Query gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter asiaticus str. psy62] Match_columns 340 No_of_seqs 142 out of 1377 Neff 5.5 Searched_HMMs 23785 Date Tue May 24 02:40:14 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780237.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3lu0_A DNA-directed RNA polyme 100.0 0 0 810.3 20.7 324 2-331 1-328 (329) 2 2a6h_A DNA-directed RNA polyme 100.0 0 0 755.4 22.6 298 20-318 13-314 (315) 3 1bdf_A RNA polymerase alpha su 100.0 0 0 589.1 24.6 230 2-234 1-234 (235) 4 2pa8_D DNA-directed RNA polyme 100.0 1E-36 4.3E-41 256.6 10.0 208 22-233 7-258 (265) 5 3h0g_C DNA-directed RNA polyme 100.0 1.9E-32 8.1E-37 228.9 7.6 211 19-233 8-261 (297) 6 1twf_C B44.5, DNA-directed RNA 100.0 3.8E-31 1.6E-35 220.5 10.7 211 19-233 9-260 (318) 7 1coo_A RNA polymerase alpha su 99.9 2.9E-27 1.2E-31 195.4 5.0 85 247-331 13-97 (98) 8 3k4g_A DNA-directed RNA polyme 99.9 7.8E-27 3.3E-31 192.6 4.7 83 249-331 3-85 (86) 9 3gfk_B DNA-directed RNA polyme 99.9 6.4E-22 2.7E-26 160.8 6.5 74 247-320 5-78 (79) 10 1z3e_B DNA-directed RNA polyme 99.8 1.2E-21 5.1E-26 158.9 7.6 70 251-320 2-71 (73) 11 1b22_A DNA repair protein RAD5 96.5 0.002 8.4E-08 41.0 4.1 56 258-313 23-81 (114) 12 3lda_A DNA repair protein RAD5 96.0 0.02 8.5E-07 34.5 6.8 58 256-313 79-139 (400) 13 1pzn_A RAD51, DNA repair and r 95.8 0.0097 4.1E-07 36.6 4.6 57 257-313 34-91 (349) 14 2zj8_A DNA helicase, putative 94.9 0.04 1.7E-06 32.6 5.4 45 267-312 657-701 (720) 15 2i1q_A DNA repair and recombin 94.3 0.098 4.1E-06 30.1 6.1 24 200-223 143-166 (322) 16 1vq8_Y 50S ribosomal protein L 93.1 0.013 5.7E-07 35.6 0.0 18 299-316 211-228 (241) 17 2pa8_L DNA-directed RNA polyme 93.0 0.24 9.9E-06 27.6 6.2 48 180-233 38-85 (92) 18 2z43_A DNA repair and recombin 93.0 0.015 6.2E-07 35.4 0.0 20 201-220 143-162 (324) 19 1dgs_A DNA ligase; AMP complex 92.6 0.32 1.3E-05 26.8 6.4 49 264-312 448-497 (667) 20 1v5w_A DMC1, meiotic recombina 91.2 0.032 1.3E-06 33.3 0.0 23 199-221 156-178 (343) 21 1twf_K B13.6, DNA-directed RNA 90.5 0.84 3.5E-05 24.0 6.8 36 198-233 68-103 (120) 22 3h0g_K DNA-directed RNA polyme 90.1 0.38 1.6E-05 26.2 4.8 36 198-233 67-102 (123) 23 2pa8_L DNA-directed RNA polyme 89.9 0.32 1.4E-05 26.7 4.3 39 22-65 7-45 (92) 24 1xpp_A TA1416, DNA-directed RN 89.5 0.69 2.9E-05 24.6 5.6 47 180-233 48-94 (115) 25 2owo_A DNA ligase; protein/DNA 89.1 0.86 3.6E-05 24.0 5.9 44 56-99 107-162 (671) 26 3h0g_K DNA-directed RNA polyme 89.0 0.5 2.1E-05 25.5 4.7 41 13-59 16-56 (123) 27 1u9l_A Transcription elongatio 88.9 0.99 4.1E-05 23.6 6.1 59 255-313 4-62 (70) 28 1z00_A DNA excision repair pro 87.4 1.1 4.6E-05 23.3 5.5 44 268-313 31-74 (89) 29 1im4_A DBH; DNA polymerase PAL 86.0 0.41 1.7E-05 26.1 2.7 40 255-294 181-221 (221) 30 3bq0_A POL IV, DBH, DNA polyme 84.8 1 4.2E-05 23.5 4.3 53 255-309 176-229 (354) 31 3gqc_A DNA repair protein REV1 84.2 1.7 7E-05 22.1 5.2 54 254-309 311-365 (504) 32 1jx4_A DNA polymerase IV (fami 83.9 0.96 4E-05 23.7 3.8 52 255-308 175-227 (352) 33 3im1_A Protein SNU246, PRE-mRN 79.8 3 0.00013 20.4 8.6 94 214-314 113-214 (328) 34 1kft_A UVRC, excinuclease ABC 79.6 2.2 9.4E-05 21.3 4.5 42 268-311 36-77 (78) 35 1wcn_A Transcription elongatio 78.7 3.3 0.00014 20.2 5.4 47 264-310 14-60 (70) 36 3osn_A DNA polymerase IOTA; ho 76.0 3.8 0.00016 19.8 4.8 49 259-309 235-284 (420) 37 1x2i_A HEF helicase/nuclease; 75.7 4 0.00017 19.6 5.1 51 259-312 18-68 (75) 38 2a1j_B DNA excision repair pro 72.7 4.6 0.00019 19.3 4.5 41 271-312 46-86 (91) 39 1feu_A 50S ribosomal protein L 70.8 2.5 0.0001 21.0 2.8 34 113-149 68-102 (206) 40 2bgw_A XPF endonuclease; hydro 69.6 5.5 0.00023 18.7 8.1 48 264-312 169-216 (219) 41 2kp7_A Crossover junction endo 69.0 4.1 0.00017 19.6 3.6 41 268-314 42-82 (87) 42 3mr3_A DNA polymerase ETA; POL 63.9 7.1 0.0003 18.0 4.3 52 257-310 252-305 (435) 43 2w9m_A Polymerase X; SAXS, DNA 60.0 6.1 0.00026 18.4 3.1 23 302-324 471-493 (578) 44 2q0z_X Protein Pro2281; SEC63, 59.0 8.7 0.00036 17.5 4.2 96 215-313 117-217 (339) 45 2zjr_S 50S ribosomal protein L 58.1 2.7 0.00011 20.7 1.0 24 114-137 147-171 (237) 46 2x7i_A Mevalonate kinase; tran 55.9 9.7 0.00041 17.1 4.5 77 260-338 207-295 (308) 47 1zco_A 2-dehydro-3-deoxyphosph 52.3 7.9 0.00033 17.7 2.6 15 77-91 70-84 (262) 48 2aq4_A DNA repair protein REV1 52.1 11 0.00047 16.8 3.8 50 257-308 240-293 (434) 49 3bz1_U Photosystem II 12 kDa e 51.3 6.1 0.00026 18.4 1.9 41 267-315 44-84 (104) 50 1s5l_U Photosystem II 12 kDa e 46.2 8.8 0.00037 17.4 2.1 39 267-313 74-112 (134) 51 2a1j_A DNA repair endonuclease 42.9 15 0.00065 15.8 3.9 47 264-312 11-57 (63) 52 3bqs_A Uncharacterized protein 42.4 16 0.00066 15.8 3.0 77 259-338 5-84 (93) 53 1kea_A Possible G-T mismatches 41.0 10 0.00044 17.0 1.8 53 256-308 78-133 (221) 54 3c1y_A DNA integrity scanning 36.0 20 0.00083 15.2 3.8 50 264-313 308-370 (377) 55 1kg2_A A/G-specific adenine gl 35.9 12 0.00051 16.5 1.5 51 258-308 75-127 (225) 56 2e1f_A Werner syndrome ATP-dep 35.6 13 0.00056 16.2 1.7 47 270-316 37-90 (103) 57 1gm5_A RECG; helicase, replica 34.3 13 0.00055 16.3 1.4 22 68-89 113-134 (780) 58 1x40_A ARAP2; ASAP-related pro 34.2 21 0.00088 15.0 3.6 40 259-299 21-62 (91) 59 1vr6_A Phospho-2-dehydro-3-deo 33.5 22 0.00091 14.9 2.6 17 204-220 217-233 (350) 60 1t94_A Polymerase (DNA directe 33.1 22 0.00092 14.8 3.8 49 255-306 279-328 (459) 61 2cz9_A Probable galactokinase; 31.7 23 0.00097 14.7 8.2 62 259-321 239-300 (350) 62 2rrd_A BLM HRDC domain, HRDC d 30.9 15 0.00063 15.9 1.3 45 269-313 43-91 (101) 63 3fsp_A A/G-specific adenine gl 30.0 18 0.00076 15.4 1.6 17 287-303 115-131 (369) 64 1vs1_A 3-deoxy-7-phosphoheptul 29.0 26 0.0011 14.4 2.3 11 82-92 54-64 (276) 65 2duy_A Competence protein come 28.0 13 0.00054 16.3 0.5 24 287-310 50-73 (75) 66 1wuu_A Galactokinase; galactos 27.9 27 0.0011 14.3 2.4 63 260-322 289-351 (399) 67 1ow5_A Serine/threonine-protei 26.9 28 0.0012 14.2 4.0 53 258-313 20-74 (85) 68 3cqj_A L-ribulose-5-phosphate 26.7 11 0.00044 16.9 -0.1 49 169-229 239-287 (295) 69 3fhf_A Mjogg, N-glycosylase/DN 25.5 30 0.0012 14.0 3.6 41 267-307 95-142 (214) 70 2kg5_A ARF-GAP, RHO-GAP domain 24.1 31 0.0013 13.8 4.4 49 260-312 33-81 (100) 71 1npy_A Hypothetical shikimate 23.6 6.4 0.00027 18.3 -1.7 15 37-51 17-31 (271) 72 1dxs_A P53-like transcription 22.6 33 0.0014 13.7 2.8 50 260-313 13-64 (80) 73 2h56_A DNA-3-methyladenine gly 22.6 34 0.0014 13.7 5.2 48 259-306 97-154 (233) 74 2abk_A Endonuclease III; DNA-r 21.6 35 0.0015 13.5 2.1 53 256-308 72-127 (211) 75 1ucv_A Ephrin type-A receptor 21.4 35 0.0015 13.5 2.6 35 260-295 14-48 (81) 76 1z00_B DNA repair endonuclease 21.4 35 0.0015 13.5 4.2 47 264-312 25-71 (84) 77 1orn_A Endonuclease III; DNA r 21.2 33 0.0014 13.7 1.5 52 256-307 76-130 (226) 78 2hfs_A Mevalonate kinase, puta 21.0 36 0.0015 13.4 8.5 114 200-339 188-312 (332) 79 2rhf_A DNA helicase RECQ; HRDC 21.0 21 0.0009 14.9 0.6 37 269-305 26-62 (77) 80 1pie_A Galactokinase; galactos 20.4 37 0.0016 13.4 3.0 61 261-321 305-365 (419) 81 2edu_A Kinesin-like protein KI 20.3 37 0.0016 13.4 7.0 54 283-336 33-90 (98) 82 2ihm_A POL MU, DNA polymerase 20.2 37 0.0016 13.3 4.6 11 38-48 68-78 (360) No 1 >3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A Probab=100.00 E-value=0 Score=810.30 Aligned_cols=324 Identities=45% Similarity=0.798 Sum_probs=304.0 Q ss_pred CCCHHHHCCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHH Q ss_conf 52205751797420158636788815899996169756678889999987416983068899988714431466462444 Q gi|254780237|r 2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81 (340) Q Consensus 2 ~~~~~~~~~~P~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~ED 81 (340) |+..|++|++|+.+++ ++.+++||||+++||+||||+|||||||||||||++|+|||+|||+||.|||++|+||+|| T Consensus 1 m~~~~~~~~~p~~i~~---~~~~~~yg~f~i~Ple~G~g~TlGnaLRRvLLssi~G~ait~vkI~gv~HEfsti~GV~Ed 77 (329) T 3lu0_A 1 MQGSVTEFLKPRLVDI---EQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQED 77 (329) T ss_dssp CCCSTTTSSSCCCCCE---EECTTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEEEEEEESSCSSTTCCCTTBSSC T ss_pred CCCHHHHHCCCCEEEE---ECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCC T ss_conf 9613666138857787---2268867899997688862636688999998856984588999989965545568996237 Q ss_pred HHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEEC-CCCEEEEEEEEECCCCCEECCC Q ss_conf 999998401141777279827999999447169963351389859988880899977-8964999999746876320344 Q gi|254780237|r 82 LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKH 160 (340) Q Consensus 82 V~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~-~~~~l~iel~ie~G~GY~~~e~ 160 (340) |++|+||||+|+|+.+++.+..++|+++|||+|||+||++|++++|+||||||||++ +++.|+|+++|++|+||++++. T Consensus 78 v~~IilNLK~i~~~~~~~~~~~~~l~~~Gpg~vtA~di~~p~~veivNpdq~IaTl~~~~~~l~~e~~i~~G~GY~~~~~ 157 (329) T 3lu0_A 78 ILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPAST 157 (329) T ss_dssp HHHHHHHHHSCCCEESSCSCEEEEECCCSSSCEETTSSCCCSSEECSCTTCEEECBCSSCCCCCEEEEEEEESSEECTTT T ss_pred HHHHHHHCCCCCEEECCCCCEEEEEEEECCCCEEECCCCCCCCEEEECCCEEEEEECCCCCEEEEEEEEEECCCEEECCC T ss_conf 99999846733156426872589999616776681136667987995899889996588926999999990565264200 Q ss_pred CC---CCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 44---655754302124311114422357764116887762189999993896177799999999999988876224444 Q gi|254780237|r 161 HR---TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237 (340) Q Consensus 161 ~~---~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~ 237 (340) ++ ....++|+||+||+||||+||||.|+++|+|++++||+|+|||||||||+|++||++||++|++||++|.++++. T Consensus 158 ~~~~~~~~~~ig~i~iDa~FsPV~kVny~Ve~~rv~~~~~~e~L~lEI~TnGsI~P~eAl~~AakiL~~~f~~f~~~~~~ 237 (329) T 3lu0_A 158 RIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237 (329) T ss_dssp SCCCSTTSSSCCCEECCEECCCEEEEEEEEEEECCSSCSCEEEEEEEEEECSSSCHHHHHHHHHHHHHHHTTTSSSCC-- T ss_pred CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 23554334667834036655563789999864355667751038999983898898999999999999999976263101 Q ss_pred CCCCCCHHHCCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCC Q ss_conf 32210000000001123331112210110588898988398371888744988886188988644999999999808312 Q gi|254780237|r 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317 (340) Q Consensus 238 ~~~~~~~~~~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~l 317 (340) ..... ..+..+.++.+.++||+||||+||+||||||||+|||||+++|++||+++||||+||++||+++|+++||+| T Consensus 238 ~~~~~---~~~~~~~~~~l~~~Ie~LeLSvRs~NcLkra~I~ti~dLv~~s~~dLl~ikNfGkKSl~EI~~kL~~~gl~l 314 (329) T 3lu0_A 238 RQPEV---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 314 (329) T ss_dssp -------------------------------------------------------------------------------- T ss_pred CCCCC---CCCCCCCCHHHHCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHCCCCC T ss_conf 34444---444444265763879885277888865757189189997647999995589976200999999999749777 Q ss_pred CCCCCCCCHHHHHH Q ss_conf 67687898677999 Q gi|254780237|r 318 GMNLPDWPPESIEE 331 (340) Q Consensus 318 g~~l~~~~~~~~~~ 331 (340) ||++++|||+++++ T Consensus 315 gm~l~~~~~~~~~~ 328 (329) T 3lu0_A 315 GMRLENWPPASIAD 328 (329) T ss_dssp -------------- T ss_pred CCCCCCCCCCCCCC T ss_conf 78789999534356 No 2 >2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* 2gho_A 1hqm_A ... Probab=100.00 E-value=0 Score=755.37 Aligned_cols=298 Identities=37% Similarity=0.567 Sum_probs=276.2 Q ss_pred CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCC Q ss_conf 36788815899996169756678889999987416983068899988714431466462444999998401141777279 Q gi|254780237|r 20 LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99 (340) Q Consensus 20 ~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~ 99 (340) .++.+++||||+++||+||||+|+||||||+||||++|+|||+|||+||.|||++||||+|||+||+||||+|+|++.++ T Consensus 13 ~~~~~~~Yg~F~i~Pl~~G~g~TlGnaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~Edv~eIllNLK~i~~k~~~~ 92 (315) T 2a6h_A 13 VRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNP 92 (315) T ss_dssp EEEETTTEEEEEEEEECTTCHHHHHHHHHHHHHHTCEEEEEEEEEESSCCSTTCBCTTBSSBHHHHHHHHHTCCEEECST T ss_pred EEECCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHCCCEEEEECC T ss_conf 88668856899996688972304678999999856985489999999954423458885105899998530446997148 Q ss_pred --CCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEECCCCCH Q ss_conf --827999999447169963351389859988880899977896499999974687632034444655754302124311 Q gi|254780237|r 100 --SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177 (340) Q Consensus 100 --~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~iDa~F 177 (340) ++..