Query         gi|254780242|ref|YP_003064655.1| 50S ribosomal protein L15 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 151
No_of_seqs    152 out of 2062
Neff          6.3 
Searched_HMMs 39220
Date          Tue May 24 04:20:20 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780242.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01071 rplO_bact ribosomal  100.0       0       0  385.4  10.7  148    2-149     1-155 (155)
  2 PRK05592 rplO 50S ribosomal pr 100.0       0       0  379.3  12.2  143    1-149     1-144 (144)
  3 COG0200 RplO Ribosomal protein 100.0       0       0  305.8  12.0  146    1-151     1-151 (152)
  4 KOG0846 consensus              100.0       0       0  305.9   9.3  149    1-150    22-174 (274)
  5 pfam01305 consensus            100.0       0       0  275.9   8.0  101    1-107     1-102 (102)
  6 pfam00828 Ribosomal_L18e Ribos 100.0       0       0  260.5  10.6  118   27-151     3-122 (122)
  7 PRK06419 rpl15p 50S ribosomal   99.8 6.9E-21 1.8E-25  129.3   9.8  127   13-151     4-145 (148)
  8 PTZ00160 60S ribosomal protein  99.7 4.5E-17 1.1E-21  109.5   7.6  127   12-151     3-146 (147)
  9 PRK04005 50S ribosomal protein  99.1 5.4E-11 1.4E-15   77.8   3.0   77   54-151    18-94  (111)
 10 COG1727 RPL18A Ribosomal prote  98.9 1.4E-09 3.6E-14   70.4   3.4   77   54-151    29-105 (122)
 11 pfam00256 consensus             98.6 1.6E-08   4E-13   64.9   1.9   32  115-146     1-32  (32)
 12 KOG1742 consensus               98.3 1.2E-06   3E-11   55.2   4.8  124   12-151     3-146 (147)
 13 PTZ00195 60S ribosomal protein  96.6  0.0032 8.1E-08   37.3   4.2   71   70-150    56-129 (198)
 14 KOG1714 consensus               90.3     0.2   5E-06   28.0   2.3   37  115-151    85-123 (188)
 15 TIGR01359 UMP_CMP_kin_fam UMP-  58.5     2.3 5.9E-05   22.4  -0.4   25   79-104    47-71  (189)
 16 TIGR01360 aden_kin_iso1 adenyl  58.1     3.4 8.6E-05   21.5   0.4   57   22-104    11-74  (191)
 17 CHL00005 rps16 ribosomal prote  49.1      15 0.00039   18.1   2.6   44   63-109    36-79  (82)
 18 TIGR00002 S16 ribosomal protei  24.9      62  0.0016   14.9   2.5   43   62-106    34-80  (81)
 19 CHL00147 rpl4 ribosomal protei  23.4      34 0.00087   16.3   0.9   36  109-144   174-211 (214)
 20 TIGR01328 met_gam_lyase methio  22.5      43  0.0011   15.7   1.3   37   96-135   161-206 (392)
 21 PRK00040 rpsP 30S ribosomal pr  22.2      71  0.0018   14.6   3.3   44   40-90      7-64  (75)
 22 COG0228 RpsP Ribosomal protein  20.3      78   0.002   14.4   3.1   57   40-105     7-78  (87)

No 1  
>TIGR01071 rplO_bact ribosomal protein L15; InterPro: IPR005749   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 , .   This entry represents ribosomal protein L15 and homologues found in bacteria, chloroplasts and mitochondria.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=100.00  E-value=0  Score=385.40  Aligned_cols=148  Identities=47%  Similarity=0.764  Sum_probs=143.1

Q ss_pred             CCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECCCCCCCCC--CCCCEEEEE
Q ss_conf             7666888-999876761020315789898578776676423689866-444316853011676355465--655214775
Q gi|254780242|r    2 KLNEISY-DKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLPKRGFVNI--AGSDFVTIS   77 (151)
Q Consensus         2 ~L~~l~~-~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~-gfEGGQ~Pl~rrlPKrGF~~~--~~~~~~~iN   77 (151)
                      +||+|+| +.||+|.+||||||+|||+|||||||||||+||||..++ |||||||||||||||+||.|.  ++.+|.+||
T Consensus         1 ~L~~L~pv~~G~~k~~KrvGRG~gSG~GKTsGRG~KGQkaRsG~~~r~GFEGGQ~PLYrRLPK~GF~~~~~~~k~~~~vN   80 (155)
T TIGR01071         1 KLHELKPVAKGAKKRRKRVGRGIGSGLGKTSGRGHKGQKARSGGKVRRGFEGGQTPLYRRLPKRGFSNKRAFKKEYAVVN   80 (155)
T ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCEEEEEE
T ss_conf             97776787430003630464257888864557788875122278754210579841321167557645326652168885


Q ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCC-EEEECCCC--CCCCEEEEEEEECHHHHHHHHHCCCEEE
Q ss_conf             112045430245553322335555430862544332-04630443--1441489999826999999997498899
Q gi|254780242|r   78 LGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRG-IRILSDGD--LKAKVVLRVSGASASAVEKVEKLGGQVI  149 (151)
Q Consensus        78 L~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~-vKiLg~Ge--l~~ki~I~v~~~S~sA~ekIE~aGG~v~  149 (151)
                      |++|+.+++.+++...++||++.|.+.++|+..... ||||++|+  ++.||+|+++++|++|.++||+|||+|+
T Consensus        81 ~~~~~~~~~~gRL~~~~~vt~~~L~e~g~i~~~~~~~vK~lg~G~~~l~~~~~~~~~~~S~~A~~~ie~aGG~~~  155 (155)
T TIGR01071        81 LGKLAKLFKDGRLSLQEVVTLETLLEKGLITKKIKLPVKVLGNGKFDLTKKLVVKAHRVSKSAKAKIEAAGGSVE  155 (155)
T ss_pred             HHHHHHHHHCCCEECCEEECHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCEEEEEEEECHHHHHHHHHCCCEEC
T ss_conf             135765640785200014177899851672432245424873275432242689872004578898887167109


