Query gi|254780292|ref|YP_003064705.1| 50S ribosomal protein L13 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 155 No_of_seqs 111 out of 1699 Neff 4.9 Searched_HMMs 23785 Date Mon May 30 08:05:55 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780292.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3ofq_J 50S ribosomal protein L 100.0 0 0 402.6 6.4 142 2-144 1-142 (142) 2 3f1f_N 50S ribosomal protein L 100.0 0 0 390.4 7.7 141 1-144 23-163 (163) 3 3bbo_L Ribosomal protein L13; 100.0 0 0 392.8 5.2 150 2-152 97-249 (250) 4 2j01_N 50S ribosomal protein L 100.0 0 0 388.8 6.9 140 2-144 1-140 (140) 5 2zjr_G 50S ribosomal protein L 100.0 0 0 383.3 11.3 147 1-150 28-174 (174) 6 2ftc_H L13MT, MRP-L13, 39S rib 100.0 0 0 377.5 10.1 144 2-146 1-147 (148) 7 1j3a_A 50S ribosomal protein L 100.0 1.2E-42 0 269.7 9.5 122 17-151 2-124 (142) 8 3jyw_M 60S ribosomal protein L 100.0 6.9E-43 0 271.1 4.2 116 17-145 1-117 (178) 9 1vq8_J 50S ribosomal protein L 100.0 1E-41 0 264.2 8.5 123 10-150 4-127 (145) 10 2zkr_j 60S ribosomal protein L 100.0 1.5E-41 0 263.2 7.5 120 13-145 3-123 (203) 11 3czq_A Putative polyphosphate 26.7 27 0.0011 15.8 2.0 20 12-31 249-268 (304) 12 2cvb_A Probable thiol-disulfid 23.8 40 0.0017 14.8 2.5 18 9-26 28-47 (188) 13 2bgw_A XPF endonuclease; hydro 23.0 40 0.0017 14.8 2.3 39 14-57 8-46 (219) 14 2ziu_A MUS81 protein; helix-ha 22.8 42 0.0017 14.7 2.6 46 17-62 22-69 (311) 15 1tul_A TLP20; telokin-like pro 21.5 32 0.0013 15.4 1.5 15 48-62 63-77 (108) 16 3czp_A Putative polyphosphate 21.4 36 0.0015 15.0 1.8 21 11-31 205-225 (500) No 1 >3ofq_J 50S ribosomal protein L13; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_H 1p86_H 1vs8_J 1vs6_J 2aw4_J 2awb_J 2gya_H 2gyc_H 1vt2_J 2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J 2qbg_J 2qbi_J* 2qbk_J* 2qov_J 2qox_J ... Probab=100.00 E-value=0 Score=402.58 Aligned_cols=142 Identities=45% Similarity=0.832 Sum_probs=139.4 Q ss_pred CEEEECCHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCC Q ss_conf 51132684360200699978987457679999999846565210345566888999751010015601211333311575 Q gi|254780292|r 2 IPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGY 81 (155) Q Consensus 2 ~kT~~~k~~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgy 81 (155) |+||++++++++|+||+|||+||+||||||.||++|+|||||+|+|++||||+||||||++|++||+||.+|.||+|||| T Consensus 1 Mkt~~~k~~~~~r~W~liDA~~~~lGRlAs~iA~~L~GK~kp~y~p~~d~Gd~VvViNa~ki~~tG~K~~~k~y~~hsgy 80 (142) T 3ofq_J 1 MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGH 80 (142) T ss_dssp CCCCCCCSSSCCCCEEECCCSSSCSSHHHHHHHHHHTTTTSSCCCTTSCCCCEEECCBGGGCCCCSSCTTTCCCCEECSS T ss_pred CCCCCCCHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCHHHCCCCCCEEEEEECHHEEECCCCHHCEEEEEEEEC T ss_conf 97505884452664799968999468889999999843788630103578867999831465861861120466784105 Q ss_pred CCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEH Q ss_conf 576336302000012487999999997308998547899962701078999713208547616 Q gi|254780292|r 82 PGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDI 144 (155) Q Consensus 82 pGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~ 144 (155) |||+++.