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 33803 Date Mon May 23 23:39:47 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780237.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >2a6h_A DNA-directed RNA polym 100.0 0 0 394.1 12.0 181 13-318 7-189 (190) 2 >3iyd_A DNA-directed RNA polym 100.0 1.4E-45 0 315.4 2.2 128 53-180 1-132 (132) 3 >1bdf_A RNA polymerase alpha s 100.0 8.4E-43 0 297.0 13.1 124 55-178 1-128 (128) 4 >2a6h_A DNA-directed RNA polym 100.0 4.7E-42 0 292.1 10.5 123 55-178 1-125 (125) 5 >3iyd_A DNA-directed RNA polym 100.0 7.5E-34 2.2E-38 239.0 4.5 109 2-241 1-109 (114) 6 >1bdf_A RNA polymerase alpha s 100.0 9.2E-32 2.7E-36 225.5 10.9 107 2-235 1-107 (107) 7 >1lb2_B DNA-directed RNA polym 99.9 2.3E-24 6.9E-29 177.5 7.9 81 251-331 3-83 (84) 8 >1coo_A RNA polymerase alpha s 99.9 9.8E-25 2.9E-29 180.0 5.0 85 246-330 12-96 (98) 9 >1z3e_B DNA-directed RNA polym 99.9 7.3E-22 2.2E-26 161.4 7.6 71 251-321 2-72 (73) 10 >3gfk_B DNA-directed RNA polym 99.8 1.3E-21 3.9E-26 159.7 6.5 74 247-320 5-78 (79) 11 >2pa8_D DNA-directed RNA polym 96.6 0.0052 1.5E-07 39.3 5.9 55 100-154 57-115 (118) 12 >1wcn_A Transcription elongati 95.7 0.024 7.2E-07 35.0 5.5 51 264-314 14-64 (70) 13 >1b22_A DNA repair protein RAD 95.5 0.015 4.5E-07 36.3 3.9 58 256-313 23-81 (114) 14 >1twf_C B44.5, DNA-directed RN 95.2 0.088 2.6E-06 31.3 7.1 123 19-233 9-132 (190) 15 >1twf_K B13.6, DNA-directed RN 95.1 0.088 2.6E-06 31.4 6.7 48 180-233 56-103 (120) 16 >1twf_C B44.5, DNA-directed RN 94.9 0.062 1.8E-06 32.4 5.4 55 101-155 56-125 (128) 17 >2pa8_L DNA-directed RNA polym 94.7 0.1 3E-06 31.0 6.2 48 180-233 38-85 (92) 18 >1twf_C B44.5, DNA-directed RN 94.5 0.087 2.6E-06 31.4 5.4 16 176-191 41-56 (190) 19 >1twf_K B13.6, DNA-directed RN 94.4 0.12 3.4E-06 30.6 5.9 54 6-65 7-63 (120) 20 >3h0g_K DNA-directed RNA polym 94.2 0.077 2.3E-06 31.7 4.7 48 180-233 55-102 (123) 21 >2pa8_L DNA-directed RNA polym 93.7 0.092 2.7E-06 31.2 4.3 41 20-65 5-45 (92) 22 >1xpp_A TA1416, DNA-directed R 93.6 0.11 3.4E-06 30.6 4.6 31 200-231 62-92 (115) 23 >3h0g_C DNA-directed RNA polym 93.6 0.071 2.1E-06 32.0 3.5 36 198-233 94-129 (165) 24 >3h0g_C DNA-directed RNA polym 93.6 0.086 2.6E-06 31.4 4.0 55 101-155 62-128 (132) 25 >3h0g_K DNA-directed RNA polym 92.8 0.14 4.1E-06 30.1 3.9 44 6-54 7-52 (123) 26 >3h0g_C DNA-directed RNA polym 92.7 0.1 3E-06 30.9 3.2 38 19-60 8-45 (165) 27 >1pzn_A RAD51, DNA repair and 92.0 0.27 7.9E-06 28.3 4.6 48 266-313 44-91 (95) 28 >2aq4_A DNA repair protein REV 84.0 0.83 2.5E-05 25.1 2.8 48 258-307 2-53 (67) 29 >1feu_A 50S ribosomal protein 82.9 1 3.1E-05 24.4 2.9 53 88-140 27-84 (113) 30 >1jx4_A DNA polymerase IV (fam 80.6 0.95 2.8E-05 24.7 2.0 40 267-308 6-45 (55) 31 >3c1y_A DNA integrity scanning 79.4 2.7 8.1E-05 21.7 4.1 44 269-313 24-67 (74) 32 >1u9l_A Transcription elongati 79.1 4.6 0.00013 20.3 6.2 59 255-313 4-62 (70) 33 >1t94_A Polymerase (DNA direct 78.0 2.6 7.7E-05 21.8 3.6 53 255-310 9-62 (70) 34 >1z00_A DNA excision repair pr 76.5 3.9 0.00012 20.7 4.2 44 269-313 31-74 (89) 35 >2zjr_S 50S ribosomal protein 72.7 1.6 4.6E-05 23.3 1.4 54 89-142 26-85 (146) 36 >1kft_A UVRC, excinuclease ABC 71.8 3.5 0.0001 21.0 3.0 34 278-311 44-77 (78) 37 >3bzc_A TEX; helix-turn-helix, 66.2 9.1 0.00027 18.3 4.9 50 285-335 5-59 (70) 38 >2pa8_D DNA-directed RNA polym 59.6 12 0.00036 17.5 7.6 48 173-229 34-81 (92) 39 >2cz9_A Probable galactokinase 53.2 15 0.00045 16.9 8.2 112 204-315 6-117 (165) 40 >1pie_A Galactokinase; galacto 52.3 16 0.00047 16.8 4.5 64 259-322 71-134 (177) 41 >3bqs_A Uncharacterized protei 52.1 16 0.00047 16.7 5.8 74 259-338 5-84 (93) 42 >2ztd_A Holliday junction ATP- 46.0 20 0.00058 16.1 3.4 45 269-313 22-67 (75) 43 >2kp7_A Crossover junction end 44.7 21 0.00061 16.0 3.0 43 268-316 42-84 (87) 44 >1szp_A DNA repair protein RAD 44.0 21 0.00062 15.9 4.1 40 279-321 1-40 (56) 45 >2kg5_A ARF-GAP, RHO-GAP domai 37.6 25 0.00074 15.5 2.5 40 260-300 33-74 (100) 46 >1eu8_A Trehalose/maltose bind 35.9 28 0.00083 15.1 2.9 21 208-228 83-103 (107) 47 >1ixr_A Holliday junction DNA 32.8 32 0.00093 14.8 4.6 45 269-313 85-130 (191) 48 >2w9m_A Polymerase X; SAXS, DN 32.1 32 0.00096 14.7 2.8 36 280-315 2-38 (123) 49 >3bz1_U Photosystem II 12 kDa 31.7 32 0.00094 14.8 2.3 39 267-313 44-82 (104) 50 >3hil_A Ephrin type-A receptor 31.6 33 0.00097 14.7 3.2 39 260-299 30-70 (82) 51 >2nrt_A Uvrabc system protein 30.8 21 0.00062 16.0 1.2 33 277-310 31-63 (64) 52 >2gha_A Maltose ABC transporte 29.9 35 0.001 14.5 2.9 43 169-230 49-91 (98) 53 >2gru_A 2-deoxy-scyllo-inosose 29.5 22 0.00064 15.9 1.1 19 299-317 111-129 (195) 54 >1s5l_U Photosystem II 12 kDa 27.4 39 0.0012 14.2 2.6 39 267-313 27-65 (87) 55 >1vdd_A Recombination protein 26.9 40 0.0012 14.2 4.3 38 290-338 12-49 (66) 56 >3dm0_A Maltose-binding peripl 26.6 36 0.0011 14.5 1.8 19 207-225 66-84 (86) 57 >1cuk_A RUVA protein; DNA repa 26.2 41 0.0012 14.1 4.2 45 269-313 21-66 (79) 58 >2w9m_A Polymerase X; SAXS, DN 25.8 14 0.00042 17.1 -0.4 27 286-312 53-79 (118) 59 >2fmp_A DNA polymerase beta; n 24.6 44 0.0013 13.9 3.6 32 286-317 53-84 (119) 60 >2vqe_M 30S ribosomal protein 24.1 45 0.0013 13.8 3.4 48 289-339 16-63 (64) 61 >3bq0_A POL IV, DBH, DNA polym 24.1 30 0.00088 15.0 1.0 27 270-296 8-34 (51) 62 >2rkh_A Putative APHA-like tra 23.7 42 0.0013 14.0 1.7 21 205-225 2-22 (99) 63 >3i0w_A 8-oxoguanine-DNA-glyco 23.6 45 0.0013 13.8 2.8 26 281-306 20-49 (58) 64 >3bbo_O Ribosomal protein L16; 23.2 46 0.0014 13.7 1.9 26 199-224 100-125 (135) 65 >1wuu_A Galactokinase; galacto 23.1 47 0.0014 13.7 5.0 80 259-338 66-155 (167) 66 >3clh_A 3-dehydroquinate synth 23.0 34 0.001 14.6 1.1 13 38-50 68-80 (183) 67 >2uyg_A 3-dehydroquinate dehyd 22.7 47 0.0014 13.7 2.2 23 299-321 22-44 (149) 68 >2p6r_A Afuhel308 helicase; pr 22.6 48 0.0014 13.7 2.1 43 267-313 9-51 (68) 69 >3i1n_M 50S ribosomal protein 22.5 48 0.0014 13.6 2.6 26 199-224 99-124 (136) 70 >2duy_A Competence protein com 22.2 47 0.0014 13.7 1.7 20 289-308 52-71 (75) 71 >3k17_A LIN0012 protein; prote 21.5 50 0.0015 13.5 2.3 79 260-338 38-131 (140) 72 >1ujn_A Dehydroquinate synthas 21.3 38 0.0011 14.3 1.1 22 260-281 105-126 (188) 73 >1gtd_A MTH169; synthetase, FG 21.2 49 0.0015 13.6 1.7 48 174-229 21-68 (85) 74 >1qme_A Penicillin-binding pro 20.9 34 0.001 14.6 0.8 33 287-319 4-36 (71) 75 >2abk_A Endonuclease III; DNA- 20.3 53 0.0016 13.4 2.4 52 256-307 50-104 (111) No 1 >>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (A:1-47,A:173-315) Probab=100.00 E-value=0 Score=394.12 Aligned_cols=181 Identities=34% Similarity=0.467 Sum_probs=162.6 Q ss_pred CCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCC Q ss_conf 42015863678881589999616975667888999998741698306889998871443146646244499999840114 Q gi|254780237|r 13 NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92 (340) Q Consensus 13 ~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I 92 (340) ..++. ..++.+++||+|+++||+||||+|||||||||||| T Consensus 7 ~~~e~-~~~~~~~~yg~f~~~Ple~G~g~TiGN~lRR~LLs--------------------------------------- 46 (190) T 2a6h_A 7 KAPVF-TVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLS--------------------------------------- 46 (190) T ss_dssp SCCEE-EEEEETTTEEEEEEEEECTTCHHHHHHHHHHHHHH--------------------------------------- T ss_pred CCCEE-EEEECCCCEEEEEEECCCCCCHHHHHHHHHHHHHH--------------------------------------- T ss_conf 89567-88756885689999568896175778899999885--------------------------------------- Q ss_pred EEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEEC Q ss_conf 17772798279999994471699633513898599888808999778964999999746876320344446557543021 Q gi|254780237|r 93 NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172 (340) Q Consensus 93 ~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~ 172 (340) T Consensus 47 -------------------------------------------------------------------------------- 46 (190) T 2a6h_A 47 -------------------------------------------------------------------------------- 46 (190) T ss_dssp -------------------------------------------------------------------------------- T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred CCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC--HHHCCCC Q ss_conf 24311114422357764116887762189999993896177799999999999988876224444322100--0000000 Q gi|254780237|r 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE--DINVKSL 250 (340) Q Consensus 173 iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~--~~~~~~~ 250 (340) |||++|||.|+++|||+.++||||+|||||||||+|++|+++||++|++||.+|.++......... ....+.. T Consensus 47 -----sPV~kVnY~Ve~~~v~~~~~~ekL~leI~TdGsItP~eAl~~Aa~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 121 (190) T 2a6h_A 47 -----SPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPP 121 (190) T ss_dssp -----TCEEEEEEEEEECCBTTBCCCEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHTTCSCC----------------- T ss_pred -----CHHHHEEEEEEEEECCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC T ss_conf -----611104457888521777766610599954886452335999999999888763353212223442111111221 Q ss_pred HHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 11233311122101105888989883983718887449888861889886449999999998083126 Q gi|254780237|r 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318 (340) Q Consensus 251 ~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg 318 (340) ..+..+.++|++|+||+|++||||+|||+|||||+++|++||++++|||+||++||+++|+++||+|. T Consensus 122 ~~~~~~~~~IeeL~Ls~R~~n~Lk~a~I~ti~dL~~~s~~dL~~i~n~G~ksl~EI~~~L~~~gl~L~ 189 (190) T 2a6h_A 122 EQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLK 189 (190) T ss_dssp -------------------------------------------------------------------- T ss_pred CHHHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHCCCCCC T ss_conf 01354268599905878888678775894799988499999845999760559999999998599888 No 2 >>3iyd_A DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} (A:49-180) Probab=100.00 E-value=1.4e-45 Score=315.44 Aligned_cols=128 Identities=45% Similarity=0.813 Sum_probs=123.8 Q ss_pred CCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCE Q ss_conf 16983068899988714431466462444999998401141777279827999999447169963351389859988880 Q gi|254780237|r 53 SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132 (340) Q Consensus 53 ssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~ 132 (340) ||++|+|||+|||+||.