No 2  
>PRK05592 rplO 50S ribosomal protein L15; Reviewed
Probab=100.00  E-value=0  Score=379.30  Aligned_cols=143  Identities=52%  Similarity=0.854  Sum_probs=137.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECCCCCCCCCCCCCEEEEEHH
Q ss_conf             97666888999876761020315789898578776676423689866-44431685301167635546565521477511
Q gi|254780242|r    1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLPKRGFVNIAGSDFVTISLG   79 (151)
Q Consensus         1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~-gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~   79 (151)
                      |+||+|+|++||++++||||||+|||+|||||||||||+||||+.++ ||||||||||||||||||+|+++.+|.+|||+
T Consensus         1 m~L~~L~~~~gs~k~~kRvGRG~gSG~GkTsGrG~KGQksRsG~~~~~gFEGGQ~PL~rRlPKrGF~n~~~~~~~~inL~   80 (144)
T PRK05592          1 MKLNELKPAPGSKKAKKRVGRGIGSGLGKTAGRGHKGQKARSGGGVRPGFEGGQMPLYRRLPKRGFTNIFRKEYAVVNLS   80 (144)
T ss_pred             CCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCEEEEECHH
T ss_conf             95355779989854773246576789985567777777466899979874379864278446436666565346898399


Q ss_pred             HHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEE
Q ss_conf             2045430245553322335555430862544332046304431441489999826999999997498899
Q gi|254780242|r   80 LLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVI  149 (151)
Q Consensus        80 ~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~  149 (151)
                      +|+.      |+++++||+++|++++||+++..+||||++|||+.+|+|+|++||++|+++||+|||+|+
T Consensus        81 ~L~~------~~~~~~I~~~~L~~~gli~~~~~~VKiLg~Gel~~ki~i~~~~~S~sA~~~Ie~aGG~v~  144 (144)
T PRK05592         81 DLAK------FEDGTEVTLEALKAAGLIRKNKKGVKVLGNGELTKKLTVKAHKFSKSAKEAIEAAGGSVE  144 (144)
T ss_pred             HHHC------CCCCCCCCHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCHHHHHHHHHCCCCCC
T ss_conf             9843------668871279999877884568754599847834555799998709999999998188439


No 3  
>COG0200 RplO Ribosomal protein L15 [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=305.83  Aligned_cols=146  Identities=50%  Similarity=0.831  Sum_probs=135.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CC-CCCCCCCCEEEECCCCCCCC-CCCC-CEEEE
Q ss_conf             976668889998767610203157898985787766764236898-66-44431685301167635546-5655-21477
Q gi|254780242|r    1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVS-VR-GFEGGQMPLYRRLPKRGFVN-IAGS-DFVTI   76 (151)
Q Consensus         1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~-~~-gfEGGQ~Pl~rrlPKrGF~~-~~~~-~~~~i   76 (151)
                      |+||+|+|..|+++.++|+|||++||.|||+|||||||+||||.. ++ +||||||||||||||+||+| .+.. +|.+|
T Consensus         1 m~l~~l~~~~G~~~~~~rvgrG~~sG~Gkt~GRG~kGqkaRsg~~~~~~gfeGgq~Pl~rrlpK~GF~~~~~~~~~~~~v   80 (152)
T COG0200           1 MRLNDLKPARGSKKTRKRVGRGIGSGLGKTGGRGHKGQKARSGHKWVRPGFEGGQMPLYRRLPKRGFTNSKFKKVEYAVV   80 (152)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCEEECCCCCHHHHCCCCCCCCCCCCCCCEEEE
T ss_conf             96433666877751457866277789998787877887555479600545525986135334888876665455314677


Q ss_pred             EHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEE-EECHHHHHHHHHCCCEEEEC
Q ss_conf             5112045430245553322335555430862544332046304431441489999-82699999999749889989
Q gi|254780242|r   77 SLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVS-GASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus        77 NL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~-~~S~sA~ekIE~aGG~v~ii  151 (151)
                      |++.|+.+++     +..+||++.|.+.++|......+|||++|+|+.++.++++ .||++|+|+||+|||+|+++
T Consensus        81 n~~~l~~~~~-----~~~~v~~~~l~~~~~i~~~~~~vKvLg~G~l~~~~~~~v~a~~S~~A~ekIe~aGG~v~~~  151 (152)
T COG0200          81 NLGKLAELLP-----EGEEVTLASLKAAGVIRKLKDLVKVLGNGKLTKAVPVKVKAKASKSAIEKIEAAGGKVELI  151 (152)
T ss_pred             EHHHHHHHCC-----CCCCCCHHHHHHCCEEECCCCCCEEECCCEECCCEEEEEEEEECHHHHHHHHHCCCEEEEC
T ss_conf             8889665415-----6651349998518947136655079606732553369986323899999999819889834


No 4  
>KOG0846 consensus
Probab=100.00  E-value=0  Score=305.94  Aligned_cols=149  Identities=49%  Similarity=0.780  Sum_probs=141.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCEEEEEHHH
Q ss_conf             97666888999876761020315789898578776676423689866444316853011676355465655214775112
Q gi|254780242|r    1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVRGFEGGQMPLYRRLPKRGFVNIAGSDFVTISLGL   80 (151)
Q Consensus         1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~~   80 (151)
                      ..|+||+|++|+++ .+|+|||++||+|||||||||||+||++.++.||||||||||||+||+||.+.+++.|.+++|..
T Consensus        22 ~~L~dLrpn~gskk-~kR~GRg~~sG~Gkt~GrG~KGqkqR~~~~~lGfEgGqtP~yrr~Pk~~~~~~~~r~~~pl~L~r  100 (274)
T KOG0846          22 VRLNDLRPNPGSKK-KKRKGRGISSGLGKTSGRGHKGQKQRGGRKILGFEGGQTPLYRRFPKFGFGNGGRRQYLPLSLGR  100 (274)
T ss_pred             HHHHCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCHHH
T ss_conf             35531689977434-24447775778764457877431103688755413688616775555566666543677546899