++++++||++|||+||++|++++|+||||||||+++++.|+||++|++||||++++.++.. .++|+|++||+| T Consensus 93 ~~~~~~~~l~~~Gp~~vtA~di~~p~~ieivNpdq~IaTl~~~~~l~~el~i~~G~Gy~~~e~~~~~-~~~g~i~iDa~F 171 (315) T 2a6h_A 93 SLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIK-DRINAIPVDAVF 171 (315) T ss_dssp TCSBCCEEEEEESSCEEEGGGSCCCTTEEESCTTCEEEEBCSSCEEEEEEEEEEEESEECHHHHCCC-SSTTCEECCEEC T ss_pred CCCEEEEEEECCCCEEEEEECCCCCCCEEEECCCEEEEEECCCCEEEEEEEEEECCCEEECCCCCCC-CCCCCCCCCCCC T ss_conf 8615999996499848995414689858997898799997789669999999925754402335664-656751677652 Q ss_pred HEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHH--CCCCHHHHH Q ss_conf 114422357764116887762189999993896177799999999999988876224444322100000--000011233 Q gi|254780237|r 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--VKSLPFNPA 255 (340) Q Consensus 178 sPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~--~~~~~~~~~ 255 (340) |||+||||.|+++|+||+++||+|+|||||||||+|++||++||+||++||.+|.++++.......... ......+.. T Consensus 172 sPV~kVny~V~~~rvg~~~~~ekL~lEIwTnGsi~P~~Al~~Aa~iL~~~f~~f~~~~~~~~~~~~~~~~~~~~~~~~~~ 251 (315) T 2a6h_A 172 SPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQEEE 251 (315) T ss_dssp CCEEEEEEEEEECCBTTBCCCEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHTTCSCC---------------------- T ss_pred CCEEEEEEEEEECCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHH T ss_conf 35257899999711367777654699998289899899999999999999997528310022333323342222200354 Q ss_pred HHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 311122101105888989883983718887449888861889886449999999998083126 Q gi|254780237|r 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318 (340) Q Consensus 256 L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg 318 (340) ++++|++|+||+|++||||+|||+|||||+++|++||+++||||+||++||+++|+++||+|. T Consensus 252 l~~~Ie~L~LSvRs~NcLk~a~I~ti~dLv~~s~~eLl~i~N~G~KSl~EI~ekL~~~Gl~L~ 314 (315) T 2a6h_A 252 LDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLK 314 (315) T ss_dssp --------------------------------------------------------------- T ss_pred HCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHCCCCCC T ss_conf 368099822879888678785994899987399999847999851039999999998599889 No 3 >1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1 Probab=100.00 E-value=0 Score=589.06 Aligned_cols=230 Identities=43% Similarity=0.757 Sum_probs=220.3 Q ss_pred CCCHHHHCCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHH Q ss_conf 52205751797420158636788815899996169756678889999987416983068899988714431466462444 Q gi|254780237|r 2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81 (340) Q Consensus 2 ~~~~~~~~~~P~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~ED 81 (340) |+.+|++|++|+.+++ ++.+++||||.++||+||||+||||||||+||||++|+|||+|||+|+.|||++||||+|| T Consensus 1 m~~~~~~~~~p~~i~~---~~~~~~~~~f~i~Ple~G~g~TlGnaLRRvLLs~i~G~ait~vkI~gv~hEfs~i~GV~Ed 77 (235) T 1bdf_A 1 MQGSVTEFLKPRLVDI---EQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEIDGVLHEYSTKEGVQED 77 (235) T ss_dssp -CCCSSCSCCCCEEEE---EESSSSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCCEEEEEEEETTCCSTTCCCTTBSSC T ss_pred CCCHHHHHCCCCEEEE---ECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCHHH T ss_conf 9504666038857887---0378867899997788962525788999988865985499999957765465468880563 Q ss_pred HHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECC-CCEEEEEEEEECCCCCEECCC Q ss_conf 9999984011417772798279999994471699633513898599888808999778-964999999746876320344 Q gi|254780237|r 82 LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKH 160 (340) Q Consensus 82 V~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~-~~~l~iel~ie~G~GY~~~e~ 160 (340) |+||+||||+|+|+.+++++..++|+++|||+|||+||++|++++|+||||||||+++ ++.|+||++|++|+||++++. T Consensus 78 v~eIilNLK~i~~~~~~~~~~~~~l~~~Gp~~vtA~di~~p~~ieivNpdq~IaTlt~~~~~l~ie~~ie~G~Gy~~~~~ 157 (235) T 1bdf_A 78 ILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPAST 157 (235) T ss_dssp HHHHHHHHHTCCEECSSCSEEEEEEEEESSEEEEGGGBCCCSSCEESCTTCEEEEECSTTCEEEEEEEEEECCSEECGGG T ss_pred HHHHHHHCCCCEEEECCCCCEEEEEEEECCCCEEEECCCCCCCEEEECCCEEEEEECCCCCEEEEEEEEECCCCEECCCC T ss_conf 99999726755367516884179999515743897156678987996899899997678957999999945786343533 Q ss_pred C---CCCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 4---4655754302124311114422357764116887762189999993896177799999999999988876224 Q gi|254780237|r 161 H---RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234 (340) Q Consensus 161 ~---~~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~ 234 (340) + +.+..++|+|++||+||||++|||.|+++|+|++++||+|+|||||||||+|++||++||++|++||++|+++ T Consensus 158 ~~~~~~~~~~~g~i~iDa~fsPV~~Vny~Ve~~rv~~~~~~e~L~leI~TdGsI~P~~Al~~Aa~iL~~~f~~f~~~ 234 (235) T 1bdf_A 158 RIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDL 234 (235) T ss_dssp TC-----CCCCSCCBCCEECCSEEEEEEECCBCCCSSCSSEEEEEEEEEECSSSCHHHHHHHHHHHHHHHGGGGC-- T ss_pred CCCCCCCCCCCCCEECCCCCCCEEEEEEEEEECCCCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCC T ss_conf 44554333567833336543555789999997124789860699999997998999999999999999999987537 No 4 >2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D Probab=100.00 E-value=1e-36 Score=256.56 Aligned_cols=208 Identities=17% Similarity=0.155 Sum_probs=177.6 Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE---------CCCCCCCCCCCCCHHHHHHHHHHHCCC Q ss_conf 78881589999616975667888999998741698306889998---------871443146646244499999840114 Q gi|254780237|r 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGI 92 (340) Q Consensus 22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI---------~gv~HEfs~i~GV~EDV~eIiLNLK~I 92 (340) +.++++.+|.+. |+|.|+||||||+|||++||+||++|+| +++.|+|+.||++.|++.++++|+|.+ T Consensus 7 ~~~~~~~~f~~~----g~~~si~NaLRR~lls~ip~~ai~~v~I~~Nts~~~dE~i~hrl~lIP~~~e~~~~~~~~~~~~ 82 (265) T 2pa8_D 7 HKDDTRIDLVFE----GYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPEEC 82 (265) T ss_dssp EECSSEEEEEEE----SSCHHHHHHHHHHHHHSCCEEEEEEEEEEEECSSSCHHHHHHHHTTSCBCCTTHHHHSCCGGGC T ss_pred ECCCCEEEEEEE----CCCCHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCCCCCEEEEECCCCCCCCCHHHHCCCHHE T ss_conf 737988999997----8882799999999997496367999999866654667750689851675013502321160210 Q ss_pred EEEECCCC--CEEEEEE---EECCEEEEEEEEECC-CCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCC--- Q ss_conf 17772798--2799999---944716996335138-98599888808999778964999999746876320344446--- Q gi|254780237|r 93 NLKMSGDS--HKRVTIF---KRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--- 163 (340) Q Consensus 93 ~~k~~~~~--~~~~~l~---~~Gp~~vtA~Di~~p-~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~--- 163 (340) ........ ....++. ..||+.++|+|++.+ +.+++++|+++||+|..+..|.+++++..|+|+..+..+.. T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~~~~~~~~~~i~I~~L~~~q~L~l~~~~~~g~Gk~hak~~~v~~~ 162 (265) T 2pa8_D 83 IECTENCEKCYTKIYIEAEAPNEPRMIYSKDIKSEDPSVVPISGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLS 162 (265) T ss_dssp TTCCSSCTTTEEEEEEEEECCSSCEEEEGGGCEESSTTCCBSCSCCEEEEECTTCEEEEEEEEEEECTTTCGGGCCEEEE T ss_pred EECCCCCCCEEEEEEEEEECCCCCCEEEHHHCCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEECCCCCCCCCCCCC T ss_conf 22158898238999998882789837873332467997221148806999379976778999996364212212766543 Q ss_pred --------------------------CCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHH Q ss_conf --------------------------557543021243111144223577641168877621899999938961777999 Q gi|254780237|r 164 --------------------------ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217 (340) Q Consensus 164 --------------------------~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl 217 (340) ........+.|+.++|+.+++|...+..+....++++++|+|||+|+++|++|+ T Consensus 163 ~y~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~f~f~IET~G~i~p~~il 242 (265) T 2pa8_D 163 VVRYYPKVEILANCEKAVNVCPEGVFELKDGKLSVKNELSCTLCEECLRYCNGSIRISFVEDKYILEIESVGSLKPERIL 242 (265) T ss_dssp EEEEEEEEEECSCCTTHHHHCTTCCEEEETTEEEESCGGGCCCCCHHHHHHTTSEEEEEEEEEEEEEEEECSSSCHHHHH T ss_pred CCCCCCCHHHHCCHHHHHHHCCCCCCCCCCCCEEECCCHHCCEEEEEEEECCCCEEECCCCCEEEEEEEECCCCCHHHHH T ss_conf 31213404330004677664732430125675267452328714676542575200033676899999974761999999 Q ss_pred HHHHHHHHHHHHHHHC Q ss_conf 9999999998887622 Q gi|254780237|r 218 ALASRILQDQLGMFIN 233 (340) Q Consensus 218 ~~Aa~iL~~~l~~f~~ 233 (340) .+|+++|+++|..|.+ T Consensus 243 ~~A~~iL~~kl~~l~~ 258 (265) T 2pa8_D 243 LEAGKSIIRKIEELEK 258 (265) T ss_dssp HHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHH T ss_conf 9999999999999999 No 5 >3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Probab=99.97 E-value=1.9e-32 Score=228.88 Aligned_cols=211 Identities=18% Similarity=0.227 Sum_probs=172.1 Q ss_pred ECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE---------CCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 63678881589999616975667888999998741698306889998---------871443146646244499999840 Q gi|254780237|r 19 VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNI 89 (340) Q Consensus 19 ~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI---------~gv~HEfs~i~GV~EDV~eIiLNL 89 (340) .+.+.+++..+|.++ |.+.|++|||||+|||++|++||+.|+| +++.|+|+.||++.|++.++.+|+ T Consensus 8 ~i~~~~~~~~~f~l~----~~~~s~aNaLRR~lls~ip~~ai~~v~I~~Nts~l~dE~i~hRl~lIPi~~~~~~~~~~~~ 83 (297) T 3h0g_C 8 TIRNISKNSVDFVLT----NTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPPVG 83 (297) T ss_dssp CCCCBCSSEEEEEEC----SCCHHHHHHHHHHHHSSCCEEEEEEEEEEEECSSSCHHHHHHHHHHSCBCCTTCSSCSSSC T ss_pred EEEECCCCEEEEEEE----CCCCHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCEEEEECCCCCEECCCCCCCHHH T ss_conf 999845987999997----8880677899999987384207999999767864555312677314675202522022001 Q ss_pred CCCEEEECCCC-----CEEEEEEE----ECCEEEEEEEEECCCCEE--------EECCCEEEEEECCCCEEEEEEEEECC Q ss_conf 11417772798-----27999999----447169963351389859--------98888089997789649999997468 Q gi|254780237|r 90 KGINLKMSGDS-----HKRVTIFK----RGPGVVTAGDIQTVNDIE--------VLNPDHVICNLDVDAVVRMELTVSKG 152 (340) Q Consensus 90 K~I~~k~~~~~-----~~~~~l~~----~Gp~~vtA~Di~~p~~ve--------ivNpd~~IaTl~~~~~l~iel~ie~G 152 (340) +...++..... ....++.+ .||+.|+|+|+++++.-+ .++|+++||+|..+..|+|++++..| T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~s~dl~~~~~~~~~~~~~~~~~~~~i~I~~L~~gq~L~le~~a~~G 163 (297) T 3h0g_C 84 LEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILADPKSRGPLICKLRKEQEISLRCIAKKG 163 (297) T ss_dssp CCCSSSCSSSSSCGGGSCEEEEEECCCCSSCEEEEGGGCBCCSCCSSCCBCCCSTTSCCSEEEEECSSCCEEEEEEEEEE T ss_pred EEEEEECCCCCCCCCCEEEEEEEEECCCCCCEEEEECCEEECCCCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEEEEEC T ss_conf 00111014456776525899998870567843676031687786430586433555689627980367369999999948 Q ss_pred CCCEECCCCC-------------CCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCC----CEEEEEEEECCCCCHHH Q ss_conf 7632034444-------------655754302124311114422357764116887762----18999999389617779 Q gi|254780237|r 153 HGYVPAKHHR-------------TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY----DKLSMTIDTDGSITGED 215 (340) Q Consensus 153 ~GY~~~e~~~-------------~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~----dkL~lEI~TnGsi~P~e 215 (340) +|+..|..+. ......+....+..+.|..++.+..+..+.++..++ ++++|+|||+|+++|++ T Consensus 164 ~Gk~hak~spvs~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~F~IES~G~l~p~~ 243 (297) T 3h0g_C 164 IAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWPKSKNADWEEPPREGEPFNFQEEPRRFYMDVESVGSIPPNE 243 (297) T ss_dssp CGGGCTTSCCBCCCCCCSSSSCSSCCSCCCCSSCSTTTSCCCGGGTTCCCCSCCSCCCSSCCCCCEEEEEEBCSSSCTTT T ss_pred CCCCCCCCCCCCEEEEEECCCHHHHCCCCCCCCCCHHHCCCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCCCCHHH T ss_conf 72222524663025653145101102433321231121356532137860455530577605768999999516659999 Q ss_pred HHHHHHHHHHHHHHHHHC Q ss_conf 999999999998887622 Q gi|254780237|r 216 SVALASRILQDQLGMFIN 233 (340) Q Consensus 216 Al~~Aa~iL~~~l~~f~~ 233 (340) ||.