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 33803
Date          Wed Jun  1 11:56:54 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780292.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >3bbo_L Ribosomal protein L13; 100.0       0       0  398.7   5.2  152    1-153    96-250 (250)
  2 >2zjr_G 50S ribosomal protein  100.0       0       0  391.9  11.1  148    2-150    27-174 (174)
  3 >3i1n_J 50S ribosomal protein  100.0       0       0  386.6  11.6  142    2-144     1-142 (142)
  4 >3f1f_N 50S ribosomal protein  100.0       0       0  386.7   7.5  141    1-144    23-163 (163)
  5 >2ftc_H L13MT, MRP-L13, 39S ri 100.0       0       0  360.0   9.8  131   15-146     1-131 (132)
  6 >1j3a_A 50S ribosomal protein  100.0       0       0  290.7   9.8  125   17-154     2-127 (142)
  7 >1vq8_J 50S ribosomal protein  100.0 1.4E-45       0  288.7   8.1  127    9-152     2-129 (145)
  8 >2j01_N 50S ribosomal protein  100.0 1.4E-45       0  289.0   6.9  111    2-144     1-111 (111)
  9 >2zkr_j 60S ribosomal protein  100.0 5.9E-44       0  278.3   7.8  124   13-149     3-127 (203)
 10 >3jyw_M 60S ribosomal protein  100.0 2.7E-44       0  280.2   4.6  122   17-151     1-123 (141)
 11 >2j01_N 50S ribosomal protein   97.3 3.9E-05 1.1E-09   50.9  -0.2   28   67-94      1-28  (29)
 12 >2ziu_A MUS81 protein; helix-h  32.4      39  0.0012   15.7   2.9   53   11-63     16-70  (229)
 13 >1tul_A TLP20; telokin-like pr  27.8      29 0.00085   16.5   1.5   13   49-61     64-76  (108)
 14 >2e31_A FBS1, F-box only prote  20.7      60  0.0018   14.6   2.0   83    3-93     38-141 (165)

No 1  
>>3bbo_L Ribosomal protein L13; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (L:)
Probab=100.00  E-value=0  Score=398.74  Aligned_cols=152  Identities=43%  Similarity=0.752  Sum_probs=146.9

Q ss_pred             CCEEEECCHHH---CCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHH
Q ss_conf             95113268436---020069997898745767999999984656521034556688899975101001560121133331
Q gi|254780292|r    1 MIPTFFQKSSE---VEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYR   77 (155)
Q Consensus         1 ~~kT~~~k~~~---~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~   77 (155)
                      ||+||+++.++   ++|+||||||+||+||||||.||++|+|||||+|||++||||+||||||++|++||+||.+|.||+
T Consensus        96 ~~~t~~~k~~~~~~~~r~W~vIDA~~~~LGRLAs~IAk~L~GKhKp~ytP~~d~Gd~VIVVNa~ki~itG~k~~~k~y~~  175 (250)
T 3bbo_L           96 WNTTWYPKSADHVPTDKKWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNADKVAVSGKKRTQKLYRR  175 (250)
T ss_dssp             ----------------CCCCEECCSSCCSSTTHHHHTTTTTTTTTTCCCTTSCCSCCCEESCCSSCCCCSGGGGTCCCBC
T ss_pred             CCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCHHEEECCCHHHHHEEEE
T ss_conf             15441367566666576489995899946888999999980477775066767785699835501050560333210011