Q ss_pred             HHHHHCCCCCCCCCCCCHHHHHHCCCCC--CCCCCEEEECCC--CCCCCEEEEEEEECHHHHHHHHHCCCEEEE
Q ss_conf             0454302455533223355554308625--443320463044--314414899998269999999974988998
Q gi|254780242|r   81 LQAYIDKDRLDCSSEIDASVLVASGLVR--RSQRGIRILSDG--DLKAKVVLRVSGASASAVEKVEKLGGQVIV  150 (151)
Q Consensus        81 L~~~i~~~~~~~~~~Id~~~L~~~gli~--~~~~~vKiLg~G--el~~ki~I~v~~~S~sA~ekIE~aGG~v~i  150 (151)
                      ||.|||.++||+.++||+++|++.+++.  ...++|.|+.+|  +|+.+|+|||++||..||++||+|||+|+.
T Consensus       101 lq~lID~grid~~q~Idm~tL~~~g~i~p~~~eyGv~L~~~G~d~~~~~i~iEvs~aS~~AiaaIEkaGG~vtt  174 (274)
T KOG0846         101 LQKLIDTGRIDPSQPIDMKTLKDSGLINPKGREYGVQLTADGADEFKAKINIEVSRASVQAIAAIEKAGGSVTT  174 (274)
T ss_pred             HHHHHHHCCCCCCCCEEHHHHHHCCCCCCCCCCCCCEEECCCCCCCCCEEEEEEHHHHHHHHHHHHHCCCEEEE
T ss_conf             99999825878567121999975468776430027154214776445037988202119999999963985899


No 5  
>pfam01305 consensus
Probab=100.00  E-value=0  Score=275.88  Aligned_cols=101  Identities=55%  Similarity=0.891  Sum_probs=96.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECCCCCCCCCCCCCEEEEEHH
Q ss_conf             97666888999876761020315789898578776676423689866-44431685301167635546565521477511
Q gi|254780242|r    1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLPKRGFVNIAGSDFVTISLG   79 (151)
Q Consensus         1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~-gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~   79 (151)
                      |+||||+|++||+++++|||||+|||+|||||||||||+||||+.++ ||||||||||||||||||+|+++.+|++|||+
T Consensus         1 M~L~~Lkp~~gs~k~~kRvGRG~gsG~GktsGrG~KGQkaRsG~~~r~gFEGGQ~Pl~rRlPKrGF~n~~~~~~~~vnl~   80 (102)
T pfam01305         1 MKLHDLKPAPGSRKKRKRVGRGPGSGLGKTAGRGHKGQKSRSGGKVRRGFEGGQTPLYRRLPKRGFTNIKRKRYAEVNLK   80 (102)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCEEEEEEHH
T ss_conf             95254778999854773610688889985688887777677898878743378740167256367678888755888599


Q ss_pred             HHHHHHCCCCCCCCCCCCHHHHHHCCCC
Q ss_conf             2045430245553322335555430862
Q gi|254780242|r   80 LLQAYIDKDRLDCSSEIDASVLVASGLV  107 (151)
Q Consensus        80 ~L~~~i~~~~~~~~~~Id~~~L~~~gli  107 (151)
                      +|+.|+|      .++||+++|++++||
T Consensus        81 ~L~~~~~------~~~v~~~~L~~~glI  102 (102)
T pfam01305        81 DLARFFE------GGEVTLETLKAKGVI  102 (102)
T ss_pred             HHHHHHC------CCEECHHHHHHCCCC
T ss_conf             9861122------785889999886699


No 6  
>pfam00828 Ribosomal_L18e Ribosomal protein L18e/L15. This family includes eukaryotic L18 as well as prokaryotic L15.
Probab=100.00  E-value=0  Score=260.52  Aligned_cols=118  Identities=41%  Similarity=0.669  Sum_probs=107.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCC--CCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHC
Q ss_conf             8985787766764236898664443168530116763554656--55214775112045430245553322335555430
Q gi|254780242|r   27 TGKTAGRGVKGQKSRSGVSVRGFEGGQMPLYRRLPKRGFVNIA--GSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVAS  104 (151)
Q Consensus        27 ~Gkt~GrG~kGqk~Rsg~~~~gfEGGQ~Pl~rrlPKrGF~~~~--~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~  104 (151)
                      .|||||||||||+||||+..++|||||||||||||||||+|.+  +.+|.+|||++|+.+.    +++..++|.+.|.+.
T Consensus         3 ~Gkt~grG~kGqk~rsg~~~~~FeGGq~pl~rrlpKrGf~~~~~~~~~~~~inL~~l~~~~----~~~~~~~~~~~~~~~   78 (122)
T pfam00828         3 IGKTRGRGRKGGRGRAGGQKHPFEGGQVPLYRRLGKRGFRRLFKSRKNRPPVNLSKLDRKM----LKDGEEVDGETLVVV   78 (122)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCEEEEEEEHHHHHHCC----CCCCCCCCHHHHHHC
T ss_conf             7564778887777789999988646866134433214766656675189998899954112----456551059999776


