) T ss_dssp TTEEEEEEEEEESSSCTTTSCE--EEEEEEEEEECTTSCEEEEEEEEEEBCCCTTCCCCHHHHHHHCCCTTCSTTCCBCH T ss_pred CCCCEEEEEEECCCCCCCCCCC--EEEEEEEEEECCCCCEECCCEEEEEECCCCCCCCCHHHHHHHCCCHHHHHHCCCCH T ss_conf 2898599983799999999832--89999998956888683353599985268899988568760252138787079861 Q ss_pred CHHHHHHHHC----------CCCCEEECCCCHHHHHHHHHHH---CC-----CCCHHHHHHHHHHHHHHCCCHHHHHHHH Q ss_conf 0677677732----------3640230100001688865420---00-----0000457898865211000000887776 Q gi|254780636|r 63 APNLVGMLVD----------EKREKIFHYGRFDIAVLFYTFG---VR-----VRPVFCTKIASRLTRTYTNQHGLKDNLK 124 (207) Q Consensus 63 ~~~L~~ll~d----------~~i~KV~Hn~~~D~~~L~~~~g---i~-----~~~i~DT~ias~l~~~~~~~~~L~~L~~ 124 (207) .+.+.++++- .....|+||++||..+|.+.+. +. +...+||+..++.. .++++|..++. T Consensus 93 ~~~~~~~~~~i~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~l~~~~~~~~~~iDt~~~~~~~---~~~~~L~~l~~ 169 (215) T 2is3_A 93 YEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLA---LGQTVLSKACQ 169 (215) T ss_dssp HHHHHHHHHHHHHHHHHHTCSEEEEEETTHHHHHHHHHHHHHHHTCTTCCEEEEEEEEHHHHHHHH---HSCCSHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH---HCCCCHHHHHH T ss_conf 253599999999998763146550100376876999999999839998865330167799999887---36324999999 Q ss_pred HHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH Q ss_conf 5420024675200365654432368999986459999999999999997491899 Q gi|254780636|r 125 ELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDL 179 (207) Q Consensus 125 ~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~~ 179 (207) + +|++++ ..+-+=|..||..+.+||.++.+++++.+.+.+ T Consensus 170 ~-~~i~~~--------------~~~~H~Al~Da~~ta~lf~~l~~~~~~~g~~~~ 209 (215) T 2is3_A 170 T-AGMDFD--------------STQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209 (215) T ss_dssp H-TTCCCC--------------TTTTTCHHHHHHHHHHHHHHHHHHHHHTTCSCC T ss_pred H-CCCCCC--------------CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 8-599999--------------997678699999999999999999997589999 No 14 >2ioc_B Three prime repair exonuclease 1; proline helix, nucleotide complex, DNAQ family, hydrolase; HET: D5M; 2.10A {Mus musculus} SCOP: c.55.3.5 PDB: 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A Probab=98.73 E-value=4.4e-08 Score=64.96 Aligned_cols=134 Identities=18% Similarity=0.101 Sum_probs=79.4 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEEC----C-----------------------CCEEEECCCCC------------- Q ss_conf 9827997177789854450799998418----9-----------------------42899746577------------- Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPG----D-----------------------GTVDIIRIAAG------------- 59 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~----~-----------------------~~~~l~~~~~~------------- 59 (207) ...|.+||||||+++.++++ ||++.- + .-..++..... T Consensus 12 ~t~v~~D~ETTGl~~~~~~I--ieia~v~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~lv~P~~~I~~~a~~ihGIt~ 89 (242) T 2ioc_B 12 QTLIFLDLEATGLPSSRPEV--TELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSK 89 (242) T ss_dssp SEEEEEEEEESSCGGGCCCE--EEEEEEEEEHHHHHTSCCCCSSSCCCCCCCSSCEEEEEECCCSSCCCHHHHHHHCCCH T ss_pred CEEEEEEEECCCCCCCCCCE--EEEEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHEECCCCCCCHHHHHHCCCCH T ss_conf 85999998889969999876--8999999876753465222111113566541101233012889979988998629999 Q ss_pred ------C--C----CCHHHHHHHHC--CCCCEEECCC-CHHHHHHHHHH---HCCC--CC--HHHHHHHHHHHHH----- Q ss_conf ------8--5----70677677732--3640230100-00168886542---0000--00--0457898865211----- Q gi|254780636|r 60 ------Q--K----NAPNLVGMLVD--EKREKIFHYG-RFDIAVLFYTF---GVRV--RP--VFCTKIASRLTRT----- 112 (207) Q Consensus 60 ------~--~----~~~~L~~ll~d--~~i~KV~Hn~-~~D~~~L~~~~---gi~~--~~--i~DT~ias~l~~~----- 112 (207) . . ..+.++.+++. ....-|+||+ .||..+|.+.+ |+.. .+ ..||+-+++-+.. T Consensus 90 ~~l~~~~~~~~~~~~~~~~~~f~~~~~~~~~lVahN~~~FD~~~L~~~~~r~~~~~~~~~~~~iDtl~~~~~~~~~~~~~ 169 (242) T 2ioc_B 90 AELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPS 169 (242) T ss_dssp HHHHHTTCCCSCHHHHHHHHHHHHTSCSSEEEEETTTTTTHHHHHHHHHHTSSSCCTTTTCEEEEHHHHHHHHHHTC--- T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHCCCCC T ss_conf 99972015505689999899999741688559983547889999999999859988877886877899999970324222 Q ss_pred ---HCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ---00000088777654200246752003656544323689999864599999999999999 Q gi|254780636|r 113 ---YTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171 (207) Q Consensus 113 ---~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L 171 (207) ...+++|.+|+++++|..... -+=|..||..+.+++.++.+.+ T Consensus 170 ~~~~~~~~~L~~l~~~~~g~~~~~----------------aH~Al~Da~~t~~l~~~~~~~~ 215 (242) T 2ioc_B 170 GNGSRKSYSLGSIYTRLYWQAPTD----------------SHTAEGDVLTLLSICQWKPQAL 215 (242) T ss_dssp ----CCCCCHHHHHHHHHSSCCSS----------------TTSHHHHHHHHHHHHTSSHHHH T ss_pred CCCCCCCCCHHHHHHHHCCCCCCC----------------CCCHHHHHHHHHHHHHHHHHHH T ss_conf 467766856899999974999987----------------8388999999999999999999 No 15 >1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 Probab=98.58 E-value=2.5e-07 Score=60.56 Aligned_cols=82 Identities=20% Similarity=0.158 Sum_probs=55.0 Q ss_pred CCCEEECCC-CHHHHHHHHHH---HCCC--C-CHHHHHHHHHHHHH---------HCCCHHHHHHHHHHHCCCCCCCCEE Q ss_conf 640230100-00168886542---0000--0-00457898865211---------0000008877765420024675200 Q gi|254780636|r 74 KREKIFHYG-RFDIAVLFYTF---GVRV--R-PVFCTKIASRLTRT---------YTNQHGLKDNLKELLGINISKAQQS 137 (207) Q Consensus 74 ~i~KV~Hn~-~~D~~~L~~~~---gi~~--~-~i~DT~ias~l~~~---------~~~~~~L~~L~~~~lg~~ldK~~q~ 137 (207) ....|+||+ +||..+|.+.+ |+.+ . ...||+-.++.+.. ...+++|.+|++++.|.. T Consensus 113 ~~~~v~hn~~~FD~~~L~~~~~r~~~~~~~~~~~iDtl~~~~~l~~~~~~~~~~~~~~~~~L~~l~~~~~~~~------- 185 (238) T 1y97_A 113 PICLVAHNGFDYDFPLLCAELRRLGARLPRDTVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLFHRYFRAE------- 185 (238) T ss_dssp SEEEEETTTTTTHHHHHHHHHHHHTCCCCTTCEEEEHHHHHHHHHHHC----------CCSHHHHHHHHHSSC------- T ss_pred CCEEEEECCHHHHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCCC------- T ss_conf 8269996518778999999999808988889878778999999735075444566668858999999964999------- Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 3656544323689999864599999999999999 Q gi|254780636|r 138 SDWSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171 (207) Q Consensus 138 SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L 171 (207) ..+-+-|..||..+.+|+.++...+ T Consensus 186 ---------~~~aH~Al~Da~~t~~i~~~l~~~~ 210 (238) T 1y97_A 186 ---------PSAAHSAEGDVHTLLLIFLHRAAEL 210 (238) T ss_dssp ---------CC---CHHHHHHHHHHHHHHTHHHH T ss_pred ---------CCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf ---------8978898999999999999999999 No 16 >2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PSI, MCSG, protein structure initiative; 2.09A {Pseudomonas aeruginosa PAO1} SCOP: c.55.3.5 Probab=98.58 E-value=3.9e-07 Score=59.44 Aligned_cols=86 Identities=16% Similarity=0.181 Sum_probs=53.5 Q ss_pred CEEECCCCHHHHHHHHHH---HCCC--CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHH Q ss_conf 023010000168886542---0000--00045789886521100000088777654200246752003656544323689 Q gi|254780636|r 76 EKIFHYGRFDIAVLFYTF---GVRV--RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQL 150 (207) Q Consensus 76 ~KV~Hn~~~D~~~L~~~~---gi~~--~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi 150 (207) .-|+||..||..++...+ |+.. .+.+|+....+......+..+|.++++. +|++++.. + . T Consensus 128 ~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~~---------~-----a 192 (224) T 2f96_A 128 ILVGHNSSFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQA-AGMEFDNR---------E-----A 192 (224) T ss_dssp EEEETTHHHHHHHHHHHHHHHTCCCCCEEEEEEEEHHHHHHHHHSCCSHHHHHHH-TTCCCCTT---------S-----C T ss_pred EECCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHH-CCCCCCCC---------C-----C T ss_conf 2215347889999999999819998864113589999998754796439999998-29999989---------7-----6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 99986459999999999999997491 Q gi|254780636|r 151 QYAASDVVHLHALRLQFTEKLQRLGR 176 (207) Q Consensus 151 ~YAA~Dv~~l~~L~~~l~~~L~~~~~ 176 (207) +=|..