HHsearch alignment for GI: 254780254 and conserved domain: TIGR01164

>TIGR01164 rplP_bact ribosomal protein L16; InterPro: IPR000114 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 L16 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L16 is known to bind directly the 23S rRNA and to be located at the A site of the peptidyltransferase centre. L16 is a protein of 133 to 185 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=100.00  E-value=0  Score=365.60  Aligned_cols=126  Identities=56%  Similarity=0.944  Sum_probs=125.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCEEECCCEEECHHHHHHHHHHHHHHCCCCCEEEEEECCCCEEEEECCCC
Q ss_conf             88877551067898972347787531213103274053132599999999999974267846898754986078621544
Q gi|254780254|r    3 RQPKNTKYPKQFKGRIKGVAKGGSRICFGNFALKAQEANRIGSSEIEAARRAISRGMKRAGRVWICVFPDVPVTAKPTEV   82 (138)
Q Consensus         3 l~Pk~~KyrK~~kgr~~g~~~~~~~l~fG~yGL~a~e~g~it~~qiEaaR~~i~R~lkk~gkiwirv~P~~pvTkKp~e~   82 (138)
T Consensus         1 L~Pkr~kyRK~~~G~~~G~a~~G~~~~FG~ygl~a~e~~wit~rQIEaaR~A~~R~~kr~Gk~WIRiFPd~p~T~KP~Et   80 (126)
T TIGR01164         1 LSPKRTKYRKQQRGRLKGKAKRGNTVAFGEYGLQALEPAWITARQIEAARVAMTRYIKRGGKLWIRIFPDKPYTKKPAET   80 (126)
T ss_pred             CCCCCEEEEECEECCEEEEECCCCEECCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEECCCCCCCCCCCCC
T ss_conf             99971035313001213320159840015322222034202268889999999886520670689967888832788852


Q ss_pred             CCCCCCCCCCEEEEEECCCEEEEEECCCCHHHHHHHHHHHHHHCCC
Q ss_conf             0014478811069983215089997497999999999998543895
Q gi|254780254|r   83 RMGKGKGNVEKWVCRVKPGRILFEIDGVSEEVARRAFRLGAAKLSV  128 (138)
Q Consensus        83 RMGkGKG~~~~wv~~Vk~G~ilfEi~gi~~~~a~~al~~a~~KLP~  128 (138)
T Consensus        81 RMG~GKG~~E~Wva~vk~G~vlFE~~Gv~e~~A~~A~~~A~~KLPi  126 (126)
T TIGR01164        81 RMGKGKGSPEYWVAVVKPGKVLFEIAGVPEEVAREALRLAASKLPI  126 (126)
T ss_pred             CCCCCCCCCCEEEEEECCCCEEEEECCCHHHHHHHHHHHHHHCCCC
T ss_conf             2588779976147873488079886186088899999985431789