Q ss_pred             CCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC
Q ss_conf             86254433204630443144148999982699999999749889989
Q gi|254780242|r  105 GLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus       105 gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii  151 (151)
                      ++++   ++||||++|+++.||+|+|++||++|+|+||+|||+|++|
T Consensus        79 ~~~~---~~vKlLg~G~l~~~i~I~a~~~S~sA~e~Ie~aGG~v~~i  122 (122)
T pfam00828        79 GTVT---DDVKVLGNGELTKPLTVKALKFSKSAREKIEKAGGEVILL  122 (122)
T ss_pred             CCCC---CCEEEEECCCCCCEEEEEEEECCHHHHHHHHHCCCEEEEC
T ss_conf             8665---3469985883473489999976999999999859989979


No 7  
>PRK06419 rpl15p 50S ribosomal protein L15P; Reviewed
Probab=99.85  E-value=6.9e-21  Score=129.32  Aligned_cols=127  Identities=28%  Similarity=0.426  Sum_probs=80.6

Q ss_pred             CCCCCCCCCCC---CCCC-CCCCCCCCCCCCCCCCCCCCCCCCCC--CCEEEECCCCCCCCCCC--CCEEEEEHHHHHHH
Q ss_conf             76761020315---7898-98578776676423689866444316--85301167635546565--52147751120454
Q gi|254780242|r   13 CKVKKRVARGI---GSGT-GKTAGRGVKGQKSRSGVSVRGFEGGQ--MPLYRRLPKRGFVNIAG--SDFVTISLGLLQAY   84 (151)
Q Consensus        13 ~~~~kR~GRG~---gsg~-Gkt~GrG~kGqk~Rsg~~~~gfEGGQ--~Pl~rrlPKrGF~~~~~--~~~~~iNL~~L~~~   84 (151)
                      +.++.|.=||.   |-|. |+--|.||+|..-++|..-.-|..-.  .|-|  +.|+||+++++  .+|.+|||++|+++
T Consensus         4 r~kK~rK~RG~rt~G~G~~~khRgaG~rGGrG~AG~~kH~~~~~~k~~p~~--fGK~GF~~~~~~~~~~~~INl~~L~~l   81 (148)
T PRK06419          4 RRKKSRKLRGSRTHGWGTHKQHRGAGNRGGRGMAGMHKHKWTWTVKYGPDH--YGKHGFKRPPKTIKEVSTINVGELDEL   81 (148)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCC--CCCCCCCCCCCCCCCCEEEEHHHHHHH
T ss_conf             541243567671527998777888989976823489866636524456300--377776576001663167789999998


Q ss_pred             HCCCC----CCC---CCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC
Q ss_conf             30245----553---32233555543086254433204630443144148999982699999999749889989
Q gi|254780242|r   85 IDKDR----LDC---SSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus        85 i~~~~----~~~---~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii  151 (151)
                      ++...    ++.   ..+||   |.+.+       .+||||+|+++.|++|+|++||++|+|+||+|||+|+++
T Consensus        82 i~~l~~~g~a~~~~~~~vID---l~~~G-------y~KvLg~G~~~~~~~v~a~~~S~~A~ekIe~aGG~~~l~  145 (148)
T PRK06419         82 IEELKEEGKAEEEDGKIVVD---LTELG-------YDKVLGGGKVTRPLVIKAPAFSEKAIEKIEAAGGEVILL  145 (148)
T ss_pred             HHHHHHHHHEECCCCCEEEE---CHHCC-------CEEEECCCCCCCCEEEEEEECCHHHHHHHHHCCCEEEEE
T ss_conf             88887531223369976986---04449-------548908975187689999723888999999839989998


No 8  
>PTZ00160 60S ribosomal protein L27; Provisional
Probab=99.70  E-value=4.5e-17  Score=109.48  Aligned_cols=127  Identities=22%  Similarity=0.294  Sum_probs=86.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----EEEE----CCCCCCCCCCCC---CE-EEEEHH
Q ss_conf             87676102031578989857877667642368986644431685----3011----676355465655---21-477511
Q gi|254780242|r   12 SCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVRGFEGGQMP----LYRR----LPKRGFVNIAGS---DF-VTISLG   79 (151)
Q Consensus        12 ~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~gfEGGQ~P----l~rr----lPKrGF~~~~~~---~~-~~iNL~   79 (151)
                      ++.++.|.=||.-     |+|.|..||- |....-+|.-|||.-    +..-    +-|.||.+++..   .| .+|||+
T Consensus         3 tr~kKtRK~RG~~-----s~G~GrvGkH-Rkh~GGrG~aGg~~Hhr~~~~KyhPgyfGK~G~r~~h~~~n~~~~p~INl~   76 (147)
T PTZ00160          3 TRFKKCRKQRGHV-----SHGYGRVGKH-RKHPSGRGNAGGLHHHRINFDKYHPGYFGKVGMRHFHLKKNTLHKPTVNID   76 (147)
T ss_pred             CCCCCCCCCCCCC-----CCCCCCCCCC-CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHH
T ss_conf             5432122456654-----3178887767-889988855465522145200208563467765468736664427721099


Q ss_pred             HHHHHHCCCCCCCC----CCCCHHHHHHCCCCCCCCCCEEEECCCCC-CCCEEEEEEEECHHHHHHHHHCCCEEEEC
Q ss_conf             20454302455533----22335555430862544332046304431-44148999982699999999749889989
Q gi|254780242|r   80 LLQAYIDKDRLDCS----SEIDASVLVASGLVRRSQRGIRILSDGDL-KAKVVLRVSGASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus        80 ~L~~~i~~~~~~~~----~~Id~~~L~~~gli~~~~~~vKiLg~Gel-~~ki~I~v~~~S~sA~ekIE~aGG~v~ii  151 (151)
                      +|.++++....+..    +..-.-+|.+.|.       .||||.|.| +.|+.|+|-+||++|+|+||+|||.|+|+
T Consensus        77 kLw~lv~~~~~~~~~~~~~~~pVIDl~~~Gy-------~KvLG~G~lp~~P~iVKa~~fS~~AeeKIk~aGG~~vL~  146 (147)
T PTZ00160         77 KLWSLVPEETREKYAKKKDTAPVIDVTKSGY-------FKVLGNGHLPQQPVIVKARYFSKLAEKKIKAAGGACVLV  146 (147)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEHHCCC-------EEEECCCCCCCCCEEEEEEECCHHHHHHHHHCCCEEEEE
T ss_conf             9999867999988740469986887112371-------077028746998889997222888999999709779983