|||++||||+|||++|+||||+|+|++.++++++++++++||++|||+||++|++++|+|||| T Consensus 1 Ssi~G~aIt~vkI~gv~HEfsti~GV~Edv~eIiLNLK~i~~k~~~~~~~~~~l~~~Gp~~VtA~di~~p~~ieivnpd~ 80 (132) T 3iyd_A 1 SSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQH 80 (132) T ss_dssp SSCCCCEEEECCCSSCCSSSSCCTTBSSCTTHHHHGGGTCCEEESSCSCEECCBCEESSSCCCGGGBCCCTTEEESCTTC T ss_pred HCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCEEEECCCCCEEEEEEECCCCCEEECCCCCCCCEEEECCCE T ss_conf 66984589999999954430238770452999998557550665268851799960686666822676788889926988 Q ss_pred EEEEEC-CCCEEEEEEEEECCCCCEECCCCC---CCCCCCCEECCCCCHHEE Q ss_conf 899977-896499999974687632034444---655754302124311114 Q gi|254780237|r 133 VICNLD-VDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPI 180 (340) Q Consensus 133 ~IaTl~-~~~~l~iel~ie~G~GY~~~e~~~---~~~~~ig~i~iDa~FsPV 180 (340) |||||+ +++.|+|+++|++||||++++.++ .+..++|+|++||+|||| T Consensus 81 ~Iatl~~~~~~l~~el~i~~G~GY~~~~~~~~~~~~~~~~g~i~iDa~fsPV 132 (132) T 3iyd_A 81 VICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV 132 (132) T ss_dssp CCCCBCSTTCEECCCCEEECCSSCCCHHHHC-----CCSSSCSBCCCCCCSC T ss_pred EEEEECCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE T ss_conf 8999757894799999998056602142244553334657733257766776 No 3 >>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} (A:51-178) Probab=100.00 E-value=8.4e-43 Score=296.98 Aligned_cols=124 Identities=44% Similarity=0.799 Sum_probs=119.4 Q ss_pred CCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEE Q ss_conf 98306889998871443146646244499999840114177727982799999944716996335138985998888089 Q gi|254780237|r 55 LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134 (340) Q Consensus 55 i~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~I 134 (340) ++|+|||+|||+|+.|||++||||+|||++|+||||+|+|++++++++.+++.++||++|||+||++|+++||+|||||| T Consensus 1 i~G~aI~~vkI~Gv~HEfs~i~GV~EDv~eIilNLK~i~~~~~~~~~~~~~l~~~gp~~VtA~di~~p~~veIvnpd~~I 80 (128) T 1bdf_A 1 MPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVI 80 (128) T ss_dssp CCCEEEEEEEETTCCSTTCCCTTBSSCHHHHHHHHHTCCEECSSCSEEEEEEEEESSEEEEGGGBCCCSSCEESCTTCEE T ss_pred CCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCEEEECCCCCCEEEEECCCCCCEEECCCCCCCCEEEECCCEEE T ss_conf 97639999962787664320653667699999971765367427886069994388741895166688988992698789 Q ss_pred EEEC-CCCEEEEEEEEECCCCCEECCCCC---CCCCCCCEECCCCCHH Q ss_conf 9977-896499999974687632034444---6557543021243111 Q gi|254780237|r 135 CNLD-VDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178 (340) Q Consensus 135 aTl~-~~~~l~iel~ie~G~GY~~~e~~~---~~~~~ig~i~iDa~Fs 178 (340) |||+ +++.|+|+++|++||||+++++++ .+..++|+||+||+|| T Consensus 81 aTl~~~~~~l~~el~i~~GrGYv~ae~~~~~~~~~~~ig~i~iDa~fS 128 (128) T 1bdf_A 81 CHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYS 128 (128) T ss_dssp EEECSTTCEEEEEEEEEECCSEECGGGTC-----CCCCSCCBCCEECC T ss_pred EEECCCCCEEEEEEEEECCCCEECCCCCCCCCCCCCCCCCEECCCCCC T ss_conf 997578947999999974555130432334432246667250464566 No 4 >>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (A:48-172) Probab=100.00 E-value=4.7e-42 Score=292.11 Aligned_cols=123 Identities=40% Similarity=0.673 Sum_probs=117.1 Q ss_pred CCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCC--CCEEEEEEEECCEEEEEEEEECCCCEEEECCCE Q ss_conf 983068899988714431466462444999998401141777279--827999999447169963351389859988880 Q gi|254780237|r 55 LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132 (340) Q Consensus 55 i~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~--~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~ 132 (340) ++|+|||+|||+|+.|||++||||+|||++|+||||+|+|+.+.+ ++.+++++++||++|||+||++|++++|+|||| T Consensus 1 l~G~AIt~vkI~Gv~hEf~~i~GV~EDv~eIilNLK~i~~~~~~~~~~~~~~~l~~~Gp~~vtA~di~~p~~ieivNp~~ 80 (125) T 2a6h_A 1 IPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDL 80 (125) T ss_dssp CEEEEEEEEEESSCCSTTCBCTTBSSBHHHHHHHHHTCCEEECSTTCSBCCEEEEEESSCEEEGGGSCCCTTEEESCTTC T ss_pred CCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHCEEEEECCCCCCEEEEEEECCCCEEEEECCCCCCCCEEEECCCE T ss_conf 98538999999994343020898521699999853051899615886249999943898279802356888589976988 Q ss_pred EEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEECCCCCHH Q ss_conf 8999778964999999746876320344446557543021243111 Q gi|254780237|r 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178 (340) Q Consensus 133 ~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~iDa~Fs 178 (340) |||||++++.|+|+++|++||||+++++++.. .++|+|++||+|| T Consensus 81 ~Iatl~~~~~l~~el~i~~GrGYv~a~~~~~~-~~~g~i~iDa~fS 125 (125) T 2a6h_A 81 HIATLEEGGRLNMEVRVDRGVGYVPAEKHGIK-DRINAIPVDAVFS 125 (125) T ss_dssp EEEEBCSSCEEEEEEEEEEEESEECHHHHCCC-SSTTCEECCEECC T ss_pred EEEEECCCCEEEEEEEEECCEEEEEECCCCCC-CCCCCCCCCCCCH T ss_conf 89995568628899997058012220103674-5577654464430 No 5 >>3iyd_A DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} (A:1-48,A:181-246) Probab=100.00 E-value=7.5e-34 Score=239.03 Aligned_cols=109 Identities=38% Similarity=0.674 Sum_probs=101.1 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~~~m~~~~~p~~~~---~~~~~~~~g~f~~ePLerG~g~TlGNaLRRvLL----------------------------- 48 (114) T 3iyd_A 1 MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILL----------------------------- 48 (114) T ss_dssp -CCCSCCSCCCCEEE---CCCSSSSEECCEESCBCTTHHHHHHHTTTTSSS----------------------------- T ss_pred CCCHHHHHCCCCEEE---EECCCCCEEEEEEECCCCCCHHHHHHHHHHHHH----------------------------- T ss_conf 960466623896778---722788678999966899617677889999998----------------------------- Q ss_pred HHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCC Q ss_conf 99999840114177727982799999944716996335138985998888089997789649999997468763203444 Q gi|254780237|r 82 LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161 (340) Q Consensus 82 V~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~ 161 (340) T Consensus 49 -------------------------------------------------------------------------------- 48 (114) T 3iyd_A 49 -------------------------------------------------------------------------------- 48 (114) T ss_dssp -------------------------------------------------------------------------------- T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred CCCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 46557543021243111144223577641168877621899999938961777999999999999888762244443221 Q gi|254780237|r 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241 (340) Q Consensus 162 ~~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~ 241 (340) +||||.||++|||++++||||+|||||||||+|++|+++||+||++||.+|.++++..... T Consensus 49 -------------------kkVnY~VE~~rv~~~~~~erLileI~TnGsI~P~dAl~~Aa~iL~~~f~~f~~~~~~~e~~ 109 (114) T 3iyd_A 49 -------------------ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPE 109 (114) T ss_dssp -------------------SCEEECCCBCCCSSCSCCBCCCEEEECCSSSCHHHHHHHHHHHHHHTTTTTTTCCCCCCCC T ss_pred -------------------EEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf -------------------8898889860334667544237998316750336337899999999999754002221102 No 6 >>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} (A:1-50,A:179-235) Probab=99.97 E-value=9.2e-32 Score=225.51 Aligned_cols=107 Identities=40% Similarity=0.697 Sum_probs=100.0 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~~~~~~~~~~~~~~~---~~~~~~~~~f~~~Ple~g~g~TlGNaLRRvLLs---------------------------- 49 (107) T 1bdf_A 1 MQGSVTEFLKPRLVDI---EQVSSTHAKVTLEPLERGFGHTLGNALRAILLS---------------------------- 49 (107) T ss_dssp -CCCSSCSCCCCEEEE---EESSSSEEEEEEEEEETTHHHHHHHHHHHHHTT---------------------------- T ss_pred CCHHHHHHCCCCEEEE---CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHH---------------------------- T ss_conf 9605667218857786---257885789999578996353678899999886---------------------------- Q ss_pred HHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCC Q ss_conf 99999840114177727982799999944716996335138985998888089997789649999997468763203444 Q gi|254780237|r 82 LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161 (340) Q Consensus 82 V~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~ 161 (340) T Consensus 50 -------------------------------------------------------------------------------- 49 (107) T 1bdf_A 50 -------------------------------------------------------------------------------- 49 (107) T ss_dssp -------------------------------------------------------------------------------- T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred CCCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 46557543021243111144223577641168877621899999938961777999999999999888762244 Q gi|254780237|r 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235 (340) Q Consensus 162 ~~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~ 235 (340) |||++|+|.|+++++|+.++||+|+|||||||||+|+||+.+||++|++||.+|.+++ T Consensus 50 ----------------sPV~~v~Y~Ve~~~~~~~~~~ekL~leI~TdGsI~P~eAl~~Aa~iL~~~~~~~~~~n 107 (107) T 1bdf_A 50 ----------------SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLR 107 (107) T ss_dssp ----------------SSEEEEEEECCBCCCSSCSSEEEEEEEEEECSSSCHHHHHHHHHHHHHHHGGGGC--- T ss_pred ----------------CCEEEEEECCEEECCCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC T ss_conf ----------------4434235110420247898606999999979989999999999999999999875479 No 7 >>1lb2_B DNA-directed RNA polymerase alpha chain; protein-DNA complex, gene-regulatory, gene regulation/DNA complex; HET: CMP; 3.10A {Escherichia coli} (B:) Probab=99.91 E-value=2.3e-24 Score=177.54 Aligned_cols=81 Identities=57% Similarity=1.030 Sum_probs=77.7 Q ss_pred HHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHH Q ss_conf 11233311122101105888989883983718887449888861889886449999999998083126768789867799 Q gi|254780237|r 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330 (340) Q Consensus 251 ~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~ 330 (340) ..