++.+++ +++|++||++||+||||+|++|+.+|+||+||+|++|||+||+|+.||+ T Consensus 81 pGg~k~~~~~~~~-~k~P~~il~~aV~gMLPkn~lgr~~~krLkvy~g~~hp~~aq~P~~l~i 142 (142) T 3ofq_J 81 IGGIKQATFEEMI-ARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI 142 (142) T ss_dssp SSCEECCCHHHHS-SSCGGGHHHHTTTTTSCCSTTHHHHHTTEECCBSSCCSCGGGCCCCCCC T ss_pred CCCCCCCCHHHHH-HHCHHHHHHHHHHHHCCCCHHHHHHHHCCEEECCCCCCCCCCCCEEECC T ss_conf 9998678989998-5287899999998817998359999848889698999965679877169 No 2 >3f1f_N 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_N Probab=100.00 E-value=0 Score=390.42 Aligned_cols=141 Identities=45% Similarity=0.894 Sum_probs=136.9 Q ss_pred CCEEEECCHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCC Q ss_conf 95113268436020069997898745767999999984656521034556688899975101001560121133331157 Q gi|254780292|r 1 MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTG 80 (155) Q Consensus 1 ~~kT~~~k~~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htg 80 (155) +||||+|+ +++|+||||||+||+||||||.||++|+|||||+|+|++||||+||||||++|.+||+||.++.||+||| T Consensus 23 ~~kt~~p~--~~~r~W~vIDA~~~~LGRLAS~IAk~L~GKhkp~y~p~~d~Gd~VvViNa~ki~itG~K~~~k~y~~~tg 100 (163) T 3f1f_N 23 LVKTYVPK--QVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSG 100 (163) T ss_dssp --CCCCCC--CCCCCBCBBCCTTCBHHHHHHHHHHHHSCTTSTTCCTTTCCCCBCEECCGGGCBCSTTHHHHCEECCBCS T ss_pred HHCCCCCC--CCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCEEEEEECCCCCCEEEEEEEC T ss_conf 41110776--5554089994899945888999999984345343155666773799943527798468541267899824 Q ss_pred CCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEH Q ss_conf 5576336302000012487999999997308998547899962701078999713208547616 Q gi|254780292|r 81 YPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDI 144 (155) Q Consensus 81 ypGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~ 144 (155) ||||+++.++.++. +++|++||++||+||||+|++|+.+|+||+||+|++|||+||+|+.|++ T Consensus 101 ~pGg~k~~~~~~~~-~r~P~~ii~raVrGMLPkn~lgr~~lkrLkvy~G~~hph~aQ~P~~l~i 163 (163) T 3f1f_N 101 YPGGLKKIPLEKML-ATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV 163 (163) T ss_dssp STTCBCCEEHHHHH-HSSCHHHHHHHHHTTSCSSHHHHHHHHTCEECSSSCCCCCSCCCBCC-- T ss_pred CCCCCCCCCHHHHC-CCCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEEECC T ss_conf 79988646524431-3488999999998658898469999848589698999845689877279 No 3 >3bbo_L Ribosomal protein L13; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Probab=100.00 E-value=0 Score=392.81 Aligned_cols=150 Identities=43% Similarity=0.758 Sum_probs=145.1 Q ss_pred CEEEECCHHH---CCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHC Q ss_conf 5113268436---0200699978987457679999999846565210345566888999751010015601211333311 Q gi|254780292|r 2 IPTFFQKSSE---VEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRH 78 (155) Q Consensus 2 ~kT~~~k~~~---~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~h 78 (155) |+||+||.++ ++|+||||||+||+||||||.||++|+|||||+|+|++||||+||||||++|++||+||.+|.