Q ss_pred             CCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCCCCCC
Q ss_conf             1575576336302000012487999999997308998547899962701078999713208547616652813123
Q gi|254780292|r   78 HTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSR  153 (155)
Q Consensus        78 htgypGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~kn~~  153 (155)
                      |||||||+++.++.+++ .++|++||++||+||||+|++|+.+|+||+||+|++|||++|+|+.+++.++++++.+
T Consensus       176 htg~pGg~k~~~~~~~~-~r~P~~Ii~~aVrgMLPkn~lgr~~lkrLkvy~g~~hp~~~qkp~~l~~~~~~~~~kr  250 (250)
T 3bbo_L          176 HSGRPGGLKEETFDQLQ-KRIPERIIEHAVRGMLPKGRLGRYLFNHLKVYKGAEHPHQAQQPIDLPLRDKRIRVEK  250 (250)
T ss_dssp             CCSSSSCCCBCCHHHHT-TSCTTHHHHHHHHTTSCSSSSHHHHHTTCCCCSSSCCSCTTSCC--------------
T ss_pred             ECCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEECCHHHHHHHHCC
T ss_conf             11333445543223224-5688899999987418998459999749789689999712359715366674443049


No 2  
>>2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (G:)
Probab=100.00  E-value=0  Score=391.85  Aligned_cols=148  Identities=43%  Similarity=0.739  Sum_probs=144.9

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        27 ~~t~~~~~~~~~r~W~viDA~~~~lGRLAs~iA~~L~GKhKp~y~P~~d~Gd~ViVINa~~v~~tG~k~~~k~y~~htg~  106 (174)
T 2zjr_G           27 FKVKTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGY  106 (174)
T ss_dssp             ---CCCCCCCSCCCEEEEECTTSBHHHHHHHHHHHHHCSSCSSCCSSSCCCCEEEEECCTTCBCSSCSSSSCEEEECCSS
T ss_pred             EEEEECCCCCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCEEEEECCCEEEECCCCEEEEEEEEECCC
T ss_conf             11243158867655899969999468899999999726887646513457867999435336854863135676640124


Q ss_pred             CCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCCC
Q ss_conf             576336302000012487999999997308998547899962701078999713208547616652813
Q gi|254780292|r   82 PGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPK  150 (155)
Q Consensus        82 pGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~k  150 (155)
                      |||+++.++++++ .++|++||++||+||||+|++|+.+|+||+||+|++|||++|+|+.+++.++++|
T Consensus       107 pgg~k~~~~~~~~-~r~P~~ii~~aV~gMLPkn~~gr~~l~rL~vy~g~~hp~~~qkp~~l~i~~~~~k  174 (174)
T 2zjr_G          107 QGGLKTETAREAL-SKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK  174 (174)
T ss_dssp             CSSCCEEEESTTT-TSCHHHHHHHHHGGGSCCSHHHHHHHTTCEECSCSTGGGGSCCSCCCCCCCC---
T ss_pred             CCCCCCCCHHHHC-CCCHHHHHHHHHHHHCCCCHHHHHHHHCCEEECCCCCCHHHCCCCEECCCCCCCC
T ss_conf             5543321024430-2377899999999628998669999848868589999843239817524357779


No 3  
>>3i1n_J 50S ribosomal protein L13; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_H 1p86_H 1vs8_J 2aw4_J 2awb_J 2gya_H 2gyc_H 1vs6_J 2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J 2qbg_J 2qbi_J* 2qbk_J* 2qov_J 2qox_J 2qoz_J* ... (J:)
Probab=100.00  E-value=0  Score=386.56  Aligned_cols=142  Identities=45%  Similarity=0.832  Sum_probs=139.7

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 m~t~~~~~~~~~r~W~viDA~~~~lGRlAs~iA~~L~GK~kp~y~p~~d~Gd~VvViNa~~i~~tG~k~~~k~y~~htg~   80 (142)
T 3i1n_J            1 MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGH   80 (142)
T ss_dssp             CCCCCCCTTTCCCCEEEEECSSCBTTHHHHHHHHHHHTTTSSCCCTTSCCCCEEEEECGGGCBCCTTHHHHCCCEEECSS
T ss_pred             CCCCCCCHHHHCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCEECCCCEEEEEEEEEEEC
T ss_conf             97625885671652899969999579999999999864788751002467757999966301213874047898864225