+|+++|+++|..|.. T Consensus 244 il~~A~~iL~~kl~~~~~ 261 (297) T 3h0g_C 244 IMVQGLRILQEKLAVLVR 261 (297) T ss_dssp TTHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHH T ss_conf 999999999999999999 No 6 >1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ... Probab=99.97 E-value=3.8e-31 Score=220.53 Aligned_cols=211 Identities=17% Similarity=0.186 Sum_probs=161.2 Q ss_pred ECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE---------CCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 63678881589999616975667888999998741698306889998---------871443146646244499999840 Q gi|254780237|r 19 VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNI 89 (340) Q Consensus 19 ~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI---------~gv~HEfs~i~GV~EDV~eIiLNL 89 (340) ++.+.++++.+|.++ |++.|+||||||+|||++|++||+.|+| +++.|+|+.||++.||+.++..|+ T Consensus 9 ~i~~~~~~~~~f~l~----g~~~siaNaLRR~lLseIp~~Ai~~V~I~~Nts~l~dE~i~HRlglIPi~~~d~~~~~~~~ 84 (318) T 1twf_C 9 KIREASKDNVDFILS----NVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSR 84 (318) T ss_dssp CCSCCCSSEECCEEB----SSCHHHHHHHHHHHHHCCCEEEEEEEEEEEECSSSCHHHHHHHHHTSCEEETTGGGSCCTT T ss_pred EEEECCCCEEEEEEE----CCCHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCEEEEEECCCCCCCCHHHHHHCC T ss_conf 999867998999997----8881799999999987395127999999767764566623688632676335777832111 Q ss_pred CCCEEEECCCCCEEEEEEEEC----CEEEEEEEEECCCCE-----------EEECCCEEEEEECCCCEEEEEEEEECCCC Q ss_conf 114177727982799999944----716996335138985-----------99888808999778964999999746876 Q gi|254780237|r 90 KGINLKMSGDSHKRVTIFKRG----PGVVTAGDIQTVNDI-----------EVLNPDHVICNLDVDAVVRMELTVSKGHG 154 (340) Q Consensus 90 K~I~~k~~~~~~~~~~l~~~G----p~~vtA~Di~~p~~v-----------eivNpd~~IaTl~~~~~l~iel~ie~G~G 154 (340) +.+.+...+.......|++++ |..|+|+|+..++.. .+.+++.+||+|..+..|+|++++..|+| T Consensus 85 ~~~~~~~~~~~~v~~~L~v~~~~~~~~~Vts~Di~~~~~~~~~~~~~p~~~~~~~~~IlI~kL~~gq~l~l~~~~~~G~g 164 (318) T 1twf_C 85 DCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIA 164 (318) T ss_dssp TSSSSSCCTTTEEEEEEEEECCSSSCEEEEGGGEEECSCCTTCSEEEECCCSTTSCCSEEEEECTTCEEEEEEEEEEECT T ss_pred CCCCCCCCCCCEEEEEEEEECCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEEECCC T ss_conf 34210368873599999964577765401135534567544467788655466789759999668957999999983873 Q ss_pred CEECCCC-------------CCCCCCCCEECCCCCHHEEEEEEE----EEEEECCCCCCCCCEEEEEEEECCCCCHHHHH Q ss_conf 3203444-------------465575430212431111442235----77641168877621899999938961777999 Q gi|254780237|r 155 YVPAKHH-------------RTENDPIGLITIDALYSPIKKVSY----TVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217 (340) Q Consensus 155 Y~~~e~~-------------~~~~~~ig~i~iDa~FsPV~~Vny----~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl 217 (340) +..|..+ +...........+..+.|..+... ..+..++......+++.|+|||+|+++|+++| T Consensus 165 kehak~~pvs~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~F~IET~G~~~p~~il 244 (318) T 1twf_C 165 KEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVV 244 (318) T ss_dssp TTCGGGCCEEEEEEEECSSTTSCCSCCCCSSCHHHHSCCCGGGTTSCCCCSSSCCCTTCCCCCEEEEEEECSSSCHHHHH T ss_pred CCCCEECCCCEEEEEECCCCCCCCCCCCEECCCHHHCCCCCCEEEECCCCCCCEEEEECCCCEEEEEEEECCCCCHHHHH T ss_conf 33556555412676515543335553332204331088653036862344554058743664899999945877999999 Q ss_pred HHHHHHHHHHHHHHHC Q ss_conf 9999999998887622 Q gi|254780237|r 218 ALASRILQDQLGMFIN 233 (340) Q Consensus 218 ~~Aa~iL~~~l~~f~~ 233 (340) .+|+++|++.|..|.. T Consensus 245 ~~A~~iL~~Kl~~l~~ 260 (318) T 1twf_C 245 VRGIDTLQKKVASILL 260 (318) T ss_dssp HHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHH T ss_conf 9999999999999999 No 7 >1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} SCOP: a.60.3.1 PDB: 2jzb_A Probab=99.93 E-value=2.9e-27 Score=195.40 Aligned_cols=85 Identities=54% Similarity=0.970 Sum_probs=79.1 Q ss_pred CCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCH Q ss_conf 00001123331112210110588898988398371888744988886188988644999999999808312676878986 Q gi|254780237|r 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326 (340) Q Consensus 247 ~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~ 326 (340) .+....++.|.++|++|+||+|++|||+++||+|||||+++|++||+++||||+||++||+++|+++||+|||++++||| T Consensus 13 ee~~~~~~~L~~~I~eL~LSvRs~N~L~~~gI~tvgdLv~~se~dLl~~~n~G~KSl~EIk~~L~~~gL~lgm~l~~~~p 92 (98) T 1coo_A 13 EEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPP 92 (98) T ss_dssp -----CCHHHHSBGGGGTCCTTTHHHHHTTTCCBHHHHHTSCHHHHTTSTTCCHHHHHHHHHHHHHTTCCTTCCCSSSSC T ss_pred CCCHHHHHHHCCCHHHHCCCHHHHHHHHHHCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCC T ss_conf 00034528860969882778999998738179389999857999997588976878999999999859777997899893 Q ss_pred HHHHH Q ss_conf 77999 Q gi|254780237|r 327 ESIEE 331 (340) Q Consensus 327 ~~~~~ 331 (340) .++++ T Consensus 93 ~~~~~ 97 (98) T 1coo_A 93 ASIAD 97 (98) T ss_dssp STTCC T ss_pred CCCCC T ss_conf 13235 No 8 >3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} PDB: 1lb2_B* 1xs9_D Probab=99.93 E-value=7.8e-27 Score=192.58 Aligned_cols=83 Identities=53% Similarity=0.938 Sum_probs=78.3 Q ss_pred CCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHH Q ss_conf 00112333111221011058889898839837188874498888618898864499999999980831267687898677 Q gi|254780237|r 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328 (340) Q Consensus 249 ~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~ 328 (340) ..+.++.|.++|++|+||+|++|||+++||+|||||+++|++||+++||||+||++||+++|+++||+|||++++|||.+ T Consensus 3 ~~e~~~~L~~~I~eL~LSvR~~N~Lk~~gI~tvgdLv~~se~dLl~i~NfG~kSl~EI~~~L~~~gL~lgm~l~~~~p~~ 82 (86) T 3k4g_A 3 XPEFDPILLRPVDDLELTVRSANCLXAEAIHYIGDLVQRTEVELLXTPNLGXXSLTEIXDVLASRGLSLGMRLENWPPAS 82 (86) T ss_dssp CCCCCGGGGSBGGGGCCCHHHHHHHHHTTCCBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHTTTCCSSCCEESBSCCE T ss_pred CCCCCHHHCCCHHHHCCCHHHHHHHCCCCCCCHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCC T ss_conf 42108887196987278899998725543937999984899998178898772699999999985988899799989412 Q ss_pred HHH Q ss_conf 999 Q gi|254780237|r 329 IEE 331 (340) Q Consensus 329 ~~~ 331 (340) +++ T Consensus 83 ~~~ 85 (86) T 3k4g_A 83 IAD 85 (86) T ss_dssp ECC T ss_pred CCC T ss_conf 133 No 9 >3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} Probab=99.85 E-value=6.4e-22 Score=160.79 Aligned_cols=74 Identities=41% Similarity=0.565 Sum_probs=69.7 Q ss_pred CCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCC Q ss_conf 00001123331112210110588898988398371888744988886188988644999999999808312676 Q gi|254780237|r 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320 (340) Q Consensus 247 ~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~ 320 (340) .++.+.++.|.++|++|+||+|++|||+++||+||+||+++|++||++++|||+||++||+++|+++||+|||+ T Consensus 5 ~~~~~~~~~L~~~I~~L~LS~R~~n~L~~~gI~tv~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~~~gL~l~~~ 78 (79) T 3gfk_B 5 KEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKD 78 (79) T ss_dssp CCCSSCCCGGGCBGGGSCCBHHHHHHHHHTTCCBHHHHTTCCHHHHTTSTTCHHHHHHHHHHHHHHTTCCCC-- T ss_pred CCCCHHHHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCC T ss_conf 42024678854959984798999999989289679999868899997578986737999999999858989999 No 10 >1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B Probab=99.85 E-value=1.2e-21 Score=158.95 Aligned_cols=70 Identities=43% Similarity=0.616 Sum_probs=67.6 Q ss_pred HHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCC Q ss_conf 1123331112210110588898988398371888744988886188988644999999999808312676 Q gi|254780237|r 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320 (340) Q Consensus 251 ~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~ 320 (340) +.++.|+++|++|+||+|++|||+++||+|||||+++|++||+++||||+||++||+++|+++||+|||+ T Consensus 2 e~~~~L~~~I~~L~LS~R~~N~L~~~~I~tv~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~~~gl~l~~~ 71 (73) T 1z3e_B 2 EKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKD 71 (73) T ss_dssp -CHHHHTCBGGGSCCBHHHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHHTTCCCC-- T ss_pred CHHHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCC T ss_conf 5067626889884698999999989489679999868999997478986605999999999849987999 No 11 >1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1 Probab=96.53 E-value=0.002 Score=41.02 Aligned_cols=56 Identities=5% Similarity=0.145 Sum_probs=51.8 Q ss_pred CCHHHC---CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 112210---11058889898839837188874498888618898864499999999980 Q gi|254780237|r 258 KKVEEL---ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 258 ~~IeeL---eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) .+|+.| .++....+-|+.|||+||.+|+..+..+|.++++||.+..+-|.+.-..+ T Consensus 23 ~~I~~L~~~Gvg~~~i~KL~~aG~~Tv~~Ia~~t~~eL~~i~Gi~e~~A~KIi~aark~ 81 (114) T 1b22_A 23 QPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKL 81 (114) T ss_dssp CCHHHHHHTTCSHHHHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHHHH T ss_pred CCHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 22899976899999999999969744999984899999766698899999999999987 No 12 >3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A* Probab=95.97 E-value=0.02 Score=34.51 Aligned_cols=58 Identities=10% Similarity=0.194 Sum_probs=49.7 Q ss_pred HHCCHHHCC---CCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 311122101---1058889898839837188874498888618898864499999999980 Q gi|254780237|r 256 LLKKVEELE---LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 256 L~~~IeeLe---LSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) ...+|++|. .+....+-|+.|||+|+.+|+..+..+|.++++++..-++.|.+.-.++ T Consensus 79 ~~~~~~~l~~~gi~~~~i~kL~~aG~~t~~~i~~~~~~~L~~~~g~s~~~a~ki~~~a~k~ 139 (400) T 3lda_A 79 SFVPIEKLQVNGITMADVKKLRESGLHTAEAVAYAPRKDLLEIKGISEAKADKLLNEAARL 139 (400) T ss_dssp CSCBGGGGCCTTCCHHHHHHHHHTTCCBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHHH T ss_pred CCCCHHHHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHHH T ss_conf 8766999986699989999999869851999971799999872399999999999999986 No 13 >1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11 Probab=95.82 E-value=0.0097 Score=36.58 Aligned_cols=57 Identities=11% Similarity=0.196 Sum_probs=38.4 Q ss_pred HCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 1112210-11058889898839837188874498888618898864499999999980 Q gi|254780237|r 257 LKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 257 ~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) ..++++| .++....+-|+.|||+|+.||+..+..+|.++.+++...+.+|.....+. T Consensus 34 ~~~l~~l~gv~~~~~~kL~~aG~~t~~~l~~~~~~~L~~~~gis~~~a~kii~~a~~~ 91 (349) T 1pzn_A 34 IRSIEDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAARKA 91 (349) T ss_dssp -CCSSCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_pred CCCHHHCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 1576337996999999999869972999970899999986498999999999999975 No 14 >2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Probab=94.93 E-value=0.04 Score=32.57 Aligned_cols=45 Identities=20% Similarity=0.330 Sum_probs=38.9 Q ss_pred HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 5888989883983718887449888861889886449999999998 Q gi|254780237|r 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340) Q Consensus 267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340) +|+..|+ ++|+.++.|++..++++|.+++++|.|..+.|.+.+.. T Consensus 657 ~~ar~L~-~~G~~s~~~i~~~~~~~l~~v~g~g~k~a~~i~~~~~~ 701 (720) T 2zj8_A 657 RRARALY-NSGFRSIEDISQARPEELLKIEGIGVKTVEAIFKFLGK 701 (720) T ss_dssp HHHHHHH-TTTCCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHC- T ss_pred HHHHHHH-HCCCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHCH T ss_conf 9999999-87999999997499889852769489999999974450 No 15 >2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ewa_A* 3ew9_A* 3etl_A* 2gdj_A* Probab=94.30 E-value=0.098 Score=30.08 Aligned_cols=24 Identities=25% Similarity=0.382 Sum_probs=16.5 Q ss_pred EEEEEEEECCCCCHHHHHHHHHHH Q ss_conf 899999938961777999999999 Q gi|254780237|r 200 KLSMTIDTDGSITGEDSVALASRI 223 (340) Q Consensus 200 kL~lEI~TnGsi~P~eAl~~Aa~i 223 (340) .