HHsearch alignment for GI: 254780258 and conserved domain: TIGR01171

>TIGR01171 rplB_bact ribosomal protein L2; InterPro: IPR005880 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 , . The protein L2 is found in all ribosomes and is one of the best conserved proteins of this mega-dalton complex. L2 is elongated, exposing one end of the protein to the surface of the intersubunit interface of the 50 S subunit and is essential for the association of the ribosomal subunits and might participate in the binding and translocation of the tRNAs . This entry represents bacterial, chloroplast and mitochondrial forms.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0016740 transferase activity, 0006412 translation, 0015934 large ribosomal subunit.
Probab=100.00  E-value=0  Score=1018.21  Aligned_cols=272  Identities=57%  Similarity=0.995  Sum_probs=266.4

Q ss_pred             CEECCCCCCCCCCEEECCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCEEEEEEEEE-CCCCCCEEEE
Q ss_conf             5011588841051087045764168--872221115543677588984878864787510268798863-3777604788
Q gi|254780258|r    3 LKNFNPDTSGRRQLVMVDRNSLHSG--KPIKSLTRGLCSKGGRNNTGRVTMRFRGGGHKNRYRLVDFKR-GEYGLEGVVK   79 (278)
Q Consensus         3 ~k~~kP~Tp~~R~~~~~~~~~l~k~--~p~K~L~~~~~~~~GRNn~GrITvrhRGGGhKr~yR~IDf~r-~~~~~~~~V~   79 (278)
T Consensus         1 ik~ykP~TpG~R~~~~~~f~ei~k~~~~P~KsL~~~~~~~~GRNn~GrIT~RHrGGGHKr~YR~IDFKR~~K~~I~AkV~   80 (279)
T TIGR01171         1 IKKYKPYTPGRRGAVVSDFEEITKGRSKPEKSLLEKLHKTGGRNNRGRITSRHRGGGHKRLYRIIDFKRRDKDGIPAKVA   80 (279)
T ss_pred             CCEECCCCCCCCEEEEEECCCCEECCCCCCCCHHCCCCCCCCCCCCCEEEEEEECCCCCCCCCEEEEEECCCCCCCEEEE
T ss_conf             91120478885313353056521047886311001676467848887188887158844124314321036578735999


Q ss_pred             EEEECCCCEEEEEEEECCCCCEEEEECCCCCCCCCEEEEC-CCCCCCCCCCCHHHHHCCCCCEEEEEEEECCCCEEEEEE
Q ss_conf             7641588525889841477634675164566104578836-667675757411044357463776233303688258863
Q gi|254780258|r   80 RLEYDPNRTAFIALISYSNGSLAYILAPQRLSVGDKVISS-DSAVDVKPGNAMPLRFIPVGSIVHNVEMKPGKGGQISRS  158 (278)
Q Consensus        80 ~IeYDPnRsa~IALv~~~~g~~~YIlAp~gl~vGd~I~s~-~~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pG~Ggkl~Rs  158 (278)
T Consensus        81 ~IEYDPNRsA~IALl~Y~DGEKRYILaP~Gl~vGd~v~SG~~~a-~IK~GNaLPL~~IP~Gt~VHNiEl~PGkGGQlaRS  159 (279)
T TIGR01171        81 AIEYDPNRSARIALLHYADGEKRYILAPKGLKVGDTVISGEPEA-PIKPGNALPLKNIPVGTTVHNIELKPGKGGQLARS  159 (279)
T ss_pred             EEEECCCCCEEEEEEECCCCCEEEEECCCCCCCCCEEEECCCCC-CCCCCCCCCCCCCCCCEEEEEEEEEECCCCHHHEE
T ss_conf             97227876602224432787676643278777078898678788-80332227756476240688898830796032211


Q ss_pred             CCCEEEEEEECC-CEEEEEECCCCEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCC
Q ss_conf             465189967508-8899994897589985678099985125533230013134410057799701233268747888888
Q gi|254780258|r  159 AGSYARLVERDR-SRALLRLSSGEMRFVHSSCMASIGAVSNQDHSNVNHAKAGRARWLGMRSHVRGVAMNPVDHPHGGGE  237 (278)
Q Consensus       159 AGt~a~Ii~k~~-~~~~ikLPSGe~r~i~~~c~AtIG~vsN~~~~~~~~gKAG~~Rwlg~RP~VRGvAMNpvDHPhGGGe  237 (278)
T Consensus       160 AG~~aqi~aKe~~~Yv~lrLpSGE~R~v~~~C~ATiG~VGN~d~~n~~~GKAGR~RWlG~RP~VRG~AMNPVDHPHGGGE  239 (279)
T TIGR01171       160 AGTSAQILAKEGTKYVTLRLPSGEVRMVLKECRATIGEVGNEDHNNIVLGKAGRSRWLGIRPTVRGVAMNPVDHPHGGGE  239 (279)
T ss_pred             CCCEEEEEEECCCCEEEEEECCCCEEEECCCCEEEECCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCC
T ss_conf             14078989763875499982687245422332274122333344422205211331677479511237088877878840


Q ss_pred             CCCCCCC-CCCCCCCEECCCCCCCCCCC-CCEEEEEECCC
Q ss_conf             8888888-78878873437725488888-86149962346
Q gi|254780258|r  238 GKTSGGR-NPCSPWGKLTKGKRTRSNKS-TDVFIARSRHK  275 (278)
Q Consensus       238 Gkt~~gr-~~~spwG~~~kg~kTr~~k~-~~~~i~~~r~~  275 (278)
T Consensus       240 Gr~~~Gr~~PvtPWG~ptkG~KTR~~kk~Sd~fIvrrR~~  279 (279)
T TIGR01171       240 GRTPGGRRHPVTPWGKPTKGYKTRKKKKYSDKFIVRRRKK  279 (279)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCC
T ss_conf             6785578888788861006641334778776000562689