||..+.+||.+|.+++++.+. T Consensus 193 H~Al~Da~~ta~l~~kl~~~~~~~~~ 218 (224) T 2f96_A 193 HSARYDTEKTAELFCGIVNRWKEMGG 218 (224) T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHTTS T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 78899999999999999999998189 No 17 >2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, product bound structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli K12} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A* 3hp9_A* Probab=98.39 E-value=3.6e-06 Score=53.86 Aligned_cols=134 Identities=19% Similarity=0.070 Sum_probs=75.6 Q ss_pred CCCCCEEEECCCCCCCCCCCEEEEEEEEE----CCC----C--EEEECCCCCCCCC------------------------ Q ss_conf 48982799717778985445079999841----894----2--8997465778570------------------------ Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRRDRLCIVQLSP----GDG----T--VDIIRIAAGQKNA------------------------ 63 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~~~l~LiQl~~----~~~----~--~~l~~~~~~~~~~------------------------ 63 (207) .....|.+|+||||++|.++++ ||+|. .+. . .+...+....... T Consensus 7 ~~~~~v~~D~ETTGl~~~~d~i--iq~~ai~~d~~~~~~~~~~~~~~~~~~~~~p~~~a~~v~gi~~~~~~~~~~~~~e~ 84 (482) T 2qxf_A 7 QQSTFLFHDYETFGTHPALDRP--AQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAF 84 (482) T ss_dssp CCCEEEEEEEEESSSCTTTSCE--EEEEEEEECTTSCBCSCCEEEEBCCCTTCCCCHHHHHHHCCCHHHHHHHCBCHHHH T ss_pred CCCCEEEEEEECCCCCCCCCCE--EEEEEEEECCCCCEEEEEEEEEECCCCCCCCCHHHHHHHCCCHHHHHCCCCCHHHH T ss_conf 6897899998878979999822--89999999899858514567763479999988789688494999997399999999 Q ss_pred -HHHHHHHHCCCCCEEECC-CCHHHHHHHHHHH---CCC--------CCHHHHHHHHHHHHH-------------HCCCH Q ss_conf -677677732364023010-0001688865420---000--------000457898865211-------------00000 Q gi|254780636|r 64 -PNLVGMLVDEKREKIFHY-GRFDIAVLFYTFG---VRV--------RPVFCTKIASRLTRT-------------YTNQH 117 (207) Q Consensus 64 -~~L~~ll~d~~i~KV~Hn-~~~D~~~L~~~~g---i~~--------~~i~DT~ias~l~~~-------------~~~~~ 117 (207) ..+.++++.+...-|||| +.||..+|...+- ..| ....||......+.. ...++ T Consensus 85 ~~~i~~~~~~~~~~~vg~N~~~FD~~~l~~~~~r~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (482) T 2qxf_A 85 AARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSF 164 (482) T ss_dssp HHHHHHHHTSTTEEEEESSTTTTHHHHHHHHHHHTTSCSSGGGTGGGCEEEEHHHHHHHHHHHCCTTSCCCBCTTSSBCC T ss_pred HHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC T ss_conf 99999998448976999676334799999998874478501220268750256888888864044221243234686646 Q ss_pred HHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 08877765420024675200365654432368999986459999999999999 Q gi|254780636|r 118 GLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 118 ~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) .|..++.. .|+. ...-+=|..||.+|.+|...+.+. T Consensus 165 kL~~l~~~-~~i~----------------~~~aHdA~~D~~~t~~l~~~l~~~ 200 (482) T 2qxf_A 165 RLEHLTKA-NGIE----------------HSNAHDAMADVYATIAMAKLVKTR 200 (482) T ss_dssp CHHHHHHH-TTCC----------------CC---CTTHHHHHHHHHHHHHHHH T ss_pred CHHHHHHH-CCCC----------------CCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 69999998-1998----------------778866355179999999999874 No 18 >3ikm_A DNA polymerase subunit gamma-1; human mitochondrial DNA polymerase, disease mutation, DNA replication, DNA-binding, DNA-directed DNA polymerase; HET: DNA; 3.24A {Homo sapiens} Probab=98.19 E-value=2.3e-06 Score=54.93 Aligned_cols=99 Identities=16% Similarity=0.132 Sum_probs=68.4 Q ss_pred CCCCEEECCCCHHHHHHHHHHHCCCCC--HHHHHHHHHHHHH-------------------------------------- Q ss_conf 364023010000168886542000000--0457898865211-------------------------------------- Q gi|254780636|r 73 EKREKIFHYGRFDIAVLFYTFGVRVRP--VFCTKIASRLTRT-------------------------------------- 112 (207) Q Consensus 73 ~~i~KV~Hn~~~D~~~L~~~~gi~~~~--i~DT~ias~l~~~-------------------------------------- 112 (207) +++ -||||..||-......+.+...+ ++|||=++--..| T Consensus 194 ~rl-VVGHNVsyDRaRi~EeY~l~~s~~rFlDTMSLHvavsGm~S~QR~~w~~~kk~~~~~~~~~~~~~~~~~~~~~~~~ 272 (1172) T 3ikm_A 194 EQL-VVGHNVSFDRAHIREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQPPTKQGQKSQRKARRGPA 272 (1172) T ss_dssp CCC-CBCBCSSSSTTGGGTSSCSSCCCCCCCBTTHHHHHHSCCCHHHHHHHHHHHHC----------------------- T ss_pred CCE-EEECCCCCCHHHHHHHHHHCCCCCEEEEHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 637-9856755108888888731456763221034655402566242689987423132200123333321333212652 Q ss_pred --------HCC--CHHHHHHHHHHH-CCCCCCCCEECCCCCCCC------CHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf --------000--000887776542-002467520036565443------2368999986459999999999999997 Q gi|254780636|r 113 --------YTN--QHGLKDNLKELL-GINISKAQQSSDWSADDL------SDEQLQYAASDVVHLHALRLQFTEKLQR 173 (207) Q Consensus 113 --------~~~--~~~L~~L~~~~l-g~~ldK~~q~SdW~~rpL------s~~Qi~YAA~Dv~~l~~L~~~l~~~L~~ 173 (207) .+. ..||.++.+-+| |+.+||+.|- .+..-++ -++-+.|||.||.++.++|.++-+...+ T Consensus 273 ~~~~~W~~~sS~~~NSL~dV~~lhcg~~~ldK~~Rd-~Fv~~~~~dI~~~fq~Lm~YCA~DV~aT~~V~~kl~P~Fle 349 (1172) T 3ikm_A 273 ISSWDWLDISSVNSNSLAEVHRLYVGGPPLEKEPRE-LFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLFLE 349 (1172) T ss_dssp ---CCCCCCCCTTSHHHHHHHTCSSCSCS--SCSSS-STTTTCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT T ss_pred CCCCCHHHCCCCCCCCHHHHHHHHCCCCCCCHHHHH-HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH T ss_conf 234330002344536499999974799877877888-88529999999989999999998899999999987768785 No 19 >2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading domain, transferase; HET: DNA U5P; 1.60A {Escherichia coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A* Probab=97.89 E-value=3.5e-05 Score=48.14 Aligned_cols=133 Identities=20% Similarity=0.208 Sum_probs=75.1 Q ss_pred CCCCCEEEECCCCCCCCCCCE---EEEEEEEEC---C-----CCE-EEECCCCCC-CC---------------------C Q ss_conf 489827997177789854450---799998418---9-----428-997465778-57---------------------0 Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRRDR---LCIVQLSPG---D-----GTV-DIIRIAAGQ-KN---------------------A 63 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~~~---l~LiQl~~~---~-----~~~-~l~~~~~~~-~~---------------------~ 63 (207) +....|.|||||||+++.... =.+||++.- + ..+ .++...... .. . T Consensus 7 ~~~r~vv~D~ETTGl~~~~~~~~~drIieigav~~~~~~~~~~~~~~~v~P~~~~~~~~~~i~gi~~e~~~~~~~~~~v~ 86 (194) T 2gui_A 7 AITRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVA 86 (194) T ss_dssp -CCEEEEEEEEESCCCSSSSTTTTCCEEEEEEEEEETTEECSCCEEEECCCSSCCCHHHHHHHCCCHHHHTTSCCHHHHH T ss_pred CCCCEEEEEEECCCCCCCCCCCCCCEEEEEEEEEEECCEEECEEEEEEECCCCCCCHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 88837999973799987645678954999999999999997407899989998655778987075576643345589988 Q ss_pred HHHHHHHHCCCCCEEECCCCHHHHHHHHHHH---CC--CC----CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCC Q ss_conf 6776777323640230100001688865420---00--00----004578988652110000008877765420024675 Q gi|254780636|r 64 PNLVGMLVDEKREKIFHYGRFDIAVLFYTFG---VR--VR----PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKA 134 (207) Q Consensus 64 ~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~g---i~--~~----~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~ 134 (207) ..+.+++.+. ..|+||..+|..++...+. .. .. .+.||...++-... ..+++|..+++. +|+..