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~~~~~~~~~~-~r~P~~i~~~aVrgMLPkn~~g~~~l~rL~iy~g~~hp~~~q~p~~l~~  142 (142)
T 3i1n_J           81 IGGIKQATFEEMI-ARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI  142 (142)
T ss_dssp             TTCEEECCHHHHH-HSCTHHHHHHHHHHHSCSSHHHHHHHTTEECCSSSCCSCGGGCCEECCC
T ss_pred             CCCCCCCCHHHHH-HHHHHHHHHHHHHHHCCCCHHHHHHHHCCEEECCCCCCCCCCCCEEECC
T ss_conf             9975300279998-6678899999997417998559999848789698999844569877269


No 4  
>>3f1f_N 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_N (N:)
Probab=100.00  E-value=0  Score=386.69  Aligned_cols=141  Identities=45%  Similarity=0.891  Sum_probs=136.6

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~~~--~~~~r~W~viDA~~~~lGRLAs~IAk~L~GKhKp~y~P~~d~Gd~VIVINa~ki~~tG~k~~~k~y~~htg  100 (163)
T 3f1f_N           23 LVKTYVP--KQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSG  100 (163)
T ss_dssp             --CCCCC--CCCCCCBCBBCCTTCBHHHHHHHHHHHHSCTTSTTCCTTTCCCCBCEECCGGGCBCSTTHHHHCEECCBCS
T ss_pred             HEEEECC--CCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCEEEEECCCCCEEEEEEEEC
T ss_conf             1112168--76565379994899936888999999984456464265666698899975822798368431067899824


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~~~~~~~~~-k~P~~ii~~aV~gMLPkn~lgr~~lkrL~vy~g~~hp~~~qkp~~l~i  163 (163)
T 3f1f_N          101 YPGGLKKIPLEKMLA-THPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV  163 (163)
T ss_dssp             STTCBCCEEHHHHHH-SSCHHHHHHHHHTTSCSSHHHHHHHHTCEECSSSCCCCCSCCCBCC--
T ss_pred             CCCCCCCCCHHHHHC-CCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEEECC
T ss_conf             799876372566512-388999999998637998669999858879698999855679867169


No 5  
>>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} (H:17-148)
Probab=100.00  E-value=0  Score=360.04  Aligned_cols=131  Identities=40%  Similarity=0.710  Sum_probs=128.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCC
Q ss_conf             06999789874576799999998465652103455668889997510100156012113333115755763363020000
Q gi|254780292|r   15 KWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEIL   94 (155)
Q Consensus        15 ~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~~~~   94 (155)
                      .||||||+||+||||||.||++|+|||||+|||++||||+||||||++|++||+||.+|.|++|||||||+++.++.+++
T Consensus         1 ~W~viDA~~~~lGRlAs~vA~~L~GKhKp~y~P~~d~Gd~ViViNa~~i~~tG~k~~~k~y~~ht~~~gg~~~~~~~~~~   80 (132)
T 2ftc_H            1 IWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLH   80 (132)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEECCCCEEEEEEEEEEEECCHHHHHHHHHHCCCCCCCCCCCCHHHHH
T ss_conf             69999489993688999999998448863157641267589996111268612155555443101123555655588875


Q ss_pred             CCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHH
Q ss_conf             1248799999999730899854789996270107899971320854761665
Q gi|254780292|r   95 AGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAK  146 (155)
Q Consensus        95 ~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~  146 (155)
                       .++|++|+++||+||||+|++|+.+|+||+||+|++|||++|+|+.+++.+
T Consensus        81 -~r~P~~ii~~aVkgMLPkn~~gr~~l~rL~vy~g~~hp~~~q~p~~~~i~q  131 (132)
T 2ftc_H           81 -LRDPVAIVKLAIYGMLPKNLHRRTMMERLHLFPDEYIPEDILKNLVEELPQ  131 (132)
T ss_pred             -CCCHHHHHHHHHHHHCCCCHHHHHHHHCCEECCCCCCCHHHHCCCCCCCCC
T ss_conf             -158379999999984799720999985857768999986772844125789


