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 39220
Date          Tue May 24 16:17:44 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780292.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01066 rplM_bact ribosomal  100.0       0       0  458.8   6.9  141    4-144     1-145 (145)
  2 CHL00159 rpl13 ribosomal prote 100.0       0       0  420.6  10.1  143    1-144     1-143 (143)
  3 PRK09216 rplM 50S ribosomal pr 100.0       0       0  419.6  10.3  144    2-146     1-144 (144)
  4 COG0102 RplM Ribosomal protein 100.0       0       0  384.0  10.1  147    2-148     1-147 (148)
  5 pfam00572 Ribosomal_L13 Riboso 100.0       0       0  354.5   9.8  128   16-144     1-128 (128)
  6 KOG3203 consensus              100.0       0       0  342.2   8.4  132   10-142    17-154 (165)
  7 cd00392 Ribosomal_L13 Ribosoma 100.0       0       0  313.2   9.1  114   16-130     1-114 (114)
  8 PRK06394 rpl13p 50S ribosomal  100.0 1.4E-41       0  264.8  10.1  125   17-154     2-128 (143)
  9 TIGR01077 L13_A_E ribosomal pr 100.0 2.2E-29 5.6E-34  193.3   8.0  122   17-151     1-125 (144)
 10 PTZ00068 60S ribosomal protein  99.9 3.2E-25   8E-30  168.9   8.1  119   15-149     4-130 (201)
 11 KOG3204 consensus               99.6 3.2E-15 8.1E-20  110.3   5.6  107   13-139     4-111 (197)
 12 TIGR02845 spore_V_AD stage V s  45.8      20 0.00051   17.8   2.7   43   25-69    231-276 (331)
 13 TIGR01704 MTA/SAH-Nsdase MTA/S  41.7      26 0.00066   17.2   2.8   38   26-63     49-97  (229)
 14 TIGR02743 TraW type-F conjugat  28.8      35 0.00089   16.4   1.7   57   11-81    132-189 (217)
 15 TIGR01135 glmS glucosamine--fr  28.3      32 0.00082   16.6   1.5   13   46-58     88-100 (628)
 16 PRK10793 D-alanyl-D-alanine ca  24.9      50  0.0013   15.5   2.0   26    2-27     34-61  (403)
 17 PRK05461 apaG ApaG; Reviewed    23.7      44  0.0011   15.8   1.5   14   12-25     45-58  (124)
 18 KOG3834 consensus               22.0      71  0.0018   14.6   2.4   53   12-82    107-159 (462)
 19 pfam06303 MatP Organiser of ma  21.5      61  0.0016   15.0   1.9   51   96-146    48-100 (148)
 20 pfam06088 TLP-20 Nucleopolyhed  21.0      51  0.0013   15.4   1.4   26   36-62     53-78  (162)
 21 PRK05097 hypothetical protein;  20.6      65  0.0017   14.8   1.9   51   96-146    48-100 (150)

No 1  
>TIGR01066 rplM_bact ribosomal protein L13; InterPro: IPR005823   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    Ribosomal protein L13 is one of the proteins from the large ribosomal subunit . In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit. This entry represents ribosomal protein L13 from bacteria, mitochondria and chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=100.00  E-value=0  Score=458.75  Aligned_cols=141  Identities=55%  Similarity=0.930  Sum_probs=137.3

Q ss_pred             EEECC-HHHCCEEEEEEECC--CCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCC
Q ss_conf             13268-43602006999789--8745767999999984656521034556688899975101001560121133331157
Q gi|254780292|r    4 TFFQK-SSEVEKKWILVDAK--GLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTG   80 (155)
Q Consensus         4 T~~~k-~~~~~r~W~iiDA~--~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htg   80 (155)
                      |++++ .++++|+||||||+  |++||||||+||.+|||||||+||||+||||||||||||+|.|||+|.++|+||+|||
T Consensus         1 T~~~k~~~~~~r~WyvvDA~rdg~~LGRLA~~vA~~LRGKHKp~YTP~~D~GD~VIvINA~Kv~lTG~K~~~K~Yy~HSg   80 (145)
T TIGR01066         1 TTLAKAEDEVERKWYVVDAARDGKTLGRLASEVAKLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKLYYRHSG   80 (145)
T ss_pred             CCCCCCHHHCCCCCEEEEEEECCCEEHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCEEECCCCCCCCEEEEECC
T ss_conf             94447632444530688643188361078898999843788884347861487269970475786387656837888668