|++| T Consensus 97 n~T~~pk~ad~~~~~K~W~VIDA~gqiLGRLAS~IAk~L~GKhKp~YtP~~D~GD~VVVINAekIviTG~K~~~K~Y~~h 176 (250) T 3bbo_L 97 NTTWYPKSADHVPTDKKWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNADKVAVSGKKRTQKLYRRH 176 (250) T ss_dssp ---------------CCCCEECCSSCCSSTTHHHHTTTTTTTTTTCCCTTSCCSCCCEESCCSSCCCCSGGGGTCCCBCC T ss_pred CCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCEEEEECCCEEEEEEEEEE T ss_conf 65514775667665764899959999448889999999806886763667776878999558046863750233568996 Q ss_pred CCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCCCCC Q ss_conf 57557633630200001248799999999730899854789996270107899971320854761665281312 Q gi|254780292|r 79 TGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNS 152 (155) Q Consensus 79 tgypGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~kn~ 152 (155) ||||||+++.++.+++ +++|++||++||+||||||++|+.+|+||+||+|++|||+||+|+.+++++.+.++. T Consensus 177 sGypGG~k~~~~~~l~-~R~P~~IlkrAVrGMLPKn~lGR~alKRLkVY~G~~HPheaQkP~~l~~~~~~~r~k 249 (250) T 3bbo_L 177 SGRPGGLKEETFDQLQ-KRIPERIIEHAVRGMLPKGRLGRYLFNHLKVYKGAEHPHQAQQPIDLPLRDKRIRVE 249 (250) T ss_dssp CSSSSCCCBCCHHHHT-TSCTTHHHHHHHHTTSCSSSSHHHHHTTCCCCSSSCCSCTTSCC------------- T ss_pred ECCCCCCCCCCCCCCC-CCCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCHHHCCCEECCHHHHHHHCC T ss_conf 0447887664444123-568899999999761899834999984888969999982104982525566444204 No 4 >2j01_N 50S ribosomal protein L13; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: c.21.1.1 PDB: 2hgq_M 2hgj_M 2hgu_M 2j03_N 2jl6_N 2jl8_N 2v47_N 2v49_N 2wdi_N 2wdj_N 2wdl_N 2wdn_N 2wh2_N 2wh4_N 2wrj_N 2wrl_N 2wro_N 2wrr_N 2x9s_N 2x9u_N ... Probab=100.00 E-value=0 Score=388.79 Aligned_cols=140 Identities=46% Similarity=0.892 Sum_probs=136.3 Q ss_pred CEEEECCHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCC Q ss_conf 51132684360200699978987457679999999846565210345566888999751010015601211333311575 Q gi|254780292|r 2 IPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGY 81 (155) Q Consensus 2 ~kT~~~k~~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgy 81 (155) ||||+|+ +++|+||||||+||+||||||.||++|+|||||+|+|++||||+||||||++|++||+||.++.||+|||| T Consensus 1 mkt~~p~--~~~r~W~viDA~~~~lGRLAs~vAk~L~GK~kp~y~p~~d~Gd~ViViNa~ki~itG~k~~~k~y~~~tg~ 78 (140) T 2j01_N 1 MKTYVPK--QVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGY 78 (140) T ss_dssp CCCCCCC--CCCCCCCEECCTTSBTTHHHHHHHHHHTTSSSSSCCTTTCCCCCCEECSCSCCBCSSCCSSSSBCCCCCCS T ss_pred CCCCCCC--CCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCEEEEECCCCCCEEEEEEEECC T ss_conf 9853766--34541899959999458889999999851330242668777847999656344871688651789998447 Q ss_pred CCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEH Q ss_conf 576336302000012487999999997308998547899962701078999713208547616 Q gi|254780292|r 82 PGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDI 144 (155) Q Consensus 82 pGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~ 144 (155) |||+++.++.++. .++|++||++||+||||+|++|+.+|+||+||+|++|||+||+|+.