No 6  
>>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly, ribosome; 1.60A {Pyrococcus horikoshii} (A:)
Probab=100.00  E-value=0  Score=290.73  Aligned_cols=125  Identities=24%  Similarity=0.371  Sum_probs=120.2

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~~~~lGRlAs~IAk~L~g------------Gd~VvViNa~~i~~tG~k~~~k~y~~ht~~~gg~~~~~~~~~~-~   68 (142)
T 1j3a_A            2 RIINADGLILGRLASRVAKMLLE------------GEEVVIVNAEKAVITGNREVIFSKYKQRTGLRTLTNPRRGPFY-P   68 (142)
T ss_dssp             EEEECTTBBHHHHHHHHHHHHHT------------TCCEEEECGGGCEEESCHHHHHHHHHHHC-------------C-C
T ss_pred             EEEECCCCCHHHHHHHHHHHHHC------------CCEEEEEECHHEEEECCCHHEEEEEECCCCCCCCCCCCHHHHC-C
T ss_conf             79978998227899999999808------------9969999742418717840201234202345643663067651-4


Q ss_pred             CCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCCCCCCC
Q ss_conf             4879999999973089-985478999627010789997132085476166528131236
Q gi|254780292|r   97 ASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSRR  154 (155)
Q Consensus        97 ~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~kn~~~  154 (155)
                      ++|++|+++||+|||| +|++|+.+|+||+||+|++|||++|+|+.++++++++++.++
T Consensus        69 r~P~~ii~~aV~gMLP~k~~~gr~~l~rL~vy~g~~hp~~~~~~~~~~~~~~~~~~~rk  127 (142)
T 1j3a_A           69 KRSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQDKQLETIVEAHVSRLSRPK  127 (142)
T ss_dssp             CSHHHHHHHHHHTTTTTTSHHHHHHHTTEEECSSCCGGGTTSCCBCCGGGBGGGSSSCC
T ss_pred             CCHHHHHHHHHHCCCCCCCHHHHHHHHCCEEECCCCCCHHHCCCCCCCHHHHHHHCCCC
T ss_conf             48899999998556888985799998388897799997221687016678876304896


No 7  
>>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} (J:)
Probab=100.00  E-value=1.4e-45  Score=288.71  Aligned_cols=127  Identities=22%  Similarity=0.321  Sum_probs=118.6

Q ss_pred             HHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEE
Q ss_conf             43602006999789874576799999998465652103455668889997510100156012113333115755763363
Q gi|254780292|r    9 SSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKT   88 (155)
Q Consensus         9 ~~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~   88 (155)
                      +.+++|+||||||+||+||||||.||+.|+            |||+||||||++|++||+||.+|.|++|||||||++..
T Consensus         2 a~~~~r~w~viDA~~~~lGRlAs~iA~~l~------------~Gd~VvVvNa~~i~~tG~k~~~k~y~~ht~~~g~~~~~   69 (145)
T 1vq8_J            2 SVAEFDADVIVDARDCIMGRVASQVAEQAL------------DGETVAVVNAERAVITGREEQIVEKYEKRVDIGNDNGY   69 (145)
T ss_dssp             --CCCCCSEEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGCEEESCHHHHHHHHHHHHHCCCSSCC
T ss_pred             CHHHCCCEEEEECCCCCHHHHHHHHHHHHC------------CCCEEEEEECHHHCCCCCHHHHHHHHEEEECCCCCCCE
T ss_conf             633427639997999873887999999863------------89879999671312257324421110355136885425


