HHsearch alignment for GI: 254780331 and conserved domain: TIGR00158

>TIGR00158 L9 ribosomal protein L9; InterPro: IPR000244 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 L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities , . The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker . Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=99.92  E-value=3.5e-25  Score=179.36  Aligned_cols=147  Identities=36%  Similarity=0.623  Sum_probs=138.8

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q ss_conf             3346520111758778388827763211014378730122014688877899999842234-678999988765432100
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEK-KAKYEGISKDLAKKNFSL   92 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~-~~~a~~~~~~L~~~~l~i   92 (179)
T Consensus         1 ~~~~~~~~~~~~g~~g~~~~~~~g~~~~~l~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (151)
T TIGR00158         1 MKVILLEDVKNLGKRGDVVEVKDGYARNFLIPKGLAVPATKKNIEKFEARRKKLEEKEAANLKAAAARLKEVLELGTLTI   80 (151)
T ss_pred             CCCHHHHHHHHCCCCCCEEECCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEE
T ss_conf             91001213431253245111144410110011331001105678877788888888888888988777877664431135


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHH--CCCCCCHHHHCCCC-CCCCEEEEEEEEEECCCEEEEEEEEEEEC
Q ss_conf             0255654310034107899999986--08876866630265-64320549999996397299999999725
Q gi|254780331|r   93 IRAAGDTGYLYGSVSSRDIADLLIE--EGFDVNRGQINLKS-PIKSVGIHNIMISLHADVSTTITLNVARS  160 (179)
Q Consensus        93 ~~k~~e~gkLfGsVt~~dI~~~L~~--~gi~I~k~~I~l~~-pIk~~G~y~V~I~L~~~V~a~i~V~V~~~  160 (179)
T Consensus        81 ~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  151 (151)
T TIGR00158        81 SLKSGDGGKLFGSITTKEIADALKADHAGLDLDKKKIELPDGVLRTFGDYEVTLKLHPEVTAVLKVEVVPE  151 (151)
T ss_pred             EECCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHCCCCCCCCCCCCCCCEEEEEEECCCEEEEEEEEEECC
T ss_conf             42037654310002357889988875405410000220466630014631467876365256788776349