Q ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCC-HHHCCCEEEEH
Q ss_conf             55763363020000124879999999973089985478999627010789997-13208547616
Q gi|254780292|r   81 YPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHP-HEAQKPVFMDI  144 (155)
Q Consensus        81 ypGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hp-h~aq~P~~l~~  144 (155)
                      ||||+|+.|+.+|+++|.|+++|+.||+||||||+|||++|++|+||.|++|| |+||||+.+|+
T Consensus        81 ypGG~k~~t~~~m~~~r~P~~~~~~AVkGMLPkn~Lgr~~~~kLkVY~G~~Hp~h~AQ~P~~l~~  145 (145)
T TIGR01066        81 YPGGLKSRTFEEMIADRKPEKVLELAVKGMLPKNRLGRKLFKKLKVYAGSEHPYHEAQKPIVLDI  145 (145)
T ss_pred             CCCCCCHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHCCCEECCCCCCCCCCCCCEECCC
T ss_conf             34887003489997427810247865016899883212121104224489874001478450479


No 2  
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=100.00  E-value=0  Score=420.57  Aligned_cols=143  Identities=50%  Similarity=0.863  Sum_probs=140.7

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         1 m~kT~~~~~~~~~r~W~viDA~~~~lGRLAs~iA~~L~GK~Kp~ytP~~d~GD~VVViNa~ki~~TG~K~~~K~y~~htg   80 (143)
T CHL00159          1 MNKTFIPSKNYKKRKWYIIDAKDQKLGRLATEISSLLRGKNKPSYTPSVDTGDYVIVINADKIIVTGNKNTQKFYVRHSG   80 (143)
T ss_pred             CCCCCCCCHHHCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECHHEEEECCCCCCEEEEEEEE
T ss_conf             97433188202466689996999944889999999975478773567887799999983714187177300108899876


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        81 ypGg~k~~~~~~~~-~r~P~~il~~AVkgMLPkn~lgr~~lkrLkVy~G~~Hph~aQ~P~~l~i  143 (143)
T CHL00159         81 RPGGLKVETFKELQ-NRLPNRIIEKAVKGMLPKGPLGRKLFKKLKVYAGSSHPHEAQKPIIINI  143 (143)
T ss_pred             CCCCCCCCCHHHHH-HCCCHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEEECC
T ss_conf             25887565678964-2280579999998618998129999858888698999855689877279


No 3  
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=100.00  E-value=0  Score=419.56  Aligned_cols=144  Identities=51%  Similarity=0.931  Sum_probs=141.1

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 ~kT~~~k~~~~~~~W~vIDA~~~~lGRLAs~iA~~L~GKhKp~ytP~~d~GD~VVVINa~ki~itG~K~~~K~y~~htgy   80 (144)
T PRK09216          1 MKTFSAKPAEVERKWYVVDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIYYRHSGY   80 (144)
T ss_pred             CCCCCCCHHHCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECHHEEEECCCCCCEEEEEECCC
T ss_conf             96423882015676599969998118999999999747887843688758988999700582773672011368860456


Q ss_pred             CCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHH
Q ss_conf             57633630200001248799999999730899854789996270107899971320854761665
Q gi|254780292|r   82 PGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAK  146 (155)
Q Consensus        82 pGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~  146 (155)
                      |||++++++++++ .++|++||++||+||||+|+||+.+|+||+||+|++|||+||+|+.+++++
T Consensus        81 pGg~k~~~~~~~~-~r~P~~il~~AVkgMLPkn~lgr~~~krLkvy~g~~Hph~aQ~P~~~~~~~  144 (144)
T PRK09216         81 PGGLKERTFGELL-AKKPERVIEKAVKGMLPKNPLGRAMLKKLKVYAGAEHPHAAQQPEVLDIKS  144 (144)
T ss_pred             CCCCEECCHHHHH-CCCCHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEEECCCC
T ss_conf             8884011689974-038268999999712899736999984867848999985557985750459


No 4  
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=384.01  Aligned_cols=147  Identities=52%  Similarity=0.909  Sum_probs=143.5

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 ~~t~~~k~~~~~r~w~vIDA~g~vLGRLAs~VA~~Lrgkhkp~ytP~~d~Gd~ViVINAeKv~iTG~K~~~k~yy~hs~~   80 (148)
T COG0102           1 MKTFTAKPSEVERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYYRHSGY   80 (148)
T ss_pred             CCEECCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECEEEEEECCCHHCEEEEEEECC
T ss_conf             95222575100351899958997668889999999965898876867677878999856026886261000357776316