-.+-|+|+++.+|...-..|... T Consensus 143 ~~~l~i~t~~~~~~~~~~~~~~~~ 166 (322) T 2i1q_A 143 PKAVYIDTEGTFRPERIMQMAEHA 166 (322) T ss_dssp EEEEEEESSSCCCHHHHHHHHHHH T ss_pred CEEEEEECCCCCCHHHHHHHHHHC T ss_conf 649999778888989999999764 No 16 >1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Probab=93.12 E-value=0.013 Score=35.65 Aligned_cols=18 Identities=17% Similarity=0.207 Sum_probs=7.5 Q ss_pred CHHHHHHHHHHHHHHCCC Q ss_conf 864499999999980831 Q gi|254780237|r 299 GRKSLVEIKGVLGTMGLF 316 (340) Q Consensus 299 G~KSl~EI~~~L~~~gl~ 316 (340) |+|.=-.|.++=+++|+. T Consensus 211 SsKtd~lIl~KA~eLGIk 228 (241) T 1vq8_Y 211 GARKRERIEEEAEDAGIR 228 (241) T ss_dssp CHHHHHHHHHHHHHTTCC T ss_pred CCCCCHHHHHHHHHCCCC T ss_conf 466779999999985994 No 17 >2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L Probab=93.02 E-value=0.24 Score=27.60 Aligned_cols=48 Identities=29% Similarity=0.317 Sum_probs=37.3 Q ss_pred EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC Q ss_conf 442235776411688776218999999389617779999999999998887622 Q gi|254780237|r 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 (340) Q Consensus 180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~ 233 (340) |.-+.|.+.. ...++..|-|.|+|+.+|.+||..|++-+++.+..|.+ T Consensus 38 V~fagY~~pH------Pl~~~i~i~i~t~~~~~p~~~l~~a~~~l~~~~~~~~~ 85 (92) T 2pa8_L 38 VSFASYYQPH------PLSDKIIVKILTDGSITPKDALLKAIENIRGMTSHYID 85 (92) T ss_dssp EEEEEEECSS------TTSCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHH T ss_pred CEEEEEECCC------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 1698875678------87781599999699999899999999999999999999 No 18 >2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular switch, RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus P2} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A* Probab=92.97 E-value=0.015 Score=35.42 Aligned_cols=20 Identities=30% Similarity=0.368 Sum_probs=12.3 Q ss_pred EEEEEEECCCCCHHHHHHHH Q ss_conf 99999938961777999999 Q gi|254780237|r 201 LSMTIDTDGSITGEDSVALA 220 (340) Q Consensus 201 L~lEI~TnGsi~P~eAl~~A 220 (340) -++-|.|.|+.+|+.....+ T Consensus 143 ~vvyidtE~~f~~~rl~~~~ 162 (324) T 2z43_A 143 KAVYIDTEGTFRWERIENMA 162 (324) T ss_dssp EEEEEESSSCCCHHHHHHHH T ss_pred EEEEEECCCCCHHHHHHHHH T ss_conf 49999743511799999999 No 19 >1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Probab=92.62 E-value=0.32 Score=26.78 Aligned_cols=49 Identities=18% Similarity=0.255 Sum_probs=30.0 Q ss_pred CCCHHHHHHHHHCC-CCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 11058889898839-83718887449888861889886449999999998 Q gi|254780237|r 264 ELSVRSTNCLRGEN-IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340) Q Consensus 264 eLSvRs~NcLk~a~-I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340) +|+.....-|-.+| |.++.||..++.++|+++.+||.||.+-+.+.++. T Consensus 448 GlG~~~i~~L~e~g~I~~i~Diy~L~~~~l~~l~gfg~ksa~nll~sIe~ 497 (667) T 1dgs_A 448 GLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEE 497 (667) T ss_dssp TCCHHHHHHHHHTTSCSSGGGGGGGCCHHHHTTSSCCSTTHHHHHHHHHH T ss_pred CCCHHHHHHHHHCCCCCCHHHHHCCCHHHHHCCCCCCCHHHHHHHHHHHH T ss_conf 60899999998678727678841378877635776340237899999876 No 20 >1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A Probab=91.21 E-value=0.032 Score=33.26 Aligned_cols=23 Identities=17% Similarity=0.206 Sum_probs=13.5 Q ss_pred CEEEEEEEECCCCCHHHHHHHHH Q ss_conf 18999999389617779999999 Q gi|254780237|r 199 DKLSMTIDTDGSITGEDSVALAS 221 (340) Q Consensus 199 dkL~lEI~TnGsi~P~eAl~~Aa 221 (340) +..++-|-|.|+..|.-....+. T Consensus 156 ~g~vvyIdTE~~f~~~Rl~~i~~ 178 (343) T 1v5w_A 156 GGKIIFIDTENTFRPDRLRDIAD 178 (343) T ss_dssp CCEEEEEESSSCCCHHHHHHHHH T ss_pred CCCEEEEECCCCCCHHHHHHHHH T ss_conf 88468997789888999999998 No 21 >1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ... Probab=90.48 E-value=0.84 Score=24.01 Aligned_cols=36 Identities=17% Similarity=0.355 Sum_probs=31.5 Q ss_pred CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC Q ss_conf 218999999389617779999999999998887622 Q gi|254780237|r 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 (340) Q Consensus 198 ~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~ 233 (340) .++.+|-|.|+++.+|.+||..|++-|++.+..+.. T Consensus 68 ~~~i~lrI~t~~~~~p~~~l~~a~~~l~~~~~~i~~ 103 (120) T 1twf_K 68 FARFKLRIQTTEGYDPKDALKNACNSIINKLGALKT 103 (120) T ss_dssp SCEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHHHH T ss_pred CCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 781279999699999999999999999999999999 No 22 >3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Probab=90.14 E-value=0.38 Score=26.23 Aligned_cols=36 Identities=11% Similarity=0.100 Sum_probs=31.4 Q ss_pred CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC Q ss_conf 218999999389617779999999999998887622 Q gi|254780237|r 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 (340) Q Consensus 198 ~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~ 233 (340) .++.++-|.|+|+.+|.+|+..|++-|+..+..+.. T Consensus 67 ~~~i~irI~t~~~~~p~~~l~~a~~~li~~~~~i~~ 102 (123) T 3h0g_K 67 NHNFILRVQTVEDCSPKQVIVDAAKSLITHLEEIKV 102 (123) T ss_dssp SCEEEEEEECCSSSCSHHHHHHHHHHHHHHHHHHHH T ss_pred CCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 880389999699999999999999999999999999 No 23 >2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L Probab=89.94 E-value=0.32 Score=26.70 Aligned_cols=39 Identities=26% Similarity=0.295 Sum_probs=29.2 Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE Q ss_conf 78881589999616975667888999998741698306889998 Q gi|254780237|r 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65 (340) Q Consensus 22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI 65 (340) +.+++...|.+ .|.+||+||+||..|+.. ++....+-++ T Consensus 7 ~~~~n~~~i~i----~~EdhTlgnlL~~~L~~~-~~V~fagY~~ 45 (92) T 2pa8_L 7 KSESNYLELEI----EGEDHTLGNLIAGTLRRI-SGVSFASYYQ 45 (92) T ss_dssp EEETTEEEEEE----ETCCHHHHHHHHHHHHTS-TTEEEEEEEC T ss_pred ECCCCEEEEEE----ECCCCHHHHHHHHHHHCC-CCCEEEEEEC T ss_conf 37998899999----489822999999999449-9916988756 No 24 >1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2 Probab=89.45 E-value=0.69 Score=24.57 Aligned_cols=47 Identities=11% Similarity=0.147 Sum_probs=33.7 Q ss_pred EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC Q ss_conf 442235776411688776218999999389617779999999999998887622 Q gi|254780237|r 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 (340) Q Consensus 180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~ 233 (340) |.-+.|.+.. .--++..|-|.|+|. +|.+||..|++-|.+.+.-|.. T Consensus 48 V~fAgY~ipH------Pl~~~~~lrIkt~~~-~p~e~l~~a~~~l~~~~~~l~~ 94 (115) T 1xpp_A 48 VDEARYYIKH------PVIDNPQIYVRVKSG-KPQSAIKRAVRKLSKLYEDLGT 94 (115) T ss_dssp EEEEEEECSS------TTTSCCEEEEEESSS-CHHHHHHHHHHHHHHHHHHHHH T ss_pred CEEEEEECCC------CCCCCEEEEEEECCC-CHHHHHHHHHHHHHHHHHHHHH T ss_conf 1699867799------887852899996799-9799999999999999999999 No 25 >2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Probab=89.05 E-value=0.86 Score=23.97 Aligned_cols=44 Identities=25% Similarity=0.416 Sum_probs=27.5 Q ss_pred CCEEEEEEEECCCCCC-----------CCCCCCC-HHHHHHHHHHHCCCEEEECCC Q ss_conf 8306889998871443-----------1466462-444999998401141777279 Q gi|254780237|r 56 RGAAITAVQIDGVLHE-----------ISSIKGV-HEDLTDIILNIKGINLKMSGD 99 (340) Q Consensus 56 ~G~ait~vkI~gv~HE-----------fs~i~GV-~EDV~eIiLNLK~I~~k~~~~ 99 (340) .+.-+..-||||+.=. +|.=.|. =|||++-+..++.|..+.... T Consensus 107 ~~~~~~e~KiDGls~~L~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~ip~~~~~~ 162 (671) T 2owo_A 107 KVTWCCELKLDGLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGE 162 (671) T ss_dssp CCCEEEEEEESSEEEEEEEETTEEEEEECCTTSSEEEBCHHHHHTCTTSCSBCCSS T ss_pred CCEEEEEEECCEEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHCCCCCCCCCC T ss_conf 82289986135279999998999989764799964348476565531577642335 No 26 >3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Probab=89.02 E-value=0.5 Score=25.47 Aligned_cols=41 Identities=24% Similarity=0.332 Sum_probs=30.9 Q ss_pred CCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEE Q ss_conf 42015863678881589999616975667888999998741698306 Q gi|254780237|r 13 NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59 (340) Q Consensus 13 ~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~a 59 (340) .+|.+ ..+...+|.+.|.+ .|..|||||+||..|+.. ++.. T Consensus 16 ~ki~~-~~~tk~~N~~~~~i----~~EDHTLGNlL~~~L~~~-~~V~ 56 (123) T 3h0g_K 16 PKVTY-ELDSKSPNAAVVTL----EKEDHTLANMLANQLLSD-ERVL 56 (123) T ss_dssp CSCCE-EECSSSTTEEEEEE----ESCCSSHHHHHHHTGGGS-TTCS T ss_pred CCEEE-EECCCCCCEEEEEE----ECCCCHHHHHHHHHHHCC-CCCE T ss_conf 51698-64478885689999----589842999999999539-9834 No 27 >1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A Probab=88.93 E-value=0.99 Score=23.57 Aligned_cols=59 Identities=10% Similarity=0.138 Sum_probs=52.4 Q ss_pred HHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 33111221011058889898839837188874498888618898864499999999980 Q gi|254780237|r 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 255 ~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) .+++-++.|++.--..+.|-..|+.+|.++.--+.++|+.|.+|...-.+|+++.=+++ T Consensus 4 ~~~~F~e~LdvDe~iA~lLv~EGF~siEeIAy~~~~eL~~IegfDee~a~eL~~RA~~~ 62 (70) T 1u9l_A 4 AIDTFTKYLDIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERAKNA 62 (70) T ss_dssp HHHHHHHHHTCCHHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHHHH T ss_pred HHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 89999998486399999999865597999875999999763155899999999999999 No 28 >1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Probab=87.39 E-value=1.1 Score=23.29 Aligned_cols=44 Identities=18% Similarity=0.190 Sum_probs=36.7 Q ss_pred HHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 8889898839837188874498888618898864499999999980 Q gi|254780237|r 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 268 Rs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) ++.+-+++ ..++.+|.+-+.++|.+++++|.+..+.|.+.+.+- T Consensus 31 ~a~~L~~~--Fgsl~~i~~As~eeL~~i~GiG~~~A~~I~~~f~~p 74 (89) T 1z00_A 31 DSQTLLTT--FGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEP 74 (89) T ss_dssp HHHHHHHH--TCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSC T ss_pred HHHHHHHH--HCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCH T ss_conf 99999999--488899999878777268996999999999998084 No 29 >1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix, fidelity, processivity, transferase; 2.30A {Sulfolobus solfataricus} SCOP: e.8.1.7 Probab=85.99 E-value=0.41 Score=26.06 Aligned_cols=40 Identities=10% Similarity=0.160 Sum_probs=34.5 Q ss_pred HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHC Q ss_conf 331112210-1105888989883983718887449888861 Q gi|254780237|r 255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294 (340) Q Consensus 255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ 294 (340) +-.++|++| .+.-|..-.|++.||+|+|||.+++.++|.+ T Consensus 181 L~~lpl~~l~GiG~~~~~~L~~~Gi~ti~dl~~~~~~~L~r 221 (221) T 1im4_A 181 LNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEK 221 (221) T ss_dssp HHTCBGGGSTTCCHHHHHHHHHTTCCBTTC----------- T ss_pred HHCCCHHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHCC T ss_conf 85798754189479999999992992099985799998119 No 30 >3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} SCOP: d.240.1.1 e.8.1.7 PDB: 3bq1_A* 3bq2_A* 1k1q_A 1k1s_A Probab=84.84 E-value=1 Score=23.52 Aligned_cols=53 Identities=9% Similarity=0.142 Sum_probs=41.9 Q ss_pred HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHH Q ss_conf 331112210-1105888989883983718887449888861889886449999999 Q gi|254780237|r 255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309 (340) Q Consensus 255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~ 309 (340) .-..+|++| .+.-|...-|++.||+|++||.+.+.++|.+ -||.+....+.