HHsearch alignment for GI: 254780257 and conserved domain: TIGR01050
>TIGR01050 rpsS_bact ribosomal protein S19; InterPro: IPR005732 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 small ribosomal subunit protein S19 contains 88-144 amino acid residues. In Escherichia coli, S19 is known to form a complex with S13 that binds strongly to 16S ribosomal RNA. Experimental evidence has revealed that S19 is moderately exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=8.4e-45 Score=277.35 Aligned_cols=91 Identities=56% Similarity=0.978 Sum_probs=87.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEECCCEECCCCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCCCCC
Q ss_conf 97787767562589999999862168983598750374781022264899970862689998525110101253364363
Q gi|254780257|r 1 MARSVRKGPFVTKSLLKKVSQARDSGGRGVVRVWCRNCDIMPQFIGLTFGVYNGRKHVPVSVSEEMVGFKLGDFAPTRHC 80 (92)
Q Consensus 1 MsRS~~Kgpfv~~~L~~ki~~~~~~~~~~~IkT~sR~s~IlP~~vg~~i~VyNGk~f~~v~I~~~MVGhklGEFa~TRk~ 80 (92)
T Consensus 1 M~RS~kKGPFvd~~LlkKv~~~~~~~~~~~iKtwSRrS~I~P~mvG~t~~vhNG~~~ipvyi~e~mVGhKLGEFapTR~f 80 (92)
T TIGR01050 1 MSRSLKKGPFVDKHLLKKVEKLNESGKKKVIKTWSRRSTIIPEMVGHTIAVHNGKKFIPVYITEEMVGHKLGEFAPTRTF 80 (92)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCEEECCCCCCCEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCC
T ss_conf 98766566214578999999875036762368861110325631230678703966742686033124201675543342
Q ss_pred CCCC-CCCCCCC
Q ss_conf 5766-6653125
Q gi|254780257|r 81 PGHG-SDKKAKR 91 (92)
Q Consensus 81 ~~H~-~~kk~k~ 91 (92)
T Consensus 81 ~~H~~~~kk~~~ 92 (92)
T TIGR01050 81 KGHAKSDKKAKR 92 (92)
T ss_pred CCCCCCCCCCCC
T ss_conf 345423246789