+..+.++|++|+||+|++|||+++||+|||||+++|++||++++|||+||++||+++|+++|++|||++++|+|..++ T Consensus 3 ~~~~~l~~~I~~L~Ls~R~~n~L~~agI~ti~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~~~gl~lg~~~~~~~~~~~e 82 (84) T 1lb2_B 3 EFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIA 82 (84) T ss_dssp --CCTTTSBGGGGCCCHHHHHHHHHTTCCBHHHHHTCCHHHHHHSTTCCHHHHHHHHHHHHHTTCCSSCCCSCC------ T ss_pred CCCHHHCCCHHHHCCCHHHHHHHHHHCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC T ss_conf 53678629798707889999999891894699987289999974889878899999999998598789989998921223 Q ss_pred H Q ss_conf 9 Q gi|254780237|r 331 E 331 (340) Q Consensus 331 ~ 331 (340) + T Consensus 83 ~ 83 (84) T 1lb2_B 83 D 83 (84) T ss_dssp - T ss_pred C T ss_conf 4 No 8 >>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} (A:) Probab=99.90 E-value=9.8e-25 Score=179.98 Aligned_cols=85 Identities=54% Similarity=0.963 Sum_probs=78.5 Q ss_pred HCCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 00000112333111221011058889898839837188874498888618898864499999999980831267687898 Q gi|254780237|r 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325 (340) Q Consensus 246 ~~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~ 325 (340) .....+..+.+.++|++|+||+|++|||+++||+|||||+++|++||+++||||+||++||+++|+++|++|||++++|+ T Consensus 12 ~~~~~~~~~~l~~~I~~L~Ls~Rs~N~Lk~~gI~ti~dL~~~s~~dLl~i~n~G~kSl~Ei~~~L~~~gl~lg~~~~~~~ 91 (98) T 1coo_A 12 KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWP 91 (98) T ss_dssp ------CCHHHHSBGGGGTCCTTTHHHHHTTTCCBHHHHHTSCHHHHTTSTTCCHHHHHHHHHHHHHTTCCTTCCCSSSS T ss_pred CCCCCCHHHHHHCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCC T ss_conf 33330034674094998268899998999939975999985899999867798787899999999982867688789999 Q ss_pred HHHHH Q ss_conf 67799 Q gi|254780237|r 326 PESIE 330 (340) Q Consensus 326 ~~~~~ 330 (340) +..++ T Consensus 92 ~~~~~ 96 (98) T 1coo_A 92 PASIA 96 (98) T ss_dssp CSTTC T ss_pred CCCCC T ss_conf 74555 No 9 >>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} (B:) Probab=99.86 E-value=7.3e-22 Score=161.39 Aligned_cols=71 Identities=42% Similarity=0.589 Sum_probs=67.7 Q ss_pred HHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 11233311122101105888989883983718887449888861889886449999999998083126768 Q gi|254780237|r 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321 (340) Q Consensus 251 ~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l 321 (340) +.++.+.++|++|+||+|++|||+++||+|||||+++|++||+++||||+||++||+++|+++|++|||+- T Consensus 2 ~~~~~l~~~I~~L~Ls~R~~N~L~~~gI~ti~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~~~gl~l~~~~ 72 (73) T 1z3e_B 2 EKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKDD 72 (73) T ss_dssp -CHHHHTCBGGGSCCBHHHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHHTTCCCC--- T ss_pred CCHHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCC T ss_conf 50566268898835889999999883894799998779999975889766059999999998599889999 No 10 >>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} (B:) Probab=99.85 E-value=1.3e-21 Score=159.70 Aligned_cols=74 Identities=41% Similarity=0.565 Sum_probs=69.6 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~nlG~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 31015679864949984688999999989189679999878999998578986736999999999859989999 No 11 >>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 (D:36-153) Probab=96.62 E-value=0.0052 Score=39.31 Aligned_cols=55 Identities=18% Similarity=0.291 Sum_probs=50.6 Q ss_pred CCEEEEEEEECCE---EEEEEEEEC-CCCEEEECCCEEEEEECCCCEEEEEEEEECCCC Q ss_conf 8279999994471---699633513-898599888808999778964999999746876 Q gi|254780237|r 100 SHKRVTIFKRGPG---VVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154 (340) Q Consensus 100 ~~~~~~l~~~Gp~---~vtA~Di~~-p~~veivNpd~~IaTl~~~~~l~iel~ie~G~G 154 (340) .....+|++++|. .|+++|+++ ++.+.-++++-.|+.|..+-.++++....+|.| T Consensus 57 c~v~~~L~v~~~~~~~~VyS~dL~~~~~~v~pv~~~I~I~KL~~gQ~i~l~~~a~kGiG 115 (118) T 2pa8_D 57 CYTKIYIEAEAPNEPRMIYSKDIKSEDPSVVPISGDIPIVLLGTNQKISLEARLRLGYG 115 (118) T ss_dssp TEEEEEEEEECCSSCEEEEGGGCEESSTTCCBSCSCCEEEEECTTCEEEEEEEEEEECT T ss_pred EEEEEEEEEECCCCCCEEEHHHCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEEECCC T ss_conf 48999999884899847984452036997312148806999179956999999995820 No 12 >>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B (A:) Probab=95.70 E-value=0.024 Score=34.96 Aligned_cols=51 Identities=8% Similarity=0.062 Sum_probs=46.7 Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHC Q ss_conf 110588898988398371888744988886188988644999999999808 Q gi|254780237|r 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314 (340) Q Consensus 264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~g 314 (340) .++....+-|..+||+|+.||...+.++|..++++|++..+.|.....+.| T Consensus 14 Gig~~~a~~L~~aGi~TvedLa~a~~~eL~~i~Gi~~~~A~~ii~~Ar~~~ 64 (70) T 1wcn_A 14 GVDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMAARNIC 64 (70) T ss_dssp TCCHHHHHHHHTTTCCSHHHHHTSCHHHHHTSSSCCHHHHHHHHHHHHHHH T ss_pred CCCHHHHHHHHHCCCCCHHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHHCC T ss_conf 989999999999699759999872999997651799999999999998655 No 13 >>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; NMR {Homo sapiens} (A:) Probab=95.52 E-value=0.015 Score=36.29 Aligned_cols=58 Identities=5% Similarity=0.041 Sum_probs=49.7 Q ss_pred HHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 31112210-11058889898839837188874498888618898864499999999980 Q gi|254780237|r 256 LLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 256 L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) ...++.++ +...+...-|+.+||+|++||...+.++|.++.+||.+....|.+....+ T Consensus 23 ~~~~l~~i~GVG~~~~~~L~~~Gi~Tv~~la~~~~~~L~~i~G~~~~~a~~i~~~ar~~ 81 (114) T 1b22_A 23 QPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKL 81 (114) T ss_dssp CCHHHHHHTTCSHHHHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHHHH T ss_pred CCHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHHH T ss_conf 24899976899989999999969853999985899999862063699999999999986 No 14 >>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (C:1-40,C:169-318) Probab=95.24 E-value=0.088 Score=31.35 Aligned_cols=123 Identities=17% Similarity=0.184 Sum_probs=73.3 Q ss_pred ECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHC-CCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEC Q ss_conf 63678881589999616975667888999998741-69830688999887144314664624449999984011417772 Q gi|254780237|r 19 VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMS-SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97 (340) Q Consensus 19 ~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLs-si~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~ 97 (340) .+.+.++.+-+|.+. |--..++|||||+||+ --.-+|..+.|..-..+==.++.++.++..... T Consensus 9 ~I~~~~~~~v~F~L~----~vd~s~ANalRRimiAEKWsPva~v~y~y~P~i~i~~~~~~~e~cp~~v~----------- 73 (190) T 1twf_C 9 KIREASKDNVDFILS----NVDLAMANSLRRVMIAEKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEW----------- 73 (190) T ss_dssp CCSCCCSSEECCEEB----SSCHHHHHHHHHHHHHCGGCCEEEEEEEECSSTTSCCSCCCCSSCHHHHS----------- T ss_pred EEEECCCCEEEEEEE----CCCHHHHHHHHHHHHHCEECCCEEEEEEECCCCCCCCCCCCCCCCCHHHC----------- T ss_conf 999767998999997----88838999999999972554530378752554333445333102423218----------- Q ss_pred CCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEECCCCCH Q ss_conf 79827999999447169963351389859988880899977896499999974687632034444655754302124311 Q gi|254780237|r 98 GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177 (340) Q Consensus 98 ~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~iDa~F 177 (340) | |+.. +-+ .+..... T Consensus 74 -------------~-----------------------~s~~--------------~~~---~~~~~~~------------ 88 (190) T 1twf_C 74 -------------P-----------------------QSKN--------------CEY---EDPPNEG------------ 88 (190) T ss_dssp -------------C-----------------------CCGG--------------GTT---SCCCCSS------------ T ss_pred -------------C-----------------------CCCC--------------EEE---ECCCCCC------------ T ss_conf -------------7-----------------------6542--------------358---6123335------------ Q ss_pred HEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC Q ss_conf 11442235776411688776218999999389617779999999999998887622 Q gi|254780237|r 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 (340) Q Consensus 178 sPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~ 233 (340) ...++... -++.+|.|+|.|++.|++.+.+|.++|+.-+..|.. T Consensus 89 ----------~~i~v~~~--~d~FiF~VES~Gsl~p~~Iv~~Ai~vLk~Kl~~l~~ 132 (190) T 1twf_C 89 ----------DPFDYKAQ--ADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILL 132 (190) T ss_dssp ----------SCCCTTCC--CCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHH T ss_pred ----------CCEEEECC--CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf ----------40576336--548999999458879999999999999999999999 No 15 >>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (K:) Probab=95.07 E-value=0.088 Score=31.36 Aligned_cols=48 Identities=19% Similarity=0.314 Sum_probs=38.5 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 56 V~fagY~ipH------Pl~~~~~lrIqT~~~~~p~eal~~a~~~l~~~~~~l~~ 103 (120) T 1twf_K 56 VLFAAYKVEH------PFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKT 103 (120) T ss_dssp EEEEEEECSC------TTSCEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHHHH T ss_pred CEEEEECCCC------CCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 3386641688------88880389999699999999999999999999999999 No 16 >>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (C:41-168) Probab=94.86 E-value=0.062 Score=32.36 Aligned_cols=55 Identities=16% Similarity=0.178 Sum_probs=46.3 Q ss_pred CEEEEEEE----ECCEEEEEEEEECCC-----------CEEEECCCEEEEEECCCCEEEEEEEEECCCCC Q ss_conf 27999999----447169963351389-----------85998888089997789649999997468763 Q gi|254780237|r 101 HKRVTIFK----RGPGVVTAGDIQTVN-----------DIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155 (340) Q Consensus 101 ~~~~~l~~----~Gp~~vtA~Di~~p~-----------~veivNpd~~IaTl~~~~~l~iel~ie~G~GY 155 (340) +...