++ T Consensus 87 ~~~~~~l~~~--~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~p-~~~~~L~~l~~~-~~i~~~~- 161 (194) T 2gui_A 87 DEFMDYIRGA--ELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFP-GKRNSLDALCAR-YEIDNSK- 161 (194) T ss_dssp HHHHHHHTTS--EEEETTHHHHHHHHHHHHHHTCSCCCCGGGTSEEEEHHHHHHHHST-TSCCSHHHHHHH-TTCCCTT- T ss_pred HHHHHHHCCC--EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEHHHHHHHHCC-CCCCCHHHHHHH-CCCCCCC- T ss_conf 9999870897--3899785131999999999809997655544200019999999748-987889999998-5999899- Q ss_pred CEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2003656544323689999864599999999999 Q gi|254780636|r 135 QQSSDWSADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 135 ~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) .+.+=|..||..+.+||.+|. T Consensus 162 -------------~~~H~Al~Da~~t~~l~~~m~ 182 (194) T 2gui_A 162 -------------RTLHGALLDAQILAEVYLAMT 182 (194) T ss_dssp -------------CSSCCHHHHHHHHHHHHHHHT T ss_pred -------------CCCCCHHHHHHHHHHHHHHHH T ss_conf -------------987488999999999999997 No 20 >2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase, antiproliferative protein, transcription; 2.50A {Homo sapiens} SCOP: c.55.3.9 Probab=97.58 E-value=0.00033 Score=42.41 Aligned_cols=141 Identities=17% Similarity=0.174 Sum_probs=84.9 Q ss_pred HCCCCCCEEEECCCCCCCCCC-------------------CEEEEEEEE----ECCC------CEEEECC--C--CCCCC Q ss_conf 424898279971777898544-------------------507999984----1894------2899746--5--77857 Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPRR-------------------DRLCIVQLS----PGDG------TVDIIRI--A--AGQKN 62 (207) Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~~-------------------~~l~LiQl~----~~~~------~~~l~~~--~--~~~~~ 62 (207) ..+..+.||+|||++|+.... +.+.+||++ ..++ .++-+.+ . ..... T Consensus 20 ~i~~~~fvAiDtEfpGl~~~~~~~~~~~~~~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~~~~~~~w~FNf~f~~~~d~~~ 99 (252) T 2d5r_A 20 VIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYA 99 (252) T ss_dssp HHHHCCEEEEEEECCCCCCCCCSCCSSHHHHHHHHHHHHHTTCCCCEEEEEEECTTSCCCSSCCEEEEEBCCCTTTSCCC T ss_pred HHHCCCEEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCCCC T ss_conf 98649989998670684578876557998999999998775403037898986247877888612779987779766537 Q ss_pred CH-----------------------HHHHH------HHCCCCCEEECCCCHHHHHHHHHH-H-CCC-------------- Q ss_conf 06-----------------------77677------732364023010000168886542-0-000-------------- Q gi|254780636|r 63 AP-----------------------NLVGM------LVDEKREKIFHYGRFDIAVLFYTF-G-VRV-------------- 97 (207) Q Consensus 63 ~~-----------------------~L~~l------l~d~~i~KV~Hn~~~D~~~L~~~~-g-i~~-------------- 97 (207) +. .+.++ .-++++.||.|++-+|+..|.+.+ | -.| T Consensus 100 ~~Si~fL~~~GfDF~k~~~~GI~~~~f~ell~~s~~~~~~~v~wv~f~g~yD~~~L~k~l~g~~LP~~~~~F~~~~~~~F 179 (252) T 2d5r_A 100 QDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFF 179 (252) T ss_dssp HHHHHHHHHHTCCHHHHHHHCBCHHHHHHHHHTTTSSSSSSCEEEESSCHHHHHHHHHHHHTSCCCSSHHHHHHHHHHHC T ss_pred HHHHHHHHHCCCCHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHC T ss_conf 78999999869977899980973899999888611432589737871345789999999809999977899999999977 Q ss_pred CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 00045789886521100000088777654200246752003656544323689999864599999999999999974 Q gi|254780636|r 98 RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRL 174 (207) Q Consensus 98 ~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~ 174 (207) ..++||...++-+.+ .+-||..+++. ||+. .. -+. +=|..|+..+..+|-++.+.+-.. T Consensus 180 p~~yD~K~i~~~~~~--~~~~L~~la~~-L~v~---r~---------g~~---H~AG~DSllT~~~F~~l~~~~~~~ 238 (252) T 2d5r_A 180 PVIYDVKYLMKSCKN--LKGGLQEVAEQ-LELE---RI---------GPQ---HQAGSDSLLTGMAFFKMREMFFED 238 (252) T ss_dssp SCEEEHHHHGGGCTT--CCSSHHHHHHH-HTCC---CC---------SST---TSHHHHHHHHHHHHHHHHHHTSCS T ss_pred CHHEEHHHHHHHCCC--CCCHHHHHHHH-CCCC---CC---------CCC---CCCHHHHHHHHHHHHHHHHHHHCC T ss_conf 346046989844566--57649999997-6999---87---------987---653678999999999999997147 No 21 >2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} Probab=97.57 E-value=0.00034 Score=42.38 Aligned_cols=133 Identities=14% Similarity=0.123 Sum_probs=72.4 Q ss_pred CEEEECCCCCCCCCCCEEEEEEEEE-----CCCC----E-EEECCCCCCCCCH------------------------HHH Q ss_conf 2799717778985445079999841-----8942----8-9974657785706------------------------776 Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLCIVQLSP-----GDGT----V-DIIRIAAGQKNAP------------------------NLV 67 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~LiQl~~-----~~~~----~-~l~~~~~~~~~~~------------------------~L~ 67 (207) .|.+|+||||.++....-..|||+. .++. + .++.+.......+ .+. T Consensus 33 ~vv~D~EtTg~~~~~~~~eIIEiGaV~~d~~~~~i~~~f~~~vkP~~~~~i~~~~~~itgIt~e~l~~a~~~~ev~~~f~ 112 (224) T 2xri_A 33 FLVLDFEATCDKPQIHPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVD 112 (224) T ss_dssp EEEECCEECCCC-CCSSCCEEEEEEEEEETTTCCEEEEEEEECCCSSSCSCCHHHHHHHCCCHHHHTTCCCHHHHHHHHH T ss_pred EEEEEEECCCCCCCCCCCCEEEEEEEEEECCCCEEEEEEEEEECCCCCCCCCHHHHEECCCCHHHCCCCCCHHHHHHHHH T ss_conf 99999836899998897818999999998999869889999999798887896781530113565113463777899999 Q ss_pred HHHHCCCC------CEEECCCCHHHHHH-HH---HHHCCC----CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC Q ss_conf 77732364------02301000016888-65---420000----000457898865211000000887776542002467 Q gi|254780636|r 68 GMLVDEKR------EKIFHYGRFDIAVL-FY---TFGVRV----RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISK 133 (207) Q Consensus 68 ~ll~d~~i------~KV~Hn~~~D~~~L-~~---~~gi~~----~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK 133 (207) .++++..+ .-+.++++||...+ .. ..|+.. ....||+-..+...+...+++|..+++ ++|++... T Consensus 113 ~~l~~~~lv~~~~~~~~~~~~~fD~~~~l~~~~~~~~~~~p~~~~~~iD~~~~~~~~~~~~~~~~L~~l~~-~~gi~~~~ 191 (224) T 2xri_A 113 EWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNK-GLSLQHIG 191 (224) T ss_dssp HHHHHTTTTSTTSCEEEEESSSHHHHTHHHHHHHHHTCCCCGGGSCEEEHHHHHHHHHTSCCTTTHHHHHH-HTTCCCCS T ss_pred HHHCCCEEEEECCEEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCEEEHHHHHHHHHHCCCCCCCHHHHHH-HCCCCCCC T ss_conf 99658859940552799965166657899999997499987434312349999999718777876999999-86999999 Q ss_pred CCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5200365654432368999986459999999999999 Q gi|254780636|r 134 AQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 134 ~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) +-+-|..||..+.+|+.+|.++ T Consensus 192 ---------------~~H~Al~DA~~ta~l~~~Ll~~ 213 (224) T 2xri_A 192 ---------------RPHSGIDDCKNIANIMKTLAYR 213 (224) T ss_dssp ---------------CTTCHHHHHHHHHHHHHHHHHT T ss_pred ---------------CCCCHHHHHHHHHHHHHHHHHC T ss_conf ---------------8738599999999999999977 No 22 >1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B polymerase, POL alpha family polymerase, transferase; 2.10A {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 3a2f_A* 2jgu_A* 1d5a_A Probab=97.56 E-value=0.0023 Score=37.56 Aligned_cols=165 Identities=18% Similarity=0.189 Sum_probs=91.9 Q ss_pred EEECCCCCCHHH----HC--------CCCCCEEEECCCCCCC---CCCCEEEEEEEEECCCCEEEECCCCCC-------- Q ss_conf 153257888578----42--------4898279971777898---544507999984189428997465778-------- Q gi|254780636|r 4 IRVHEGDIPAEC----AA--------RYVDAIAVDTETLGLM---PRRDRLCIVQLSPGDGTVDIIRIAAGQ-------- 60 (207) Q Consensus 4 ~~~~~~dl~~~~----~l--------~~~~~iaiDtEt~~l~---~~~~~l~LiQl~~~~~~~~l~~~~~~~-------- 60 (207) +.+++.|+|-.. +. ..-.++++|.||.+.. +..+++..|.++...... ++...... T Consensus 107 ~~~~E~dI~~~~r~lid~~l~p~~~~~~l~i~s~DIE~~~~~~~~~~~d~I~~Is~~~~~~~~-vi~~~~~d~~~v~~~~ 185 (775) T 1qht_A 107 VDIYEYDIPFAKRYLIDKGLIPMEGDEELTMLAFAIATLYHEGEEFGTGPILMISYADGSEAR-VITWKKIDLPYVDVVS 185 (775) T ss_dssp EEEESCSSCHHHHHHHHTTCCTTCSCCCCCEEEEEEEECCCTTCCTTCSCEEEEEEECSSCEE-EEESSCCCCSSEEECS T ss_pred CCEECCCCCCHHEEEEECCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCE-EEECCCCCCCEEEECC T ss_conf 635715888054277877878567899836999998757876888777988999996389707-9967787876278719 Q ss_pred ---CCCHHHHHHH--HCCCCCEEECCC-CHHHHHHHHH---HHCC----------------------CCC--HHHHHHHH Q ss_conf ---5706776777--323640230100-0016888654---2000----------------------000--04578988 Q gi|254780636|r 61 ---KNAPNLVGML--VDEKREKIFHYG-RFDIAVLFYT---FGVR----------------------VRP--VFCTKIAS 107 (207) Q Consensus 61 ---~~~~~L~~ll--~d~~i~KV~Hn~-~~D~~~L~~~---~gi~----------------------~~~--i~DT~ias 107 (207) .....