|+| T Consensus 79 pgg~k~~~~~~~~-~k~P~~il~~aVrgMLPkn~lgr~~lkrLkvy~g~~hp~~aq~p~~l~i 140 (140) T 2j01_N 79 PGGLKKIPLEKML-ATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV 140 (140) T ss_dssp SSCCCCCBHHHHH-HSSCSHHHHHHHHTTSCSSHHHHHHHTTCEECSSSCCTTCSCCCCCC-- T ss_pred CCCCCCCCHHHHH-CCCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEEECC T ss_conf 9998647788875-1278999999998747898569999858889698999855679877169 No 5 >2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.21.1.1 PDB: 1nwx_H* 1nwy_H* 1sm1_H* 1xbp_H* 2zjp_G* 2zjq_G 1nkw_H 3cf5_G* 3dll_G* 1pnu_H 1pny_H 1vor_K 1vou_K 1vow_K 1voy_K 1vp0_K Probab=100.00 E-value=0 Score=383.31 Aligned_cols=147 Identities=44% Similarity=0.792 Sum_probs=142.0 Q ss_pred CCEEEECCHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCC Q ss_conf 95113268436020069997898745767999999984656521034556688899975101001560121133331157 Q gi|254780292|r 1 MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTG 80 (155) Q Consensus 1 ~~kT~~~k~~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htg 80 (155) .||||+|+ +++|+||||||+||+||||||.||++|+|||||+|+|++||||+||||||+++.+||+||.+|.|++||| T Consensus 28 ~~kt~~pk--~~~r~W~vIDA~g~~LGRLAS~VAk~L~GK~Kp~y~p~~d~GD~ViViNa~ki~~tG~k~~~K~y~~htg 105 (174) T 2zjr_G 28 KVKTYIPK--NDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTG 105 (174) T ss_dssp --CCCCCC--CSCCCEEEEECTTSBHHHHHHHHHHHHHCSSCSSCCSSSCCCCEEEEECCTTCBCSSCSSSSCEEEECCS T ss_pred EEEEECCC--CCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCEECCCCCCCCEEEEECCEEEEECCCCEEEEEEEEEEC T ss_conf 45785478--7766689996999946888999999984588750556856676699961417898265200036888703 Q ss_pred CCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCCC Q ss_conf 5576336302000012487999999997308998547899962701078999713208547616652813 Q gi|254780292|r 81 YPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPK 150 (155) Q Consensus 81 ypGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~k 150 (155) ||||++++++.+++ +++|++||++||+||||+|++|+.+|+||+||+|++|||++|+|+.|+++.+|.| T Consensus 106 ~pGg~k~~~~~~~~-~r~P~~Il~rAVrGMLPKn~lgr~~lkrLkVy~G~~HPh~aq~P~~l~~~~~~~k 174 (174) T 2zjr_G 106 YQGGLKTETAREAL-SKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK 174 (174) T ss_dssp SCSSCCEEEESTTT-TSCHHHHHHHHHGGGSCCSHHHHHHHTTCEECSCSTGGGGSCCSCCCCCCCC--- T ss_pred CCCCCCCCCCCHHH-HCCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCHHHCCCCEECCCCCCCC T ss_conf 36886434321434-2173678999998718998659999848878589999932139836424357779 No 6 >2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Probab=100.00 E-value=0 Score=377.45 Aligned_cols=144 Identities=37% Similarity=0.676 Sum_probs=139.1 Q ss_pred CEEEECCHH---HCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHC Q ss_conf 511326843---60200699978987457679999999846565210345566888999751010015601211333311 Q gi|254780292|r 2 IPTFFQKSS---EVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRH 78 (155) Q Consensus 2 ~kT~~~k~~---~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~h 78 (155) |+||+.++. +++|+||||||+|++||||||.||++|+|||||+|+|++||||+||||||++|++||+||.+|.