Q ss_pred             ECCCCCCCCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCCCCC
Q ss_conf             020000124879999999973089-9854789996270107899971320854761665281312
Q gi|254780292|r   89 TAKEILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNS  152 (155)
Q Consensus        89 ~~~~~~~~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~kn~  152 (155)
                      .     +.++|++||++||+|||| ++.+|+.+|+||+||+|++|||++|+|+.+++...++.+.
T Consensus        70 ~-----~~r~P~~ii~~aV~gMLP~k~~~gr~~l~rL~vy~g~~hp~~~~~~~~~~~~~~~~~~~  129 (145)
T 1vq8_J           70 F-----YPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLDGTSLDRLSNIKF  129 (145)
T ss_dssp             C-----CCCSHHHHHHHHHHTTTTTTSHHHHHHHHTEEECSSCCSSSCCBCCTTCBCCTTSCCSE
T ss_pred             E-----HHCCHHHHHHHHHHCCCCCCCCHHHHHHHCCEEECCCCCCCCCCCCCHHHHHCCCCCCE
T ss_conf             5-----11298899999984516789904789973757807999964456776356641489856


No 8  
>>2j01_N 50S ribosomal protein L13; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (N:1-63,N:93-140)
Probab=100.00  E-value=1.4e-45  Score=289.05  Aligned_cols=111  Identities=43%  Similarity=0.867  Sum_probs=105.8

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~~~--~~~~r~W~iiDA~~q~lGrlA~~ia~~L~GKhKp~y~P~~d~GD~VVViNa~~i~~t---------------   63 (111)
T 2j01_N            1 MKTYVP--KQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVT---------------   63 (111)
T ss_dssp             CCCCCC--CCCCCCCCEECCTTSBTTHHHHHHHHHHTTSSSSSCCTTTCCCCCCEECSCSCCBCS---------------
T ss_pred             CCCCCC--CCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCHHCEEECCCCCCEEEEEEHHHEEEC---------------
T ss_conf             986575--535530899969999558889999999846431103113578737999500445742---------------


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        64 ---------------R~P~~I~~r~VRGMLPK~~~G~~alkrLkvy~G~P~~~~~~~~~~ipi  111 (111)
T 2j01_N           64 ---------------THPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV  111 (111)
T ss_dssp             ---------------SSCSHHHHHHHHTTSCSSHHHHHHHTTCEECSSSCCTTCSCCCCCC--
T ss_pred             ---------------CCHHHHHHHHHHHHCCCCHHHHHHHHCCEEECCCCCCCCCCCCEEECC
T ss_conf             ---------------486899999999618997569999848789698999855689867169


No 9  
>>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} (j:)
Probab=100.00  E-value=5.9e-44  Score=278.30  Aligned_cols=124  Identities=20%  Similarity=0.297  Sum_probs=117.1

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 ~r~w~viDA~~~~lGRlAs~iAk~L~------------~G~~VvVvn~e~i~isG~k~~~k~~~~h~~~~g~~~~~~~g~   70 (203)
T 2zkr_j            3 EVQVLVLDGRGHLLGRLAAIVAKQVL------------LGRKVVVVRCEGINISGNFYRNKLNYLAFLRKRMNTNPSRGP   70 (203)
T ss_dssp             ----CEEECTTBBHHHHHHHHHHHHH------------HTCCEEEECGGGCEEESCHHHHHHHSSSSSCHHHHCCCSSCC
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHC------------CCCEEEEEEHHHHEECCCHHHHHHHHHCCCCCCCCCCCCHHH
T ss_conf             74499997899805888999999862------------799699988689045560776655530102589887688788


Q ss_pred             CCCCCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCC
Q ss_conf             00124879999999973089-9854789996270107899971320854761665281
Q gi|254780292|r   93 ILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNP  149 (155)
Q Consensus        93 ~~~~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~  149 (155)
                      +. .++|++|+++||+|||| ++.+|+.+|+||+||+|++|||++|+|+.+++.....
T Consensus        71 ~~-~r~P~~I~~raVrgMLP~k~~rg~~~l~rL~vy~g~p~p~~~~k~~~~~~~~~~~  127 (203)
T 2zkr_j           71 YD-FRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAALKVV  127 (203)
T ss_dssp             CC-CCSHHHHHHHHHHHHSCTTSHHHHHHHHTEEECSCSSCSSSSCCBCCGGGBCCSS
T ss_pred             HH-CCCHHHHHHHHHHCCCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEECCCHHHHH
T ss_conf             62-5586799999873527899836899984777825899976454332023005765