Q ss_pred             CCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCC
Q ss_conf             5763363020000124879999999973089985478999627010789997132085476166528
Q gi|254780292|r   82 PGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMN  148 (155)
Q Consensus        82 pGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~  148 (155)
                      |||++..++.++++++.|++|+++||+||||+|+|||++|+||+||.|++|||++|+|+.+++..++
T Consensus        81 ~gglk~~t~~~~~~~r~P~ri~~~AVrGMLPk~~lGr~~~krLkVy~G~~h~~~aq~p~~l~~~~~~  147 (148)
T COG0102          81 PGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPHPHEAQKPEALELKLLK  147 (148)
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHCCEEECCCCCCCCCCCCHHHHHHCCC
T ss_conf             7764456401145667889999999702188986599997471586489986022466334330257


No 5  
>pfam00572 Ribosomal_L13 Ribosomal protein L13.
Probab=100.00  E-value=0  Score=354.51  Aligned_cols=128  Identities=56%  Similarity=0.960  Sum_probs=125.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCC
Q ss_conf             69997898745767999999984656521034556688899975101001560121133331157557633630200001
Q gi|254780292|r   16 WILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILA   95 (155)
Q Consensus        16 W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~~~~~   95 (155)
                      ||||||+||+||||||.||++|+|||||+|||++||||+||||||++|++||+||.++.|++|||||||+++.+++++++
T Consensus         1 w~viDA~~~~lGRlAs~iAk~L~GK~kp~y~p~~d~Gd~VvViNa~~i~itG~k~~~k~y~~htg~pgg~~~~~~~~~~~   80 (128)
T pfam00572         1 WHVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVVNAEKIVLTGKKRDQKKYYRHTGYPGGLKNPTAKGPLE   80 (128)
T ss_pred             CEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEHHHEEEECCHHHHHEEEEEECCCCCCCCCCHHHHHH
T ss_conf             98995899943889999999983467886478987787899983168176065565200003440568640167799874


Q ss_pred             CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEH
Q ss_conf             2487999999997308998547899962701078999713208547616
Q gi|254780292|r   96 GASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDI  144 (155)
Q Consensus        96 ~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~  144 (155)
                       ++|++||++||+||||+|++|+.+|+||+||+|++|||++|+|+.+++
T Consensus        81 -r~P~~il~~aVrgMLP~n~~g~~~~krLkiy~g~~hp~~~q~p~~~~~  128 (128)
T pfam00572        81 -RKPERILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHAAQKPEVLEI  128 (128)
T ss_pred             -HCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEECCC
T ss_conf             -077899999998628997449999858789699998856679876179


No 6  
>KOG3203 consensus
Probab=100.00  E-value=0  Score=342.21  Aligned_cols=132  Identities=49%  Similarity=0.847  Sum_probs=125.0

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        17 ~afaRvW~vvDa~~q~lGrLAs~ia~~L~GkhKPiYhP~~DcGD~VVV~N~~~Ia~sG~K~~qk~Y~~HsGyPG~lk~~~   96 (165)
T KOG3203          17 LAFARVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFSGKKWEQKIYRSHSGYPGGLKQTT   96 (165)
T ss_pred             HHHHHHHEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCHHHEECCCHHHHHHHHHCCCCCCCHHHHH
T ss_conf             87766512533456756899999999986046776487667788799954556441220042340110178987302308


Q ss_pred             CCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCC------HHHCCCEEE
Q ss_conf             20000124879999999973089985478999627010789997------132085476
Q gi|254780292|r   90 AKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHP------HEAQKPVFM  142 (155)
Q Consensus        90 ~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hp------h~aq~P~~l  142 (155)
                      +++ +++++|++|+++||+||||+|+||+.+|.|||+|.|++||      +++++|..+
T Consensus        97 ~~q-~~~rdp~~Iv~~AV~gMLPkN~Lrr~~~~rL~lf~g~e~p~~~Ni~~~~~q~~~v  154 (165)
T KOG3203          97 ADQ-LADRDPCRIVRLAVYGMLPKNLLRRRRMQRLHLFPGEEHPEKVNIGSELHQPQGV  154 (165)
T ss_pred             HHH-HHHHCHHHHHHHHHHHHCCCCHHHHHHHHEEECCCCCCCCHHHHHHHHHCCCCCC
T ss_conf             999-8541779999999970276233788776503435886570132067774366687


No 7  
>cd00392 Ribosomal_L13 Ribosomal protein L13.  Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site.  It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer.  L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.
Probab=100.00  E-value=0  Score=313.23  Aligned_cols=114  Identities=52%  Similarity=0.913  Sum_probs=111.8