+. T Consensus 176 l~~lpv~~l~GiG~~~~~~L~~~Gi~t~~dl~~~~~~~l~~--~fG~~~g~~l~~~ 229 (354) T 3bq0_A 176 LNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEK--ITGKAKALYLLKL 229 (354) T ss_dssp HHHCBSTTSTTCCHHHHHHHTTTTCCBGGGGGGSCHHHHHH--HHCHHHHHHHHHH T ss_pred HHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHH--HHCHHHHHHHHHH T ss_conf 98610666159647899999981896999954589878998--8481788999998 No 31 >3gqc_A DNA repair protein REV1; protein-DNA complex, alternative splicing, DNA damage, DNA repair, DNA synthesis; HET: DNA DOC DCP; 2.50A {Homo sapiens} Probab=84.19 E-value=1.7 Score=22.09 Aligned_cols=54 Identities=22% Similarity=0.111 Sum_probs=42.9 Q ss_pred HHHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHH Q ss_conf 3331112210-1105888989883983718887449888861889886449999999 Q gi|254780237|r 254 PALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309 (340) Q Consensus 254 ~~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~ 309 (340) -+...+|.+| .+.-+...-|++.||+|++||...+.+.|.+. ||.+....+.+. T Consensus 311 fL~~lpv~~lpGIG~~~~~kL~~lGI~Ti~DL~~l~~~~L~~~--fG~k~g~~L~~~ 365 (504) T 3gqc_A 311 FIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKE--FGPKTGQMLYRF 365 (504) T ss_dssp HHHHSBGGGSTTCCHHHHHHHHHTTCCBHHHHTTSCHHHHHHH--HCHHHHHHHHHH T ss_pred HHHHHCCCCCCCCCHHHHHHHHHHCCCCHHHHHCCCHHHHHHH--HCCHHHHHHHHH T ss_conf 8864133344787878999998616850999855999999988--471789999996 No 32 >1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family, transferase/DNA complex; HET: DNA MSE ADI; 1.70A {Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB: 1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A* 1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A* 2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ... Probab=83.87 E-value=0.96 Score=23.66 Aligned_cols=52 Identities=8% Similarity=0.012 Sum_probs=42.2 Q ss_pred HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHH Q ss_conf 331112210-110588898988398371888744988886188988644999999 Q gi|254780237|r 255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308 (340) Q Consensus 255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~ 308 (340) +-..+|.+| .+.-++..-|++.||+|++||.+.+.+.|.+ -||.+....+.+ T Consensus 175 L~~lpv~~l~Gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~--~fG~~~~~~l~~ 227 (352) T 1jx4_A 175 IRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKG--MIGEAKAKYLIS 227 (352) T ss_dssp HHHSBGGGSTTCCHHHHHHHHTTTCCBGGGGGSSCHHHHHH--HHCHHHHHHHHH T ss_pred CCCCCEEEECCCCCHHHHHHHHHCCCCHHHHHCCCHHHHHH--HHCHHHHHHHHH T ss_conf 02676024148870468899984686825413279789997--858487999999 No 33 >3im1_A Protein SNU246, PRE-mRNA-splicing helicase BRR2; ATPase, RNA helicase, rnpase, RNA unwindase, molecular modeling; 1.65A {Saccharomyces cerevisiae} PDB: 3im2_A* 3hib_A Probab=79.83 E-value=3 Score=20.41 Aligned_cols=94 Identities=5% Similarity=0.104 Sum_probs=62.3 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCCCHHHHHH-------HCCHHHC-CCCHHHHHHHHHCCCCCHHHHH Q ss_conf 7999999999999888762244443221000000000112333-------1112210-1105888989883983718887 Q gi|254780237|r 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL-------LKKVEEL-ELSVRSTNCLRGENIVYMGDLI 285 (340) Q Consensus 214 ~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~~~~~~~~~~L-------~~~IeeL-eLSvRs~NcLk~a~I~tigdLv 285 (340) ...+..|.+++...+.......-.. .. ......+-+ ..++-+| .+..+...-|++.+|.++++|. T Consensus 113 ~~I~~~~~Ril~al~ei~~~~~~~~-a~------~~l~l~q~i~q~~w~~~~~L~Qlp~i~~~~~~~l~~~~i~~l~~l~ 185 (328) T 3im1_A 113 KDILEKVVPLINVVVDILSANGYLN-AT------TAMDLAQMLIQGVWDVDNPLRQIPHFNNKILEKCKEINVETVYDIM 185 (328) T ss_dssp HHHHHHHHHHHHHHHHHHHHTTBTT-HH------HHHHHHHHHHHTSCTTSCGGGGSTTCCHHHHHHHHHTTCCSHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHH-HH------HHHHHHHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHCCCCCHHHHH T ss_conf 9999999999999999996168799-99------9999999988655899866676620799999999975999999998 Q ss_pred HCCHHHHHCCCCCCHHHHHHHHHHHHHHC Q ss_conf 44988886188988644999999999808 Q gi|254780237|r 286 QRTEADMLRMANFGRKSLVEIKGVLGTMG 314 (340) Q Consensus 286 ~~s~~dLl~ikNfG~KSl~EI~~~L~~~g 314 (340) ..+++++..+-++...-.++|.+.+..+- T Consensus 186 ~~~~~~~~~~l~~~~~~~~~i~~~~~~~P 214 (328) T 3im1_A 186 ALEDEERDEILTLTDSQLAQVAAFVNNYP 214 (328) T ss_dssp HSCHHHHHHHCCCCHHHHHHHHHHHHHCC T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHCC T ss_conf 75176799997107789999999986489 No 34 >1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Probab=79.62 E-value=2.2 Score=21.29 Aligned_cols=42 Identities=12% Similarity=0.060 Sum_probs=35.1 Q ss_pred HHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHH Q ss_conf 88898988398371888744988886188988644999999999 Q gi|254780237|r 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311 (340) Q Consensus 268 Rs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~ 311 (340) |+..-++. ..++.++..-+.+||.+++++|++..++|.+.|. T Consensus 36 ~ak~Ll~~--F~si~~i~~As~eeL~~v~GIg~~~A~~I~~~l~ 77 (78) T 1kft_A 36 RRQMLLKY--MGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK 77 (78) T ss_dssp HHHHHHHH--HSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT T ss_pred HHHHHHHH--HCCHHHHHHHCHHHHHCCCCCCHHHHHHHHHHHC T ss_conf 99999999--2994999883799998079989999999999966 No 35 >1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B Probab=78.66 E-value=3.3 Score=20.18 Aligned_cols=47 Identities=9% Similarity=0.067 Sum_probs=39.7 Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH Q ss_conf 11058889898839837188874498888618898864499999999 Q gi|254780237|r 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310 (340) Q Consensus 264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L 310 (340) .++....--|..+||+|+.||...+-++|+.+-++.......+.-+- T Consensus 14 G~~~~~~~~L~e~gI~t~edLAdls~dEL~ei~~i~ee~A~~lIM~A 60 (70) T 1wcn_A 14 GVDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMAA 60 (70) T ss_dssp TCCHHHHHHHHTTTCCSHHHHHTSCHHHHHTSSSCCHHHHHHHHHHH T ss_pred CCCHHHHHHHHHCCCCCHHHHHHHCHHHHHHHCCCCHHHHHHHHHHH T ss_conf 98999999999969974999987289999876168999999999999 No 36 >3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex, Y-family DNA polym translesion synthesis, nucleoside triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens} PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A* 2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A* 3gv5_B* 3h4d_A* 3h4b_A* 2alz_A* 3h40_A* 1t3n_A* 1zet_A* Probab=75.99 E-value=3.8 Score=19.78 Aligned_cols=49 Identities=16% Similarity=0.293 Sum_probs=39.0 Q ss_pred CHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHH Q ss_conf 12210-1105888989883983718887449888861889886449999999 Q gi|254780237|r 259 KVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309 (340) Q Consensus 259 ~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~ 309 (340) +|.+| .+.-+....|++.||+|++||...+..+|. +-||.+.-..+.+. T Consensus 235 pv~~l~GiG~~~~~~L~~~Gi~ti~dl~~~~~~~L~--~~fG~~~g~~l~~~ 284 (420) T 3osn_A 235 HIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILE--KELGISVAQRIQKL 284 (420) T ss_dssp SGGGSTTCCHHHHHHHHHTTCCSHHHHHHSCHHHHH--HHHHHHHHHHHHHH T ss_pred CHHHHCCCCHHHHHHHHHHCCCCHHHHHCCCHHHHH--HHHCCHHHHHHHHH T ss_conf 688856888789999864256609987527553699--88593999999999 No 37 >1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Probab=75.68 E-value=4 Score=19.65 Aligned_cols=51 Identities=14% Similarity=0.223 Sum_probs=38.9 Q ss_pred CHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 122101105888989883983718887449888861889886449999999998 Q gi|254780237|r 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340) Q Consensus 259 ~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340) .|..++- ...+.|-+. ..++.++..-|.++|++++++|.+..+.|.+.+.. T Consensus 18 ~IpgIG~--~~a~~L~~~-F~s~~~i~~As~eeL~~v~GIG~~~a~~i~~~~~~ 68 (75) T 1x2i_A 18 GLPHVSA--TLARRLLKH-FGSVERVFTASVAELMKVEGIGEKIAKEIRRVITA 68 (75) T ss_dssp TSTTCCH--HHHHHHHHH-HCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHS T ss_pred CCCCCCH--HHHHHHHHH-HCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCC T ss_conf 8999429--999999999-68889899978999985589799999999999857 No 38 >2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Probab=72.73 E-value=4.6 Score=19.26 Aligned_cols=41 Identities=17% Similarity=0.201 Sum_probs=34.5 Q ss_pred HHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 989883983718887449888861889886449999999998 Q gi|254780237|r 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340) Q Consensus 271 NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340) ..|-+. ..++.+|..-+.++|.+++++|.+-.+.|.+.+.+ T Consensus 46 ~~L~~~-F~Si~~l~~As~eeL~~i~GIG~~~A~~I~~~f~~ 86 (91) T 2a1j_B 46 QTLLTT-FGSLEQLIAASREDLALCPGLGPQKARRLFDVLHE 86 (91) T ss_dssp HHHHHH-HSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHS T ss_pred HHHHHH-HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHC T ss_conf 999999-58829899989997557799699999999999848 No 39 >1feu_A 50S ribosomal protein L25; general stress protein CTC, 5S rRNA-protein complex, cadmium IONS, ribosome; 2.30A {Thermus thermophilus} SCOP: b.53.1.1 PDB: 2j01_Z 1vsp_T 2hgj_Y 2hgq_Y 2hgu_Y 1vsa_T 2j03_Z 2jl6_Z 2jl8_Z 2v47_Z 2v49_Z 2wdi_Z 2wdj_Z 2wdl_Z 2wdn_Z 2wh2_Z 2wh4_Z 2wrj_Z 2wrl_Z 2wro_Z ... Probab=70.80 E-value=2.5 Score=20.98 Aligned_cols=34 Identities=12% Similarity=0.082 Sum_probs=17.4 Q ss_pred EEEEEEEECC-CCEEEECCCEEEEEECCCCEEEEEEEE Q ss_conf 6996335138-985998888089997789649999997 Q gi|254780237|r 113 VVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTV 149 (340) Q Consensus 113 ~vtA~Di~~p-~~veivNpd~~IaTl~~~~~l~iel~i 149 (340) .+--+|+|.. -.=.++.=|.|.. + +..+.+++-| T Consensus 68 ~vlikevQ~~pv~~~i~HvDF~~v--~-~~~i~v~VPv 102 (206) T 1feu_A 68 PTLVRQVNLDKRRRRPEHVDFFVL--S-DEPVEMYVPL 102 (206) T ss_dssp EEEEEEEEECSSSSCEEEEEEEEC--C-SSCEEEEEEE T ss_pred EEEEEEEEECCCCCCCEEEEEEEC--C-CCEEEEEECE T ss_conf 999999874122577379998815--8-9769999665 No 40 >2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Probab=69.64 E-value=5.5 Score=18.74 Aligned_cols=48 Identities=19% Similarity=0.297 Sum_probs=38.0 Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 1105888989883983718887449888861889886449999999998 Q gi|254780237|r 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340) Q Consensus 264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340) +.|......|-+. ..++.+|.+.+.++|.+++++|.+-..+|.+.|.. T Consensus 169 gi~~~~A~~Ll~~-f~Sl~~l~~as~~eL~~v~giG~~~A~~I~~~l~~ 216 (219) T 2bgw_A 169 GIGRRTAERILER-FGSLERFFTASKAEISKVEGIGEKRAEEIKKILMT 216 (219) T ss_dssp TCCHHHHHHHHHH-HSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHS T ss_pred CCCHHHHHHHHHH-CCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHCC T ss_conf 9899999999998-69999998688999960899799999999999638 No 41 >2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} Probab=68.96 E-value=4.1 Score=19.58 Aligned_cols=41 Identities=15% Similarity=0.135 Sum_probs=30.5 Q ss_pred HHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHC Q ss_conf 88898988398371888744988886188988644999999999808 Q gi|254780237|r 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314 (340) Q Consensus 268 Rs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~g 314 (340) ||.+.|++-- +--.+.+|+..++++|.+..+-|.++|+++- T Consensus 42 kA~~sLk~~p------~~I~s~~~l~~l~GIG~~i~~ki~e~L~~yc 82 (87) T 2kp7_A 42 KALRSLQRYP------LPLRSGKEAKILQHFGDRLCRMLDEKLKQHL 82 (87) T ss_dssp HHHHHHHHCC------SCCCSHHHHHTCTTTCHHHHHHHHHHHHHHH T ss_pred HHHHHHHHCC------CCCCCHHHHHHCCCCCHHHHHHHHHHHHHHH T ss_conf 9999999789------9888899997279977899999999999999 No 42 >3mr3_A DNA polymerase ETA; POL ETA, polymerase, thymine dimer, CPD, XPV, xeroderma PIGM variant, DNA damage; HET: DNA TTD DZ4; 1.75A {Homo sapiens} PDB: 3mr2_A* 3mr5_A* 3mr6_A* Probab=63.86 E-value=7.1 Score=18.01 Aligned_cols=52 Identities=23% Similarity=0.306 Sum_probs=37.8 Q ss_pred HCCHHHC-CCCHHH-HHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH Q ss_conf 1112210-110588-89898839837188874498888618898864499999999 Q gi|254780237|r 257 LKKVEEL-ELSVRS-TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310 (340) Q Consensus 257 ~~~IeeL-eLSvRs-~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L 310 (340) ..+|.+| ...-+. ..-|++.||+|++||...+..+|.+. ||.+.-..+.