+..++ .||+|+ +|||. .||+..|... +|+. ..+ ++|+.-.. T Consensus 186 ~E~~LL~~F~~~i~~~dPDII-~GyN~~~FDlpyL~~R~~~l~i~~~~~r~~~~~~~~~~~~~~~~~i~Gri~iDl~~~~ 264 (775) T 1qht_A 186 TEKEMIKRFLRVVREKDPDVL-ITYNGDNFDFAYLKKRCEELGIKFTLGRDGSEPKIQRMGDRFAVEVKGRIHFDLYPVI 264 (775) T ss_dssp CHHHHHHHHHHHHHHHCCSEE-EESSTTTTHHHHHHHHHHHTTCCCCCSTTSCCCEEEEETTEEEEECTTSEEEEHHHHH T ss_pred CHHHHHHHHHHHHHHCCCCEE-EECCCCCCCHHHHHHHHHHHCCCCEECCCCCCCCEEECCCEEEEEECCEEEEEHHHHH T ss_conf 999999999999987199889-8708877529999999998298101035688765434486689988798999839999 Q ss_pred HHHHHHCCCHHHHHHHHHHHCCCCCCC--CE-ECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 652110000008877765420024675--20-03656544323689999864599999999999999 Q gi|254780636|r 108 RLTRTYTNQHGLKDNLKELLGINISKA--QQ-SSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171 (207) Q Consensus 108 ~l~~~~~~~~~L~~L~~~~lg~~ldK~--~q-~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L 171 (207) +-. ....+++|.+++++++|.....- .. .--|...+-...-+.|+..||..+..|..++.... T Consensus 265 ~~~-~~l~sy~L~~Va~~~lg~~K~d~~~~~i~~~~~~~~~~~~~~~Y~~~D~~lv~~L~~kl~~~~ 330 (775) T 1qht_A 265 RRT-INLPTYTLEAVYEAVFGKPKEKVYAEEIAQAWESGEGLERVARYSMEDAKVTYELGREFFPME 330 (775) T ss_dssp HHH-SCCSCCCHHHHHHHHHCCCCCCCCHHHHHHHHTTTCSHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred HHH-CCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 764-667666689999998499755569999999875263299999996999999999988787999 No 23 >1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9 Probab=97.50 E-value=0.0014 Score=38.81 Aligned_cols=140 Identities=14% Similarity=0.197 Sum_probs=80.8 Q ss_pred HCCCCCCEEEECCCCCCCCCC-------------------CEEEEEEEE----ECC-------CCEEEECCC--CCC--C Q ss_conf 424898279971777898544-------------------507999984----189-------428997465--778--5 Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPRR-------------------DRLCIVQLS----PGD-------GTVDIIRIA--AGQ--K 61 (207) Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~~-------------------~~l~LiQl~----~~~-------~~~~l~~~~--~~~--~ 61 (207) .+...+.||+|||++|+.... +.+.+||++ ..+ ..++.+.+. ... . T Consensus 34 ~i~~~~fVAiD~Ef~Gi~~~~~~~~~~t~~~rY~~lk~nv~~~~iiQlGlt~f~~~g~~~~~~~~~w~FNf~~~~~~~~~ 113 (289) T 1uoc_A 34 LVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVDFLNPIQLGLSLSDANGNKPDNGPSTWQFNFEFDPKKEIM 113 (289) T ss_dssp HTTTSCEEEEEEEEEC----------CHHHHHHHHHHHHHTTCEEEEEEEEEECTTCCCCSSSCSEEEEEBCCCTTCCCC T ss_pred HHHCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCCCC T ss_conf 98339989996251784578886668999999999998664363246999987048876888714789977448620232 Q ss_pred CCH-----------------------HHHH------HHHCCCCCEEECCCCHHHHHHHHHH-HC-CC------------- Q ss_conf 706-----------------------7767------7732364023010000168886542-00-00------------- Q gi|254780636|r 62 NAP-----------------------NLVG------MLVDEKREKIFHYGRFDIAVLFYTF-GV-RV------------- 97 (207) Q Consensus 62 ~~~-----------------------~L~~------ll~d~~i~KV~Hn~~~D~~~L~~~~-gi-~~------------- 97 (207) .+. ...+ ++.++++.||+||+-+|+..|.+.+ |- .| T Consensus 114 ~~~Si~fL~~~G~DFnk~~~~GI~~~~f~~~~~~s~l~~~~~~~wv~f~g~yD~~yl~k~l~~~~LP~~~~~F~~~~~~~ 193 (289) T 1uoc_A 114 STESLELLRKSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVHQY 193 (289) T ss_dssp CHHHHHHHHHTTCCHHHHHHHCBCHHHHHHHHHTSSCSSCTTSEEEESSTTHHHHHHHHHHTTSCCCSSHHHHHHHHHHH T ss_pred CHHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHCCHHHCCCCEEEEECCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH T ss_conf 57789999985998689997199888888998750044247862896043557999999971898999999999999998 Q ss_pred -CCHHHHHHHHHHHHHHCC-------------CHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf -000457898865211000-------------000887776542002467520036565443236899998645999999 Q gi|254780636|r 98 -RPVFCTKIASRLTRTYTN-------------QHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHAL 163 (207) Q Consensus 98 -~~i~DT~ias~l~~~~~~-------------~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L 163 (207) ..++||...++.+.+... +.||..+++. +|++ +. ..-+=|+.|+..+-.+ T Consensus 194 Fp~iyDtK~~~~~~~~l~~~~~~~~~~~~~~~~~~L~~va~~-l~v~-------------r~--g~~HeAG~DS~lTg~~ 257 (289) T 1uoc_A 194 MPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADE-LGLP-------------RF--SIFTTTGGQSLLMLLS 257 (289) T ss_dssp CSSEEEHHHHHHHHTTTCC-------------CCSHHHHHHH-TTCC-------------CC--GGGGSHHHHHHHHHHH T ss_pred CCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHH-CCCC-------------CC--CCCCCCHHHHHHHHHH T ss_conf 762613999998621335754343322101234888899987-2998-------------77--8886607899999999 Q ss_pred HHHHHHHH Q ss_conf 99999999 Q gi|254780636|r 164 RLQFTEKL 171 (207) Q Consensus 164 ~~~l~~~L 171 (207) +-++.+.+ T Consensus 258 F~~l~~~~ 265 (289) T 1uoc_A 258 FCQLSKLS 265 (289) T ss_dssp HHHHHHHT T ss_pred HHHHHHHH T ss_conf 99999987 No 24 >1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET: DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5 e.8.1.1 Probab=97.45 E-value=0.0011 Score=39.34 Aligned_cols=145 Identities=17% Similarity=0.203 Sum_probs=76.7 Q ss_pred CCCCEEEECCCCCC------CCCCCEEEEEEEEEC--CC--CEEEECCC------------------CCCCCCHHHHHHH Q ss_conf 89827997177789------854450799998418--94--28997465------------------7785706776777 Q gi|254780636|r 19 YVDAIAVDTETLGL------MPRRDRLCIVQLSPG--DG--TVDIIRIA------------------AGQKNAPNLVGML 70 (207) Q Consensus 19 ~~~~iaiDtEt~~l------~~~~~~l~LiQl~~~--~~--~~~l~~~~------------------~~~~~~~~L~~ll 70 (207) .-.+++||.|+.+- +|.+++..+||++.. ++ .+++.... ........+..++ T Consensus 189 ~lrilsfDIE~~s~~~~~fPdp~~~~~~ii~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~f~sEkeLL~~F~~~i 268 (847) T 1s5j_A 189 KIKRVAIDIEVYTPVKGRIPDSQKAEFPIISIALAGSDGLKKVLVLNRNDVNEGSVKLDGISVERFNTEYELLGRFFDIL 268 (847) T ss_dssp CCCEEEEEEEECCSSSSCCCCTTTCCSCEEEEEEEETTSCEEEEEECSSCCCCCCEEETTEEEEEESSHHHHHHHHHHHH T ss_pred CCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHC T ss_conf 84499999887888889998943477428999999568998999981677776654579958999898999999999742 Q ss_pred HCCCCCEEECCC-CHHHHHHHHH---HHCCCCC----------------H-HHH-HHH----HHHHH--HHCCCHHHHHH Q ss_conf 323640230100-0016888654---2000000----------------0-457-898----86521--10000008877 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYT---FGVRVRP----------------V-FCT-KIA----SRLTR--TYTNQHGLKDN 122 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~---~gi~~~~----------------i-~DT-~ia----s~l~~--~~~~~~~L~~L 122 (207) .||+|+ +|||+ .||+..|.+. +|+.... + +|. ... .+... ....+++|.++ T Consensus 269 ~dpDII-~GyNi~~FDlpYL~~Ra~~lg~~~~~~~~~~~g~~~~~~~~~~~~d~~~~~~~d~~~~~~~~~~l~sy~L~~V 347 (847) T 1s5j_A 269 LEYPIV-LTFNGDDFDLPYIYFRALKLGYFPEEIPIDVAGKDEAKYLAGLHIDLYKFFFNKAVRNYAFEGKYNEYNLDAV 347 (847) T ss_dssp TTCSEE-EESSTTTTHHHHHHHHHHTTTCCGGGCSEECCSTTCCEETTSEEEEHHHHHTSHHHHHHTSTTCCSSCSHHHH T ss_pred CCCCEE-EEEECCCCCHHHHHHHHHHCCCCCCCCEEECCCCEEEEEEEEEEEEEEEEEHHHHHHHHHHHCCCCCCCHHHH T ss_conf 289979-8831056658999999998099832042530573235786206886533575989999876413020779999 Q ss_pred HHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 765420024675200365654432368999986459999999999 Q gi|254780636|r 123 LKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 123 ~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) ++++||..- ..-...+.... .+.-+.|+..||..+..|...