No 9  
>PRK04005 50S ribosomal protein L18e; Provisional
Probab=99.09  E-value=5.4e-11  Score=77.79  Aligned_cols=77  Identities=23%  Similarity=0.395  Sum_probs=58.9

Q ss_pred             CCEEEECCCCCCCCCCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEE
Q ss_conf             85301167635546565521477511204543024555332233555543086254433204630443144148999982
Q gi|254780242|r   54 MPLYRRLPKRGFVNIAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGA  133 (151)
Q Consensus        54 ~Pl~rrlPKrGF~~~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~  133 (151)
                      .|+++.+-+|=+.  ++.++.+|||+.|+.+..     ++++|         +|     +-||||+|+++.+++|.+..|
T Consensus        18 a~iwk~Va~rL~~--prr~r~~vnLskI~r~~k-----~~~~v---------vV-----pGKVLg~g~l~~kvtV~A~~f   76 (111)
T PRK04005         18 APIWKDVAERLEK--PRRKRAEVNLSKINRYAK-----EGDVV---------VV-----PGKVLGSGKLDKKVTVAALSF   76 (111)
T ss_pred             CHHHHHHHHHHHC--CCCCCCCCCHHHHHHHCC-----CCCEE---------EE-----EEEECCCCEECCCEEEEEEEC
T ss_conf             8789999999825--554689867999998577-----89989---------99-----888818877867779999757


Q ss_pred             CHHHHHHHHHCCCEEEEC
Q ss_conf             699999999749889989
Q gi|254780242|r  134 SASAVEKVEKLGGQVIVI  151 (151)
Q Consensus       134 S~sA~ekIE~aGG~v~ii  151 (151)
                      |++|+++||+|||+|..+
T Consensus        77 S~~A~~kI~~aGG~~it~   94 (111)
T PRK04005         77 SETAKEKIEEAGGECLTI   94 (111)
T ss_pred             CHHHHHHHHHCCCEEEEH
T ss_conf             989999999809989779


No 10 
>COG1727 RPL18A Ribosomal protein L18E [Translation, ribosomal structure and biogenesis]
Probab=98.87  E-value=1.4e-09  Score=70.42  Aligned_cols=77  Identities=22%  Similarity=0.404  Sum_probs=60.7

Q ss_pred             CCEEEECCCCCCCCCCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEE
Q ss_conf             85301167635546565521477511204543024555332233555543086254433204630443144148999982
Q gi|254780242|r   54 MPLYRRLPKRGFVNIAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGA  133 (151)
Q Consensus        54 ~Pl~rrlPKrGF~~~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~  133 (151)
                      -|+++.+-+|=|.  ++.++++|||++|+.+..     +++++         +|     +=||||+|.+..+++|-+-.|
T Consensus        29 a~iwk~vaerL~~--prr~ra~VnlsKI~r~ak-----~~d~v---------vV-----pGkVLg~g~l~~kVtVaAl~F   87 (122)
T COG1727          29 APIWKDVAERLEK--PRRNRAEVNVSKINRYAK-----EGDTV---------VV-----PGKVLGDGKLDKKVTVAALRF   87 (122)
T ss_pred             CHHHHHHHHHHHC--CCCCCCCEEHHHHHHHCC-----CCCEE---------EE-----EEEEECCCCCCCCEEEEEEEC
T ss_conf             7799999999835--434588463899996547-----99889---------99-----556844764236569999861


Q ss_pred             CHHHHHHHHHCCCEEEEC
Q ss_conf             699999999749889989
Q gi|254780242|r  134 SASAVEKVEKLGGQVIVI  151 (151)
Q Consensus       134 S~sA~ekIE~aGG~v~ii  151 (151)
                      |++|.++|++|||+|..|
T Consensus        88 S~~A~~KI~~aGGe~~tl  105 (122)
T COG1727          88 SKTAREKIEEAGGECLTL  105 (122)
T ss_pred             CHHHHHHHHHCCCEEEEH
T ss_conf             778999999729858649


No 11 
>pfam00256 consensus
Probab=98.60  E-value=1.6e-08  Score=64.92  Aligned_cols=32  Identities=38%  Similarity=0.553  Sum_probs=31.3

Q ss_pred             EEECCCCCCCCEEEEEEEECHHHHHHHHHCCC
Q ss_conf             46304431441489999826999999997498
Q gi|254780242|r  115 RILSDGDLKAKVVLRVSGASASAVEKVEKLGG  146 (151)
Q Consensus       115 KiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG  146 (151)
                      ||||+|+|+.|++|+++.||++|+++||+|||
T Consensus         1 KvLG~G~l~~~v~v~a~~~S~~A~~kIe~aGG   32 (32)
T pfam00256         1 KVLGSGKLTKPVTVKALKFSKSAEEKIEAAGG   32 (32)
T ss_pred             CCCCCCEECCCEEEEHHHHHHHHHHHHHHHCC
T ss_conf             91568634765898826735789999987169


