HHsearch alignment for GI: 254780266 and conserved domain: TIGR00981
>TIGR00981 rpsL_bact ribosomal protein S12; InterPro: IPR005679 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 S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This family consists of ribosomal protein S12 from bacteria, mitochondria, and chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=0 Score=401.23 Aligned_cols=123 Identities=72% Similarity=1.132 Sum_probs=119.7
Q ss_pred CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCE
Q ss_conf 95502354268737864666677000686212478756751845674424328899966996999980788875464678
Q gi|254780266|r 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80 (124)
Q Consensus 1 MpTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~ 80 (124)
T Consensus 1 mpT~~Ql~r~~r~~~~-~~~~~paL~~~P~krGvc~~V~t~tPkKPNSAlRK~a~vrL~~~~~V~aYIpG~gH~lqEHs~ 79 (124)
T TIGR00981 1 MPTINQLIRKGRKKKV-KKSKSPALEKCPQKRGVCTRVYTVTPKKPNSALRKVARVRLTNGFEVTAYIPGEGHNLQEHSV 79 (124)
T ss_pred CCCHHHHHCCCCHHHH-HHHCCCHHHHCCCCCCEEEEEEEECCCCCCHHHCCEEEEEECCCCEEEEEECCCCCCCCCCCE
T ss_conf 9303645505530222-310240456088767737887753599986201314678724884898851887766443327
Q ss_pred EEEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99953783888875478980400144334200121125610789
Q gi|254780266|r 81 VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK 124 (124)
Q Consensus 81 VLvrGGrv~DlPGVry~ivRG~~D~~gv~~Rk~~RSkYG~kkpk 124 (124)
T Consensus 80 vl~rGGrv~dLPGVrYhivrGa~D~~GV~~R~~~Rs~YG~k~~~ 123 (124)
T TIGR00981 80 VLVRGGRVKDLPGVRYHIVRGALDTAGVKNRKQSRSKYGAKKPK 123 (124)
T ss_pred EEECCCEECCCCCCEEEEEECCCCHHHHHHHHHCCCCCCCCCCC
T ss_conf 88507844278983279984551013465432011104744788