+.. T Consensus 252 ~lpi~~l~GiG~k~~~~~L~~~gi~ti~dl~~~~~~~L~~~--~G~~~g~~l~~~a 305 (435) T 3mr3_A 252 QMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSH--FGEKNGSWLYAMC 305 (435) T ss_dssp TCBGGGSTTCSSHHHHHHHHHHTCCBGGGGGGSCHHHHHHH--HCHHHHHHHHHHT T ss_pred HCCCCEECCCCHHHHHHHHHHHCCCCHHHHHHCCHHHHHHH--HCHHHHHHHHHHH T ss_conf 37677607767578999999958947899873999899999--7868899999996 No 43 >2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Probab=60.03 E-value=6.1 Score=18.43 Aligned_cols=23 Identities=17% Similarity=0.177 Sum_probs=14.9 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 49999999998083126768789 Q gi|254780237|r 302 SLVEIKGVLGTMGLFLGMNLPDW 324 (340) Q Consensus 302 Sl~EI~~~L~~~gl~lg~~l~~~ 324 (340) -+++|.+.+++.|..+=+|-..| T Consensus 471 d~e~v~~~~~~~g~~lEINts~~ 493 (578) T 2w9m_A 471 DLDAVLGACEANGTVVEINANAA 493 (578) T ss_dssp CHHHHHHHHHHHTCEEEEECSTT T ss_pred HHHHHHHHHHHHCCEEEEECCCC T ss_conf 79999999998199999949999 No 44 >2q0z_X Protein Pro2281; SEC63, SEC, NESG, HR1979, structural genomics, translocase, northeast structural genomics consortium, PSI-2; 2.00A {Homo sapiens} SCOP: a.289.1.1 b.1.18.22 Probab=59.00 E-value=8.7 Score=17.47 Aligned_cols=96 Identities=6% Similarity=0.067 Sum_probs=59.9 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCH---HHCCC-CHHHHHHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCH Q ss_conf 999999999999888762244443221000---00000-01123331112210-11058889898839837188874498 Q gi|254780237|r 215 DSVALASRILQDQLGMFINFEEPKKEVKED---INVKS-LPFNPALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTE 289 (340) Q Consensus 215 eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~---~~~~~-~~~~~~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~ 289 (340) -.+..|.+++...+................ .-..+ .-.+ ..++-+| .++....+-|.+.+|.++.||...+. T Consensus 117 ~I~~~~~Ril~al~ei~~~~~~~~~~~~~l~l~q~i~q~~w~~---~~pL~Qlp~i~~~~~~~l~~~~i~sl~~l~~~~~ 193 (339) T 2q0z_X 117 EILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSK---DSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMED 193 (339) T ss_dssp HHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHTCCTT---SCGGGGSTTCCHHHHHHHHHTTCCSHHHHHHSCH T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCC---CCHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCH T ss_conf 9999899999999999986598999999999999988663899---7732324658999999998669998999972899 Q ss_pred HHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 888618898864499999999980 Q gi|254780237|r 290 ADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 290 ~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) +++..+-++......+|.+.+..+ T Consensus 194 ~~~~~~l~l~~~~~~~i~~~~~~~ 217 (339) T 2q0z_X 194 EERNALLQLTDSQIADVARFCNRY 217 (339) T ss_dssp HHHHHHHCCCHHHHHHHHHHHTTS T ss_pred HHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 999877523768999999988758 No 45 >2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W 1vou_W 1vow_W ... Probab=58.09 E-value=2.7 Score=20.75 Aligned_cols=24 Identities=25% Similarity=0.536 Sum_probs=8.1 Q ss_pred EEEEEEECCCCEEEE-CCCEEEEEE Q ss_conf 996335138985998-888089997 Q gi|254780237|r 114 VTAGDIQTVNDIEVL-NPDHVICNL 137 (340) Q Consensus 114 vtA~Di~~p~~veiv-Npd~~IaTl 137 (340) ++++||.+|.+++++ +|+..||++ T Consensus 147 i~v~Dl~lp~gv~l~~d~d~~V~~V 171 (237) T 2zjr_S 147 ITAGDIKLPEGCTLAADPELTVVSV 171 (237) T ss_dssp EETTTSCCSTTCCCCSCTTCEEEEE T ss_pred EEEEEECCCCCEEECCCCCCEEEEE T ss_conf 9998442799808825999579999 No 46 >2x7i_A Mevalonate kinase; transferase; HET: CIT; 2.20A {Staphylococcus aureus} Probab=55.85 E-value=9.7 Score=17.13 Aligned_cols=77 Identities=13% Similarity=0.274 Sum_probs=53.9 Q ss_pred HHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCC--CC---------CHH Q ss_conf 2210-11058889898839837188874498888618898864499999999980831267687--89---------867 Q gi|254780237|r 260 VEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP--DW---------PPE 327 (340) Q Consensus 260 IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~--~~---------~~~ 327 (340) ++.+ ++..++..+|++.++..+++|+..+...|.++ +.....++++.+...+.|- +|.++. +| +.+ T Consensus 207 ~~~i~~~~~~~~~al~~~d~~~lg~lm~~~~~~l~~l-~vs~p~l~~l~~~~~~~Ga-~gaklsGaG~Gg~~~al~~~~~ 284 (308) T 2x7i_A 207 VKHIGKLVLRASDVIEHHKFEALADIFNECHADLKAL-TVSHDKIEQLMKIGKENGA-IAGKLTGAGRGGSMLLLAKDLP 284 (308) T ss_dssp HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHTTC-SEEEESBTTTCSSEEEEESSHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHCCC-CEEEEECCCCCCEEEEEECCHH T ss_conf 9997478999999998657789999999999999871-7898899999999997899-5899977785226999979878 Q ss_pred HHHHHHHHHHC Q ss_conf 79999987750 Q gi|254780237|r 328 SIEELAKKYED 338 (340) Q Consensus 328 ~~~~~~~~~~~ 338 (340) ..+.+.+++++ T Consensus 285 ~a~~i~~~l~~ 295 (308) T 2x7i_A 285 TAKNIVKAVEK 295 (308) T ss_dssp HHHHHHHHHHH T ss_pred HHHHHHHHHHH T ss_conf 99999999997 No 47 >1zco_A 2-dehydro-3-deoxyphosphoheptonate aldolase; arabino-heptulosonate, synthase, shikimate, DAHP, DAH7P, dahps, DAH7PS, lyase; HET: PEP; 2.25A {Pyrococcus furiosus} Probab=52.30 E-value=7.9 Score=17.71 Aligned_cols=15 Identities=13% Similarity=0.085 Sum_probs=8.8 Q ss_pred CCHHHHHHHHHHHCC Q ss_conf 624449999984011 Q gi|254780237|r 77 GVHEDLTDIILNIKG 91 (340) Q Consensus 77 GV~EDV~eIiLNLK~ 91 (340) |.-|.-++++...|+ T Consensus 70 g~g~~gl~~l~~ik~ 84 (262) T 1zco_A 70 GYGEKALRWMREAAD 84 (262) T ss_dssp CCTHHHHHHHHHHHH T ss_pred CCHHHHHHHHHHHHH T ss_conf 761588999998776 No 48 >2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A* Probab=52.13 E-value=11 Score=16.75 Aligned_cols=50 Identities=18% Similarity=0.131 Sum_probs=35.7 Q ss_pred HCCHHHC-CCCHHHHHHHHHC--CCCCHHHHHH-CCHHHHHCCCCCCHHHHHHHHH Q ss_conf 1112210-1105888989883--9837188874-4988886188988644999999 Q gi|254780237|r 257 LKKVEEL-ELSVRSTNCLRGE--NIVYMGDLIQ-RTEADMLRMANFGRKSLVEIKG 308 (340) Q Consensus 257 ~~~IeeL-eLSvRs~NcLk~a--~I~tigdLv~-~s~~dLl~ikNfG~KSl~EI~~ 308 (340) ..++.+| ...-++..-|++. ||+|++||.+ .+.+.|.+. ||.|.-..+.+ T Consensus 240 ~lpv~~LpGIG~~~~~kL~~~~~Gi~ti~DL~~~~~~~~L~~~--fG~~~g~~l~~ 293 (434) T 2aq4_A 240 SFKLDDLPGVGHSTLSRLESTFDSPHSLNDLRKRYTLDALKAS--VGSKLGMKIHL 293 (434) T ss_dssp TCCGGGSTTCCHHHHHHHHHHTTCCCSHHHHHHHCCHHHHHHH--HCSSHHHHHHH T ss_pred CCCCCCCCCCCHHHHHHHHHHHCCCEEHHHHHHHCCHHHHHHH--HCCHHHHHHHH T ss_conf 6672106686789999999876588079997632829899999--67489999999 No 49 >3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3kzi_U* 3a0b_U* 3a0h_U* Probab=51.27 E-value=6.1 Score=18.43 Aligned_cols=41 Identities=7% Similarity=0.126 Sum_probs=28.5 Q ss_pred HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCC Q ss_conf 5888989883983718887449888861889886449999999998083 Q gi|254780237|r 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315 (340) Q Consensus 267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl 315 (340) ..|....+...+. +-+||++++++|.+.++-|+..|..+-. T Consensus 44 ~~A~~Iv~~gpf~--------s~~dL~~V~Gig~~~~e~ik~yl~~~~~ 84 (104) T 3bz1_U 44 TLAKLIVKNAPYE--------SVEDVLNIPGLTERQKQILRENLEHFTV 84 (104) T ss_dssp HHHHHHHHSCCCS--------SGGGGGGCTTCCHHHHHHHHHHGGGEEC T ss_pred HHHHHHHHCCCCC--------CHHHHHCCCCCCHHHHHHHHHHHCCCEE T ss_conf 9999999749979--------8999963899899999999986545544 No 50 >1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} Probab=46.18 E-value=8.8 Score=17.43 Aligned_cols=39 Identities=8% Similarity=0.127 Sum_probs=27.4 Q ss_pred HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 58889898839837188874498888618898864499999999980 Q gi|254780237|r 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) .++....++..+. +-+||++++++|.|.++-+++.|..+ T Consensus 74 ~~A~~Iv~~gpf~--------svedl~~v~Gig~~~~e~l~~~l~~f 112 (134) T 1s5l_U 74 TLAKLIVKNAPYE--------SVEDVLNIPGLTERQKQILRENLEHF 112 (134) T ss_dssp HHHHHHHHTCCCS--------SGGGGGGCTTCCHHHHHHHHHHHTTE T ss_pred HHHHHHHHCCCCC--------CHHHHHCCCCCCHHHHHHHHHHHCCC T ss_conf 9999999827848--------79999617757999999999865353 No 51 >2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A* Probab=42.90 E-value=15 Score=15.84 Aligned_cols=47 Identities=6% Similarity=0.191 Sum_probs=37.2 Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 1105888989883983718887449888861889886449999999998 Q gi|254780237|r 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340) Q Consensus 264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340) +.+......|-+ ...++.+|.+.|.+||.++.+ |++....|.+.|.. T Consensus 11 GIg~~~~~~Ll~-~fgSi~~l~~as~eeL~~v~G-~~~~A~~i~~~l~~ 57 (63) T 2a1j_A 11 GVNAKNCRSLMH-HVKNIAELAALSQDELTSILG-NAANAKQLYDFIHT 57 (63) T ss_dssp TCCHHHHHHHHH-HCSSHHHHHTCCHHHHHHHHS-CHHHHHHHHHHHHC T ss_pred CCCHHHHHHHHH-HCCCHHHHHHCCHHHHHHCCC-CHHHHHHHHHHHCC T ss_conf 988999999999-867999998799999987869-89999999999802 No 52 >3bqs_A Uncharacterized protein; 10114F, NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.42A {Listeria monocytogenes str} PDB: 3bqt_A 3mab_A Probab=42.41 E-value=16 Score=15.79 Aligned_cols=77 Identities=17% Similarity=0.123 Sum_probs=46.9 Q ss_pred CHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHH-HCCCCCCHH-HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 12210-11058889898839837188874498888-618898864-4999999999808312676878986779999987 Q gi|254780237|r 259 KVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADM-LRMANFGRK-SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335 (340) Q Consensus 259 ~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dL-l~ikNfG~K-Sl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~~~~ 335 (340) .+.+| +++..+..-|.+.||+++.||......++ .+++-.|.. ++.- -..--|.--|..-...+.+.-++|++. T Consensus 5 ~L~~LPNig~~~e~~L~~iGI~~~~~L~~~ga~~~y~rLk~~~~~~~~~~---L~aL~gAl~g~~w~~l~~e~K~~L~~~ 81 (93) T 3bqs_A 5 NLSELPNIGKVLEQDLIKAGIKTPVELKDVGSKEAFLRIWENDSSVCMSE---LYALEGAVQGIRWHGLDEAKKIELKKF 81 (93) T ss_dssp CGGGSTTCCHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHTTCTTCCHHH---HHHHHHHHHTSCGGGSCHHHHHHHHHH T ss_pred HHHHCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHHHCCCCCHHH---HHHHHHHHCCCCHHHCCHHHHHHHHHH T ss_conf 77248999999999999939998999986799999999998689960999---999999994998676999999999999 Q ss_pred HHC Q ss_conf 750 Q gi|254780237|r 336 YED 338 (340) Q Consensus 336 ~~~ 338 (340) |.. T Consensus 82 ~~~ 84 (93) T 3bqs_A 82 HQS 84 (93) T ss_dssp HHH T ss_pred HHH T ss_conf 998 No 53 >1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} SCOP: a.96.1.2 Probab=40.96 E-value=10 Score=16.96 Aligned_cols=53 Identities=19% Similarity=0.326 Sum_probs=36.7 Q ss_pred HHCCHHHCCCC-HHHHHHHHHCCCC--CHHHHHHCCHHHHHCCCCCCHHHHHHHHH Q ss_conf 31112210110-5888989883983--71888744988886188988644999999 Q gi|254780237|r 256 LLKKVEELELS-VRSTNCLRGENIV--YMGDLIQRTEADMLRMANFGRKSLVEIKG 308 (340) Q Consensus 256 L~~~IeeLeLS-vRs~NcLk~a~I~--tigdLv~~s~~dLl~ikNfG~KSl~EI~~ 308 (340) +..-|..++|. .||.+..+-+.+- .-+.-+..+.++|+++|+.|+|+..-|-. T Consensus 78 l~~~i~~~G~~~~KA~~l~~~a~~i~~~~~g~vp~~~~eL~~LPGVG~ktA~~vl~ 133 (221) T 1kea_A 78 IAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYTCAAVMC 133 (221) T ss_dssp HHHHTGGGSCHHHHHHHHHHHHHHHHHHHTTSCCSCHHHHHTSTTCCHHHHHHHHH T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCHHHHHHHHH T ss_conf 99999987899999999999999998860587301288874489876567999999 No 54 >3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* Probab=36.03 E-value=20 Score=15.15 Aligned_cols=50 Identities=14% Similarity=0.252 Sum_probs=40.2 Q ss_pred CCCHHHHHHHHH-------------CCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 110588898988-------------39837188874498888618898864499999999980 Q gi|254780237|r 264 ELSVRSTNCLRG-------------ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 264 eLSvRs~NcLk~-------------a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) -+|.|-|-.|.+ ....++..|+.-|.+||.++.+.|++-..-|++-|..+ T Consensus 308 ~v~pRGyRiLskiprlp~~vienLV~~FgsLq~Ll~AS~EeL~eVeGIGe~RAr~IreGL~Rl 370 (377) T 3c1y_A 308 LVSARGYRLLKTVARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISSL 370 (377) T ss_dssp BCCCCSHHHHHHTSCCCHHHHHHHHHHHCSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHHH T ss_pred CCCCHHHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 657417888723899978899999998468999985899889645885899999999999998 No 55 >1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A Probab=35.92 E-value=12 Score=16.49 Aligned_cols=51 Identities=18% Similarity=0.183 Sum_probs=34.8 Q ss_pred CCHHHCCCCHHHHHHHHHCCCC--CHHHHHHCCHHHHHCCCCCCHHHHHHHHH Q ss_conf 1122101105888989883983--71888744988886188988644999999 Q gi|254780237|r 258 KKVEELELSVRSTNCLRGENIV--YMGDLIQRTEADMLRMANFGRKSLVEIKG 308 (340) Q Consensus 258 ~~IeeLeLSvRs~NcLk~a~I~--tigdLv~~s~~dLl~ikNfG~KSl~EI~~ 308 (340) .