+ T Consensus 348 a~~~Lg~~K--~~~~~~~~~~d-~~~l~~Y~~~D~~l~~~L~~~~ 389 (847) T 1s5j_A 348 AKALLGTSK--VKVDTLISFLD-VEKLIEYNFRDAEITLQLTTFN 389 (847) T ss_dssp HHHHHCCCC--C--SSCTTTCC-HHHHHHHHHHHHHHHHHTTTHH T ss_pred HHHHHCCCC--CCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHH T ss_conf 999838884--22222020100-6889888755568888999875 No 25 >2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP: c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A* 2pyj_A* 2pyl_A* 2pzs_A* Probab=97.34 E-value=0.0035 Score=36.51 Aligned_cols=142 Identities=11% Similarity=0.049 Sum_probs=74.6 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEECCCC-EEEECCCCCCCCCHHHHHHHH--CCCCCEEECCCCHHHHHHHHHHHC- Q ss_conf 9827997177789854450799998418942-899746577857067767773--236402301000016888654200- Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGT-VDIIRIAAGQKNAPNLVGMLV--DEKREKIFHYGRFDIAVLFYTFGV- 95 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~-~~l~~~~~~~~~~~~L~~ll~--d~~i~KV~Hn~~~D~~~L~~~~gi- 95 (207) -+++.+|.||+ .+....++..+-+....+. .+-+. .....+.+.+. ||.| +|||.+||..++..++.. T Consensus 6 ~~~~~~D~Et~-~~~~~~~~~~~~~~~~~~~~~~~~~-----~~l~~f~~~i~~~dpdi--~~hNl~FD~~~i~~~~~~~ 77 (575) T 2py5_A 6 RKMYSCAFETT-TKVEDCRVWAYGYMNIEDHSEYKIG-----NSLDEFMAWVLKVQADL--YFHNLKFAGAFIINWLERN 77 (575) T ss_dssp CCEEEEEEEEC-CBTTBCCEEEEEEEESSCTTCEEEE-----SCHHHHHHHHHHHCCEE--EETTHHHHHHHHHHHHHHT T ss_pred CEEEEEEEEEC-CCCCCCEEEEEEEEECCCCEEEEHH-----HHHHHHHHHHHHCCCCE--EEECCCCCHHHHHHHHHHC T ss_conf 51799999706-8977731479999717984077708-----99999999998659979--9988757999999999970 Q ss_pred --CCCCHHH----------H-HHH---------------HHHHHHHC-CCHHHHHHHHHHHCCCCCCCC---EECCCCCC Q ss_conf --0000045----------7-898---------------86521100-000088777654200246752---00365654 Q gi|254780636|r 96 --RVRPVFC----------T-KIA---------------SRLTRTYT-NQHGLKDNLKELLGINISKAQ---QSSDWSAD 143 (207) Q Consensus 96 --~~~~i~D----------T-~ia---------------s~l~~~~~-~~~~L~~L~~~~lg~~ldK~~---q~SdW~~r 143 (207) ....-.+ . .+. -.+.+++. .+.||.++++.+ +....|.. ...+|... T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~DS~~l~~~SL~~va~~f-~l~~~K~~~~~~~~~~~~~ 156 (575) T 2py5_A 78 GFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDF-KLTVLKGDIDYHKERPVGY 156 (575) T ss_dssp TCEECTTCCTTEEEEEEBTTCCEEEEEEEEEEETTEEEEEEEEEHHHHSCSCHHHHHHHT-TCCCCSSCCCTTSCCCTTC T ss_pred CCCCEECCCCCCCCCEEEECCEEEEEEEEEEECCEEEEEEEEEECCCCCCCCHHHHHHHH-CCCCCCCCCCHHHCCHHHH T ss_conf 986203246766652267354579998999603301368999842144844799999873-7454556477444102233 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 432368999986459999999999999 Q gi|254780636|r 144 DLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 144 pLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) .+.++.+.|+..||..|.+++..+.+. T Consensus 157 ~~~~~~~~Y~~~Dv~ll~~i~~~~~~~ 183 (575) T 2py5_A 157 KITPEEYAYIKNDIQIIAEALLIQFKQ 183 (575) T ss_dssp CCCHHHHHHHHHHHHHHHHHHHHHHHT T ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 232989999999999999999999998 No 26 >2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A Probab=97.31 E-value=0.00094 Score=39.80 Aligned_cols=140 Identities=18% Similarity=0.244 Sum_probs=84.0 Q ss_pred HCCCCCCEEEECCCCCCCCC-----C--------------CEEEEEEEE----ECCC------CEEEECCC----CCCCC Q ss_conf 42489827997177789854-----4--------------507999984----1894------28997465----77857 Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPR-----R--------------DRLCIVQLS----PGDG------TVDIIRIA----AGQKN 62 (207) Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~-----~--------------~~l~LiQl~----~~~~------~~~l~~~~----~~~~~ 62 (207) .++..+.||+|||++|+... . +.+.+||++ ..++ .++-+.+. ..... T Consensus 41 ~I~~~~fVAiDtEFpGiv~~p~~~~~~t~d~rY~~lr~nVd~l~iIQlGLt~~~~~g~~p~~~~twqFNF~f~~~~d~~~ 120 (333) T 2p51_A 41 LIERYPVVSMDTEFPGVVARPLGVFKSSDDYHYQTLRANVDSLKIIQIGLALSDEEGNAPVEACTWQFNFTFNLQDDMYA 120 (333) T ss_dssp HTTTSCEEEEEEECCCCCCCCCSCCSSSHHHHHHHHHHHHHHSCCCEEEEEEECTTSCCCTTCSEEEEEBCCCTTTSCCC T ss_pred HHHCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEEEEEECCCCCCCCCEEEEEEEEECCCCCCCC T ss_conf 98459989995331772567876668978999999997542145147999977258887888637999879778665504 Q ss_pred C-----------------------HHHHH------HHHCCCCCEEECCCCHHHHHHHHHHH----------------CCC Q ss_conf 0-----------------------67767------77323640230100001688865420----------------000 Q gi|254780636|r 63 A-----------------------PNLVG------MLVDEKREKIFHYGRFDIAVLFYTFG----------------VRV 97 (207) Q Consensus 63 ~-----------------------~~L~~------ll~d~~i~KV~Hn~~~D~~~L~~~~g----------------i~~ 97 (207) + ..+.+ ++-++++.||.|++.+|+..|.+.+- ... T Consensus 121 ~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~sglv~~~~v~Wvtfhg~yD~~yLlk~l~g~~LP~~~~eF~~~l~~~F 200 (333) T 2p51_A 121 PESIELLTKSGIDFKKHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAMTQIPLPAEYEEFYKILCIYF 200 (333) T ss_dssp HHHHHHHHHTTCCHHHHHHHCBCHHHHHHHHHTTTSSSCTTCEEEESSCHHHHHHHHHHHHCSCCCSSHHHHHHHHHHHS T ss_pred HHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC T ss_conf 78999999749677889860998888899998505541688739980661679999999708878867899999999977 Q ss_pred CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0004578988652110000008877765420024675200365654432368999986459999999999999997 Q gi|254780636|r 98 RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQR 173 (207) Q Consensus 98 ~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~ 173 (207) ..++||...++-+.+ .+-||..+++. ||+. .. -++ +=|..|+..+..+|-+|.+..-. T Consensus 201 P~vYD~Kyia~~~~~--~~~gL~~lA~~-L~v~---r~---------g~~---HqAGsDSllT~~~F~kl~~~~f~ 258 (333) T 2p51_A 201 PKNYDIKYIMKSVLN--NSKGLQDIADD-LQIH---RI---------GPQ---HQAGSDALLTARIFFEIRSRYFD 258 (333) T ss_dssp SSEEEHHHHHTTTTC--CCCCHHHHHHH-TTCC---CC---------SCT---TSHHHHHHHHHHHHHHHHHHHHT T ss_pred CHHHHHHHHHHHCCC--CCCCHHHHHHH-CCCC---CC---------CCC---CCCHHHHHHHHHHHHHHHHHHCC T ss_conf 628718999976156--67659999997-4998---76---------776---45305899999999999998659 No 27 >3nae_A DNA polymerase, GP43; RB69 DNA polymerase; HET: DNA G35 DOC DTP; 2.00A {Enterobacteria phage RB69} PDB: 3lzi_A* 3lzj_A* 1ig9_A* 1q9x_A* 2atq_A* 2dy4_A* 2oyq_A* 2ozm_A* 2ozs_A* 2p5g_A* 2p5o_A* 1q9y_A* 3l8b_A* 3lds_A* 3cq8_A* 1ih7_A* 1clq_A* 1waf_A* 1waj_A* 3cfr_A* ... Probab=96.79 E-value=0.0059 Score=35.15 Aligned_cols=97 Identities=10% Similarity=-0.041 Sum_probs=55.0 Q ss_pred HCCCCCEEECCC-CHHHHHHHHHHHCC-------------------------------C--CCHHHHHHHHH-HHHHHCC Q ss_conf 323640230100-00168886542000-------------------------------0--00045789886-5211000 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYTFGVR-------------------------------V--RPVFCTKIASR-LTRTYTN 115 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~~gi~-------------------------------~--~~i~DT~ias~-l~~~~~~ 115 (207) .||+|+ +|||+ .||+..|.+..... + ..++|.+-..+ ....... T Consensus 208 ~dPDII-~GyN~~~FD~pYL~~R~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~i~G~~~lD~~~l~~k~~~~~~~ 286 (903) T 3nae_A 208 KTPVIL-TGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQP 286 (903) T ss_dssp TCCSEE-ECSSTTTTHHHHHHHHHHHHHCHHHHGGGSTTSCEEEEEEEETTEEEEEEEETTCEECCHHHHHHHHSCCCCS T ss_pred CCCCEE-EECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEEECEEEEEHHHHHHHHHHHCCC T ss_conf 599899-9689877679999999998557632211254567652100002355314666043675289999998760201 Q ss_pred CHHHHHHHHHHHCCCCCCCC-EECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00088777654200246752-0036565443236899998645999999999999 Q gi|254780636|r 116 QHGLKDNLKELLGINISKAQ-QSSDWSADDLSDEQLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 116 ~~~L~~L~~~~lg~~ldK~~-q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) +++|..++..++|..-.+.. ...++.... ...-+.|...|+..+.+|.+++.