|++| T Consensus 1 m~~~~~~~q~~~~~~r~W~viDA~~~~lGRLAs~VAk~L~GK~kp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~h 80 (148) T 2ftc_H 1 MSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFSGNKWEQKVYSSH 80 (148) T ss_pred CCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCEEEECCCHHHHEEEEEE T ss_conf 97634575533321417999948999268889999999835876535546567868999735128972621220466775 Q ss_pred CCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHH Q ss_conf 57557633630200001248799999999730899854789996270107899971320854761665 Q gi|254780292|r 79 TGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAK 146 (155) Q Consensus 79 tgypGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~ 146 (155) ||||||+++.+++++. .++|++||++||+||||+|++|+.+|+||+||+|++|||++|+|+.+++.+ T Consensus 81 tg~pgg~k~~~~~~~~-~r~P~~il~raVrgMLPkn~~gr~~lkrLkvy~g~~hP~~~q~p~~~~i~q 147 (148) T 2ftc_H 81 TGYPGGFRQVTAAQLH-LRDPVAIVKLAIYGMLPKNLHRRTMMERLHLFPDEYIPEDILKNLVEELPQ 147 (148) T ss_pred EEECCCCCCCCCCHHC-CCCHHHHHHHHHHHHCCCCHHHHHHHHCCEECCCCCCCHHHHCCCCCCCCC T ss_conf 3216862124520001-357689999999984899811999985857768999986774855346799 No 7 >1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly, ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1 Probab=100.00 E-value=1.2e-42 Score=269.68 Aligned_cols=122 Identities=25% Similarity=0.385 Sum_probs=115.4 Q ss_pred EEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCCC Q ss_conf 99978987457679999999846565210345566888999751010015601211333311575576336302000012 Q gi|254780292|r 17 ILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAG 96 (155) Q Consensus 17 ~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~~~~~~ 96 (155) -||||+||+||||||.||++|+ |||+||||||+++++||+||..+.||+|+++|||++..+..+++ + T Consensus 2 ~vIDA~g~~LGRlAs~iAk~L~------------~Gd~VvVvNaekv~~tG~k~~~~~~~~~~~~~~~~~~~~~~~~~-~ 68 (142) T 1j3a_A 2 RIINADGLILGRLASRVAKMLL------------EGEEVVIVNAEKAVITGNREVIFSKYKQRTGLRTLTNPRRGPFY-P 68 (142) T ss_dssp EEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGCEEESCHHHHHHHHHHHC-------------C-C T ss_pred EEEECCCCCHHHHHHHHHHHHC------------CCCEEEEEECCEEEEECCCCEEEEEEECCCCCCCCCCCCHHHHC-C T ss_conf 7996899832789999999980------------89969999750058837763010214435755532552067652-4 Q ss_pred CCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCCCC Q ss_conf 4879999999973089-985478999627010789997132085476166528131 Q gi|254780292|r 97 ASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKN 151 (155) Q Consensus 97 ~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~kn 151 (155) ++|++||++||+|||| +|++|+.+|+||+||+|++|||++|+|+.++.+++++.+ T Consensus 69 ~~P~~il~~aVrgMLP~k~~lgr~~~~rLkvy~G~ph~~~~q~~~~i~~a~~~~~~ 124 (142) T 1j3a_A 69 KRSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQDKQLETIVEAHVSRLS 124 (142) T ss_dssp CSHHHHHHHHHHTTTTTTSHHHHHHHTTEEECSSCCGGGTTSCCBCCGGGBGGGSS T ss_pred CCHHHHHHHHHHCCCCCCCHHHHHHHHCCEEECCCCCCHHHCCCCCCCHHHHHHHC T ss_conf 47599999998546888986799998388897799997221697126678876404 No 8 >3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_M Probab=100.00 E-value=6.9e-43 Score=271.13 Aligned_cols=116 Identities=25% Similarity=0.404 Sum_probs=109.6 Q ss_pred EEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCCC Q ss_conf 99978987457679999999846565210345566888999751010015601211333311575576336302000012 Q gi|254780292|r 17 ILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAG 96 (155) Q Consensus 17 ~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~~~~~~ 96 (155) .