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCC
Q ss_conf             69997898745767999999984656521034556688899975101001560121133331157557633630200001
Q gi|254780292|r   16 WILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILA   95 (155)
Q Consensus        16 W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~~~~~   95 (155)
                      ||||||+||+||||||.||++|+|||||+|+|++||||+||||||++|++||+||.++.||+|||||||+++.++++++ 
T Consensus         1 w~viDA~~~~lGRLAs~iA~~L~GK~kp~y~p~~d~Gd~ViViNa~~i~~tG~k~~~k~y~~~~~~~gg~~~~~~~~~~-   79 (114)
T cd00392           1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVYYRHTGYPGGLKNPTAGPLH-   79 (114)
T ss_pred             CEEEECCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEHHHEEEECCHHHCEEEEEEECCCCCCCCCCCHHHH-
T ss_conf             9899589993588999999999637578867787689889998326836605312101246750478987347704544-


Q ss_pred             CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             24879999999973089985478999627010789
Q gi|254780292|r   96 GASPTNILKKAIARMLPRGPLARKQMKNLHIYAED  130 (155)
Q Consensus        96 ~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~  130 (155)
                      +++|++||++||+||||+|++|+.+|+||+||+|+
T Consensus        80 ~~~P~~il~~aV~gMLPkn~~gr~~lkrL~vy~G~  114 (114)
T cd00392          80 PRAPERILKRAVRGMLPKNKLGRAALKRLKVYEGA  114 (114)
T ss_pred             CCCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCC
T ss_conf             13989999999986189972399998598882799


No 8  
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=100.00  E-value=1.4e-41  Score=264.75  Aligned_cols=125  Identities=28%  Similarity=0.381  Sum_probs=113.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHH-HHHHHCCCCCCCCEEEECCCCCC
Q ss_conf             99978987457679999999846565210345566888999751010015601211-33331157557633630200001
Q gi|254780292|r   17 ILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQ-KTYYRHTGYPGGIKKTTAKEILA   95 (155)
Q Consensus        17 ~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~-k~y~~htgypGG~k~~~~~~~~~   95 (155)
                      .||||+|++||||||.||++|+|            ||+|||||||+|.+||+|... +.|++|++++|+.....+... +
T Consensus         2 ivIDA~~~vlGRLAs~vAk~L~g------------Gd~ViVINAeKi~iTG~K~~~~~~Y~~~~~~~~~~~~~~~~~~-~   68 (143)
T PRK06394          2 VVIDAEGAILGRLASYVAKLLLS------------GEEVVIVNAEKAVITGNREFIFEKYKQRRERKTISNPRRFGPY-Y   68 (143)
T ss_pred             EEEECCCCEEHHHHHHHHHHHHC------------CCEEEEEECCCEEEECCHHHHHHHEEEECCCCCCCCCCCCCCC-C
T ss_conf             89978998808899999999858------------9979999761348846537744340453578989886212100-0


Q ss_pred             CCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCCCCCCC
Q ss_conf             24879999999973089-985478999627010789997132085476166528131236
Q gi|254780292|r   96 GASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSRR  154 (155)
Q Consensus        96 ~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~kn~~~  154 (155)
                      .+.|++|+++||+|||| ||++|+++|+||+||+|.+|||++|+|+.++++.++++|..+
T Consensus        69 ~r~P~~il~~aVrGMLP~K~~lGr~~~k~LkvY~G~ph~~~aqkp~~~~~a~~~~~~~~k  128 (143)
T PRK06394         69 PKRPDNIVKRTIRGMLPYKKDRGREAFKRLKVYVGVPKELEGKEFETIDDADVSRLSGIK  128 (143)
T ss_pred             CCCHHHHHHHHHHCCCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEECCHHHHHCCCCCC
T ss_conf             029599999988334899985799998498897689986356787505778850648984


No 9  
>TIGR01077 L13_A_E ribosomal protein L13; InterPro: IPR005755   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    Ribosomal protein L13 is one of the proteins from the large ribosomal subunit . In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=99.96  E-value=2.2e-29  Score=193.31  Aligned_cols=122  Identities=28%  Similarity=0.436  Sum_probs=97.7