+|++ .+|..|+++|+++.. .+.-++++-.|+.|..+-.++|++...+|.|= T Consensus 56 tv~~~L~v~~~~~~~~~V~s~dL~~~~~~~~~~~~~~~~~~p~~~~I~I~KL~~gQ~I~l~~~a~kGiGk 125 (128) T 1twf_C 56 SVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAK 125 (128) T ss_dssp EEEEEEEEECCSSSCEEEEGGGEEECSCCTTCSEEEECCCSTTSCCSEEEEECTTCEEEEEEEEEEECTT T ss_pred CEEEEEEEECCCCCCCEEECHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEECCCCC T ss_conf 2689999624777763345000211144444677886654677897699995798479999999547234 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 (L:) Probab=94.75 E-value=0.1 Score=30.99 Aligned_cols=48 Identities=29% Similarity=0.317 Sum_probs=39.0 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~ipH------Pl~~~~~i~Iqt~~~~~p~~~l~~a~~~l~~~~~~l~~ 85 (92) T 2pa8_L 38 VSFASYYQPH------PLSDKIIVKILTDGSITPKDALLKAIENIRGMTSHYID 85 (92) T ss_dssp EEEEEEECSS------TTSCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHH T ss_pred EEEEEEECCC------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 0698887777------88780599999689999899999999999999999999 No 18 >>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (C:1-40,C:169-318) Probab=94.47 E-value=0.087 Score=31.40 Aligned_cols=16 Identities=6% Similarity=0.322 Sum_probs=8.8 Q ss_pred CHHEEEEEEEEEEEEC Q ss_conf 1111442235776411 Q gi|254780237|r 176 LYSPIKKVSYTVESAR 191 (340) Q Consensus 176 ~FsPV~~Vny~Ve~~r 191 (340) =|+||--|.|.-.+-. T Consensus 41 KWsPva~v~y~y~P~i 56 (190) T 1twf_C 41 KWGPAAAIEFEYDPWN 56 (190) T ss_dssp GGCCEEEEEEEECSST T ss_pred EECCCEEEEEEECCCC T ss_conf 5545303787525543 No 19 >>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (K:) Probab=94.40 E-value=0.12 Score=30.59 Aligned_cols=54 Identities=19% Similarity=0.297 Sum_probs=38.4 Q ss_pred HHHCCCCC---CCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE Q ss_conf 57517974---2015863678881589999616975667888999998741698306889998 Q gi|254780237|r 6 WQELIKPN---NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65 (340) Q Consensus 6 ~~~~~~P~---~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI 65 (340) +.-|+.|. ++++. +.+.++++++|.+ .|..|||||+||-.||.. |+.-..+-+| T Consensus 7 ~e~~~l~~~e~ki~i~-~~~~~~n~~~f~i----~~EDHTLgNlLr~~Ll~~-p~V~fagY~i 63 (120) T 1twf_K 7 FELFLLGEGESKLKID-PDTKAPNAVVITF----EKEDHTLGNLIRAELLND-RKVLFAAYKV 63 (120) T ss_dssp GGGTSCCTTCCSCCEE-ECSSSTTEEEEEE----ESCCHHHHHHHHHHHTTC-TTEEEEEEEC T ss_pred HHHCCCCCCCCCEEEE-ECCCCCCEEEEEE----ECCCCHHHHHHHHHHHCC-CCCEEEEECC T ss_conf 1200058998515998-5588885699999----289704899999999439-9833866416 No 20 >>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (K:) Probab=94.22 E-value=0.077 Score=31.73 Aligned_cols=48 Identities=13% Similarity=0.093 Sum_probs=39.5 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 55 V~fagY~ipH------Pl~~~~~lrIqT~~~~~p~~al~~A~~~l~~~~~~l~~ 102 (123) T 3h0g_K 55 VLFAGYKVPH------PLNHNFILRVQTVEDCSPKQVIVDAAKSLITHLEEIKV 102 (123) T ss_dssp CSCBCCBCSC------TTSCEEEEEEECCSSSCSHHHHHHHHHHHHHHHHHHHH T ss_pred CEEEEEECCC------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 2498876789------98782079999699999999999999999999999999 No 21 >>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 (L:) Probab=93.71 E-value=0.092 Score=31.24 Aligned_cols=41 Identities=24% Similarity=0.267 Sum_probs=32.2 Q ss_pred CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE Q ss_conf 3678881589999616975667888999998741698306889998 Q gi|254780237|r 20 LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65 (340) Q Consensus 20 ~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI 65 (340) +.+.+++++.|.+ .|..|||||+||-.|+.. |++-..+-+| T Consensus 5 i~~~~~n~~~~~i----~~EdHTlgN~Lr~~L~~~-~~V~fagY~i 45 (92) T 2pa8_L 5 ILKSESNYLELEI----EGEDHTLGNLIAGTLRRI-SGVSFASYYQ 45 (92) T ss_dssp EEEEETTEEEEEE----ETCCHHHHHHHHHHHHTS-TTEEEEEEEC T ss_pred EEECCCCEEEEEE----ECCCCHHHHHHHHHHHCC-CCEEEEEEEC T ss_conf 9607997899999----289944999999998359-9806988877 No 22 >>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} (A:) Probab=93.60 E-value=0.11 Score=30.63 Aligned_cols=31 Identities=10% Similarity=0.120 Sum_probs=14.1 Q ss_pred EEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 89999993896177799999999999988876 Q gi|254780237|r 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMF 231 (340) Q Consensus 200 kL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f 231 (340) +..|-|.|+|+ +|.+||..|++-|++.+..| T Consensus 62 ~~~lrIqT~~~-~p~~al~~A~~~l~~~~~~l 92 (115) T 1xpp_A 62 NPQIYVRVKSG-KPQSAIKRAVRKLSKLYEDL 92 (115) T ss_dssp CCEEEEEESSS-CHHHHHHHHHHHHHHHHHHH T ss_pred CCEEEEECCCC-CHHHHHHHHHHHHHHHHHHH T ss_conf 71899981899-97999999999999999999 No 23 >>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (C:1-38,C:171-297) Probab=93.59 E-value=0.071 Score=31.96 Aligned_cols=36 Identities=25% Similarity=0.471 Sum_probs=32.4 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 94 ~d~FiF~VES~Gsl~p~~Iv~~Al~iLk~K~~~l~~ 129 (165) T 3h0g_C 94 PRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVR 129 (165) T ss_dssp CCCEEEEEEBCSSSCTTTTTHHHHHHHHHHHHHHHH T ss_pred CCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 878999999505659999999999999999999998 No 24 >>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (C:39-170) Probab=93.59 E-value=0.086 Score=31.42 Aligned_cols=55 Identities=15% Similarity=0.214 Sum_probs=45.9 Q ss_pred CEEEEEEE----ECCEEEEEEEEECCC-CE-------EEECCCEEEEEECCCCEEEEEEEEECCCCC Q ss_conf 27999999----447169963351389-85-------998888089997789649999997468763 Q gi|254780237|r 101 HKRVTIFK----RGPGVVTAGDIQTVN-DI-------EVLNPDHVICNLDVDAVVRMELTVSKGHGY 155 (340) Q Consensus 101 ~~~~~l~~----~Gp~~vtA~Di~~p~-~v-------eivNpd~~IaTl~~~~~l~iel~ie~G~GY 155 (340) +...+|++ .|+..|+++|+++.+ +. +-++++-.|+.|..+-.++|++...+|.|= T Consensus 62 tv~f~L~v~~~~~~~~~V~S~dL~~~~~~~~~~~~~~~p~~~~I~I~KL~~gQ~i~l~~~a~kGiGk 128 (132) T 3h0g_C 62 SVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILADPKSRGPLICKLRKEQEISLRCIAKKGIAK 128 (132) T ss_dssp SCEEEEEECCCCSSCEEEEGGGCBCCSCCSSCCBCCCSTTSCCSEEEEECSSCCEEEEEEEEEECGG T ss_pred EEEEEEEEEECCCCCEEEEECCEEECCCCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEEEEECCCC T ss_conf 6898887893577745774041662786340586443555788458970577359999999978411 No 25 >>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (K:) Probab=92.76 E-value=0.14 Score=30.11 Aligned_cols=44 Identities=20% Similarity=0.289 Sum_probs=32.7 Q ss_pred HHHCCCC--CCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCC Q ss_conf 5751797--420158636788815899996169756678889999987416 Q gi|254780237|r 6 WQELIKP--NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSS 54 (340) Q Consensus 6 ~~~~~~P--~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLss 54 (340) ...|..| .++++.. .+.+++.+.|.+ .|..|||||+||-.||.. T Consensus 7 ~e~~~l~~~~km~i~~-~~~~~n~~~~~i----~~EDHTLgNlLr~~Ll~~ 52 (123) T 3h0g_K 7 YELIELMGLPKVTYEL-DSKSPNAAVVTL----EKEDHTLANMLANQLLSD 52 (123) T ss_dssp GGTSSCSSCCSCCEEE-CSSSTTEEEEEE----ESCCSSHHHHHHHTGGGS T ss_pred CCEECCCCCCEEEEEE-CCCCCCEEEEEE----ECCCCHHHHHHHHHHHCC T ss_conf 1131148986079873-477884699999----489856999999999549 No 26 >>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (C:1-38,C:171-297) Probab=92.68 E-value=0.1 Score=30.94 Aligned_cols=38 Identities=18% Similarity=0.274 Sum_probs=29.9 Q ss_pred ECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEE Q ss_conf 636788815899996169756678889999987416983068 Q gi|254780237|r 19 VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60 (340) Q Consensus 19 ~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ai 60 (340) .+.+.++.+-+|.+. |--..++|||||+|++=.|-+++ T Consensus 8 ~i~e~~~~~i~F~l~----~vd~s~ANalRRimiaWsPV~~a 45 (165) T 3h0g_C 8 TIRNISKNSVDFVLT----NTSLAVANSLRRVVLAWSPTSAV 45 (165) T ss_dssp CCCCBCSSEEEEEEC----SCCHHHHHHHHHHHHSSCCBCCC T ss_pred EEEECCCCEEEEEEE----CCCHHHHHHHHHHHHHECCCEEE T ss_conf 999856988999997----89837888999999876332025 No 27 >>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} (A:1-95) Probab=92.00 E-value=0.27 Score=28.25 Aligned_cols=48 Identities=8% Similarity=0.094 Sum_probs=42.4 Q ss_pred CHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 058889898839837188874498888618898864499999999980 Q gi|254780237|r 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 266 SvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) .......|-.+++.|+.++..-+.+||.+++++|.+..+.|.+.+.+. T Consensus 44 G~~~a~~L~~~~~~s~e~i~~As~e~L~~i~Gig~~~A~~I~~~~~~~ 91 (95) T 1pzn_A 44 GPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAARKA 91 (95) T ss_dssp CHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_pred CHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 999999999859971999982899999975498999999999999873 No 28 >>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A* (A:240-306) Probab=84.01 E-value=0.83 Score=25.05 Aligned_cols=48 Identities=23% Similarity=0.263 Sum_probs=34.1 Q ss_pred CCHHHC-CCCHHHHHHHHHC--CCCCHHHHHHC-CHHHHHCCCCCCHHHHHHHH Q ss_conf 112210-1105888989883--98371888744-98888618898864499999 Q gi|254780237|r 258 KKVEEL-ELSVRSTNCLRGE--NIVYMGDLIQR-TEADMLRMANFGRKSLVEIK 307 (340) Q Consensus 258 ~~IeeL-eLSvRs~NcLk~a--~I~tigdLv~~-s~~dLl~ikNfG~KSl~EI~ 307 (340) .+|.++ ..--|+..-|++. ||+|++||.++ +.+.|. +-||.|.-..