No 10 
>>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_M (M:1-141)
Probab=100.00  E-value=2.7e-44  Score=280.24  Aligned_cols=122  Identities=24%  Similarity=0.361  Sum_probs=115.2

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~~~~lGRlAs~iA~~L~------------~Gd~ViViNa~ki~ltG~k~~~k~y~~ht~~~gg~~~~~~~~~~-~   67 (141)
T 3jyw_M            1 VVIDGKGHLVGRLASVVAKQLL------------NGQKIVVVRAEELNISGEFFRNKLKYHDFLRKATAFNKTRGPFH-F   67 (141)
T ss_dssp             CCCCCCSSCSHHHHHHHHHHHT------------TTCCCCEECSTTSCCCCCSSHHHHSCSSSSSSTTSCCCSSSCCC-C
T ss_pred             CEEECCCCCHHHHHHHHHHHHC------------CCCEEEEEEEEEEEECCCCCEEEEEEEEEEECCCCCCCCHHHHH-C
T ss_conf             9894899975788999999971------------89979999810079758501368999851007754441688773-1


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        68 r~P~~ii~~aV~gMLP~k~~~gr~~lkrL~vy~g~~hp~~~~~~~~~~~~~~~~~~  123 (141)
T 3jyw_M           68 RAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQALRVLRL  123 (141)
T ss_dssp             SSTTTHHHHHTTSSSCSSSHHHHHHHHHCCEESSCCCCSCCSCSSSCCSSCCCCCS
T ss_pred             CCHHHHHHHHHHCCCCCCCHHHHHHHHCCEEECCCCCCHHCCCCEECCHHHHHHCC
T ss_conf             38389999998356999990599997297897799996320798737468776133


No 11 
>>2j01_N 50S ribosomal protein L13; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (N:64-92)
Probab=97.29  E-value=3.9e-05  Score=50.89  Aligned_cols=28  Identities=54%  Similarity=0.981  Sum_probs=25.8

Q ss_pred             CCHHHHHHHHHCCCCCCCCEEEECCCCC
Q ss_conf             6012113333115755763363020000
Q gi|254780292|r   67 GKKYDQKTYYRHTGYPGGIKKTTAKEIL   94 (155)
Q Consensus        67 G~K~~~k~y~~htgypGG~k~~~~~~~~   94 (155)
                      |+|..+|+|.++||||||+|+++++.|+
T Consensus         1 gkkl~qkiytrysgy~gglk~ip~ekml   28 (29)
T 2j01_N            1 GKKLEQKIYTRYSGYPGGLKKIPLEKML   28 (29)
T ss_dssp             SCCSSSSBCCCCCCSSSCCCCCBHHHHH
T ss_pred             CCCCCEEEEEEEECCCCCCCCCCHHHHH
T ss_conf             7763027999860356765555577762


No 12 
>>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 (A:1-229)
Probab=32.43  E-value=39  Score=15.71  Aligned_cols=53  Identities=11%  Similarity=0.026  Sum_probs=40.6

Q ss_pred             HCCEEEEEEECCCCCHH--HHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             60200699978987457--679999999846565210345566888999751010
Q gi|254780292|r   11 EVEKKWILVDAKGLIVG--RLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV   63 (155)
Q Consensus        11 ~~~r~W~iiDA~~~~lG--RlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki   63 (155)
                      ...+-=.|||-..+.-+  +..+.+...|..+.-+.---...+|||+.|.++...
T Consensus        16 ~~~~~~iiVD~RE~~~~~~~~~~~~~~~l~~~gv~~~~~~L~~GDyiwv~~~~~~   70 (229)
T 2ziu_A           16 GSYDIVLCVDLCETTGGSSVRKQELVKELQRNSVTFDVRKLNVGDFLWVARERVT   70 (229)
T ss_dssp             TSEEEEEEECGGGSCC-----CCHHHHHHHTTTCCEECCCCSSCSEEEEEEECCC
T ss_pred             CCCEEEEEEECCCCCCCCCCHHHHHHHHHHHCCCEEEEEECCCCCEEEEECCCCC
T ss_conf             9837999998888766664118999999997899589985686888999326654


