HHsearch alignment for GI: 254780244 and conserved domain: TIGR01021

>TIGR01021 rpsE_bact ribosomal protein S5; InterPro: IPR005712 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 chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00  E-value=0  Score=442.78  Aligned_cols=157  Identities=52%  Similarity=0.875  Sum_probs=154.5

Q ss_pred             CCCCEEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCCCCCCCEECC
Q ss_conf             11602100002244401278738467999998089983899704744247899999999963012522016687620011
Q gi|254780244|r   19 DNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGV   98 (199)
Q Consensus        19 ~~~l~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~~~TI~h~v~   98 (199)
T Consensus         1 ~~~l~Ervv~vnRvsKVVKGGRrfsF~ALvVVGd~~G~VG~G~GKA~EV~~AI~Ka~~~A~Knl~~Vp~~~~~tI~H~V~   80 (157)
T TIGR01021         1 ESELEERVVAVNRVSKVVKGGRRFSFSALVVVGDKKGRVGFGFGKAKEVPDAIKKAVEDAKKNLIKVPLVKGNTIPHEVI   80 (157)
T ss_pred             CCCCEEEEEEEEEEEEEEECCCCEEEEEEEEEECCCCEEEEEEEEHHHHHHHHHHHHHHHHHCEEEEEEECCCEEECCEE
T ss_conf             96615688986027876428940368999997178743788650120047899886875312517888608974502148


Q ss_pred             CCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHH
Q ss_conf             03376799996367544850304899999980944100454689888899999999995069989999861997989
Q gi|254780244|r   99 GRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSL  175 (199)
Q Consensus        99 gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~~t~~~iA~~RG~~i~~  175 (199)
T Consensus        81 G~~~aa~vllkPA~~GTGvIAGGa~RavlE~AGv~DIlaK~LGSnNP~N~vrAt~~AL~~l~~~~~vA~~Rg~~v~e  157 (157)
T TIGR01021        81 GKSGAAKVLLKPASPGTGVIAGGAVRAVLELAGVKDILAKSLGSNNPINVVRATFDALLKLKSPEDVAEERGKSVEE  157 (157)
T ss_pred             EEECCEEEEEECCCCCCCEEECCCHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCC
T ss_conf             87778289986589989579477457887753841256651568774689999999997236967999845886679