-|..+.+..|+.|-.+.+.+- .-+.-+..+.++|+++|+.|+|+.+-|-. T Consensus 75 ~~i~~~gy~~ka~~l~~~a~~i~~~~~g~~p~~~~~L~~LpGVG~kTA~~il~ 127 (225) T 1kg2_A 75 HLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILS 127 (225) T ss_dssp HHHTTSCCTHHHHHHHHHHHHHHHHSTTSCCCSHHHHHTSTTCCHHHHHHHHH T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCHHHHHHHHH T ss_conf 99861673277999999999999870799974299997589874789999999 No 56 >2e1f_A Werner syndrome ATP-dependent helicase; HRDC domain, hydrolase; 2.00A {Homo sapiens} SCOP: a.60.8.1 PDB: 2e1e_A Probab=35.58 E-value=13 Score=16.24 Aligned_cols=47 Identities=15% Similarity=0.089 Sum_probs=29.5 Q ss_pred HHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHH-------HHHHHHHHHCCC Q ss_conf 89898839837188874498888618898864499-------999999980831 Q gi|254780237|r 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV-------EIKGVLGTMGLF 316 (340) Q Consensus 270 ~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~-------EI~~~L~~~gl~ 316 (340) +..+.+.-+.-+....-.|.++|..+++||.+-++ -|.+...+.++. T Consensus 37 ~~I~~d~~L~~ia~~~P~t~~eL~~I~G~g~~k~~ryG~~l~~I~~~~~~~~~~ 90 (103) T 2e1f_A 37 AILATNKILVDMAKMRPTTVENVKRIDGVSEGKAAMLAPLLEVIKHFCQTNSVQ 90 (103) T ss_dssp HHHCCHHHHHHHHHHCCCSHHHHTTSTTCCHHHHHHTHHHHHHHHHHHHHTTCC T ss_pred EEEECHHHHHHHHHHCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 044789999999987899999993789989999999989999999999984998 No 57 >1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19 Probab=34.27 E-value=13 Score=16.29 Aligned_cols=22 Identities=18% Similarity=0.270 Sum_probs=15.2 Q ss_pred CCCCCCCCCCCHHHHHHHHHHH Q ss_conf 1443146646244499999840 Q gi|254780237|r 68 VLHEISSIKGVHEDLTDIILNI 89 (340) Q Consensus 68 v~HEfs~i~GV~EDV~eIiLNL 89 (340) ....-+.++||=.-..+.+-.| T Consensus 113 l~~~i~~lkGVGpk~a~~L~kl 134 (780) T 1gm5_A 113 LSTDIQYAKGVGPNRKKKLKKL 134 (780) T ss_dssp SCCCSSSSSSCCHHHHHHHHTT T ss_pred CCCCCCCCCCCCHHHHHHHHHC T ss_conf 9998601788159999999976 No 58 >1x40_A ARAP2; ASAP-related protein2, GTPase activity, signal transduction, SAM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.1.2 Probab=34.23 E-value=21 Score=14.97 Aligned_cols=40 Identities=8% Similarity=0.100 Sum_probs=31.3 Q ss_pred CHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCC--CCCC Q ss_conf 1221011058889898839837188874498888618--8988 Q gi|254780237|r 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM--ANFG 299 (340) Q Consensus 259 ~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~i--kNfG 299 (340) =++.+.|+ +=...+++.+|.++.+|...++++|.++ .++| T Consensus 21 WL~~igL~-~Y~~~F~~~~~~~~~~l~~l~~~dL~~lGI~~~g 62 (91) T 1x40_A 21 FLMSINLE-QYLLHFHESGFTTVKDCAAINDSLLQKIGISPTG 62 (91) T ss_dssp HHHTTTCG-GGHHHHHHHTCCBSGGGGGCCHHHHHHHTCCCHH T ss_pred HHHHCCCH-HHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHH T ss_conf 99888559-9999999949982899987999999786999899 No 59 >1vr6_A Phospho-2-dehydro-3-deoxyheptonate aldolase; TM0343, structural genomics, joint center for structural genomics, JCSG; 1.92A {Thermotoga maritima} SCOP: c.1.10.4 PDB: 1rzm_A* Probab=33.46 E-value=22 Score=14.89 Aligned_cols=17 Identities=18% Similarity=-0.097 Sum_probs=7.4 Q ss_pred EEEECCCCCHHHHHHHH Q ss_conf 99938961777999999 Q gi|254780237|r 204 TIDTDGSITGEDSVALA 220 (340) Q Consensus 204 EI~TnGsi~P~eAl~~A 220 (340) .+.-.-..+|++-+.-| T Consensus 217 ~lKkG~~~s~~e~l~aa 233 (350) T 1vr6_A 217 LLKRGFMNTIEEFLLSA 233 (350) T ss_dssp EEECCTTCCHHHHHHHH T ss_pred EECCCCCCCHHHHHHHH T ss_conf 94175548999987789 No 60 >1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family DNA polymerase, translesion DNA synthesis, lesion bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7 PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A* Probab=33.06 E-value=22 Score=14.85 Aligned_cols=49 Identities=14% Similarity=0.108 Sum_probs=36.3 Q ss_pred HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHH Q ss_conf 331112210-1105888989883983718887449888861889886449999 Q gi|254780237|r 255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306 (340) Q Consensus 255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI 306 (340) +-..+|.+| +..-+...-|++.||.|++||.+.. ..|. +-||++...-+ T Consensus 279 L~~lpv~~l~GIG~~~~~~L~~~gI~ti~dL~~~~-~~l~--~~~g~~~~~~~ 328 (459) T 1t94_A 279 IKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQR-ALLS--LLFSETSWHYF 328 (459) T ss_dssp HTTCBGGGCTTSCHHHHHHHHHTTCCBHHHHHHTH-HHHH--HHSCHHHHHHH T ss_pred HHHCCCCEECCCCCHHHHHHHHHCCCCHHHHHHHH-HHHH--HHHCCHHHHHH T ss_conf 86298353368884137889870784999999858-8899--98451366646 No 61 >2cz9_A Probable galactokinase; structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.50A {Pyrococcus horikoshii} PDB: 2dei_A* 2dej_A* 1s4e_A* Probab=31.66 E-value=23 Score=14.70 Aligned_cols=62 Identities=18% Similarity=0.193 Sum_probs=48.0 Q ss_pred CHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 122101105888989883983718887449888861889886449999999998083126768 Q gi|254780237|r 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321 (340) Q Consensus 259 ~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l 321 (340) -+.+-+........|++.++..+|+|+..+-..|++.-+..-..++++.+...+.|. +|-++ T Consensus 239 v~~e~~~~~~~~~~~~~~d~~~~g~lm~~~~~~L~~~~~vs~~~ld~lv~~a~~~Ga-~GaKl 300 (350) T 2cz9_A 239 IVRENARVLEVRDALKEGNVEEVGKILTTAHWDLAKNYEVSCKELDFFVERALKLGA-YGARL 300 (350) T ss_dssp HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTC-SEEEE T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCC-CEEEE T ss_conf 999999999999875027899999999999999987208996899999999997799-38998 No 62 >2rrd_A BLM HRDC domain, HRDC domain from bloom syndrome protein; DNA helicase, RECQ family, HRDC DOMA binding protein; NMR {Homo sapiens} Probab=30.85 E-value=15 Score=15.91 Aligned_cols=45 Identities=13% Similarity=0.187 Sum_probs=31.3 Q ss_pred HHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHH----HHHHHHHHH Q ss_conf 889898839837188874498888618898864499----999999980 Q gi|254780237|r 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV----EIKGVLGTM 313 (340) Q Consensus 269 s~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~----EI~~~L~~~ 313 (340) .+..+.+..+.-+....-.|.++|++|++||.+.++ +|.+.+.++ T Consensus 43 ~~~I~~d~~L~eia~~~P~t~~eL~~I~Gv~~~k~~~yG~~il~~I~~~ 91 (101) T 2rrd_A 43 YFNIFNTVTLKKLAESLSSDPEVLLQIDGVTEDKLEKYGAEVISVLQKY 91 (101) T ss_dssp HHHHCCHHHHHHHHHHCCCCHHHHHTSTTCCHHHHHHTHHHHHHHHHHH T ss_pred CEEEECHHHHHHHHHHCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 5455779999999986859999982677879999999999999999999 No 63 >3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A* Probab=30.05 E-value=18 Score=15.38 Aligned_cols=17 Identities=12% Similarity=0.307 Sum_probs=6.4 Q ss_pred CCHHHHHCCCCCCHHHH Q ss_conf 49888861889886449 Q gi|254780237|r 287 RTEADMLRMANFGRKSL 303 (340) Q Consensus 287 ~s~~dLl~ikNfG~KSl 303 (340) .+.++|+++++.|+++. T Consensus 115 ~~~~~L~~LpGVG~~TA 131 (369) T 3fsp_A 115 DDPDEFSRLKGVGPYTV 131 (369) T ss_dssp CSHHHHHTSTTCCHHHH T ss_pred CCHHHHHHCCCHHHHHH T ss_conf 87999852422588999 No 64 >1vs1_A 3-deoxy-7-phosphoheptulonate synthase; (beta/alpha)8 barrel, transferase; HET: PEP; 2.30A {Aeropyrum pernix} Probab=29.03 E-value=26 Score=14.42 Aligned_cols=11 Identities=18% Similarity=0.338 Sum_probs=4.4 Q ss_pred HHHHHHHHCCC Q ss_conf 99999840114 Q gi|254780237|r 82 LTDIILNIKGI 92 (340) Q Consensus 82 V~eIiLNLK~I 92 (340) ..++..-+|++ T Consensus 54 ~~~~a~~~k~~ 64 (276) T 1vs1_A 54 VREAALAVKEA 64 (276) T ss_dssp HHHHHHHHHHH T ss_pred HHHHHHHHHHH T ss_conf 99999999984 No 65 >2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} SCOP: a.60.2.7 Probab=28.02 E-value=13 Score=16.33 Aligned_cols=24 Identities=21% Similarity=0.421 Sum_probs=16.3 Q ss_pred CCHHHHHCCCCCCHHHHHHHHHHH Q ss_conf 498888618898864499999999 Q gi|254780237|r 287 RTEADMLRMANFGRKSLVEIKGVL 310 (340) Q Consensus 287 ~s~~dLl~ikNfG~KSl~EI~~~L 310 (340) .|-+||.+++++|.+.++.|+..| T Consensus 50 ~s~~dL~~v~gi~~~~~~~i~~~l 73 (75) T 2duy_A 50 ARVEDLLKVKGIGPATLERLRPYL 73 (75) T ss_dssp SSGGGGGGSTTCCHHHHHHHGGGE T ss_pred CCHHHHHHCCCCCHHHHHHHHHHC T ss_conf 989999757898999999999772 No 66 >1wuu_A Galactokinase; galactosemia, GHMP superfamily, transferase; HET: GLA ANP; 2.50A {Homo sapiens} SCOP: d.14.1.5 d.58.26.7 Probab=27.93 E-value=27 Score=14.29 Aligned_cols=63 Identities=13% Similarity=0.149 Sum_probs=48.8 Q ss_pred HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 221011058889898839837188874498888618898864499999999980831267687 Q gi|254780237|r 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322 (340) Q Consensus 260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~ 322 (340) +.+.....++..+|+..+...+|+|+..+-+.|+..-+..--+|+.|.+...+.+=.+|-++- T Consensus 289 ~~e~~~~~~~~~al~~~d~~~lG~Lm~~~h~~L~~~lgVS~p~Ld~lv~~a~~~~Ga~gaKlt 351 (399) T 1wuu_A 289 VGEIRRTAQAAAALRRGDYRAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMT 351 (399) T ss_dssp HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTSCCCCHHHHHHHHHHHTSTTEEEEEEC T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEC T ss_conf 778888888998775389999999999999999986479979999999999874997398973 No 67 >1ow5_A Serine/threonine-protein kinase STE11; MAP kinase, MAPKKK, SAM domain, pointed domain, SCM domain, STE50 regulator, transferase; NMR {Saccharomyces cerevisiae} SCOP: a.60.1.2 PDB: 1x9x_A Probab=26.86 E-value=28 Score=14.17 Aligned_cols=53 Identities=11% Similarity=0.154 Sum_probs=36.8 Q ss_pred CCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCC--CCCCHHHHHHHHHHHHHH Q ss_conf 11221011058889898839837188874498888618--898864499999999980 Q gi|254780237|r 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM--ANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 258 ~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~i--kNfG~KSl~EI~~~L~~~ 313 (340) .=++++.|+ +-..++.++|+.+...|+..+++||..+ .++|.+ .-|...+..+ T Consensus 20 ~WL~~igL~-~Y~~~F~~~g~i~~~~L~~L~~~dL~~lGI~~~ghR--~rIl~ai~~L 74 (85) T 1ow5_A 20 LFLEEIGCT-QYLDSFIQCNLVTEEEIKYLDKDILIALGVNKIGDR--LKILRKSKSF 74 (85) T ss_dssp HHHHHHSCT-HHHHHHHHHTCCCHHHHHHCCHHHHHHHTCCCHHHH--HHHHHHHHHT T ss_pred HHHHHCCCH-HHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHH--HHHHHHHHHH T ss_conf 999998449-999999984887399967389999978599988999--9999999999 No 68 >3cqj_A L-ribulose-5-phosphate 3-epimerase ULAE; TIM-barrel, isomerase, phosphate-binding motif, structural genomics; 2.04A {Escherichia coli} PDB: 3cqi_A 3cqh_A 3cqk_A Probab=26.69 E-value=11 Score=16.92 Aligned_cols=49 Identities=12% Similarity=0.259 Sum_probs=29.1 Q ss_pred CEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHH Q ss_conf 3021243111144223577641168877621899999938961777999999999999888 Q gi|254780237|r 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229 (340) Q Consensus 169 g~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~ 229 (340) |.|+.+..|.-++..+|.. -+++|+|+.+.-.|.+++..|...|.+.+. T Consensus 239 G~id~~~~~~~L~~~gy~G------------~~~~E~~~~~~~~~~~~~~~~~~~l~~~l~ 287 (295) T 3cqj_A 239 GVVDFERCFETLKQSGYCG------------PYLIEMWSETAEDPAAEVAKARDWVKARMA 287 (295) T ss_dssp SSCCHHHHHHHHHHTTCCS------------CEEECCCGGGSSCHHHHHHHHHHHHHHHHH T ss_pred CCCCHHHHHHHHHHHCCCE------------EEEEEECCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 4619999999999969971------------799972687677999999999999999999 No 69 >3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} PDB: 3knt_A* Probab=25.51 E-value=30 Score=14.01 Aligned_cols=41 Identities=12% Similarity=0.130 Sum_probs=28.8 Q ss_pred HHHHHHHHHCCCCCHHHHH-------HCCHHHHHCCCCCCHHHHHHHH Q ss_conf 5888989883983718887-------4498888618898864499999 Q gi|254780237|r 267 VRSTNCLRGENIVYMGDLI-------QRTEADMLRMANFGRKSLVEIK 307 (340) Q Consensus 267 vRs~NcLk~a~I~tigdLv-------~~s~~dLl~ikNfG~KSl~EI~ 307 (340) .||.+....+.+....++. ..++++|+++|+.|+|+.