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECC-CCCC
Q ss_conf             999789874576799999998465652103455668889997510100156012113333115755763363020-0001
Q gi|254780292|r   17 ILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAK-EILA   95 (155)
Q Consensus        17 ~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~-~~~~   95 (155)
                      .||||+|.+||||||.||+.|+            .|..|||||||+|++||++...+.-|..+ +-+....-+-. ..++
T Consensus         1 ~ViDa~G~ilGRLAS~VAK~lL------------~G~~vVvVnAE~~vItG~~~~~~~~Y~~~-~~~~~~~n~~r~GP~~   67 (144)
T TIGR01077         1 TVIDASGHILGRLASVVAKRLL------------NGERVVVVNAEKIVITGNKYMVFEKYKEF-LRKRTKTNPRRFGPYF   67 (144)
T ss_pred             CEECCCCCHHHHHHHHHHHHHH------------CCCEEEEEECCEEEECCCCHHHHHHHHHH-HHHHHHCCCCCCCCCC
T ss_conf             9567874313768999999875------------79867897226025227830456877887-6313213773679989


Q ss_pred             CCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHH-CCCCC
Q ss_conf             24879999999973089-9854789996270107899971320854761665-28131
Q gi|254780292|r   96 GASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAK-MNPKN  151 (155)
Q Consensus        96 ~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~-~~~kn  151 (155)
                      +|.|++|+++||+|||| |+..|+++|+||+||.|-+-|++.++-+.++-+. ..+-+
T Consensus        68 PR~P~rIf~rtvRGMLP~K~~RGr~Al~RLkVy~G~P~el~~k~~~~v~~A~~~~rL~  125 (144)
T TIGR01077        68 PRRPDRIFKRTVRGMLPWKTARGRAALRRLKVYVGIPKELQGKEFVTVPEALKVSRLS  125 (144)
T ss_pred             CCCCHHHHHHHHCCCCCCCCHHHHHHHHHCEECCCCCCCCCCCEEEEHHHHHHHHCCC
T ss_conf             9870789998640358877743588885150015875851576056610122111268


No 10 
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=99.92  E-value=3.2e-25  Score=168.94  Aligned_cols=119  Identities=25%  Similarity=0.445  Sum_probs=92.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHH-C--CCCCCCCEEEECC
Q ss_conf             069997898745767999999984656521034556688899975101001560121133331-1--5755763363020
Q gi|254780292|r   15 KWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYR-H--TGYPGGIKKTTAK   91 (155)
Q Consensus        15 ~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~-h--tgypGG~k~~~~~   91 (155)
                      +=.||||+|++||||||.||+.|+            .|..|||||||+|.+||+...++.-|. .  ..--+.    +..
T Consensus         4 k~iVIDa~ghllGRLAS~VAK~lL------------~G~kVvVVncE~i~ISG~~~r~k~ky~~~lrkr~~~n----p~~   67 (201)
T PTZ00068          4 KIIVIDGKGHLLGRLASVVAKELL------------LGQKIVVVRCELINISGSLFRNKLKYLEFLRKRTNTN----PRR   67 (201)
T ss_pred             CCEEEECCCCHHHHHHHHHHHHHH------------CCCEEEEEECHHHEECCCHHHHHHHHHHHHHHHHCCC----CCC
T ss_conf             618996887389889999999995------------6995999962041222628999999999999987279----999


Q ss_pred             CCCCCCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCC----CEEEEHHHCCC
Q ss_conf             000124879999999973089-98547899962701078999713208----54761665281
Q gi|254780292|r   92 EILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQK----PVFMDIAKMNP  149 (155)
Q Consensus        92 ~~~~~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~----P~~l~~~~~~~  149 (155)
                      ..++.+.|++|++++|+|||| |+..|+.+|+||+||+|.+.|++-++    |..+-+-.+++
T Consensus        68 GPf~~R~Ps~I~~RtVRGMLP~Kt~RG~~Al~rLkvyeGvP~pyd~~kr~vvP~Alrv~rlkp  130 (201)
T PTZ00068         68 GPFHHRAPSKIFWRVVRGMLPHKTKRGAAALKRLKVYEGVPPPYDTGKRVVVPSALRHLRLKP  130 (201)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEECHHHHHHHCCC
T ss_conf             999888988999998637577687679999970744258996502588678025789875289


No 11 
>KOG3204 consensus
Probab=99.57  E-value=3.2e-15  Score=110.34  Aligned_cols=107  Identities=28%  Similarity=0.477  Sum_probs=89.7

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         4 ~~~~~vidg~~hllGrlAa~vaK~ll------------~g~kvvvvr~E~i~isg~f~r~k~~lrk---~~~~n-----g   63 (197)
T KOG3204           4 EVKLVVIDGRGHLLGRLAAIVAKQLL------------LGRKVVVVRCEEINISGNFYRNKLFLRK---RLNRN-----G   63 (197)
T ss_pred             EEEEEECCCHHHHHHHHHHHHHHHHH------------CCCEEEEEEEEEEEEEEEEECCHHHHHH---HHCCC-----C
T ss_conf             37875313403566358999999996------------1882899997668886001001577764---53046-----7