+- T Consensus 2 Lpi~~i~GVG~~t~~kL~~~~~Gi~ti~dL~~~~~~~~L~--~~~G~k~G~~l~ 53 (67) T 2aq4_A 2 FKLDDLPGVGHSTLSRLESTFDSPHSLNDLRKRYTLDALK--ASVGSKLGMKIH 53 (67) T ss_dssp CCGGGSTTCCHHHHHHHHHHTTCCCSHHHHHHHCCHHHHH--HHHCSSHHHHHH T ss_pred CCCCCHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH--HHHCCHHHHHHH T ss_conf 5423012027899999998774357699999887777888--750228999999 No 29 >>1feu_A 50S ribosomal protein L25; general stress protein CTC, 5S rRNA-protein complex, cadmium IONS, ribosome; 2.30A {Thermus thermophilus} (A:94-206) Probab=82.86 E-value=1 Score=24.40 Aligned_cols=53 Identities=17% Similarity=0.213 Sum_probs=41.0 Q ss_pred HHCCCEEEECCC-CCEEEEEEEEC---CEEEEEEEEECCCCEEEE-CCCEEEEEECCC Q ss_conf 401141777279-82799999944---716996335138985998-888089997789 Q gi|254780237|r 88 NIKGINLKMSGD-SHKRVTIFKRG---PGVVTAGDIQTVNDIEVL-NPDHVICNLDVD 140 (340) Q Consensus 88 NLK~I~~k~~~~-~~~~~~l~~~G---p~~vtA~Di~~p~~veiv-Npd~~IaTl~~~ 140 (340) .+..|.++.... -|..+.+++.| -..++.+||.+|.+++++ +++..|||+... T Consensus 27 ~~~~i~v~~~p~~iP~~i~VDvs~l~~Gd~i~v~Di~lp~gv~~~~d~~~vV~sv~~~ 84 (113) T 1feu_A 27 IHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVVPP 84 (113) T ss_dssp CCSEEEEEECGGGCCSCEEEECTTCCTTEEEEGGGSCCCTTCEESSCTTCEEEEEECS T ss_pred EEEEEEEEEEHHCCCCEEEEECCCCCCCCEEEEEEECCCCCCEECCCCCCEEEEEECC T ss_conf 8637889710322982799975127689869998332899948905899669999689 No 30 >>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family, transferase/DNA complex; HET: DNA MSE ADI; 1.70A {Sulfolobus solfataricus} (A:183-237) Probab=80.56 E-value=0.95 Score=24.67 Aligned_cols=40 Identities=10% Similarity=0.024 Sum_probs=30.5 Q ss_pred HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHH Q ss_conf 588898988398371888744988886188988644999999 Q gi|254780237|r 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308 (340) Q Consensus 267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~ 308 (340) -++.--|++.||+|++||.+.+++.|. +.||++.-..+-+ T Consensus 6 ~~t~~kL~~~GI~ti~dl~~~~~~~L~--~~~G~~~g~~l~~ 45 (55) T 1jx4_A 6 NITAEKLKKLGINKLVDTLSIEFDKLK--GXIGEAKAKYLIS 45 (55) T ss_dssp HHHHHHHHTTTCCBGGGGGSSCHHHHH--HHHCHHHHHHHHH T ss_pred HHHHHHHHHHCCCCCHHCCCCCHHHHH--HHHCCHHHHHHHH T ss_conf 679999998489682312137999999--8968077899999 No 31 >>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* (A:304-377) Probab=79.36 E-value=2.7 Score=21.71 Aligned_cols=44 Identities=9% Similarity=0.162 Sum_probs=36.3 Q ss_pred HHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 889898839837188874498888618898864499999999980 Q gi|254780237|r 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 269 s~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) ...-|-+. ..++.++.+-+.++|..++++|++..+.|.+.+..- T Consensus 24 ~a~~L~~~-fgsl~~i~~as~~~L~~v~GiG~~~A~~i~~~~~~~ 67 (74) T 3c1y_A 24 IGYNVVRM-FKTLDQISKASVEDLKKVEGIGEKRARAISESISSL 67 (74) T ss_dssp HHHHHHHH-HCSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHHH T ss_pred HHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 99999998-538999985799888544784699999999999998 No 32 >>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} (A:) Probab=79.07 E-value=4.6 Score=20.26 Aligned_cols=59 Identities=10% Similarity=0.138 Sum_probs=51.1 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 ~~~lF~e~LdvDe~iA~lLV~EGFtslEEiAyvp~~El~~IegfDee~a~eL~~RAk~~ 62 (70) T 1u9l_A 4 AIDTFTKYLDIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERAKNA 62 (70) T ss_dssp HHHHHHHHHTCCHHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHHHH T ss_pred HHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHHH T ss_conf 89999998387499999999846587999865899999760044799999999999999 No 33 >>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family DNA polymerase, translesion DNA synthesis, lesion bypass; 2.40A {Homo sapiens} (A:271-340) Probab=77.99 E-value=2.6 Score=21.83 Aligned_cols=53 Identities=13% Similarity=0.086 Sum_probs=39.6 Q ss_pred HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH Q ss_conf 331112210-11058889898839837188874498888618898864499999999 Q gi|254780237|r 255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310 (340) Q Consensus 255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L 310 (340) +-.++|.++ ..--++.--|++.||+|++||.+.+.+-+.+ +|.++-..+.+.+ T Consensus 9 l~~lpi~~i~GIG~~~~~~L~~~gI~ti~dl~~~~~~~~~~---~~~~~g~~l~~~a 62 (70) T 1t94_A 9 IKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLL---FSETSWHYFLHIS 62 (70) T ss_dssp HTTCBGGGCTTSCHHHHHHHHHTTCCBHHHHHHTHHHHHHH---SCHHHHHHHHHHH T ss_pred HHHCCCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHH---HHHHHHHHHHHHH T ss_conf 97397140257631100454541358699999867778888---5111245656652 No 34 >>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (A:) Probab=76.47 E-value=3.9 Score=20.70 Aligned_cols=44 Identities=16% Similarity=0.184 Sum_probs=36.8 Q ss_pred HHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 889898839837188874498888618898864499999999980 Q gi|254780237|r 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 269 s~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) ....|-+. ..++.++..-+.++|.+++++|.+...+|.+.+..- T Consensus 31 ~a~~L~~~-F~s~~~i~~A~~~~L~~v~GiG~~~A~~i~~~~~~~ 74 (89) T 1z00_A 31 DSQTLLTT-FGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEP 74 (89) T ss_dssp HHHHHHHH-TCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSC T ss_pred HHHHHHHH-HCCCHHHHHHHHHHHCHHCCCCHHHHHHHHHHHHCH T ss_conf 99999999-099478766547510000332799999999998183 No 35 >>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (S:92-237) Probab=72.70 E-value=1.6 Score=23.27 Aligned_cols=54 Identities=11% Similarity=0.207 Sum_probs=42.2 Q ss_pred HCCCEEEE-C-CCCCEEEEEEEEC---CEEEEEEEEECCCCEEEE-CCCEEEEEECCCCE Q ss_conf 01141777-2-7982799999944---716996335138985998-88808999778964 Q gi|254780237|r 89 IKGINLKM-S-GDSHKRVTIFKRG---PGVVTAGDIQTVNDIEVL-NPDHVICNLDVDAV 142 (340) Q Consensus 89 LK~I~~k~-~-~~~~~~~~l~~~G---p~~vtA~Di~~p~~veiv-Npd~~IaTl~~~~~ 142 (340) +..|.++. . .+-|..+.+++.| -..++++||.+|.+++++ +++..||++..... T Consensus 26 ~~~i~V~~l~P~~IPe~I~VDVs~L~iGdsi~v~Dl~lp~gv~~~~d~d~vVvsV~~p~~ 85 (146) T 2zjr_S 26 VHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPRL 85 (146) T ss_dssp CSEEEEECCCTTCCCSCCEEECTTCCSSCEEETTTSCCSTTCCCCSCTTCEEEEEECCC- T ss_pred HHHHHHHCCCHHHCCHHHCCCCCCCCCCCCEEEEEEECCCCEEEECCCCCEEEEEECCCC T ss_conf 243665423843575230236434658984588777269984981489847999967874 No 36 >>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} (A:) Probab=71.81 E-value=3.5 Score=21.01 Aligned_cols=34 Identities=9% Similarity=0.040 Sum_probs=31.8 Q ss_pred CCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHH Q ss_conf 8371888744988886188988644999999999 Q gi|254780237|r 278 IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311 (340) Q Consensus 278 I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~ 311 (340) ..++.++.+-+.+||.++.++|.+..+.|.+.|. T Consensus 44 Fgs~~~i~~As~eeL~~v~gIG~~~A~~I~~~l~ 77 (78) T 1kft_A 44 MGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK 77 (78) T ss_dssp HSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT T ss_pred CCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC T ss_conf 0998999857899997389989999999999976 No 37 >>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} (A:499-568) Probab=66.22 E-value=9.1 Score=18.30 Aligned_cols=50 Identities=14% Similarity=0.085 Sum_probs=39.7 Q ss_pred HHCCHHHHHCCCCCCHHHHHHHHHHHHHHCC-----CCCCCCCCCCHHHHHHHHHH Q ss_conf 7449888861889886449999999998083-----12676878986779999987 Q gi|254780237|r 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGL-----FLGMNLPDWPPESIEELAKK 335 (340) Q Consensus 285 v~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl-----~lg~~l~~~~~~~~~~~~~~ 335 (340) =.-+.++|.+++++|.+....|.+.....|. .|. .++++++..++.++.- T Consensus 5 N~A~~~~L~~lpgig~~~A~~Ii~~R~~~G~f~s~~dL~-~v~gl~~~~~~~l~~~ 59 (70) T 3bzc_A 5 NTASAALLARISGLNSTLAQNIVAHRDANGAFRTRDELK-KVSRLGEKTFEQAAGF 59 (70) T ss_dssp TTCCHHHHHTSTTCCHHHHHHHHHHHHHHCCCSSGGGGG-GSTTCCHHHHHHHGGG T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHH-HCCCCCHHHHHHCCEE T ss_conf 875488886606978899999999999669957799998-5678881289871808 No 38 >>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 (D:1-35,D:154-168,D:224-265) Probab=59.56 E-value=12 Score=17.53 Aligned_cols=48 Identities=19% Similarity=0.236 Sum_probs=33.5 Q ss_pred CCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHH Q ss_conf 243111144223577641168877621899999938961777999999999999888 Q gi|254780237|r 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229 (340) Q Consensus 173 iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~ 229 (340) +-|-|-||.-..- +.. -++-++||+.-||..|+-.|-+|.+-+..-+. T Consensus 34 LYakfipvsl~~i--~~~-------~~kyILeiESVGSLkPeRILiEA~KSilrKie 81 (92) T 2pa8_D 34 LYAKFIPVSLSVV--RYY-------PDKYILEIESVGSLKPERILLEAGKSIIRKIE 81 (92) T ss_dssp HSGGGCCEEEEEE--EEE-------EEEEEEEEEECSSSCHHHHHHHHHHHHHHHHH T ss_pred HCCCCCCCCCEEE--ECC-------CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHH T ss_conf 7132266652001--002-------37899999975762999999999999999999 No 39 >>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* (A:179-343) Probab=53.19 E-value=15 Score=16.86 Aligned_cols=112 Identities=11% Similarity=0.018 Sum_probs=70.5 Q ss_pred EEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHH Q ss_conf 99938961777999999999999888762244443221000000000112333111221011058889898839837188 Q gi|254780237|r 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283 (340) Q Consensus 204 EI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigd 283 (340) =++|+-.-+-.++.......-.+....+................-..........-+.+-.++..+..+|++.++..