||||+|++||||||.||++|+ +||+|||||||+|.+||+||.+|.||+|||||||++..++..++ + T Consensus 1 IVIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNAeki~iTG~K~~~k~yy~~~g~~gg~k~~~~g~~~-~ 67 (178) T 3jyw_M 1 VVIDGKGHLVGRLASVVAKQLL------------NGQKIVVVRAEELNISGEFFRNKLKYHDFLRKATAFNKTRGPFH-F 67 (178) T ss_dssp CCCCCCSSCSHHHHHHHHHHHT------------TTCCCCEECSTTSCCCCCSSHHHHSCSSSSSSTTSCCCSSSCCC-C T ss_pred CEEECCCCCHHHHHHHHHHHHC------------CCCEEEEEEEEEEEECCCCCEEEEEEEEEECCCCCCCCCHHHHH-C T ss_conf 9895899966888999999972------------89979999711079747401468999842015664685778873-4 Q ss_pred CCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHH Q ss_conf 4879999999973089-985478999627010789997132085476166 Q gi|254780292|r 97 ASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIA 145 (155) Q Consensus 97 ~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~ 145 (155) ++|++||+++|+|||| ||++|+.+|+||+||+|.+|||++|+|+.++-. T Consensus 68 r~P~~Il~rAVrGMLP~K~~~Gr~alkrLkVY~G~php~~~qk~~~i~~A 117 (178) T 3jyw_M 68 RAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQA 117 (178) T ss_dssp SSTTTHHHHHTTSSSCSSSHHHHHHHHHCCEESSCCCCSCCSCSSSCCSS T ss_pred CCHHHHHHHHHHCCCCCCCHHHHHHHHCCEEECCCCCCHHCCCCEECCHH T ss_conf 37589999998456899993699998387897899997211788726447 No 9 >1vq8_J 50S ribosomal protein L13P; 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.21.1.1 PDB: 1giy_M 1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K* 1kqs_I* 1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K* 1q81_K* 1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ... Probab=100.00 E-value=1e-41 Score=264.22 Aligned_cols=123 Identities=23% Similarity=0.379 Sum_probs=111.4 Q ss_pred HHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEE Q ss_conf 36020069997898745767999999984656521034556688899975101001560121133331157557633630 Q gi|254780292|r 10 SEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTT 89 (155) Q Consensus 10 ~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~ 89 (155) ++++ +|.||||+|++||||||.||+.|. +||+||||||+++.+||+||.++.||+|+|||||.+.. T Consensus 4 ~~~~-k~ivIDA~~~~lGRLAs~vAk~ll------------~Gd~ViVvNaeki~itG~k~~~k~~y~~~~~~g~~kg~- 69 (145) T 1vq8_J 4 AEFD-ADVIVDARDCIMGRVASQVAEQAL------------DGETVAVVNAERAVITGREEQIVEKYEKRVDIGNDNGY- 69 (145) T ss_dssp CCCC-CSEEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGCEEESCHHHHHHHHHHHHHCCCSSCC- T ss_pred HHCC-CEEEEECCCCCHHHHHHHHHHHHC------------CCCEEEEEEHHHHEECCCHHHHHHEEEEECCCCCCCCE- T ss_conf 4537-619997999845888999989854------------89979999848924048616520102464357986632- Q ss_pred CCCCCCCCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCCC Q ss_conf 20000124879999999973089-98547899962701078999713208547616652813 Q gi|254780292|r 90 AKEILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPK 150 (155) Q Consensus 90 ~~~~~~~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~k 150 (155) +++++|++||++||+|||| +|++|+.+|+||+||+|++|||++|+|+..++..