No 12 
>KOG1742 consensus
Probab=98.27  E-value=1.2e-06  Score=55.18  Aligned_cols=124  Identities=31%  Similarity=0.385  Sum_probs=74.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CEEEECC----CCCCCCC----CCCCEEEEEHHHH
Q ss_conf             8767610203157898985787766764236898664443168--5301167----6355465----6552147751120
Q gi|254780242|r   12 SCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVRGFEGGQM--PLYRRLP----KRGFVNI----AGSDFVTISLGLL   81 (151)
Q Consensus        12 ~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~gfEGGQ~--Pl~rrlP----KrGF~~~----~~~~~~~iNL~~L   81 (151)
                      ++.++.|.=||.-|     +|.|.-| |.|.-..-+|-.||.+  -+-+-.|    |.|...+    +.--+.+|||+.|
T Consensus         3 s~~rKTrKLrGHVS-----hGhgrig-KhrkhpgGrg~agghhr~~fdKyhpgyfgkvgmr~yh~~rn~~~~P~vnldkL   76 (147)
T KOG1742           3 SRLRKTRKLRGHVS-----HGHGRIG-KHRKHPGGRGNAGHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFCPTVNLDKL   76 (147)
T ss_pred             CHHHHHHHHHCCCC-----CCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCHHHH
T ss_conf             13567787623301-----0455445-44568886666677630012234777555420468998735565776258999


Q ss_pred             HHHHCCCCC--------CCCCCCCHHHHHHCCCCCCCCCCEEEECCCCC--CCCEEEEEEEECHHHHHHHHHCCCEEEEC
Q ss_conf             454302455--------53322335555430862544332046304431--44148999982699999999749889989
Q gi|254780242|r   82 QAYIDKDRL--------DCSSEIDASVLVASGLVRRSQRGIRILSDGDL--KAKVVLRVSGASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus        82 ~~~i~~~~~--------~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel--~~ki~I~v~~~S~sA~ekIE~aGG~v~ii  151 (151)
                      -.++.+..-        ...-.||.   .+.|.       .|+||.|.+  +.|+.|++.+||..|.|+|.++||.+++.
T Consensus        77 Wtlv~~~~~~~~~~~k~g~aPvidv---~~~Gy-------~kvlGkgklp~~~PvIvKak~~s~~AeekIk~~gg~~~~~  146 (147)
T KOG1742          77 WTLVREQTRVKAAKNKTGAAPVIDV---VQSGY-------YKVLGKGKLPEETPVIVKAKYFSRRAEEKIKKAGGAVVLT  146 (147)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCEEEE---EECCE-------EEEECCCCCCCCCCEEEECCCCCCCCHHHHHHCCCCEEEC
T ss_conf             9870699999875158887751555---51130-------5651246478778678760203762359887306602544


No 13 
>PTZ00195 60S ribosomal protein L18; Provisional
Probab=96.57  E-value=0.0032  Score=37.28  Aligned_cols=71  Identities=15%  Similarity=0.196  Sum_probs=41.5

Q ss_pred             CCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCE-EEECCCCC-CC-CEEEEEEEECHHHHHHHHHCCC
Q ss_conf             552147751120454302455533223355554308625443320-46304431-44-1489999826999999997498
Q gi|254780242|r   70 GSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGI-RILSDGDL-KA-KVVLRVSGASASAVEKVEKLGG  146 (151)
Q Consensus        70 ~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~v-KiLg~Gel-~~-ki~I~v~~~S~sA~ekIE~aGG  146 (151)
                      +.+-.+++|+.|..+..+........      .+..++    --| .|+.+-.+ .. +++|-|..||++|++.|++|||
T Consensus        56 r~nRpPlSlSrl~~~mk~~~~~~~~g------~~~kia----VvVGtVTDD~Rl~evPkl~VcALrfT~~AR~RIlkaGG  125 (198)
T PTZ00195         56 RSNRAPISLSRIAVVMKRKAVFTAKG------KKAPIA----VVVGDVLDDVRMARIPAMRVCALRFSKSARQSIVAAGG  125 (198)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCCCCC------CCCCEE----EEEEEECCCHHHHCCCCCEEEEEEECHHHHHHHHHCCC
T ss_conf             45799611999999986312334788------768779----99830326534313765148876513889999996398


Q ss_pred             EEEE
Q ss_conf             8998
Q gi|254780242|r  147 QVIV  150 (151)
Q Consensus       147 ~v~i  150 (151)
                      +|..
T Consensus       126 e~lT  129 (198)
T PTZ00195        126 ECLT  129 (198)
T ss_pred             EEEE
T ss_conf             5886


No 14 
>KOG1714 consensus
Probab=90.28  E-value=0.2  Score=27.96  Aligned_cols=37  Identities=16%  Similarity=0.318  Sum_probs=28.8

Q ss_pred             EEECCCCC-C-CCEEEEEEEECHHHHHHHHHCCCEEEEC
Q ss_conf             46304431-4-4148999982699999999749889989
Q gi|254780242|r  115 RILSDGDL-K-AKVVLRVSGASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus       115 KiLg~Gel-~-~ki~I~v~~~S~sA~ekIE~aGG~v~ii  151 (151)
                      +|+++-.+ . -++.|.+..||++|.+.|++|||+|..+
T Consensus        85 TvtdD~rv~~vPkl~v~al~~t~~ar~rI~kagg~i~Tl  123 (188)
T KOG1714          85 TVTDDLRVQEVPKLKVAALRFTKGARARILKAGGEILTL  123 (188)
T ss_pred             EECCCCEEEECCCCEEEEEECCCCHHHHHHCCCCEEEEE
T ss_conf             651650024313202444100442145553068669754


No 15 
>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family; InterPro: IPR006266   This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic. ; GO: 0005524 ATP binding, 0016776 phosphotransferase activity phosphate group as acceptor, 0019201 nucleotide kinase activity, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=58.50  E-value=2.3  Score=22.37  Aligned_cols=25  Identities=20%  Similarity=0.434  Sum_probs=19.1