+|. T Consensus 6 i~dsgv~~~t~~~~~~~r~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~al~~~d~~~lg~ 85 (165) T 2cz9_A 6 VFYTGVRRELASSEYAERKHIAEESLKILGKGSSKEVREGELSKLPPLHRKFFGYIVRENARVLEVRDALKEGNVEEVGK 85 (165) T ss_dssp EEECSCC----CHHHHHHHHHHHHHHHHHTCSCGGGCCGGGGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHH T ss_pred EEECCCEECCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH T ss_conf 97324200112102566789999999762432146777877752678999999999986067899998762141778888 Q ss_pred HHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCC Q ss_conf 87449888861889886449999999998083 Q gi|254780237|r 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315 (340) Q Consensus 284 Lv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl 315 (340) |+..+...|...-+..--.++.+.+.-.+.|. T Consensus 86 lm~~~~~~l~~~~~vs~p~ld~l~~~a~~~Ga 117 (165) T 2cz9_A 86 ILTTAHWDLAKNYEVSCKELDFFVERALKLGA 117 (165) T ss_dssp HHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTC T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCC T ss_conf 99999999987506687899999999997699 No 40 >>1pie_A Galactokinase; galactose, galactosemia, transferase; HET: GLA; 2.10A {Lactococcus lactis} (A:233-409) Probab=52.35 E-value=16 Score=16.77 Aligned_cols=64 Identities=14% Similarity=0.144 Sum_probs=52.9 Q ss_pred CHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 1221011058889898839837188874498888618898864499999999980831267687 Q gi|254780237|r 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322 (340) Q Consensus 259 ~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~ 322 (340) -+.+-....++..+|+..++..+|.|+..+...|...-+..-..++-+.+...+.+=.+|-++. T Consensus 71 ~~~e~~rv~~a~~al~~~d~~~lG~lm~~sh~~l~~~~~vS~peld~lv~~a~~~~Ga~GaKlt 134 (177) T 1pie_A 71 AVYENNRTKIAQKAFVAGNLTKFGELLNASHASLKDDYEVTGLELDTLAETAQKQAGVLGARMT 134 (177) T ss_dssp HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTSCCCCHHHHHHHHHHHHSTTEEEEEEC T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEEC T ss_conf 5068899999998753277888999999999999997579979999999999984895798970 No 41 >>3bqs_A Uncharacterized protein; 10114F, NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.42A {Listeria monocytogenes str} PDB: 3bqt_A (A:) Probab=52.07 E-value=16 Score=16.74 Aligned_cols=74 Identities=15% Similarity=0.108 Sum_probs=47.9 Q ss_pred CHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHH---HCCCCC--CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH Q ss_conf 12210-11058889898839837188874498888---618898--8644999999999808312676878986779999 Q gi|254780237|r 259 KVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADM---LRMANF--GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332 (340) Q Consensus 259 ~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dL---l~ikNf--G~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~ 332 (340) ++.+| ++...+..-|.+.||+|+.||......++ ++-.+. ....|--+.-++. |.....|+++.-++| T Consensus 5 ~l~~LPNiG~~~e~~L~~iGI~tv~~L~~~ga~~~~~~l~~~~~~~~~~~Lyal~~Ai~------g~~w~~l~~~~K~~L 78 (93) T 3bqs_A 5 NLSELPNIGKVLEQDLIKAGIKTPVELKDVGSKEAFLRIWENDSSVCMSELYALEGAVQ------GIRWHGLDEAKKIEL 78 (93) T ss_dssp CGGGSTTCCHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHTTCTTCCHHHHHHHHHHHH------TSCGGGSCHHHHHHH T ss_pred HHHHCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHC------CCCHHHCCHHHHHHH T ss_conf 78568999999999999839998999987799999999998589997999999999995------998677999999999 Q ss_pred HHHHHC Q ss_conf 987750 Q gi|254780237|r 333 AKKYED 338 (340) Q Consensus 333 ~~~~~~ 338 (340) ...++. T Consensus 79 ~~~~~~ 84 (93) T 3bqs_A 79 KKFHQS 84 (93) T ss_dssp HHHHHH T ss_pred HHHHHH T ss_conf 999999 No 42 >>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A (A:80-154) Probab=46.02 E-value=20 Score=16.14 Aligned_cols=45 Identities=11% Similarity=0.161 Sum_probs=32.1 Q ss_pred HHHHHHHCCCCCHHHHHHC-CHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 8898988398371888744-98888618898864499999999980 Q gi|254780237|r 269 STNCLRGENIVYMGDLIQR-TEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 269 s~NcLk~a~I~tigdLv~~-s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) +.++|..-+...+.+.+.- ...-|.++|+.|+|..+-|.--|+.. T Consensus 22 Al~iLs~~~~~el~~aI~~~D~~~L~~ipGIG~KtA~rii~ELk~k 67 (75) T 2ztd_A 22 AMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDK 67 (75) T ss_dssp HHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHTTT T ss_pred HHHHHCCCCHHHHHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHCC T ss_conf 6232215776777788853688998508883568899999998411 No 43 >>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} (A:) Probab=44.67 E-value=21 Score=16.01 Aligned_cols=43 Identities=12% Similarity=0.088 Sum_probs=30.5 Q ss_pred HHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCC Q ss_conf 8889898839837188874498888618898864499999999980831 Q gi|254780237|r 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316 (340) Q Consensus 268 Rs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~ 316 (340) ||.+.|++-.. --.+..|+..++++|.+...-|.+.|+..-.. T Consensus 42 kA~~slk~~p~------pi~s~~~l~~lpgiG~~ia~kI~e~l~tg~~e 84 (87) T 2kp7_A 42 KALRSLQRYPL------PLRSGKEAKILQHFGDRLCRMLDEKLKQHLAS 84 (87) T ss_dssp HHHHHHHHCCS------CCCSHHHHHTCTTTCHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHCCC------CCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 99999997898------87889998738998789999999999999987 No 44 >>1szp_A DNA repair protein RAD51; homologous recombination, asymmetry, RAD51 filament, DNA binding protein; HET: DNA; 3.25A {Saccharomyces cerevisiae} (A:26-81) Probab=44.02 E-value=21 Score=15.95 Aligned_cols=40 Identities=8% Similarity=0.120 Sum_probs=33.7 Q ss_pred CCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 3718887449888861889886449999999998083126768 Q gi|254780237|r 279 VYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321 (340) Q Consensus 279 ~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l 321 (340) +||..+..-+..+|..+++++.--.+-|.+.-.++ ++|.. T Consensus 1 ~Tve~ia~at~k~L~~ikGisE~ka~KIi~aA~kl---~~~gF 40 (56) T 1szp_A 1 HTAEAVAYAPRKDLLEIKGISEAKADKLLNEAARL---VPMGF 40 (56) T ss_dssp CSHHHHHHSCSHHHHTSTTCCHHHHHHHHHHHHHH---SCCSC T ss_pred CCHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHH---HCCCC T ss_conf 63999973899999876399999999999999987---44799 No 45 >>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} (A:) Probab=37.56 E-value=25 Score=15.47 Aligned_cols=40 Identities=10% Similarity=0.219 Sum_probs=31.4 Q ss_pred HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCC--CCCCH Q ss_conf 221011058889898839837188874498888618--89886 Q gi|254780237|r 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM--ANFGR 300 (340) Q Consensus 260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~i--kNfG~ 300 (340) ++.++|+. -..++.+.+|..+..|...+.+||..+ .++|- T Consensus 33 L~~igl~~-Y~~~F~~~~i~g~~~L~~l~~~dL~~lgI~~~gh 74 (100) T 2kg5_A 33 LATVHLEQ-YADTFRRHGLATAGAARGLGHEELKQLGISATGH 74 (100) T ss_dssp HGGGTCGG-GHHHHHHTTCCBHHHHTTCCHHHHHHHTCCCHHH T ss_pred HHHCCCHH-HHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHH T ss_conf 99884499-9999998699848999877899998749998899 No 46 >>1eu8_A Trehalose/maltose binding protein; protein-carbohydrate complex, MBP 2 fold, ABC transporter fold, thermophilic protein; HET: TRE; 1.90A {Thermococcus litoralis} (A:175-230,A:359-409) Probab=35.94 E-value=28 Score=15.14 Aligned_cols=21 Identities=14% Similarity=0.338 Sum_probs=12.3 Q ss_pred CCCCCHHHHHHHHHHHHHHHH Q ss_conf 896177799999999999988 Q gi|254780237|r 208 DGSITGEDSVALASRILQDQL 228 (340) Q Consensus 208 nGsi~P~eAl~~Aa~iL~~~l 228 (340) .|..+|++||..|++-+...+ T Consensus 83 ~G~~tpeeAl~~a~~~i~~il 103 (107) T 1eu8_A 83 AGKISPQEALDKAQKEAEELV 103 (107) T ss_dssp HTSSCHHHHHHHHHHHHHHHH T ss_pred CCCCCHHHHHHHHHHHHHHHH T ss_conf 599999999999999999999 No 47 >>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} (A:) Probab=32.79 E-value=32 Score=14.82 Aligned_cols=45 Identities=13% Similarity=0.069 Sum_probs=30.1 Q ss_pred HHHHHHHCCCCCHH-HHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 88989883983718-8874498888618898864499999999980 Q gi|254780237|r 269 STNCLRGENIVYMG-DLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 269 s~NcLk~a~I~tig-dLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) +..-|..-+...+- .+.+.+.+.|.++|+.|+|..+.|...|+.. T Consensus 85 Al~iL~~~~~~el~~aI~~~d~~~L~~ipGIG~KtA~rIi~eLk~k 130 (191) T 1ixr_A 85 ALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELKGK 130 (191) T ss_dssp HHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHTTT T ss_pred HHHHHHCCCHHHHHHHHHCCCHHHHCCCCCCCHHHHHHHHHHHHHH T ss_conf 9999855999999999982899985138884568899999999864 No 48 >>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:119-241) Probab=32.11 E-value=32 Score=14.75 Aligned_cols=36 Identities=19% Similarity=0.192 Sum_probs=26.1 Q ss_pred CHHHHHHCCH-HHHHCCCCCCHHHHHHHHHHHHHHCC Q ss_conf 7188874498-88861889886449999999998083 Q gi|254780237|r 280 YMGDLIQRTE-ADMLRMANFGRKSLVEIKGVLGTMGL 315 (340) Q Consensus 280 tigdLv~~s~-~dLl~ikNfG~KSl~EI~~~L~~~gl 315 (340) |+.||-..-+ ..+..+|+||.|+-+-|...|+.+.- T Consensus 2 tleeL~~a~~~~~i~~l~gfG~K~~~~il~gl~~~~~ 38 (123) T 2w9m_A 2 SLERLREAAESGELAGLKGFGAKSAATILENVVFLFE 38 (123) T ss_dssp SHHHHHHHHHHTTTTTSTTCCHHHHHHHHHHHHHHHH T ss_pred CHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 8999999876088012110138899999987878887 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* 3a0b_U* 3a0h_U* (U:) Probab=31.65 E-value=32 Score=14.79 Aligned_cols=39 Identities=8% Similarity=0.128 Sum_probs=29.8 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 44 ~~A~~Iv~~gpf~s~--------~dL~~v~gi~~~~~~~i~~~l~v~ 82 (104) T 3bz1_U 44 TLAKLIVKNAPYESV--------EDVLNIPGLTERQKQILRENLEHF 82 (104) T ss_dssp HHHHHHHHSCCCSSG--------GGGGGCTTCCHHHHHHHHHHGGGE T ss_pred HHHHHHHHCCCCCCH--------HHHHCCCCCCHHHHHHHHHHHCCC T ss_conf 999999970897879--------999617998999999999876145 No 50 >>3hil_A Ephrin type-A receptor 1; ATP-binding, kinase, nucleotide-binding, transferase, tyrosine-protein kinase, signal, sterIle alpha motif; 2.00A {Homo sapiens} PDB: 3kka_A (A:) Probab=31.64 E-value=33 Score=14.70 Aligned_cols=39 Identities=18% Similarity=0.261 Sum_probs=30.1 Q ss_pred HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCC--CCCC Q ss_conf 221011058889898839837188874498888618--8988 Q gi|254780237|r 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM--ANFG 299 (340) Q Consensus 260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~i--kNfG 299 (340) ++.