- T Consensus 287 sy~Ld~va~~~Lg~~k~~~~~~~~~~~~~~-~~~~~~Y~~~D~~L~~~L~~kl~~ 340 (903) T 3nae_A 287 SYSLDYISEFELNVGKLKYDGPISKLRESN-HQRYISYNIIAVYRVLQIDAKRQF 340 (903) T ss_dssp CCCHHHHHHHHHCCCCCCCSSCGGGHHHHH-HHHHHHHHHHHHHHHHHHHHHHCH T ss_pred CCHHHHHHHHHCCCCCCCCCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 123999999972888764421032330467-888988743279999999999878 No 28 >2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1 strain kos} PDB: 1dml_B* Probab=96.73 E-value=0.0046 Score=35.82 Aligned_cols=97 Identities=10% Similarity=-0.026 Sum_probs=56.2 Q ss_pred HCCCCCEEECCC-CHHHHHHHHHHH----CCC------------------------------CC--HHHHHHHHHHHHHH Q ss_conf 323640230100-001688865420----000------------------------------00--04578988652110 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYTFG----VRV------------------------------RP--VFCTKIASRLTRTY 113 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~~g----i~~------------------------------~~--i~DT~ias~l~~~~ 113 (207) .||+|+ +|||+ .||+..|..... ..+ .+ ++|++-..+-- .. T Consensus 415 ~dPDII-tGYNi~~FDlpYL~~Ra~~l~~~~~~~~gR~~~~~~~~~~~~~~~~~~~~~~~~i~Gri~iDl~~~~k~~-~k 492 (1193) T 2gv9_A 415 YGPEFV-TGYNIINFDWPFLLAKLTDIYKVPLDGYGRMNGRGVFRVWDIGQSHFQKRSKIKVNGMVNIDMYGIITDK-IK 492 (1193) T ss_dssp HCCSEE-EESSTTTTHHHHHHHHHHHTTCCCCTTTSSBSSSCCEEECC----------CEEETTBEEEEHHHHHTTT-CC T ss_pred CCCCEE-EEECCCCCCHHHHHHHHHHHCCCCHHHHCCCCCCCCCEECCCCCCCCCCCCEEEECCEEEEEHHHHHHHH-CC T ss_conf 399889-9725547747899999999779987882755765662020356665565404623466998437887663-04 Q ss_pred CCCHHHHHHHHHHHCCCCCC-CC-EEC-CCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00000887776542002467-52-003-6565443-236899998645999999999999 Q gi|254780636|r 114 TNQHGLKDNLKELLGINISK-AQ-QSS-DWSADDL-SDEQLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 114 ~~~~~L~~L~~~~lg~~ldK-~~-q~S-dW~~rpL-s~~Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) ..+++|.++++++||.+-.. +. ... -|...|- ...-..|+..|+..+..|+.++.. T Consensus 493 L~sY~L~~Va~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~lv~~L~~kl~~ 552 (1193) T 2gv9_A 493 LSSYKLNAVAEAVLKDKKKDLSYRDIPAYYATGPAQRGVIGEYCIQDSLLVGQLFFKFLP 552 (1193) T ss_dssp CSCCCHHHHHHHTSCCCCCCCCTTTHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHCH T ss_pred CCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 666889999999727777666888888887656778999999998879999999999878 No 29 >3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA- binding, DNA-directed DNA polymerase, exonuclease; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae} Probab=96.52 E-value=0.012 Score=33.43 Aligned_cols=102 Identities=17% Similarity=0.056 Sum_probs=60.0 Q ss_pred HHHHH--HCCCCCEEECCC-CHHHHHHHHHH---HCC----------------------------------CCC--HHHH Q ss_conf 76777--323640230100-00168886542---000----------------------------------000--0457 Q gi|254780636|r 66 LVGML--VDEKREKIFHYG-RFDIAVLFYTF---GVR----------------------------------VRP--VFCT 103 (207) Q Consensus 66 L~~ll--~d~~i~KV~Hn~-~~D~~~L~~~~---gi~----------------------------------~~~--i~DT 103 (207) +..++ .||+|+ +|||+ .||+..|.+.. |+. +.+ ++|+ T Consensus 320 F~~~i~~~DPDII-~GyNi~~FDlpYL~~Ra~~l~i~~~~~~gr~~~~~~~~~~~~~~~~~~g~~~~~~~~i~Gr~~iDl 398 (919) T 3iay_A 320 WRNFIIKVDPDVI-IGYNTTNFDIPYLLNRAKALKVNDFPYFGRLKTVKQEIKESVFSSKAYGTRETKNVNIDGRLQLDL 398 (919) T ss_dssp HHHHHHHHCCSEE-EESSTTTTHHHHHHHHHHHTTCTTCSCCSSBTTCCCCBCCEEEEETTTEEEEECCBCCTTCEEEEH T ss_pred HHHHHHHCCCCEE-EEECCCCCCHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCEEEEEH T ss_conf 9999866299879-875785753799999999858751433176577664456564345433564422898737899877 Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-C-CEECC-CCCCC-CCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 898865211000000887776542002467-5-20036-56544-3236899998645999999999999 Q gi|254780636|r 104 KIASRLTRTYTNQHGLKDNLKELLGINISK-A-QQSSD-WSADD-LSDEQLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 104 ~ias~l~~~~~~~~~L~~L~~~~lg~~ldK-~-~q~Sd-W~~rp-Ls~~Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) .-..+-. ....+++|.+++++++|.+-.. . ...++ |...+ -...-+.|+..||..+..|.+++.- T Consensus 399 ~~~~~~~-~kl~sy~L~~Va~~~lg~~K~dv~~~~i~~~~~~~~e~~~~l~~Y~l~Da~l~~~L~~kl~~ 467 (919) T 3iay_A 399 LQFIQRE-YKLRSYTLNAVSAHFLGEQKEDVHYSIISDLQNGDSETRRRLAVYCLKDAYLPLRLMEKLMA 467 (919) T ss_dssp HHHHHHH-CCCSCCCHHHHHHHHHCCC------CCHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHTTH T ss_pred HHHHHHH-CCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999875-65672328999987715887643044435777535267999999985436889999999999 No 30 >2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, X-RAY diffraction, hydrolase; 2.30A {Xanthomonas campestris PV} Probab=96.14 E-value=0.0022 Score=37.62 Aligned_cols=28 Identities=29% Similarity=0.387 Sum_probs=22.7 Q ss_pred CCCCCCEEEECCCCCCCCCCCEEEEEEEEE Q ss_conf 248982799717778985445079999841 Q gi|254780636|r 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSP 46 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~ 46 (207) ....+.|.+||||||++|.++++ ||+|. T Consensus 6 ~~~~~lV~lD~ETTGLdp~~d~I--IEIaa 33 (194) T 2gbz_A 6 AGNDRLIWIDLEMTGLDTDRDSI--IEIAT 33 (194) T ss_dssp --CCEEEEEEEEESCSCTTTCCE--EEEEE T ss_pred CCCCCEEEEEEECCCCCCCCCEE--EEEEE T ss_conf 77899899987789999999837--99999 No 31 >2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli K12} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A Probab=96.01 E-value=0.0028 Score=37.09 Aligned_cols=27 Identities=33% Similarity=0.572 Sum_probs=21.8 Q ss_pred CCCCCEEEECCCCCCCCCCCEEEEEEEEE Q ss_conf 48982799717778985445079999841 Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRRDRLCIVQLSP 46 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~~~l~LiQl~~ 46 (207) ++.++|.+|+||||++|.++++ ||||. T Consensus 3 ~~~~lv~lD~ETTGL~p~~D~I--IeIaa 29 (180) T 2igi_A 3 NENNLIWIDLEMTGLDPERDRI--IEIAT 29 (180) T ss_dssp GGGCEEEEEEEESSSCTTTCCE--EEEEE T ss_pred CCCCEEEEEEECCCCCCCCCEE--EEEEE T ss_conf 8897899986789999999847--99999 No 32 >3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia coli k-12} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 3maq_A* 1q8i_A* Probab=95.83 E-value=0.0074 Score=34.60 Aligned_cols=142 Identities=15% Similarity=0.098 Sum_probs=73.7 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEECCCC-EEEECCCC-CC--------------CCCHHHHHHH--HCCCCCEEECC Q ss_conf 9827997177789854450799998418942-89974657-78--------------5706776777--32364023010 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGT-VDIIRIAA-GQ--------------KNAPNLVGML--VDEKREKIFHY 81 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~-~~l~~~~~-~~--------------~~~~~L~~ll--~d~~i~KV~Hn 81 (207) -.+++||.|+.+-+ ++.-|.+...... ++.+.... .. .....+..++ .||+|+ +||| T Consensus 153 l~vlsfDIE~~~~~----~i~~I~~~~~~~~~v~~~~~~~~~~~~~~~~v~~~~sE~~LL~~F~~~i~~~DPDII-~GyN 227 (786) T 3k59_A 153 LKWVSIDIETTRHG----ELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKLNAWFANYDPDVI-IGWN 227 (786) T ss_dssp CCEEEEEEEECTTS----CEEEEEEEETTEEEEEEESSCCSCCTTCSSEEEEESSHHHHHHHHHHHHHHHCCSEE-EESS T ss_pred CEEEEEEEEECCCC----CEEEEEEECCCCCEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHHHHHCCCCEE-EECC T ss_conf 14899988975889----889999856998389999467777777753899969999999999999997099999-9728 Q ss_pred C-CHHHHHHHHHH---HCC-------------------------CCC--HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC Q ss_conf 0-00168886542---000-------------------------000--0457898865211000000887776542002 Q gi|254780636|r 82 G-RFDIAVLFYTF---GVR-------------------------VRP--VFCTKIASRLTRTYTNQHGLKDNLKELLGIN 130 (207) Q Consensus 82 ~-~~D~~~L~~~~---gi~-------------------------~~~--i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ 130 (207) . .||+..|.+.. |+. ..+ ++|+.-..+-.-....+++|.++++++||.. T Consensus 228 i~~FDlpyL~~Ra~~~~i~~~lgr~~~~~~~~~~~~~~~~~~~~i~Gr~~iD~~~~~~~~~~~~~sy~L~~va~~~L~~~ 307 (786) T 3k59_A 228 VVQFDLRMLQKHAERYRLPLRLGRDNSELEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEG 307 (786) T ss_dssp TTTTHHHHHHHHHHHHTCCCCCBTTTBCCEEEECSSSTTCEEEECTTCEEEEHHHHHHHTTCCCSCCSHHHHHHHHHCCC T ss_pred CCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCEEEHHHHHHHHHHHHCCCCCCHHHHHHHHCCCC T ss_conf 86867999999999818973026767502300134346537871076880899999999752554378899999975788 Q ss_pred CCC--C-CEECC----CCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 467--5-20036----56544323689999864599999999999 Q gi|254780636|r 131 ISK--A-QQSSD----WSADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 131 ldK--~-~q~Sd----W~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) ..