HHsearch alignment for GI: 254780244 and conserved domain: TIGR01020

>TIGR01020 rpsE_arch ribosomal protein S5; InterPro: IPR005711 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 model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00  E-value=0  Score=337.59  Aligned_cols=149  Identities=29%  Similarity=0.422  Sum_probs=141.6

Q ss_pred             HHCCCC-CCC---E-EEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECC
Q ss_conf             100001-160---2-10000224440127873846799999808998389970474424789999999996301252201
Q gi|254780244|r   14 NREERD-NSI---V-DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLL   88 (199)
Q Consensus        14 ~~~~~~-~~l---~-ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~   88 (199)
T Consensus        44 IvD~LLGP~L~aren~eVldv~lVQrmt~sGRrtrFra~vvVGn~dGYVGlG~gkA~eV~~AIrKAI~~AKlnIi~VrRG  123 (220)
T TIGR01020        44 IVDALLGPDLNARENEEVLDVSLVQRMTDSGRRTRFRATVVVGNRDGYVGLGKGKAKEVAPAIRKAINNAKLNIIPVRRG  123 (220)
T ss_pred             HHHEECCCCCCCCCCCCEEEEECCEEECCCCCEEEEEEEEEEECCCCCEEECCCCCCHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             41101088878755652023313164234686043489999857898176234631003468999997247143566405


Q ss_pred             CC---------CCCCEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECC-CCCHHHHHHHHHHHHHC
Q ss_conf             66---------876200110337679999636754485030489999998094410045468-98888999999999950
Q gi|254780244|r   89 DG---------RTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIG-SSNPHNVIRATFEVLRS  158 (199)
Q Consensus        89 ~~---------~TI~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~G-S~N~~NvvkAt~~AL~~  158 (199)
T Consensus       124 CGsWec~cG~pHsvPfkV~Gk~GSV~V~LiPAP~G~GLVaGDV~K~~L~LAGI~DVWt~T~G~T~Tt~NFAkAtF~Al~~  203 (220)
T TIGR01020       124 CGSWECGCGRPHSVPFKVSGKSGSVRVRLIPAPKGVGLVAGDVAKKVLRLAGIKDVWTQTRGETRTTVNFAKATFEALKK  203 (220)
T ss_pred             CCCCCCCCCCCCCCCEEEEECCCEEEEEEECCCCCCEEEECCHHHHHHHHCCCCEEEECCCCCCCCCCHHHHHHHHHHHH
T ss_conf             67634657888533456500000489998749996238874644688774596235404556022330388999999987


Q ss_pred             CCCH
Q ss_conf             6998
Q gi|254780244|r  159 QSHP  162 (199)
Q Consensus       159 ~~t~  162 (199)
T Consensus       204 t~~~  207 (220)
T TIGR01020       204 TYSF  207 (220)
T ss_pred             HHCC
T ss_conf             4212