Q ss_pred             CCCCCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCC
Q ss_conf             00124879999999973089-985478999627010789997132085
Q gi|254780292|r   93 ILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKP  139 (155)
Q Consensus        93 ~~~~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P  139 (155)
                      .++.+-|.+|++++|+||+| +...|+..+.+|.+|+|-.+|++-|++
T Consensus        64 ~~hfr~ps~i~~~~vrgm~~~kt~rg~aal~~l~~~eGip~~~dk~~r  111 (197)
T KOG3204          64 PFHFRAPSRILQKAVRGMYPHKTKRGRAALERLRVFEGIPPPYDKQKR  111 (197)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHCCC
T ss_conf             401112789998855051136788607799988873778982550687


No 12 
>TIGR02845 spore_V_AD stage V sporulation protein AD; InterPro: IPR010894   This family contains the bacterial stage V sporulation protein AD (SpoVAD), which is approximately 340 residues long. This is one of six proteins encoded by the spoVA operon, which is transcribed exclusively in the forespore at about the time of dipicolinic acid (DPA) synthesis in the mother cell. The functions of the proteins encoded by the spoVA operon are unknown, but it has been suggested they are involved in DPA transport during sporulation ..
Probab=45.84  E-value=20  Score=17.83  Aligned_cols=43  Identities=26%  Similarity=0.337  Sum_probs=36.0

Q ss_pred             CHHHHHHHHHHHHHCCC-CCCCCCC-CCCCCEEEEECCCCC-CCCCCH
Q ss_conf             45767999999984656-5210345-566888999751010-015601
Q gi|254780292|r   25 IVGRLASQIALRLRGKN-KPTYTPS-ADDGDHVVIINASKV-AFSGKK   69 (155)
Q Consensus        25 ~lGRlAs~iA~~L~GKh-Kp~y~P~-~d~GD~VvViNa~ki-~~tG~K   69 (155)
                      .|||+-+.|+.-|+-|+ .-.++-. .|||  |-|=++++= +++|--
T Consensus       231 DL~rvG~~I~~~LL~e~yg~~~~~~Y~DCG--~~IY~~dqqdV~AGGS  276 (331)
T TIGR02845       231 DLARVGSEILRKLLKEEYGYDVTEKYDDCG--VMIYRPDQQDVFAGGS  276 (331)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCCCEECCCC--EEEECCCCCCCCCCCC
T ss_conf             300214899999988860875000104564--6753388781057785


No 13 
>TIGR01704 MTA/SAH-Nsdase MTA/SAH nucleosidase; InterPro: IPR010049   This entry represents the enzyme 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase which acts on its two substrates at the same active site. This enzyme is involved in the recycling of the components of S-adenosylmethionine after it has donated one of its two non-ribose sulphur ligands to an acceptor. In the case of 5'-methylthioadenosine this represents the first step of the methionine salvage pathway in bacteria , ,]. This enzyme is widely distributed in bacteria. ; GO: 0008782 adenosylhomocysteine nucleosidase activity, 0008930 methylthioadenosine nucleosidase activity, 0009164 nucleoside catabolic process, 0019509 methionine salvage.
Probab=41.74  E-value=26  Score=17.15  Aligned_cols=38  Identities=24%  Similarity=0.323  Sum_probs=29.1

Q ss_pred             HHHHHHHHH-HHHHCCCCCCC----------CCCCCCCCEEEEECCCCC
Q ss_conf             576799999-99846565210----------345566888999751010
Q gi|254780292|r   26 VGRLASQIA-LRLRGKNKPTY----------TPSADDGDHVVIINASKV   63 (155)
Q Consensus        26 lGRlAs~iA-~~L~GKhKp~y----------~P~~d~GD~VvViNa~ki   63 (155)
                      .|+++.-+. .+|+-..||+|          +|....||-||=..+.+=
T Consensus        49 IGKV~AA~~~TLLL~~~KPD~~INTGSAGGl~~TL~VGD~V~S~~~R~H   97 (229)
T TIGR01704        49 IGKVAAALSATLLLDRYKPDVVINTGSAGGLAHTLKVGDVVVSDDVRYH   97 (229)
T ss_pred             CHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCEEEECCCEEC
T ss_conf             2378999888888750799769858875442331320567871674021