- . ..... |... ...-..|+..|+..+..|.+++. T Consensus 308 k~~~~~~~~~~~~~~~~~~~--~~~~~~Y~~~D~~L~~~L~~kl~ 350 (786) T 3k59_A 308 KSIDNPWDRMDEIDRRFAED--KPALATYNLKNCELVTQIFHKTE 350 (786) T ss_dssp CC-CCHHHHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHHHHHHT T ss_pred CCCCCHHHHHHHHHHCCHHH--HHHHHHHHHHHHHHHHHHHHHHC T ss_conf 66678677534554246145--88999999888999999999856 No 33 >1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 Probab=95.45 E-value=0.11 Score=27.77 Aligned_cols=77 Identities=12% Similarity=0.223 Sum_probs=42.7 Q ss_pred EECCCCHHH-HHHHHHH---HCCC----CCHHHHHHHH-HHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHH Q ss_conf 301000016-8886542---0000----0004578988-65211000000887776542002467520036565443236 Q gi|254780636|r 78 IFHYGRFDI-AVLFYTF---GVRV----RPVFCTKIAS-RLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDE 148 (207) Q Consensus 78 V~Hn~~~D~-~~L~~~~---gi~~----~~i~DT~ias-~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~ 148 (207) +.++..+|. .+|...+ ++.. ..++|++-.. ...+....+++|..+++. +|++.+. T Consensus 109 ~~~~~~~d~~~~l~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~kL~~l~~~-~gi~~~~--------------- 172 (204) T 1w0h_A 109 LLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEK-LGMDYDG--------------- 172 (204) T ss_dssp EEESSTTTTHHHHHHHHHHHTCCCCGGGSEEEEHHHHHHHHHTCCGGGCSHHHHHHH-TTCCCCS--------------- T ss_pred HHCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEHHHHHHHHHCCCCCCCCHHHHHHH-CCCCCCC--------------- T ss_conf 211035648999999999818998642451676888888875034578899999998-6999999--------------- Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8999986459999999999999 Q gi|254780636|r 149 QLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 149 Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) +-+-|..||..+-+|+.+|.++ T Consensus 173 ~aH~Al~Da~~ta~i~~~ll~~ 194 (204) T 1w0h_A 173 RPHCGLDDSKNIARIAVRMLQD 194 (204) T ss_dssp CTTCHHHHHHHHHHHHHHHHHT T ss_pred CCCCHHHHHHHHHHHHHHHHHC T ss_conf 8848799999999999999987 No 34 >3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, cytoplasm, exonuclease, hydrolase, magnesium, metal-binding, nonsense- mediated mRNA decay; HET: 7MG GDP; 3.00A {Mus musculus} Probab=95.39 E-value=0.023 Score=31.78 Aligned_cols=99 Identities=17% Similarity=0.104 Sum_probs=58.9 Q ss_pred HHCCCCCEEECCCCHHHHHHHHHH-HCCC--------------CCHHHHHHHHHHH--HHHCCCHHHHHHHHHHHCCC-- Q ss_conf 732364023010000168886542-0000--------------0004578988652--11000000887776542002-- Q gi|254780636|r 70 LVDEKREKIFHYGRFDIAVLFYTF-GVRV--------------RPVFCTKIASRLT--RTYTNQHGLKDNLKELLGIN-- 130 (207) Q Consensus 70 l~d~~i~KV~Hn~~~D~~~L~~~~-gi~~--------------~~i~DT~ias~l~--~~~~~~~~L~~L~~~~lg~~-- 130 (207) +.+.+.+.||||+-+|+..+.+.| |..| ..++||...+... ......-+|..+.+.+-... T Consensus 272 l~~~kkpiVgHN~~~Dl~~l~~~F~gpLP~~~~eFk~~v~~lFP~i~DTK~la~~~~~~~~~~~t~L~~l~~~l~~~~~~ 351 (507) T 3d45_A 272 IANSGKLVVGHNMLLDVMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFD 351 (507) T ss_dssp HHHHCCEEEESSCHHHHHHHHHHHTCSCCSSHHHHHHHHHHHCSCEEEHHHHTTSTTHHHHCCCCCHHHHHHHTTSTTCC T ss_pred HHHCCCEEEEECCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCEEHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCC T ss_conf 97259839992438889999998428899679999999999777505888776316744467787699999998325789 Q ss_pred -----CCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf -----4675200365654432368999986459999999999999997 Q gi|254780636|r 131 -----ISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQR 173 (207) Q Consensus 131 -----ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~ 173 (207) ........+++. ++.+=|+.|++.|-.++-++...|.. T Consensus 352 ~~~i~~~~~~~~~~~~~-----~~~HeAGyDA~mTg~vF~~l~~~l~~ 394 (507) T 3d45_A 352 PPKVESAEGFPSYDTAS-----EQLHEAGYDAYITGLCFISMANYLGS 394 (507) T ss_dssp CCCEEECTTSCCCC---------CCCCHHHHHHHHHHHHHHHHHHHCC T ss_pred CCCEECCCCCCCCCCCC-----CCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 98342265666555678-----88735388899999999999999731 No 35 >1noy_A Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DNA-binding, complex (nucleotidyltransferase/DNA); HET: DNA; 2.20A {Enterobacteria phage T4} SCOP: c.55.3.5 PDB: 1noz_A* Probab=95.14 E-value=0.14 Score=27.20 Aligned_cols=95 Identities=8% Similarity=-0.043 Sum_probs=51.8 Q ss_pred HCCCCCEEECCC-CHHHHHHHHHHHCC-------------------------------CC--CHHHHHHHHHHH-HHHCC Q ss_conf 323640230100-00168886542000-------------------------------00--004578988652-11000 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYTFGVR-------------------------------VR--PVFCTKIASRLT-RTYTN 115 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~~gi~-------------------------------~~--~i~DT~ias~l~-~~~~~ 115 (207) .||+|+ +|||. .||+..|.+..... .. ..+|.+-..+.. ..... T Consensus 205 ~dPDiI-~G~N~~~FD~pYL~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~d~l~~~~~~~~~~~~ 283 (388) T 1noy_A 205 KRPAIF-TGWNIEGFDVPYIMNRVKMILGERSMKRFSPIGRVKSKLLQNMYGSKEIYSIDGVSILDYLDLYKKFAFTNLP 283 (388) T ss_dssp SCCSEE-ECSSTTTTHHHHHHHHHHHHHHHHHHGGGSTTSCEEEEECCGGGCSCEEEEETTSEECCHHHHHHHHTCCCCS T ss_pred CCCCEE-EECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEECCCCCEEEEECCCHHHHHHHHHHHHHCCCCC T ss_conf 388889-8706788517899999998526421011375676642255402565225642142167899999976303423 Q ss_pred CHHHHHHHHHHHCCCCCC-CCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 000887776542002467-5200365654432368999986459999999999 Q gi|254780636|r 116 QHGLKDNLKELLGINISK-AQQSSDWSADDLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 116 ~~~L~~L~~~~lg~~ldK-~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) +.+|.......++..... ......|.... .+.-+.|+..||..+++|.+++ T Consensus 284 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d-~~kli~Yn~~D~~l~~~L~~kl 335 (388) T 1noy_A 284 SFSLESVAQHETKKGKLPYDGPINKLRETN-HQRYISYNIIDVESVQAIDKIR 335 (388) T ss_dssp CCSHHHHHHHHHSCCCCCCSSCGGGHHHHH-HHHHHHHHHHHHHHHHHHHHHH T ss_pred CCCHHHHHHHHCCCCCCCCHHHHHHHHHHC-HHHHHHHHHHHHHHHHHHHHHH T ss_conf 202888999866887667256666665418-9999999999999999999997 No 36 >3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A Probab=94.39 E-value=0.22 Score=26.07 Aligned_cols=134 Identities=10% Similarity=0.088 Sum_probs=66.8 Q ss_pred CCEEEECCCCCCCCCCCE-EEEEEEEE-----CCCC------EE-EECCCCCCCC-----------------CH------ Q ss_conf 827997177789854450-79999841-----8942------89-9746577857-----------------06------ Q gi|254780636|r 21 DAIAVDTETLGLMPRRDR-LCIVQLSP-----GDGT------VD-IIRIAAGQKN-----------------AP------ 64 (207) Q Consensus 21 ~~iaiDtEt~~l~~~~~~-l~LiQl~~-----~~~~------~~-l~~~~~~~~~-----------------~~------ 64 (207) ..|.||+||||+++.++. --.|||+. ..+. +. ++.+...... ++ T Consensus 20 ~~vViD~ETTg~~~~~d~~~EIIEIgaV~vd~~~~~i~~~~~F~~~VkP~~~~~ls~~~~~ltGIt~e~v~~ap~f~evl 99 (308) T 3cg7_A 20 TLLILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKYVKPVLNRTLTKNCVDFTGIPQRSIDTADTFDVVY 99 (308) T ss_dssp EEEEEEEEECCBTTBCSCCCCEEEEEEEEEETTTTEEEEEEEEEEECBCSSBCSCCHHHHHHHCCCHHHHHTSCBHHHHH T ss_pred EEEEEEEEECCCCCCCCCCCEEEEEEEEEEEECCCEEEECCEEEEEECCCCCCCCCHHHHHHCCCCHHHHHCCCHHHHHH T ss_conf 18999976089987889996079999999980599897841888778988888679889987197989943110045668 Q ss_pred -HHHHHHHCCCC----CEEECCCCHHHH-HHHHHH---HCCC----CCHHHHHHHH-HHHH-----HHCCCHHHHHHHHH Q ss_conf -77677732364----023010000168-886542---0000----0004578988-6521-----10000008877765 Q gi|254780636|r 65 -NLVGMLVDEKR----EKIFHYGRFDIA-VLFYTF---GVRV----RPVFCTKIAS-RLTR-----TYTNQHGLKDNLKE 125 (207) Q Consensus 65 -~L~~ll~d~~i----~KV~Hn~~~D~~-~L~~~~---gi~~----~~i~DT~ias-~l~~-----~~~~~~~L~~L~~~ 125 (207) .