+... T Consensus 70 ----~~~r~P~~il~raVrGMLP~k~~~Gr~~lkrLkvy~G~~h~~~~q~~~~~~l~~~~~~ 127 (145) T 1vq8_J 70 ----FYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLDGTSLDRLSNI 127 (145) T ss_dssp ----CCCCSHHHHHHHHHHTTTTTTSHHHHHHHHTEEECSSCCSSSCCBCCTTCBCCTTSCC T ss_pred ----EHHCCHHHHHHHHHHCCCCCCCCHHHHHHHCCEEECCCCCCCCCCCCCHHHHHCCCCC T ss_conf ----0211889999999841589998068999838789779998723466776677525898 No 10 >2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Probab=100.00 E-value=1.5e-41 Score=263.24 Aligned_cols=120 Identities=21% Similarity=0.333 Sum_probs=112.6 Q ss_pred CEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCC Q ss_conf 20069997898745767999999984656521034556688899975101001560121133331157557633630200 Q gi|254780292|r 13 EKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKE 92 (155) Q Consensus 13 ~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~~ 92 (155) +.+|.||||+|++||||||.||+.| |+||+|||||||+|.+||+++.++.||+|++||||.+..+... T Consensus 3 e~k~ivIDA~g~iLGRLAS~VAk~L------------l~Gd~VvVVNaeki~isG~k~~~k~~y~~~~~~~~~~~~~~g~ 70 (203) T 2zkr_j 3 EVQVLVLDGRGHLLGRLAAIVAKQV------------LLGRKVVVVRCEGINISGNFYRNKLNYLAFLRKRMNTNPSRGP 70 (203) T ss_dssp ----CEEECTTBBHHHHHHHHHHHH------------HHTCCEEEECGGGCEEESCHHHHHHHSSSSSCHHHHCCCSSCC T ss_pred CCEEEEEECCCCCHHHHHHHHHHHH------------CCCCEEEEEECHHEEECCCHHHHHHHHEEEECCCCCCCCCHHH T ss_conf 7449999689980488899999986------------4899699996035487275476653430010588886787677 Q ss_pred CCCCCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHH Q ss_conf 00124879999999973089-985478999627010789997132085476166 Q gi|254780292|r 93 ILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIA 145 (155) Q Consensus 93 ~~~~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~ 145 (155) + +.++|++|+++||+|||| +|++|+.+|+||+||+|.+|||++|+|+.+.-+ T Consensus 71 ~-~~r~P~~Il~raVrGMLP~K~~~Gr~alkrLkvy~G~p~p~~~~k~~vvp~a 123 (203) T 2zkr_j 71 Y-DFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAA 123 (203) T ss_dssp C-CCCSHHHHHHHHHHHHSCTTSHHHHHHHHTEEECSCSSCSSSSCCBCCGGGB T ss_pred H-HHCCHHHHHHHHHHCCCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEECCHH T ss_conf 5-3037779999998533778985599998488796689997556765536337 No 11 >3czq_A Putative polyphosphate kinase 2; structural genomics, APC6299, PSI-2, protein structure initiative; HET: MSE GOL; 2.23A {Sinorhizobium meliloti 1021} Probab=26.69 E-value=27 Score=15.78 Aligned_cols=20 Identities=10% Similarity=0.273 Sum_probs=14.0 Q ss_pred CCEEEEEEECCCCCHHHHHH Q ss_conf 02006999789874576799 Q gi|254780292|r 12 VEKKWILVDAKGLIVGRLAS 31 (155) Q Consensus 12 ~~r~W~iiDA~~~~lGRlAs 31 (155) -.--||||+|.++-..||.. T Consensus 249 ~~APW~VI~a~dK~~arl~v 268 (304) T 3czq_A 249 EHGPWAVIRGNDKRRSRINV 268 (304) T ss_dssp SSSCEEEEECSSHHHHHHHH T ss_pred CCCCEEEECCCCCHHHHHHH T ss_conf 99993897288808999999 No 12 >2cvb_A Probable thiol-disulfide isomerase/thioredoxin; redox protein, structural genomics, riken structural genomics/proteomics initiative; 1.80A {Thermus thermophilus HB8} SCOP: c.47.1.10 PDB: 2ywo_A Probab=23.79 E-value=40 Score=14.79 Aligned_cols=18 Identities=11% Similarity=-0.016 Sum_probs=11.1 Q ss_pred HHHCCEEEEEEE--CCCCCH Q ss_conf 436020069997--898745 Q gi|254780292|r 9 SSEVEKKWILVD--AKGLIV 26 (155) Q Consensus 9 ~~~~~r~W~iiD--A~~~~l 26 (155) .