+-+- T Consensus 95 ~KAk~I~~~a~~~~~~~l~~~~~~~~~~~~~~L~~l~GIG~ktA~~~L 142 (214) T 3fhf_A 95 KRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYKEASHFL 142 (214) T ss_dssp HHHHHHHHHGGGCCHHHHHHHSSSHHHHHHHHHHHSTTCCHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCHHHHHHHH T ss_conf 999999999999999888897399898739999748887699999999 No 70 >2kg5_A ARF-GAP, RHO-GAP domain, ANK repeat and PH domain-containing protein 3; SAM domain, helix bundle, cell membrane, cell projection, cytoplasm; NMR {Homo sapiens} Probab=24.10 E-value=31 Score=13.84 Aligned_cols=49 Identities=12% Similarity=0.178 Sum_probs=33.6 Q ss_pred HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 22101105888989883983718887449888861889886449999999998 Q gi|254780237|r 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340) Q Consensus 260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340) ++.++|+--+ ..+.+.+|.++.+|...+++||.+ +|-++.-..+..|.. T Consensus 33 L~~igL~~Y~-~~F~~~gi~~~~~l~~lt~~DL~~---lGI~~~ghrkkil~a 81 (100) T 2kg5_A 33 LATVHLEQYA-DTFRRHGLATAGAARGLGHEELKQ---LGISATGHRKRILRL 81 (100) T ss_dssp HGGGTCGGGH-HHHHHTTCCBHHHHTTCCHHHHHH---HTCCCHHHHHHHHHH T ss_pred HHHCCCHHHH-HHHHHCCCCCHHHHHHCCHHHHHH---CCCCCHHHHHHHHHH T ss_conf 9988429999-999996998399997777978998---599988999999999 No 71 >1npy_A Hypothetical shikimate 5-dehydrogenase-like protein HI0607; structural genomics, PSI, protein structure initiative; 1.75A {Haemophilus influenzae} SCOP: c.2.1.7 c.58.1.5 Probab=23.59 E-value=6.4 Score=18.30 Aligned_cols=15 Identities=33% Similarity=0.363 Sum_probs=9.2 Q ss_pred CCHHHHHHHHHHHHH Q ss_conf 756678889999987 Q gi|254780237|r 37 RGFAHTLGNALRRVL 51 (340) Q Consensus 37 ~G~g~TlGNaLRRvL 51 (340) ..++-|+=|+.=+-| T Consensus 17 ~s~sp~iHn~~f~~l 31 (271) T 1npy_A 17 SNFGTTFHNYLYDKL 31 (271) T ss_dssp CSHHHHHHHHHHHHH T ss_pred CCCCHHHHHHHHHHC T ss_conf 656999999999987 No 72 >1dxs_A P53-like transcription factor; P73 SAM-like domain, gene regulation, P53 P63 homologue, sterIle alpha motif, tumour supressor; 2.54A {Homo sapiens} SCOP: a.60.1.2 PDB: 1cok_A Probab=22.62 E-value=33 Score=13.66 Aligned_cols=50 Identities=12% Similarity=0.043 Sum_probs=34.1 Q ss_pred HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHC--CCCCCHHHHHHHHHHHHHH Q ss_conf 22101105888989883983718887449888861--8898864499999999980 Q gi|254780237|r 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR--MANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~--ikNfG~KSl~EI~~~L~~~ 313 (340) ++.|.|+ .=..++..+|+.++.+|...+++||.. |+ .|- -.-|-..+..+ T Consensus 13 L~~igL~-qY~~~F~~~g~~~~~~l~~lt~~dL~~lgI~-~gH--r~kIl~~i~~l 64 (80) T 1dxs_A 13 LTGLGCP-NCIEYFTSQGLQSIYHLQNLTIEDLGALKIP-EQY--RMTIWRGLQDL 64 (80) T ss_dssp HHHTTCT-TSHHHHHTTTCCCHHHHHTCCHHHHHHTTCC-TTT--HHHHHHHHHHC T ss_pred HHHCCHH-HHHHHHHHCCCCCHHHHHCCCHHHHHHCCCC-HHH--HHHHHHHHHHH T ss_conf 9888739-9999999848865688870599999771999-999--99999999999 No 73 >2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} Probab=22.59 E-value=34 Score=13.66 Aligned_cols=48 Identities=10% Similarity=0.151 Sum_probs=34.8 Q ss_pred CHHHCCCCHHHHHHHHH------CCCCCHHHHHHCCHHH----HHCCCCCCHHHHHHH Q ss_conf 12210110588898988------3983718887449888----861889886449999 Q gi|254780237|r 259 KVEELELSVRSTNCLRG------ENIVYMGDLIQRTEAD----MLRMANFGRKSLVEI 306 (340) Q Consensus 259 ~IeeLeLSvRs~NcLk~------a~I~tigdLv~~s~~d----Ll~ikNfG~KSl~EI 306 (340) .+-++.||-|...+++. .|...+..+...+.++ |+++|++|.++.+-+ T Consensus 97 ~Lr~~Gls~~K~~~i~~la~~~~~g~~~~~~l~~~~~~e~~~~L~~ikGIGpWTA~~i 154 (233) T 2h56_A 97 ALRQAGVSKRKIEYIRHVCEHVESGRLDFTELEGAEATTVIEKLTAIKGIGQWTAEMF 154 (233) T ss_dssp HHHHTTCCHHHHHHHHHHHHHHHTTSSCHHHHTTSCHHHHHHHHHTSTTCCHHHHHHH T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHH T ss_conf 9977799787899999999999817752001012688899999880688487899999 No 74 >2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Probab=21.60 E-value=35 Score=13.53 Aligned_cols=53 Identities=13% Similarity=0.219 Sum_probs=32.6 Q ss_pred HHCCHHHCCCC-HHHHHHHHHCCCC--CHHHHHHCCHHHHHCCCCCCHHHHHHHHH Q ss_conf 31112210110-5888989883983--71888744988886188988644999999 Q gi|254780237|r 256 LLKKVEELELS-VRSTNCLRGENIV--YMGDLIQRTEADMLRMANFGRKSLVEIKG 308 (340) Q Consensus 256 L~~~IeeLeLS-vRs~NcLk~a~I~--tigdLv~~s~~dLl~ikNfG~KSl~EI~~ 308 (340) +..-|.-+++. .|+.+-...+.+- .-+.-+..+.++|+++|+.|+|+..-|-- T Consensus 72 l~~~i~~~G~y~~Ka~~l~~~a~~i~~~~~g~~p~~~~~L~~LpGVG~kTA~~il~ 127 (211) T 2abk_A 72 VKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLN 127 (211) T ss_dssp HHHHHTTSTTHHHHHHHHHHHHHHHHHHTTTSCCSCHHHHHHSTTCCHHHHHHHHH T ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCHHHHHHHHH T ss_conf 99999862179999999999999999984899983299987178873699999999 No 75 >1ucv_A Ephrin type-A receptor 8; receptor oligomerization, developmental regulation, tyrosine kinase, riken structural genomics/proteomics initiative; NMR {Homo sapiens} SCOP: a.60.1.2 Probab=21.38 E-value=35 Score=13.50 Aligned_cols=35 Identities=9% Similarity=0.286 Sum_probs=27.9 Q ss_pred HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCC Q ss_conf 221011058889898839837188874498888618 Q gi|254780237|r 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295 (340) Q Consensus 260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~i 295 (340) ++.|.|+ +-..++.+.+|.+...|...+++||..+ T Consensus 14 L~~igL~-qY~~~F~~~g~~~~~~l~~lt~~dL~~l 48 (81) T 1ucv_A 14 LDSIRMG-RYRDHFAAGGYSSLGMVLRMNAQDVRAL 48 (81) T ss_dssp HHHTTCG-GGHHHHHHTTCCBHHHHTTCCHHHHHHH T ss_pred HHHCCCH-HHHHHHHHCCCCCHHHHHHCCHHHHHHC T ss_conf 9888689-9999999969998999976789999886 No 76 >1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Probab=21.37 E-value=35 Score=13.50 Aligned_cols=47 Identities=6% Similarity=0.191 Sum_probs=37.9 Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 1105888989883983718887449888861889886449999999998 Q gi|254780237|r 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340) Q Consensus 264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340) +.+...+-.|-+ .+.++.+|...|.+||..+.+ |.+....|.+.|.. T Consensus 25 GIg~k~~~~Ll~-~f~sl~~i~~AS~eeL~~v~G-~~~~Ak~i~~~lh~ 71 (84) T 1z00_B 25 GVNAKNCRSLMH-HVKNIAELAALSQDELTSILG-NAANAKQLYDFIHT 71 (84) T ss_dssp SCCHHHHHHHHH-HSSCHHHHHHSCHHHHHHHHS-CHHHHHHHHHHHTS T ss_pred CCCHHHHHHHHH-HCCCHHHHHHCCHHHHHHCCC-CHHHHHHHHHHHCC T ss_conf 999999999999-966999998599999988759-79999999999855 No 77 >1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A* Probab=21.25 E-value=33 Score=13.73 Aligned_cols=52 Identities=13% Similarity=0.245 Sum_probs=34.9 Q ss_pred HHCCHHHCCCC-HHHHHHHHHCCC--CCHHHHHHCCHHHHHCCCCCCHHHHHHHH Q ss_conf 31112210110-588898988398--37188874498888618898864499999 Q gi|254780237|r 256 LLKKVEELELS-VRSTNCLRGENI--VYMGDLIQRTEADMLRMANFGRKSLVEIK 307 (340) Q Consensus 256 L~~~IeeLeLS-vRs~NcLk~a~I--~tigdLv~~s~~dLl~ikNfG~KSl~EI~ 307 (340) +...|..+.+. .|+.|-.+.+.+ ..-+.-+..+.++|+++|+.|.|+..-|- T Consensus 76 l~~~i~~~g~y~~ka~~i~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~kTA~~il 130 (226) T 1orn_A 76 LEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVV 130 (226) T ss_dssp HHHHTGGGSSHHHHHHHHHHHHHHHHHHSTTSCCSCHHHHTTSTTCCHHHHHHHH T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCHHHHHHHH T ss_conf 9898874221999999999999999999299798789999748775367999999 No 78 >2hfs_A Mevalonate kinase, putative; GHMP kinase, trypanosomatid parasite, transferase; 1.75A {Leishmania major} PDB: 2hfu_A* Probab=21.00 E-value=36 Score=13.45 Aligned_cols=114 Identities=16% Similarity=0.216 Sum_probs=66.7 Q ss_pred EEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCC Q ss_conf 89999993896177799999999999988876224444322100000000011233311122101105888989883983 Q gi|254780237|r 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIV 279 (340) Q Consensus 200 kL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~ 279 (340) .-++=+||+.+.+-.+.+..-..........+.. +...+. +++.++..+|+...+. T Consensus 188 ~~l~l~~tg~~~~T~~~~~~~~~~~~~~~~~~~~----------------------~~~~i~--~i~~~~~~al~~~~~~ 243 (332) T 2hfs_A 188 LYLVVVGTGINASTAKVVNDVHKMKQQQPVQFKR----------------------LYDNYT--HIVSQAREALQKGDLQ 243 (332) T ss_dssp EEEEEEECSCCCCHHHHHHHHHHHHHHCHHHHHH----------------------HHHHHH--HHHHHHHHHHHHTCHH T ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHCHHHHHH----------------------HHHHHH--HHHHHHHHHHHHHHHH T ss_conf 4799981897622499997644555534277776----------------------666789--9999999877500045 Q ss_pred CHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCC--C---------CHHHHHHHHHHHHCC Q ss_conf 71888744988886188988644999999999808312676878--9---------867799999877503 Q gi|254780237|r 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD--W---------PPESIEELAKKYEDK 339 (340) Q Consensus 280 tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~--~---------~~~~~~~~~~~~~~~ 339 (340) .+++|+..+.+-|.++ +..-..++++.+...+.|- +|.++.+ | .++..+.+.+.++++ T Consensus 244 ~lg~lm~~~~~~l~~l-~vs~p~l~~l~~~a~~~Ga-lgaklsGaG~Gg~~ial~~~~~~~~~i~~~l~~~ 312 (332) T 2hfs_A 244 RLGQLMNANHDLCRQI-DVSCRELESIVQTCRTYGA-LGAKLSGTGRGGIAVALAASSDQRDAIVKGLKAK 312 (332) T ss_dssp HHHHHHHHHHHHHHHT-TCCCHHHHHHHHHHHHTTC-SEEEEESSCSSSEEEEEESSHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHCCC-CEEEECCCCCCCEEEEEECCHHHHHHHHHHHHHH T ss_conf 6789999999999853-8998899999999997899-4899927898664999987878899999999998 No 79 >2rhf_A DNA helicase RECQ; HRDC, D. radiodurans, ATP-binding, hydrolase, nucleotide-binding; HET: DNA; 1.10A {Deinococcus radiodurans R1} Probab=20.99 E-value=21 Score=14.92 Aligned_cols=37 Identities=14% Similarity=0.214 Sum_probs=26.6 Q ss_pred HHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHH Q ss_conf 8898988398371888744988886188988644999 Q gi|254780237|r 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305 (340) Q Consensus 269 s~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~E 305 (340) .|..+.+.-+.-+....-.|.++|+.|+++|.+-++. T Consensus 26 ~~~I~~d~~L~~ia~~~P~t~~eL~~I~Gig~~k~~~ 62 (77) T 2rhf_A 26 AFVVFTNATLEALAARQPRTLAELAEVPGLGEKRIEA 62 (77) T ss_dssp HHHHCCHHHHHHHHHHCCCSHHHHTTSTTTCHHHHHH T ss_pred CEEEECHHHHHHHHHHCCCCHHHHHCCCCCCHHHHHH T ss_conf 6565789999999983978999980799979999999 No 80 >1pie_A Galactokinase; galactose, galactosemia, transferase; HET: GLA; 2.10A {Lactococcus lactis} SCOP: d.14.1.5 d.58.26.7 Probab=20.36 E-value=37 Score=13.36 Aligned_cols=61 Identities=13% Similarity=0.134 Sum_probs=46.5 Q ss_pred HHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 2101105888989883983718887449888861889886449999999998083126768 Q gi|254780237|r 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321 (340) Q Consensus 261 eeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l 321 (340) .+-....+...+|++.++..+|+|+..+...|...-+..-..|+++.+.....+=.+|-++ T Consensus 305 ~e~~rv~~~~~al~~~d~~~lG~Lm~esh~sL~~~~~vS~peLd~lv~~a~~~~Ga~GaKl 365 (419) T 1pie_A 305 YENNRTKIAQKAFVAGNLTKFGELLNASHASLKDDYEVTGLELDTLAETAQKQAGVLGARM 365 (419) T ss_dssp HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTSCCCCHHHHHHHHHHHHSTTEEEEEE T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEE T ss_conf 6889999999875327788899999999999999757997999999999998489579897 No 81 >2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7 Probab=20.28 E-value=37 Score=13.35 Aligned_cols=54 Identities=19% Similarity=0.166 Sum_probs=39.0 Q ss_pred HHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC----CCCCCCCHHHHHHHHHHH Q ss_conf 887449888861889886449999999998083126----768789867799999877 Q gi|254780237|r 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG----MNLPDWPPESIEELAKKY 336 (340) Q Consensus 283 dLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg----~~l~~~~~~~~~~~~~~~ 336 (340) +|=.-+.++|+.++++|.+-...|.+.-...|-.-. ++++++.+..++.+.+.+ T Consensus 33 ~iNtAs~~eL~~lpgIg~~~A~~Iv~~R~~~G~f~sledL~~v~Gi~~k~~eki~k~~ 90 (98) T 2edu_A 33 LLNEGSARDLRSLQRIGPKKAQLIVGWRELHGPFSQVEDLERVEGITGKQMESFLKAN 90 (98) T ss_dssp HHHHSCHHHHHHSTTCCHHHHHHHHHHHHHHCCCSSGGGGGGSTTCCHHHHHHHHHHH T ss_pred CCCCCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHCC T ss_conf 0437899999647998999999999999985992889998448998999999999838 No 82 >2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Probab=20.23 E-value=37 Score=13.35 Aligned_cols=11 Identities=9% Similarity=0.156 Sum_probs=4.0 Q ss_pred CHHHHHHHHHH Q ss_conf 56678889999 Q gi|254780237|r 38 GFAHTLGNALR 48 (340) Q Consensus 38 G~g~TlGNaLR 48 (340) |.|-.+..-+. T Consensus 68 gIG~~i~~kI~ 78 (360) T 2ihm_A 68 YFGEHSTRVIQ 78 (360) T ss_dssp TCCHHHHHHHH T ss_pred CCCHHHHHHHH T ss_conf 98789999999 Done!