+.+++.+..+ .-+.+++.+|.. ++.+.+ |+.. .+.+|++-.. .... ....+++|..++++ T Consensus 100 ~~f~~~l~~~~l~~~~~~f~~~~~~D~~~~L~~~~~~~~i~~P~~~~~~iDl~~~~~~~~~~~~~~~~~~~~~L~~l~~~ 179 (308) T 3cg7_A 100 EQFQQWLITLGLEEGKFAFVCDSRQDLWRIAQYQMKLSNIQMPAFFRQYINLYKIFTNEMDRMGPKELSATTNIGKMNEY 179 (308) T ss_dssp HHHHHHHHHHCCCTTSEEEEESSSHHHHTHHHHHHHHTTCCCCGGGSEEEEHHHHHHHHHHHHCCCCCCCCSHHHHHHHH T ss_pred HHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCEEEHHHHHHHHHHHHHHCCCCCCCCHHHHHHH T ss_conf 89999973677323289993154566999999999980999872013244599999999997432277777789999997 Q ss_pred HHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 420024675200365654432368999986459999999999999 Q gi|254780636|r 126 LLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 126 ~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) +|++.. . +-+-|..||..+.+|+.+|.++ T Consensus 180 -~gI~~~---------g------~aH~ALdDA~~tA~Il~kLl~~ 208 (308) T 3cg7_A 180 -YDLPTI---------G------RAHDAMDDCLNIATILQRMINM 208 (308) T ss_dssp -TTCCCC---------S------CTTCHHHHHHHHHHHHHHHHHT T ss_pred -CCCCCC---------C------CCCCHHHHHHHHHHHHHHHHHC T ss_conf -699999---------9------8968099999999999999977 No 37 >2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase/RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A Probab=92.85 E-value=0.18 Score=26.48 Aligned_cols=99 Identities=18% Similarity=0.097 Sum_probs=57.3 Q ss_pred HHCCCCCEEECCCCHHHHHHHHHHH-CCC--------------CCHHHHHHHHHH--HHHHCCCHHHHHHHHHHHCCCC- Q ss_conf 7323640230100001688865420-000--------------000457898865--2110000008877765420024- Q gi|254780636|r 70 LVDEKREKIFHYGRFDIAVLFYTFG-VRV--------------RPVFCTKIASRL--TRTYTNQHGLKDNLKELLGINI- 131 (207) Q Consensus 70 l~d~~i~KV~Hn~~~D~~~L~~~~g-i~~--------------~~i~DT~ias~l--~~~~~~~~~L~~L~~~~lg~~l- 131 (207) +.+.+...||||+-.|+..+...|- ..| ..++||+..+.- +......-+|..+.+.+-.... T Consensus 277 l~~~~kpiVgHN~~~Dl~~~~~~f~~~LP~~~~eFk~~v~~~FP~i~DTK~l~~~~~~~~~~~~t~L~~l~~~l~~~~~~ 356 (430) T 2a1r_A 277 IANSGKLVIGHNMLLDVMHTVHQFYCPLPADLSEFKEMTTCVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFN 356 (430) T ss_dssp HHHHCCEEEESSCHHHHHHHHHHHTCCCCSSHHHHHHHHHHHCSSEEEHHHHHTSTTTTTTCSCCSHHHHHHHTTSTTCC T ss_pred HHHCCCCEEECCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCEEEHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCC T ss_conf 98659977866428889999987158999789999999998767300437653136644678886689999997206789 Q ss_pred ------CCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ------675200365654432368999986459999999999999997 Q gi|254780636|r 132 ------SKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQR 173 (207) Q Consensus 132 ------dK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~ 173 (207) ..+.+..++ ...+.+=|+-|++.|=.++-+|...|.. T Consensus 357 ~p~i~~~~~~~~~~~-----~~~~~HeAGyDA~mTG~vF~~l~~~l~~ 399 (430) T 2a1r_A 357 PPKVESAEGFPSYDT-----ASEQLHEAGYDAYITGLCFISMANYLGS 399 (430) T ss_dssp CCCEEECTTCCCC----------CCCCHHHHHHHHHHHHHHHHHHHGG T ss_pred CCCEECCCCCCCCCC-----CCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 983433766665568-----8998617088999999999999998741 No 38 >1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} Probab=89.05 E-value=0.97 Score=22.29 Aligned_cols=74 Identities=12% Similarity=0.199 Sum_probs=41.1 Q ss_pred CCCCHHHH-HHHHHH---HCCC----CCHHHHHHHH-HHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHH Q ss_conf 10000168-886542---0000----0004578988-6521100000088777654200246752003656544323689 Q gi|254780636|r 80 HYGRFDIA-VLFYTF---GVRV----RPVFCTKIAS-RLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQL 150 (207) Q Consensus 80 Hn~~~D~~-~L~~~~---gi~~----~~i~DT~ias-~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi 150 (207) +++.+|+. +|...+ ++.. ...+|++-.. .+......+++|.++++ ++|+..+ .+ - T Consensus 229 ~~g~~Dl~~fL~~~~~~~~i~~p~~~~~~iDl~~~~~~~~~~~~~~~~L~~l~e-~lgI~~e---------G~------~ 292 (349) T 1zbu_A 229 TDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLE-KLGMDYD---------GR------P 292 (349) T ss_dssp ESSSHHHHTHHHHHHHHTTBCCCGGGSEEEEHHHHHHHHHTCCGGGGSHHHHHH-HTTCCCC---------SC------T T ss_pred ECCHHHHHHHHHHHHHHHCCCCCCCCCCEEEHHHHHHHHHCCCCCCCCHHHHHH-HCCCCCC---------CC------C T ss_conf 053888999999999995899863257666599999998568878989999999-7699999---------98------8 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 9998645999999999999 Q gi|254780636|r 151 QYAASDVVHLHALRLQFTE 169 (207) Q Consensus 151 ~YAA~Dv~~l~~L~~~l~~ 169 (207) +-|..||..+-+|+.+|.+ T Consensus 293 H~ALdDA~~tA~Il~~LL~ 311 (349) T 1zbu_A 293 HCGLDDSKNIARIAVRMLQ 311 (349) T ss_dssp TCHHHHHHHHHHHHHHHHH T ss_pred CCHHHHHHHHHHHHHHHHH T ss_conf 0969999999999999997 No 39 >1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition, structures of 3'- exonuclease and ITS RNA complex, hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens} Probab=73.52 E-value=4 Score=18.73 Aligned_cols=76 Identities=12% Similarity=0.222 Sum_probs=42.5 Q ss_pred EECCCCHHHH-HHHHHH---HCCC----CCHHHHHHHHH-HHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHH Q ss_conf 3010000168-886542---0000----00045789886-5211000000887776542002467520036565443236 Q gi|254780636|r 78 IFHYGRFDIA-VLFYTF---GVRV----RPVFCTKIASR-LTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDE 148 (207) Q Consensus 78 V~Hn~~~D~~-~L~~~~---gi~~----~~i~DT~ias~-l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~ 148 (207) +.+++.+|.. +|...+ ++.. .+.+|++.... .......+++|.++++. +|++.+ .+ T Consensus 177 ~~~~g~~D~~~fL~~~~~~~~i~~p~~~~~~iDl~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~---------G~----- 241 (299) T 1zbh_A 177 LLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEK-LGMDYD---------GR----- 241 (299) T ss_dssp EEESSSHHHHTHHHHHHHHTTBCCCGGGSEEEEHHHHHHHHHTCCGGGCSHHHHHHH-TTCCCC---------SC----- T ss_pred EECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEHHHHHHHHHCCCCCCCCHHHHHHH-CCCCCC---------CC----- T ss_conf 750507669999999999708998743574776999999984687568799999998-699989---------98----- Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 899998645999999999999 Q gi|254780636|r 149 QLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 149 Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) -+-|..||..+-+|+.+|.. T Consensus 242 -~H~AldDA~~tA~Il~klL~ 261 (299) T 1zbh_A 242 -PNCGLDDSKNIARIAVRMLQ 261 (299) T ss_dssp -TTCHHHHHHHHHHHHHHHHH T ss_pred -CCCHHHHHHHHHHHHHHHHH T ss_conf -72839999999999999997 No 40 >2hwk_A Helicase NSP2; rossman fold, alpha/beta/alpha, multi-domain, hydrolase; 2.45A {Venezuelan equine encephalitis virus} Probab=33.58 E-value=20 Score=14.63 Aligned_cols=16 Identities=13% Similarity=0.100 Sum_probs=8.7 Q ss_pred CCCCCCHHHHHHHHHH Q ss_conf 6544323689999864 Q gi|254780636|r 141 SADDLSDEQLQYAASD 156 (207) Q Consensus 141 ~~rpLs~~Qi~YAA~D 156 (207) +.|+.+..++.-...+ T Consensus 300 ~~R~~~~~~ln~~ls~ 315 (320) T 2hwk_A 300 KARTHNPYKLSSTLTN 315 (320) T ss_dssp CCCCCCHHHHHHHHHH T ss_pred CCCCCCHHHHHHHHHH T ss_conf 8665686784115455 No 41 >2vwa_A Putative uncharacterized protein PF13_0012; unknown function; HET: PTY; 2.5A {Plasmodium falciparum} Probab=27.93 E-value=25 Score=14.05 Aligned_cols=25 Identities=16% Similarity=0.231 Sum_probs=14.2 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 3236899998645999999999999 Q gi|254780636|r 145 LSDEQLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 145 Ls~~Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) ||.+|..|-..|-.|+.++-+.|.+ T Consensus 42 LSn~Qq~y~ind~dY~rkiVQ~L~E 66 (101) T 2vwa_A 42 LSNDQKDSHVNNMEYMQKFVQGLQE 66 (101) T ss_dssp SCHHHHHHHTTCHHHHHHHHHHHHH T ss_pred CCCHHHHHHHCHHHHHHHHHHHHHH T ss_conf 3768899883529999999998886 Done!