No 13 
>>1tul_A TLP20; telokin-like protein; 2.20A {Autographa californicanucleopolyhedrovirus} (A:)
Probab=27.82  E-value=29  Score=16.49  Aligned_cols=13  Identities=23%  Similarity=0.192  Sum_probs=10.7

Q ss_pred             CCCCCEEEEECCC
Q ss_conf             5668889997510
Q gi|254780292|r   49 ADDGDHVVIINAS   61 (155)
Q Consensus        49 ~d~GD~VvViNa~   61 (155)
                      +-||||+|+.|.-
T Consensus        64 v~cgdY~v~~N~~   76 (108)
T 1tul_A           64 VSCGNYGVLCNLV   76 (108)
T ss_dssp             EESSSEEEEEECC
T ss_pred             EEECCEEEEEECC
T ss_conf             9827789999700


No 14 
>>2e31_A FBS1, F-box only protein 2; ubiquitin, SCF, ubiquitin ligase, FBS1; 2.40A {Mus musculus} PDB: 2e32_A (A:133-297)
Probab=20.69  E-value=60  Score=14.64  Aligned_cols=83  Identities=16%  Similarity=0.214  Sum_probs=51.9

Q ss_pred             EEEECCHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCC------CCCCCCCCC----EEEEECCCCCCC-------
Q ss_conf             113268436020069997898745767999999984656521------034556688----899975101001-------
Q gi|254780292|r    3 PTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPT------YTPSADDGD----HVVIINASKVAF-------   65 (155)
Q Consensus         3 kT~~~k~~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~------y~P~~d~GD----~VvViNa~ki~~-------   65 (155)
                      ++.++.+-..-.+|-+||-...-+       ...|+-.-+|.      |++..|||.    .|-+.++++.++       
T Consensus        38 ~~~FvtSy~~C~k~Q~IDL~~eG~-------~~elLD~~qP~I~vsdWy~~r~d~g~~Y~l~V~LL~~~~~vi~~f~~~~  110 (165)
T 2e31_A           38 KKYFASSFEWCRKAQVIDLQAEGY-------WEELLDTTQPAIVVKDWYSGRTDAGSLYELTVRLLSENEDVLAEFATGQ  110 (165)
T ss_dssp             CEEEECCSSCEEEEEEEETTTTTC-------CHHHHHHTCCCEEEEEEEECCTTSCEEEEEEEEEECTTCCEEEEEECCC
T ss_pred             CEEEEEEECCEEEEEEECHHHCCC-------CHHHHHCCCCCEEEEEEECCCCCCCCEEEEEEEEECCCCCEEEEECCCC
T ss_conf             468985531488887744243374-------9878606599779986453788876158999998747996899973787


Q ss_pred             ----CCCHHHHHHHHHCCCCCCCCEEEECCCC
Q ss_conf             ----5601211333311575576336302000
Q gi|254780292|r   66 ----SGKKYDQKTYYRHTGYPGGIKKTTAKEI   93 (155)
Q Consensus        66 ----tG~K~~~k~y~~htgypGG~k~~~~~~~   93 (155)
                          .+++|.+-. +--++||-|.+.+.|..-
T Consensus       111 ~~~~~~~~W~~vs-h~F~~y~pGvR~V~F~h~  141 (165)
T 2e31_A          111 VAVPEDGSWMEIS-HTFIDYGPGVRFVRFEHG  141 (165)
T ss_dssp             EECCTTCCCEEEE-EEECSCCSCCCEEEEEEE
T ss_pred             CCCCCCCCEEEEE-EEECCCCCCCEEEEEEEC
T ss_conf             2025898579999-995898998369999867


Done!