Q ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHC
Q ss_conf             12045430245553322335555430
Q gi|254780242|r   79 GLLQAYIDKDRLDCSSEIDASVLVAS  104 (151)
Q Consensus        79 ~~L~~~i~~~~~~~~~~Id~~~L~~~  104 (151)
                      ..|+.+|..++|-|.+ ||.+.|.++
T Consensus        47 ~lI~~~IkeG~IVPs~-VTv~LL~ka   71 (189)
T TIGR01359        47 ELIESYIKEGKIVPSE-VTVELLKKA   71 (189)
T ss_pred             CHHHHHHHCCCEEHHE-EEHHHHHHH
T ss_conf             0377441158311122-324588877


No 16 
>TIGR01360 aden_kin_iso1 adenylate kinase; InterPro: IPR006267   Members of this family are adenylate kinase, 2.7.4.3 from EC. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (IPR006266 from INTERPRO), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in IPR006259 from INTERPRO.; GO: 0004017 adenylate kinase activity, 0005524 ATP binding, 0046034 ATP metabolic process, 0005737 cytoplasm.
Probab=58.15  E-value=3.4  Score=21.52  Aligned_cols=57  Identities=25%  Similarity=0.371  Sum_probs=40.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCC-----CCCEEEEE--HHHHHHHHCCCCCCCCC
Q ss_conf             157898985787766764236898664443168530116763554656-----55214775--11204543024555332
Q gi|254780242|r   22 GIGSGTGKTAGRGVKGQKSRSGVSVRGFEGGQMPLYRRLPKRGFVNIA-----GSDFVTIS--LGLLQAYIDKDRLDCSS   94 (151)
Q Consensus        22 G~gsg~Gkt~GrG~kGqk~Rsg~~~~gfEGGQ~Pl~rrlPKrGF~~~~-----~~~~~~iN--L~~L~~~i~~~~~~~~~   94 (151)
                      |||||+|..|-+            +             +-|+||++..     |.|...=+  =-.|++..+.+.+-+.+
T Consensus        11 GPGSGKGTQC~K------------i-------------V~KYGfTHLSsGdLLR~Ev~SgS~rg~~L~aiMe~G~LVp~~   65 (191)
T TIGR01360        11 GPGSGKGTQCEK------------I-------------VEKYGFTHLSSGDLLREEVASGSERGKQLQAIMESGELVPLD   65 (191)
T ss_pred             CCCCCCCHHHHH------------H-------------HHHCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCH
T ss_conf             888884013689------------8-------------864188645406788987415781147899998618855506


Q ss_pred             CCCHHHHHHC
Q ss_conf             2335555430
Q gi|254780242|r   95 EIDASVLVAS  104 (151)
Q Consensus        95 ~Id~~~L~~~  104 (151)
                      +| ++.|+++
T Consensus        66 ~V-L~Ll~dA   74 (191)
T TIGR01360        66 VV-LDLLKDA   74 (191)
T ss_pred             HH-HHHHHHH
T ss_conf             68-9999999


No 17 
>CHL00005 rps16 ribosomal protein S16
Probab=49.14  E-value=15  Score=18.10  Aligned_cols=44  Identities=9%  Similarity=0.243  Sum_probs=29.8

Q ss_pred             CCCCCCCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCC
Q ss_conf             35546565521477511204543024555332233555543086254
Q gi|254780242|r   63 RGFVNIAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRR  109 (151)
Q Consensus        63 rGF~~~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~  109 (151)
                      -||.|+...+ ..+|++.+..|+..+-- +.++| ...|..+|+...
T Consensus        36 lG~YnP~~~~-~~l~~eri~~Wl~~GAq-pT~tV-~~Llk~~gi~~~   79 (82)
T CHL00005         36 VGFYDPIKNQ-TYLNVPAILYFLEKGAQ-PTGTV-YDILKKAEVFKE   79 (82)
T ss_pred             EEEECCCCCC-CCCCHHHHHHHHHCCCC-CCHHH-HHHHHHCCCHHH
T ss_conf             7775799986-53389999999997698-88999-999998373776


No 18 
>TIGR00002 S16 ribosomal protein S16; InterPro: IPR000307   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 S16 is one of the proteins from the small ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups:  Eubacterial S16. Algal and plant chloroplast S16. Cyanelle S16. Neurospora crassa mitochondrial S24 (cyt-21). S16 proteins have about 100 amino-acid residues. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=24.87  E-value=62  Score=14.92  Aligned_cols=43  Identities=16%  Similarity=0.298  Sum_probs=28.9

Q ss_pred             CCCCCCCCCCC----EEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCC
Q ss_conf             63554656552----1477511204543024555332233555543086
Q gi|254780242|r   62 KRGFVNIAGSD----FVTISLGLLQAYIDKDRLDCSSEIDASVLVASGL  106 (151)
Q Consensus        62 KrGF~~~~~~~----~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gl  106 (151)
                      +-||.|+...+    ...+|...+..|+..+-- +.+++ .+.|..+++
T Consensus        34 ~lG~y~P~~~~~~~~~~~l~~~~~~~wl~~Ga~-pt~tv-~~ll~~~g~   80 (81)
T TIGR00002        34 ELGFYNPLLKEDDEERVKLDVERIKYWLSKGAQ-PTDTV-RNLLKKAGV   80 (81)
T ss_pred             HCCCCCCCCCCCCCCEEEECHHHHHHHHHCCCC-CCHHH-HHHHHHHCC
T ss_conf             315447888898752466367999999866998-57788-999886147


No 19 
>CHL00147 rpl4 ribosomal protein L4; Validated
Probab=23.42  E-value=34  Score=16.29  Aligned_cols=36  Identities=8%  Similarity=0.234  Sum_probs=24.7

