>TIGR00952 S15_bact ribosomal protein S15; InterPro: IPR005290 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 family includes specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13. Escherichia coli ribosomal protein S15 has been shown to regulate the expression of its own mRNA by a feedback mechanism at the translational level. The translational operator overlaps the ribosome binding site and folds into two mutually exclusive structures, one consisting of two stem-loops (I and II) and the other one forming a pseudoknot. The two structures, which seem to be energetically equivalent are in dynamic equilibrium, and the pseudoknot is stabilized by binding of S15. However, binding of S15 does not prevent 30 S subunit binding but traps the subunit into an incompetent translation initiation complex. Repression can be alleviated by 16 S rRNA, which is able to displace the bound S15, thus allowing translation to proceed .; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.

Probab=100.00  E-value=2.5e-43  Score=260.36  Aligned_cols=86  Identities=57%  Similarity=0.862  Sum_probs=84.7

Q ss_pred             CHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             88999999999545888788899999997799999999999778413527789999997899999998409999999999
Q gi|254780785|r    4 TLERKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKRLVQ   83 (89)
Q Consensus         4 ~~~~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~~i~   83 (89)
T Consensus         1 ~~e~K~~ii~~f~~hE~DTGS~~VQiAlLT~rI~~LteHLk~nkKDh~SRRGLL~lVg~RRrLL~Yl~~~d~e~Y~~LI~   80 (86)
T TIGR00952         1 TKERKQEIIKEFQLHEKDTGSPEVQIALLTERINQLTEHLKANKKDHHSRRGLLKLVGRRRRLLKYLKRTDVERYRSLIK   80 (86)
T ss_pred             CHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             91248999998545899855889999999999988878875178983302799999997788999971016799999998


Q ss_pred             HHCCCC
Q ss_conf             836899
Q gi|254780785|r   84 SLKLRR   89 (89)
Q Consensus        84 ~LglRk   89 (89)
T Consensus        81 ~LGLR~   86 (86)
T TIGR00952        81 KLGLRR   86 (86)
T ss_pred             HCCCCC
T ss_conf             447999