HHsearch alignment for GI: 254780257 and conserved domain: TIGR01025

>TIGR01025 rpsS_arch ribosomal protein S19; InterPro: IPR005713 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 represents eukaryotic ribosomal protein S15 and its archaeal equivalent. It excludes bacterial and organellar ribosomal protein S19. The nomenclature for the archaeal members is unresolved and given variously as S19 (after the more distant bacterial homologs) or S15.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=99.97  E-value=1.8e-31  Score=201.24  Aligned_cols=87  Identities=40%  Similarity=0.701  Sum_probs=76.2

Q ss_pred             CCCCCCCCC-CHHHHHHHHHHHC-----CCCCCEEEEEECCCEECCCCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCC
Q ss_conf             787767562-5899999998621-----6898359875037478102226489997086268999852511010125336
Q gi|254780257|r    3 RSVRKGPFV-TKSLLKKVSQARD-----SGGRGVVRVWCRNCDIMPQFIGLTFGVYNGRKHVPVSVSEEMVGFKLGDFAP   76 (92)
Q Consensus         3 RS~~Kgpfv-~~~L~~ki~~~~~-----~~~~~~IkT~sR~s~IlP~~vg~~i~VyNGk~f~~v~I~~~MVGhklGEFa~   76 (92)
T Consensus        33 R~l~RGl~~~~~~ll~k~rk~k~e~~~~g~~P~~~rTH~RdmiilPeMvG~~~~v~NGK~F~~V~i~PEMIGhylgEF~~  112 (136)
T TIGR01025        33 RRLKRGLTPKQKKLLKKLRKAKKEAKPKGEKPEVIRTHCRDMIILPEMVGLTVGVYNGKEFVEVEIKPEMIGHYLGEFAL  112 (136)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCEEECCCCCCCEEEEECCCEEEEEEEEEEEECCCHHHCCC
T ss_conf             21102877447899999999887432146888600212442157642336077872086555677420031220000001


Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             4363576666531
Q gi|254780257|r   77 TRHCPGHGSDKKA   89 (92)
Q Consensus        77 TRk~~~H~~~kk~   89 (92)
T Consensus       113 t~k~v~Hg~PG~G  125 (136)
T TIGR01025       113 TRKPVKHGAPGVG  125 (136)
T ss_pred             CCCCCCCCCCCCC
T ss_conf             1253236856966