Q ss_pred             CCCCCEEEECCCCCCC--CEEEEEEEECHHHHHHHHHC
Q ss_conf             4433204630443144--14899998269999999974
Q gi|254780242|r  109 RSQRGIRILSDGDLKA--KVVLRVSGASASAVEKVEKL  144 (151)
Q Consensus       109 ~~~~~vKiLg~Gel~~--ki~I~v~~~S~sA~ekIE~a  144 (151)
                      .+...|+++...++..  =+.-+---+|++|.++||..
T Consensus       174 RNi~~v~v~~~~~lNvyDlL~~~~vVit~~Al~~leE~  211 (214)
T CHL00147        174 RNLKNVELIAADHLNIKSLLKAKKIIITTEALKIIKEV  211 (214)
T ss_pred             HCCCCCEEEECCCCCHHHHHCCCCEEEEHHHHHHHHHH
T ss_conf             48798568625984099996699499868999999998


No 20 
>TIGR01328 met_gam_lyase methionine gamma-lyase; InterPro: IPR006237   This family of sequences is a methionine gamma-lyase subset of a family of PLP-dependent trans-sulphuration enzymes. The member from the parasite Trichomonas vaginalis is described as catalyzing alpha gamma- and alpha-beta eliminations and gamma-replacement reactions on methionine, cysteine, and some derivatives. Likewise, the enzyme from Pseudomonas degrades cysteine as well as methionine..
Probab=22.52  E-value=43  Score=15.75  Aligned_cols=37  Identities=24%  Similarity=0.448  Sum_probs=24.5

Q ss_pred             CCHHHHHHCCCCCCCCCCEEEECCCCCCCC---------EEEEEEEECH
Q ss_conf             335555430862544332046304431441---------4899998269
Q gi|254780242|r   96 IDASVLVASGLVRRSQRGIRILSDGDLKAK---------VVLRVSGASA  135 (151)
Q Consensus        96 Id~~~L~~~gli~~~~~~vKiLg~Gel~~k---------i~I~v~~~S~  135 (151)
                      ||++..+.   +.+...+|||+-+..+.+|         ++|.||+|||
T Consensus       161 iD~e~v~r---~A~~~gG~kVivDNTfatP~lt~P~alG~D~VVHSATK  206 (392)
T TIGR01328       161 IDLELVVR---VAHEKGGVKVIVDNTFATPYLTRPVALGVDVVVHSATK  206 (392)
T ss_pred             HHHHHHHH---HHHHCCCEEEEEECCCCCHHHCCHHHCCCCEEEECCCC
T ss_conf             75999999---99752982899856627700138036187768942412


No 21 
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=22.19  E-value=71  Score=14.63  Aligned_cols=44  Identities=27%  Similarity=0.483  Sum_probs=28.3

Q ss_pred             CCCCCCCCCCCCCCCCEEE------ECCC-------CCCCCCCC-CCEEEEEHHHHHHHHCCCCC
Q ss_conf             2368986644431685301------1676-------35546565-52147751120454302455
Q gi|254780242|r   40 SRSGVSVRGFEGGQMPLYR------RLPK-------RGFVNIAG-SDFVTISLGLLQAYIDKDRL   90 (151)
Q Consensus        40 ~Rsg~~~~gfEGGQ~Pl~r------rlPK-------rGF~~~~~-~~~~~iNL~~L~~~i~~~~~   90 (151)
                      +|.|..-+       |+||      |-|.       -||.++.. .+...+|++.++.|+..+--
T Consensus         7 ~R~G~k~~-------P~YrIVv~d~r~~RdGk~iE~lG~ydP~~~~~~~~l~~eri~~Wl~~GAq   64 (75)
T PRK00040          7 ARGGAKKR-------PFYRIVVADSRSPRDGRFIERVGFYNPLAKPAEVKLDEERVLYWLGQGAQ   64 (75)
T ss_pred             HCCCCCCC-------CEEEEEEEECCCCCCCCCHHEEEEECCCCCCCEEEECHHHHHHHHHCCCC
T ss_conf             00899899-------85899996266678886100004777989986699849999999987898


No 22 
>COG0228 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=20.27  E-value=78  Score=14.41  Aligned_cols=57  Identities=25%  Similarity=0.418  Sum_probs=34.9

Q ss_pred             CCCCCCCCCCCCCCCCEEE------ECCC-------CCCCCC--CCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHC
Q ss_conf             2368986644431685301------1676-------355465--655214775112045430245553322335555430
Q gi|254780242|r   40 SRSGVSVRGFEGGQMPLYR------RLPK-------RGFVNI--AGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVAS  104 (151)
Q Consensus        40 ~Rsg~~~~gfEGGQ~Pl~r------rlPK-------rGF~~~--~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~  104 (151)
                      +|-|...+       |+||      |-|.       -||.|+  ...+-..|+.+.++.|+.++-- +++++ ...|.+.
T Consensus         7 ~R~G~kk~-------P~YrIVVaDsrs~RDGr~IE~lG~ynP~~~~~~~v~l~~eri~~Wl~~GAq-pSdtV-~~ll~~~   77 (87)
T COG0228           7 ARGGSKKR-------PFYRIVVADSRSPRDGRFIERLGTYNPLLGKEERVKLDEERILYWLSQGAQ-PSDTV-RRLLKKA   77 (87)
T ss_pred             HHCCCCCC-------CEEEEEEECCCCCCCCCCHHHHCCCCCCCCCCCEEEECHHHHHHHHHCCCC-CCHHH-HHHHHHH
T ss_conf             01787669-------847999841688889864454002378878763478869999999985997-44899-9999985


Q ss_pred             C
Q ss_conf             8
Q gi|254780242|r  105 G  105 (151)
Q Consensus       105 g  105 (151)
                      |
T Consensus        78 g   78 (87)
T COG0228          78 G   78 (87)
T ss_pred             H
T ss_conf             2


Done!