No 14 
>TIGR02743 TraW type-F conjugative transfer system protein TraW; InterPro: IPR014114   This entry represents TraW, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm , ..
Probab=28.75  E-value=35  Score=16.39  Aligned_cols=57  Identities=18%  Similarity=0.311  Sum_probs=37.8

Q ss_pred             HCCEEEEEEECCC-CCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCC
Q ss_conf             6020069997898-7457679999999846565210345566888999751010015601211333311575
Q gi|254780292|r   11 EVEKKWILVDAKG-LIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGY   81 (155)
Q Consensus        11 ~~~r~W~iiDA~~-~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgy   81 (155)
                      .+++.|+.|||+| +.|......-+... |+-            .+|.++-+--.+. +.|+.++||-.-|.
T Consensus       132 ~ls~~LlFfDAdD~~Q~~wA~~~~~~~~-G~~------------K~ILt~Gs~~el~-~~L~~~IYFDQ~G~  189 (217)
T TIGR02743       132 SLSKTLLFFDADDPKQLAWAQQLLAQLP-GEV------------KWILTGGSVKELE-KRLDSRIYFDQNGK  189 (217)
T ss_pred             CCCCCEEEEECCCHHHHHHHHHHHHCCC-CCC------------EEEECCCCHHHHH-HHCCCCCEECCCCH
T ss_conf             3276178881888899999998732038-983------------0887178979999-85289604636763


No 15 
>TIGR01135 glmS glucosamine--fructose-6-phosphate aminotransferase, isomerizing; InterPro: IPR005855    Glucosamine:fructose-6-phosphate aminotransferase (2.6.1.16 from EC) catalyses the formation of glucosamine 6-phosphate and is the first and rate-limiting enzyme of the hexosamine biosynthetic pathway. The final product of the hexosamine pathway, UDP-N-acetyl glucosamine, is an active precursor of numerous macromolecules containing amino sugars.   This family of sequences belong to the MEROPS peptidase family C44 (clan PB(C)), and are classified as non-peptidase homologs.; GO: 0004360 glutamine-fructose-6-phosphate transaminase (isomerizing) activity, 0016051 carbohydrate biosynthetic process, 0005737 cytoplasm.
Probab=28.33  E-value=32  Score=16.61  Aligned_cols=13  Identities=23%  Similarity=0.815  Sum_probs=9.5

Q ss_pred             CCCCCCCCEEEEE
Q ss_conf             3455668889997
Q gi|254780292|r   46 TPSADDGDHVVII   58 (155)
Q Consensus        46 ~P~~d~GD~VvVi   58 (155)
                      |||+||+..|+||
T Consensus        88 HPH~d~~g~iaVV  100 (628)
T TIGR01135        88 HPHTDEGGRIAVV  100 (628)
T ss_pred             CCCCCCCCCEEEE
T ss_conf             8722699527999


No 16 
>PRK10793 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional
Probab=24.89  E-value=50  Score=15.46  Aligned_cols=26  Identities=23%  Similarity=0.553  Sum_probs=19.1

Q ss_pred             CEEEECCHHHCC-EEEEEEEC-CCCCHH
Q ss_conf             511326843602-00699978-987457
Q gi|254780292|r    2 IPTFFQKSSEVE-KKWILVDA-KGLIVG   27 (155)
Q Consensus         2 ~kT~~~k~~~~~-r~W~iiDA-~~~~lG   27 (155)
                      .+|+.|.+-+++ +.|+++|| +|++|.
T Consensus        34 ~~~~~p~~P~i~A~sailiD~~TG~VLy   61 (403)
T PRK10793         34 IKTMIPGVPQIDAESYILIDYNSGKVLA   61 (403)
T ss_pred             CCCCCCCCCCCCCEEEEEEECCCCCCHH
T ss_conf             4563799897554199999999994913


No 17 
>PRK05461 apaG ApaG; Reviewed
Probab=23.75  E-value=44  Score=15.80  Aligned_cols=14  Identities=36%  Similarity=0.992  Sum_probs=12.0

Q ss_pred             CCEEEEEEECCCCC
Q ss_conf             02006999789874
Q gi|254780292|r   12 VEKKWILVDAKGLI   25 (155)
Q Consensus        12 ~~r~W~iiDA~~~~   25 (155)
                      +.|.|.|.|+.|++
T Consensus        45 ~~R~W~I~d~~g~~   58 (124)
T PRK05461         45 LSRHWIITDANGRV   58 (124)
T ss_pred             EEEEEEEECCCCCE
T ss_conf             96589999699988