++|+ .-..++++.+|..+..|...++++|.++ +++| T Consensus 30 L~~~gl~-~y~~~F~~~~i~g~~~L~~l~~~dL~~lGI~~~g 70 (82) T 3hil_A 30 LESIRMK-RYILHFHSAGLDTMECVLELTAEDLTQMGITLPG 70 (82) T ss_dssp HHHTTCG-GGHHHHHHTTCCSGGGGTTCCHHHHHHTTCCCHH T ss_pred HHHCCCH-HHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHH T ss_conf 9988769-8899999969786798733889999886989889 No 51 >>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A (A:157-220) Probab=30.79 E-value=21 Score=15.96 Aligned_cols=33 Identities=6% Similarity=0.122 Sum_probs=26.2 Q ss_pred CCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH Q ss_conf 9837188874498888618898864499999999 Q gi|254780237|r 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310 (340) Q Consensus 277 ~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L 310 (340) ...++..+.+-|.+||.+++++|++. +.|.+.| T Consensus 31 ~F~s~~~i~~As~eeL~~v~gig~~A-~~I~~~f 63 (64) T 2nrt_A 31 HFGSLENIRSASLEEIARVIGSTEIA-RRVLDIL 63 (64) T ss_dssp HHCSHHHHHTSCHHHHHHHHTCHHHH-HHHHHHC T ss_pred HCCCHHHHHCCCHHHHHHCCCCHHHH-HHHHHHH T ss_conf 86899999709999998687929999-9999970 No 52 >>2gha_A Maltose ABC transporter, periplasmic maltose- binding protein; periplasmic binding protein, MBP, maltotriose, sugar binding protein; HET: MLR; 1.60A {Thermotoga maritima MSB8} PDB: 2ghb_A 2fnc_A* (A:155-206,A:337-382) Probab=29.94 E-value=35 Score=14.52 Aligned_cols=43 Identities=16% Similarity=0.341 Sum_probs=28.6 Q ss_pred CEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 30212431111442235776411688776218999999389617779999999999998887 Q gi|254780237|r 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230 (340) Q Consensus 169 g~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~ 230 (340) |.+|.-.+..|....- ..-.+|-.+|++||..|.+.+..+... T Consensus 49 g~~pM~~VW~p~~~Al-------------------~~i~~gk~~p~~al~~AV~~Ik~~I~~ 91 (98) T 2gha_A 49 GILDMAAVWAAMNDAL-------------------NLVVNGKATVEEALKNAVERIKAQIQG 91 (98) T ss_dssp TSSCGGGTHHHHHHHH-------------------HHHHTTSSCHHHHHHHHHHHHHHHHC- T ss_pred CCCCHHHHHHHHHHHH-------------------HHHHCCCCCHHHHHHHHHHHHHHHHCC T ss_conf 2678899999999999-------------------999859899999999999999999737 No 53 >>2gru_A 2-deoxy-scyllo-inosose synthase; aminoglycoside, 2-deoxystreptamine, dehydroquinate synthase, lyase; HET: NAD EXO CAK; 2.15A {Bacillus circulans} PDB: 2d2x_A* (A:174-368) Probab=29.47 E-value=22 Score=15.89 Aligned_cols=19 Identities=11% Similarity=0.125 Sum_probs=8.3 Q ss_pred CHHHHHHHHHHHHHHCCCC Q ss_conf 8644999999999808312 Q gi|254780237|r 299 GRKSLVEIKGVLGTMGLFL 317 (340) Q Consensus 299 G~KSl~EI~~~L~~~gl~l 317 (340) .+..++++.+.|..+|+.. T Consensus 111 ~~~~~~~~~~~l~~~glp~ 129 (195) T 2gru_A 111 PEHDVSAHYWLLNKIGALQ 129 (195) T ss_dssp CHHHHHHHHHHHHHTTTTT T ss_pred CHHHHHHHHHHHHHCCCCC T ss_conf 8999999999999759966 No 54 >>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} (U:48-134) Probab=27.35 E-value=39 Score=14.23 Aligned_cols=39 Identities=8% Similarity=0.127 Sum_probs=25.3 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 27 ~~A~~Iv~~g~f~--------s~~dL~~v~gi~~~~~~~i~~~l~v~ 65 (87) T 1s5l_U 27 TLAKLIVKNAPYE--------SVEDVLNIPGLTERQKQILRENLEHF 65 (87) T ss_dssp HHHHHHHHTCCCS--------SGGGGGGCTTCCHHHHHHHHHHHTTE T ss_pred HHHHHHHHCCCCC--------CHHHHHCCCCCCHHHHHHHHHHHCCC T ss_conf 9999999827848--------79999617757999999999865353 No 55 >>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} (A:1-66) Probab=26.92 E-value=40 Score=14.18 Aligned_cols=38 Identities=29% Similarity=0.361 Sum_probs=27.1 Q ss_pred HHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHC Q ss_conf 8886188988644999999999808312676878986779999987750 Q gi|254780237|r 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338 (340) Q Consensus 290 ~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~~~~~~~ 338 (340) +.|.++|+.|+||.+-+.-. +-.||++.+.++.+-+.+ T Consensus 12 ~~l~~LPGIG~KsA~Rla~~-----------lL~~~~~~~~~l~~~l~~ 49 (66) T 1vdd_A 12 RELSRLPGIGPKSAQRLAFH-----------LFEQPREDIERLASALLE 49 (66) T ss_dssp HHHHTSTTCCHHHHHHHHHH-----------HSSSCHHHHHHHHHHHHH T ss_pred HHHHHCCCCCHHHHHHHHHH-----------HHCCCHHHHHHHHHHHHH T ss_conf 99967899889999999999-----------972999999999999999 No 56 >>3dm0_A Maltose-binding periplasmic protein fused with RACK1; MBP RACK1A, receptor for activiated protein C-kinase 1, beta-propeller WD40 repeat; HET: GLC; 2.40A {Escherichia coli} (A:158-205,A:334-371) Probab=26.61 E-value=36 Score=14.48 Aligned_cols=19 Identities=21% Similarity=0.169 Sum_probs=13.3 Q ss_pred ECCCCCHHHHHHHHHHHHH Q ss_conf 3896177799999999999 Q gi|254780237|r 207 TDGSITGEDSVALASRILQ 225 (340) Q Consensus 207 TnGsi~P~eAl~~Aa~iL~ 225 (340) ++|.-+|++||..|++.+. T Consensus 66 ~~gkq~~~~AL~~A~~~I~ 84 (86) T 3dm0_A 66 ASGRQTVDAALAAAQTNAA 84 (86) T ss_dssp HHTSSCHHHHHHHHHHHHH T ss_pred HHHHCCCCCCCCCCCCCCC T ss_conf 7530033211121222223 No 57 >>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:66-144) Probab=26.23 E-value=41 Score=14.10 Aligned_cols=45 Identities=9% Similarity=0.186 Sum_probs=29.3 Q ss_pred HHHHHHHCCCCCHHHHH-HCCHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 88989883983718887-4498888618898864499999999980 Q gi|254780237|r 269 STNCLRGENIVYMGDLI-QRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340) Q Consensus 269 s~NcLk~a~I~tigdLv-~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340) ++++|..-....+.+.+ +-....|.++|+.|+|..+-|.--|+.. T Consensus 21 Al~iLs~~~~~el~~aI~~~D~~~L~~ipGIG~KtAerii~eLk~K 66 (79) T 1cuk_A 21 ALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDR 66 (79) T ss_dssp HHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHHH T ss_pred HHHHHCCCCHHHHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 9999757999999999992899998419998899999999999988 No 58 >>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:1-118) Probab=25.79 E-value=14 Score=17.07 Aligned_cols=27 Identities=7% Similarity=0.182 Sum_probs=17.2 Q ss_pred HCCHHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 449888861889886449999999998 Q gi|254780237|r 286 QRTEADMLRMANFGRKSLVEIKGVLGT 312 (340) Q Consensus 286 ~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340) ..+.+++.++++.|++..+-|.+.+.. T Consensus 53 ~~~~~~l~~lpGIG~~~a~kI~E~l~t 79 (118) T 2w9m_A 53 ELLAREFTGIPKVGKGIAAELSDFARS 79 (118) T ss_dssp ------CCSSTTCCHHHHHHHHHHHHH T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 754988625999878999999999984 No 59 >>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} (A:1-119) Probab=24.55 E-value=44 Score=13.90 Aligned_cols=32 Identities=22% Similarity=0.220 Sum_probs=24.2 Q ss_pred HCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCC Q ss_conf 44988886188988644999999999808312 Q gi|254780237|r 286 QRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317 (340) Q Consensus 286 ~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~l 317 (340) -.+.+++.+++++|.+..+-|.+.|..--+.. T Consensus 53 i~s~~~~~~lpgiG~~ia~~I~e~l~tG~~~~ 84 (119) T 2fmp_A 53 IKSGAEAKKLPGVGTKIAEKIDEFLATGKLRK 84 (119) T ss_dssp CCCHHHHHTSTTCCHHHHHHHHHHHHHSSCHH T ss_pred CCCHHHHHCCCCCCHHHHHHHHHHHHCCCHHH T ss_conf 47899984799964899999999996486589 No 60 >>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (M:1-64) Probab=24.14 E-value=45 Score=13.85 Aligned_cols=48 Identities=15% Similarity=0.233 Sum_probs=39.4 Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCC Q ss_conf 888861889886449999999998083126768789867799999877503 Q gi|254780237|r 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339 (340) Q Consensus 289 ~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~~~~~~~~ 339 (340) .-.|..+.+.|++...+| +...|++-.+++.++..++++.+.+-+++. T Consensus 16 ~~aLt~I~GIG~~~A~~I---c~~lgi~~~~k~~~Lt~~qi~~i~~~i~~~ 63 (64) T 2vqe_M 16 DVALTYIYGIGKARAKEA---LEKTGINPATRVKDLTEAEVVRLREYVENT 63 (64) T ss_dssp HHHHTTSSSCCSHHHHHH---TTTTTCCTTSBGGGCCHHHHHHHHHHHHTT T ss_pred EEEEEEEECCCHHHHHHH---HHHCCCCCCCCCCCCCHHHHHHHHHHHHCC T ss_conf 887330658189999999---998299833221513599999999987316 No 61 >>3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} (A:185-235) Probab=24.10 E-value=30 Score=14.97 Aligned_cols=27 Identities=11% Similarity=0.263 Sum_probs=21.9 Q ss_pred HHHHHHCCCCCHHHHHHCCHHHHHCCC Q ss_conf 898988398371888744988886188 Q gi|254780237|r 270 TNCLRGENIVYMGDLIQRTEADMLRMA 296 (340) Q Consensus 270 ~NcLk~a~I~tigdLv~~s~~dLl~ik 296 (340) .--|+..||+.+.|.++.+-++|.++- T Consensus 8 ~~kL~~lGInkL~Dil~~~f~klk~ii 34 (51) T 3bq0_A 8 ARRLNELGIQKLRDILSKNYNELEKIT 34 (51) T ss_dssp HHHHTTTTCCBGGGGGGSCHHHHHHHH T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHH T ss_conf 455453278747888764266788760 No 62 >>2rkh_A Putative APHA-like transcription factor; ZP_00208345.1, structural genomics, joint center for structural genomics, JCSG; 2.00A {Magnetospirillum magnetotacticum ms-1} (A:1-99) Probab=23.69 E-value=42 Score=13.99 Aligned_cols=21 Identities=19% Similarity=0.159 Sum_probs=16.8 Q ss_pred EEECCCCCHHHHHHHHHHHHH Q ss_conf 993896177799999999999 Q gi|254780237|r 205 IDTDGSITGEDSVALASRILQ 225 (340) Q Consensus 205 I~TnGsi~P~eAl~~Aa~iL~ 225 (340) .++|-|.+|+||+..+|-=++ T Consensus 2 ~~~DNtL~PkEAvRL~aLG~i 22 (99) T 2rkh_A 2 XFADNTLTPKEAVRLCALGTI 22 (99) T ss_dssp -----CCCHHHHHHHHHHHHH T ss_pred CCCCCCCCCHHHHHHHHHHHH T ss_conf 887899891779999999998 No 63 >>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A (A:111-127,A:196-236) Probab=23.64 E-value=45 Score=13.79 Aligned_cols=26 Identities=8% Similarity=0.148 Sum_probs=18.9 Q ss_pred HHHHHHCCHHH----HHCCCCCCHHHHHHH Q ss_conf 18887449888----861889886449999 Q gi|254780237|r 281 MGDLIQRTEAD----MLRMANFGRKSLVEI 306 (340) Q Consensus 281 igdLv~~s~~d----Ll~ikNfG~KSl~EI 306 (340) +..|-.++.++ |+++|+.|+|+.