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!