No 18 
>KOG3834 consensus
Probab=22.03  E-value=71  Score=14.58  Aligned_cols=53  Identities=19%  Similarity=0.172  Sum_probs=32.4

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCC
Q ss_conf             02006999789874576799999998465652103455668889997510100156012113333115755
Q gi|254780292|r   12 VEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYP   82 (155)
Q Consensus        12 ~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgyp   82 (155)
                      ..-.||+++-..-..--+|..++                -+||  ||++..+++.+.+-.-...-.|.+.|
T Consensus       107 ~~~vwHvl~V~p~SPaalAgl~~----------------~~DY--ivG~~~~~~~~~eDl~~lIeshe~kp  159 (462)
T KOG3834         107 VESVWHVLSVEPNSPAALAGLRP----------------YTDY--IVGIWDAVMHEEEDLFTLIESHEGKP  159 (462)
T ss_pred             HHHEEEEEECCCCCHHHHCCCCC----------------CCCE--EECCHHHHCCCHHHHHHHHHHCCCCC
T ss_conf             11123446438998788505533----------------6535--74354552341578999998602787


No 19 
>pfam06303 MatP Organiser of macrodomain of Terminus of chromosome. This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localizes with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial c
Probab=21.55  E-value=61  Score=14.96  Aligned_cols=51  Identities=14%  Similarity=0.167  Sum_probs=40.9

Q ss_pred             CCCHHHHHHHHHHHCCC--CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHH
Q ss_conf             24879999999973089--9854789996270107899971320854761665
Q gi|254780292|r   96 GASPTNILKKAIARMLP--RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAK  146 (155)
Q Consensus        96 ~~~P~~il~~aV~gMLP--kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~  146 (155)
                      ...|..|++.--.-|-|  .|++....-.|=+-|-.++|.|.-++.+.|++.-
T Consensus        48 e~~P~~V~~WI~~hm~p~l~nkmkQaIRArRKRhFNAE~qhTrKKSIDLey~v  100 (148)
T pfam06303        48 EHEPVKVLEWIKAHMNPELENKMKQAIRARRKRHFNAEKQHTRKKSIDLEYRV  100 (148)
T ss_pred             CCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHCCCCCCCCCCHHHH
T ss_conf             56819999999986699999999999999988106333122201342333999


No 20 
>pfam06088 TLP-20 Nucleopolyhedrovirus telokin-like protein-20 (TLP20). This family consists of several Nucleopolyhedrovirus telokin-like protein-20 (TLP20) sequences. The function of this family is unknown but TLP20 is known to shares some antigenic similarities to the smooth muscle protein telokin although the amino acid sequence shows no homologies to telokin.
Probab=21.00  E-value=51  Score=15.45  Aligned_cols=26  Identities=19%  Similarity=0.180  Sum_probs=17.1

Q ss_pred             HHHCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             984656521034556688899975101
Q gi|254780292|r   36 RLRGKNKPTYTPSADDGDHVVIINASK   62 (155)
Q Consensus        36 ~L~GKhKp~y~P~~d~GD~VvViNa~k   62 (155)
                      .|..-|.-.| -.+.||||+|+-|+-.
T Consensus        53 ~L~~L~~~~~-~ti~~GdY~v~yN~~~   78 (162)
T pfam06088        53 LLDALHNNAH-STITCGDYTVVYNLVS   78 (162)
T ss_pred             HHHHHHHCCC-EEEEECCEEEEEEEEE
T ss_conf             8788860883-3898368799987130


No 21 
>PRK05097 hypothetical protein; Provisional
Probab=20.65  E-value=65  Score=14.81  Aligned_cols=51  Identities=16%  Similarity=0.181  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHHCCC--CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHH
Q ss_conf             24879999999973089--9854789996270107899971320854761665
Q gi|254780292|r   96 GASPTNILKKAIARMLP--RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAK  146 (155)
Q Consensus        96 ~~~P~~il~~aV~gMLP--kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~  146 (155)
                      ...|..|+..--.-|-|  .|++....-.|=+-|-.++|.|.-++.+.|++.-
T Consensus        48 e~~P~~v~~WI~~hm~p~L~nkmkQ~IRArRKRhFNAE~~hTrKKSIDLey~V  100 (150)
T PRK05097         48 ENEPVKVLEWIDKHMNPELVNRMKQTIRARRKRHFNAEHQHTRKKSIDLEYAV  100 (150)
T ss_pred             CCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCHHH
T ss_conf             35828999999985698889899999999988325422100001332442899


Done!