++++-++.||+ |.+... T Consensus 28 Lsd~~gk~vvl~FwatwCp~ 47 (188) T 2cvb_A 28 LSQFHEPLLAVVFMCNHCPY 47 (188) T ss_dssp GGGCCSSEEEEEEECSSCHH T ss_pred HHHHCCCEEEEEEECCCCCC T ss_conf 89969995999998989974 No 13 >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=22.97 E-value=40 Score=14.79 Aligned_cols=39 Identities=18% Similarity=0.164 Sum_probs=28.2 Q ss_pred EEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEE Q ss_conf 00699978987457679999999846565210345566888999 Q gi|254780292|r 14 KKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVI 57 (155) Q Consensus 14 r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvV 57 (155) +.-.|||.+.. .+.+..+|..+.-..-.-..++|||++. T Consensus 8 ~~~iviD~RE~-----~s~~~~~l~~~gi~~~~~~L~~GD~~i~ 46 (219) T 2bgw_A 8 RPRVYVDVREE-----RSPVPSILESLGVQVIPKQLPMGDYLVS 46 (219) T ss_dssp SCEEEEETTTT-----TSSHHHHHHHTTCEEEEECCSSSSEEEE T ss_pred CCEEEEECCCC-----CCHHHHHHHHCCCEEEEEECCCCCEEEE T ss_conf 97799989998-----7366899997899799976797899987 No 14 >2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A Probab=22.81 E-value=42 Score=14.68 Aligned_cols=46 Identities=13% Similarity=0.106 Sum_probs=32.8 Q ss_pred EEEECCCCCHHH--HHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCC Q ss_conf 999789874576--7999999984656521034556688899975101 Q gi|254780292|r 17 ILVDAKGLIVGR--LASQIALRLRGKNKPTYTPSADDGDHVVIINASK 62 (155) Q Consensus 17 ~iiDA~~~~lGR--lAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~k 62 (155) .|||-+....++ ..+.+...|....-..-.-..++||++++.+++. T Consensus 22 lvvD~RE~~~~~~~~~~~l~~~l~~~gi~~~~~~L~vGD~i~~~~~~~ 69 (311) T 2ziu_A 22 LCVDLCETTGGSSVRKQELVKELQRNSVTFDVRKLNVGDFLWVARERV 69 (311) T ss_dssp EEECGGGSCC-----CCHHHHHHHTTTCCEECCCCSSCSEEEEEEECC T ss_pred EEEECCCCCCCCCCHHHHHHHHHHHCCCEEEEEECCCCCEEEEECCCC T ss_conf 999888876665413899999999789948999888688899941565 No 15 >1tul_A TLP20; telokin-like protein; 2.20A {Autographa californicanucleopolyhedrovirus} SCOP: b.85.5.1 Probab=21.48 E-value=32 Score=15.36 Aligned_cols=15 Identities=20% Similarity=0.233 Sum_probs=11.6 Q ss_pred CCCCCCEEEEECCCC Q ss_conf 556688899975101 Q gi|254780292|r 48 SADDGDHVVIINASK 62 (155) Q Consensus 48 ~~d~GD~VvViNa~k 62 (155) -+-||||+|+-|.-+ T Consensus 63 ~v~cGdY~V~~N~~~ 77 (108) T 1tul_A 63 TVSCGNYGVLCNLVQ 77 (108) T ss_dssp EEESSSEEEEEECCS T ss_pred EEEECCEEEEEECCC T ss_conf 999388899997113 No 16 >3czp_A Putative polyphosphate kinase 2; PPK2, MCSG, PSI-2, structural genomics, protein structure initiative; HET: MSE; 2.00A {Pseudomonas aeruginosa PAO1} Probab=21.41 E-value=36 Score=15.05 Aligned_cols=21 Identities=14% Similarity=0.178 Sum_probs=16.2 Q ss_pred HCCEEEEEEECCCCCHHHHHH Q ss_conf 602006999789874576799 Q gi|254780292|r 11 EVEKKWILVDAKGLIVGRLAS 31 (155) Q Consensus 11 ~~~r~W~iiDA~~~~lGRlAs 31 (155) +-.--||||||.++-..|+.. T Consensus 205 t~~APW~vI~addk~~a~l~v 225 (500) T 3czp_A 205 RDYAPWYVVEGADERYRALTV 225 (500) T ss_dssp BTTBCEEEEECSCHHHHHHHH T ss_pred CCCCCEEEEECCCHHHHHHHH T ss_conf 999981898078889999999 Done!