HHsearch alignment for GI: 254780626 and conserved domain: TIGR00029

>TIGR00029 S20 ribosomal protein S20; InterPro: IPR002583 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 consists of bacterial (and chloroplast) examples of the ribosomal small subunit protein S20. Bacterial ribosomal protein S20 forms part of the 30S ribosomal subunit, and interacts with 16S rRNA.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=99.93  E-value=5.7e-26  Score=175.84  Aligned_cols=87  Identities=39%  Similarity=0.538  Sum_probs=85.4

Q ss_conf             96898999999999999999999999999999999999960898-------99999999999999999865886166999
Q Consensus         1 Man~kSa~Kr~r~~~krr~~N~~~ks~~kt~iKk~~~ai~~~d~-------~~a~~~~~~~~s~lDka~kkgiihkn~As   73 (90)
T Consensus         1 maNiKSA~KR~~q~~kr~~~N~~~Ks~~kT~iK~~~~~v~~~~~dPnPekl~~A~~~~~~~~k~~D~~a~kgiihkN~Aa   80 (94)
T ss_conf             97410367778887873104730555987899999999851267998423899999999987886189850730233476

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999999999984
Q gi|254780626|r   74 RKVSRLSKRLKGIL   87 (90)
Q Consensus        74 RkKSrL~~~v~~~~   87 (90)
T Consensus        81 R~KSrL~~~l~k~~   94 (94)
T TIGR00029        81 RKKSRLAAQLNKLA   94 (94)
T ss_pred             HHHHHHHHHHHHCC
T ss_conf             79999999986209