+=| T Consensus 20 l~~L~~l~~eea~~~L~~i~GIGpwTAdci 49 (58) T 3i0w_A 20 LEYIKSLNDNECHEELKKFMGVGPQVADCI 49 (58) T ss_dssp HHHHHHSCHHHHHHHHTTSTTCCHHHHHHH T ss_pred HHHHHHCCCHHHHHHHHHCCCCHHHHHHHH T ss_conf 899731354467899982688129999999 No 64 >>3bbo_O Ribosomal protein L16; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (O:) Probab=23.17 E-value=46 Score=13.73 Aligned_cols=26 Identities=15% Similarity=0.198 Sum_probs=22.9 Q ss_pred CEEEEEEEECCCCCHHHHHHHHHHHH Q ss_conf 18999999389617779999999999 Q gi|254780237|r 199 DKLSMTIDTDGSITGEDSVALASRIL 224 (340) Q Consensus 199 dkL~lEI~TnGsi~P~eAl~~Aa~iL 224 (340) -+.+|||+++---..++||..|+..| T Consensus 100 G~iifEi~~~~~~~a~~al~~a~~KL 125 (135) T 3bbo_O 100 GRILYEISGVAENIARRAVAIAASKM 125 (135) T ss_dssp TCEEEEECSSCTTHHHHHHHHHHHHC T ss_pred CCEEEEECCCCHHHHHHHHHHHHHHC T ss_conf 91899965999999999999998728 No 65 >>1wuu_A Galactokinase; galactosemia, GHMP superfamily, transferase; HET: GLA ANP; 2.50A {Homo sapiens} (A:223-389) Probab=23.07 E-value=47 Score=13.72 Aligned_cols=80 Identities=10% Similarity=0.129 Sum_probs=61.3 Q ss_pred CHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCC--C--------CHHH Q ss_conf 12210110588898988398371888744988886188988644999999999808312676878--9--------8677 Q gi|254780237|r 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD--W--------PPES 328 (340) Q Consensus 259 ~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~--~--------~~~~ 328 (340) -+.+-+...++..+|++.+...+|.|+..+..-|..+-+..-..++.+.+...+.+=.+|-++.+ | +++. T Consensus 66 ~~~e~~rv~~a~~al~~~d~~~lg~lm~~s~~~L~~~~~vs~peld~lv~~a~~~~Ga~GaKltGaG~GGcviaLv~~~~ 145 (167) T 1wuu_A 66 VVGEIRRTAQAAAALRRGDYRAFGRLXVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRXTGGGFGGCTVTLLEASA 145 (167) T ss_dssp HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTSCCCCHHHHHHHHHHHTSTTEEEEEECSSCSEEEEEEEEEGGG T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCEEEEEEECHHH T ss_conf 52345678899987752899999999999999999853799789999999998618972888804777718999977268 Q ss_pred HHHHHHHHHC Q ss_conf 9999987750 Q gi|254780237|r 329 IEELAKKYED 338 (340) Q Consensus 329 ~~~~~~~~~~ 338 (340) +++..+.+++ T Consensus 146 ~~~v~~~~~~ 155 (167) T 1wuu_A 146 APHAXRHIQE 155 (167) T ss_dssp HHHHHHHHHH T ss_pred HHHHHHHHHH T ss_conf 9999999999 No 66 >>3clh_A 3-dehydroquinate synthase; shikimate pathway, aromatic amino acid biosynthesis, DHQS, amino-acid biosynthesis, cytoplasm, lyase, NAD; HET: NAD; 2.40A {Helicobacter pylori} (A:161-343) Probab=23.03 E-value=34 Score=14.63 Aligned_cols=13 Identities=31% Similarity=0.787 Sum_probs=5.0 Q ss_pred CHHHHHHHHHHHH Q ss_conf 5667888999998 Q gi|254780237|r 38 GFAHTLGNALRRV 50 (340) Q Consensus 38 G~g~TlGNaLRRv 50 (340) +||||+|+|+-+. T Consensus 68 n~gHt~~HalE~~ 80 (183) T 3clh_A 68 NYGHTFGHAIEKE 80 (183) T ss_dssp TTTHHHHHHHHHH T ss_pred HCCHHHHHHHHHH T ss_conf 0122687654554 No 67 >>2uyg_A 3-dehydroquinate dehydratase; typeii 3-dehydroquinase, lyase; 2.2A {Thermus thermophilus} (A:) Probab=22.69 E-value=47 Score=13.67 Aligned_cols=23 Identities=30% Similarity=0.570 Sum_probs=10.5 Q ss_pred CHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 86449999999998083126768 Q gi|254780237|r 299 GRKSLVEIKGVLGTMGLFLGMNL 321 (340) Q Consensus 299 G~KSl~EI~~~L~~~gl~lg~~l 321 (340) |+.++++|.+.+++..-.+|..+ T Consensus 22 G~~tl~~i~~~~~~~a~~~g~~v 44 (149) T 2uyg_A 22 GRTTLEELEALCEAWGAELGLGV 44 (149) T ss_dssp CSCCHHHHHHHHHHHHHHTTCCE T ss_pred CCCCHHHHHHHHHHHHHHCCCCE T ss_conf 75699999999999999739705 No 68 >>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} (A:635-702) Probab=22.59 E-value=48 Score=13.66 Aligned_cols=43 Identities=16% Similarity=0.200 Sum_probs=30.9 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 9 ~RAR-~Ly~aGiks~~dla~ap-~~l~--~~iG~k~A~~I~~~a~~~ 51 (68) T 2p6r_A 9 VRAR-KLYNAGIRNAEDIVRHR-EKVA--SLIGRGIAERVVEGISVK 51 (68) T ss_dssp HHHH-HHHTTTCCSHHHHHHTH-HHHH--HHHCHHHHHHHHHHHHHH T ss_pred HHHH-HHHHCCCCCHHHHHCCC-HHHH--HHHCCCHHHHHHHHHHHH T ss_conf 9999-99987999999997498-8789--776346389999998787 No 69 >>3i1n_M 50S ribosomal protein L16; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_K 1p86_K 1vs8_M 2aw4_M 2awb_M 1vs6_M 2i2v_M 2j28_M 2i2t_M* 2qao_M* 2qba_M* 2qbc_M* 2qbe_M 2qbg_M 2qbi_M* 2qbk_M* 2qov_M 2qox_M 2qoz_M* 2qp1_M* ... (M:) Probab=22.52 E-value=48 Score=13.65 Aligned_cols=26 Identities=19% Similarity=0.178 Sum_probs=22.7 Q ss_pred CEEEEEEEECCCCCHHHHHHHHHHHH Q ss_conf 18999999389617779999999999 Q gi|254780237|r 199 DKLSMTIDTDGSITGEDSVALASRIL 224 (340) Q Consensus 199 dkL~lEI~TnGsi~P~eAl~~Aa~iL 224 (340) .+.++||+++---.-.+||..|+..| T Consensus 99 G~iifei~~~~~~~a~~al~~a~~KL 124 (136) T 3i1n_M 99 GKVLYEMDGVPEELAREAFKLAAAKL 124 (136) T ss_dssp TCEEEEECSSCHHHHHHHHHHHHHHC T ss_pred CCEEEEECCCCHHHHHHHHHHHHHHC T ss_conf 94899966989999999999998718 No 70 >>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} (A:) Probab=22.20 E-value=47 Score=13.72 Aligned_cols=20 Identities=20% Similarity=0.469 Sum_probs=10.3 Q ss_pred HHHHHCCCCCCHHHHHHHHH Q ss_conf 88886188988644999999 Q gi|254780237|r 289 EADMLRMANFGRKSLVEIKG 308 (340) Q Consensus 289 ~~dLl~ikNfG~KSl~EI~~ 308 (340) -+||++++++|.+.++.|+. T Consensus 52 ~~dL~~v~gl~~~~~~~l~~ 71 (75) T 2duy_A 52 VEDLLKVKGIGPATLERLRP 71 (75) T ss_dssp GGGGGGSTTCCHHHHHHHGG T ss_pred HHHHHHCCCCCHHHHHHHHH T ss_conf 99996188989999999986 No 71 >>3k17_A LIN0012 protein; protein structure initiative II(PSI II), NYSGXRC, structural genomics, NEW YORK SGX research center for structural genomics; HET: PGE; 2.10A {Listeria innocua} (A:211-350) Probab=21.48 E-value=50 Score=13.51 Aligned_cols=79 Identities=11% Similarity=0.086 Sum_probs=54.2 Q ss_pred HHHCC-CCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCC-----CCCHHHHHHHHHHHHHHCCCCCCCCCC--------C- Q ss_conf 22101-10588898988398371888744988886188-----988644999999999808312676878--------9- Q gi|254780237|r 260 VEELE-LSVRSTNCLRGENIVYMGDLIQRTEADMLRMA-----NFGRKSLVEIKGVLGTMGLFLGMNLPD--------W- 324 (340) Q Consensus 260 IeeLe-LSvRs~NcLk~a~I~tigdLv~~s~~dLl~ik-----NfG~KSl~EI~~~L~~~gl~lg~~l~~--------~- 324 (340) +++++ +...+..+|.+.++..+|.|+..+..-|..+- +.....++.+.+.....|.--.+-=.+ . T Consensus 38 ~~~~~~~~~~~~~al~~~d~~~~g~l~~~~~~~l~~l~~~~~~~is~~~l~~l~~~a~~~g~gaki~GAGgGG~v~al~~ 117 (140) T 3k17_A 38 LTRNNEIXKQIIQAFHTKDEELLYSSIKENRRILQELGTKAGVNIETSLLKELADSAENXGGAGKSSGSGGGDCGIAFSK 117 (140) T ss_dssp HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHTCCCSCHHHHHHHHHHHHTTSEEEECTTCSSSEEEEEES T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCEEEEEEC T ss_conf 99986668999987741699999999999999999754303876588999999999986793899803364018999987 Q ss_pred CHHHHHHHHHHHHC Q ss_conf 86779999987750 Q gi|254780237|r 325 PPESIEELAKKYED 338 (340) Q Consensus 325 ~~~~~~~~~~~~~~ 338 (340) ++...+.+.+.+++ T Consensus 118 ~~~~~~~i~~~~~~ 131 (140) T 3k17_A 118 TKELAEKLVNEWEK 131 (140) T ss_dssp SHHHHHHHHHHHHH T ss_pred CHHHHHHHHHHHHH T ss_conf 88999999999998 No 72 >>1ujn_A Dehydroquinate synthase; riken structural genomics/proteomics initiative, RSGI, structural genomics, lyase; 1.80A {Thermus thermophilus HB8} (A:161-348) Probab=21.27 E-value=38 Score=14.29 Aligned_cols=22 Identities=9% Similarity=-0.177 Sum_probs=15.7 Q ss_pred HHHCCCCHHHHHHHHHCCCCCH Q ss_conf 2210110588898988398371 Q gi|254780237|r 260 VEELELSVRSTNCLRGENIVYM 281 (340) Q Consensus 260 IeeLeLSvRs~NcLk~a~I~ti 281 (340) .-..+...|..++|++.++-+. T Consensus 105 ~g~~~~~~~i~~~l~~~glp~~ 126 (188) T 1ujn_A 105 LGGEDLLPPVRRLLLWLSPPPL 126 (188) T ss_dssp TTCCCCHHHHHHHHHHHCCCCC T ss_pred HCCCHHHHHHHHHHHHCCCCCC T ss_conf 3896169999999996599999 No 73 >>1gtd_A MTH169; synthetase, FGAM synthetase, purine synthesis pathway, PSI, protein structure initiative, NESG; 2.56A {Methanobacterium thermoautotrophicum} (A:) Probab=21.19 E-value=49 Score=13.57 Aligned_cols=48 Identities=17% Similarity=0.132 Sum_probs=33.7 Q ss_pred CCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHH Q ss_conf 43111144223577641168877621899999938961777999999999999888 Q gi|254780237|r 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229 (340) Q Consensus 174 Da~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~ 229 (340) .|+..-..+..|.|++.|+|. .+++|-++ -++.+|..++..+..+.|. T Consensus 21 ~aI~~aL~~lG~~V~~VRvGK-------~iel~i~~-~~~e~a~~~v~~~c~~lLa 68 (85) T 1gtd_A 21 ATIERALALLGYEVEDTDTTD-------VITFTXDE-DSLEAVEREVEDXCQRLLC 68 (85) T ss_dssp HHHHHHHHHHTCCCEEEEEEE-------EEEEEECC-SCHHHHHHHHHHHHHHTTC T ss_pred HHHHHHHHHCCCCCCEEEEEE-------EEEEEECC-CCHHHHHHHHHHHHHHHCC T ss_conf 999999986598630478766-------99999778-9989999999999998639 No 74 >>1qme_A Penicillin-binding protein 2X; peptidoglycan synthesis, resistance, cell WALL, transmembrane; 2.4A {Streptococcus pneumoniae} (A:579-649) Probab=20.88 E-value=34 Score=14.62 Aligned_cols=33 Identities=9% Similarity=-0.103 Sum_probs=25.1 Q ss_pred CCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCC Q ss_conf 498888618898864499999999980831267 Q gi|254780237|r 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319 (340) Q Consensus 287 ~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~ 319 (340) .+..+...++||-..+.++.++.|+..||.... T Consensus 4 s~~~~~v~vP~~~g~~~~~A~~~l~~~gl~~~~ 36 (71) T 1qme_A 4 VSQQSPYPMPSVKDISPGDLAEELRRNLVQPIV 36 (71) T ss_dssp ---BCCCBCCCCTTCCHHHHHHHHHTTTCEEEE T ss_pred HCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEE T ss_conf 134665218867899999999999977993398 No 75 >>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} (A:23-133) Probab=20.32 E-value=53 Score=13.36 Aligned_cols=52 Identities=13% Similarity=0.197 Sum_probs=32.1 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 50 ~~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~vl 104 (111) T 2abk_A 50 VKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVL 104 (111) T ss_dssp HHHHHTTSTTHHHHHHHHHHHHHHHHHHTTTSCCSCHHHHHHSTTCCHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHH T ss_conf 7777674115677888999999999986041136779999989860635999999 Done!