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!