HHsearch alignment for GI: 254780262 and conserved domain: TIGR01049

>TIGR01049 rpsJ_bact ribosomal protein S10; InterPro: IPR005731 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 , . Included in the family are one member each from Saccharomyces cerevisiae and Schizosaccharomyces pombe. These proteins lack an N-terminal mitochondrial transit peptide but contain additional sequence C-terminal to the ribosomal S10 protein region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00  E-value=0  Score=305.52  Aligned_cols=99  Identities=57%  Similarity=0.908  Sum_probs=97.8

Q ss_conf             48999999716889999999999999971880115648982136998730678986314235223344578797699899
Q Consensus         6 ~kirIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~KksreqfE~r~hkRlI~i~~~~~~~   85 (104)
T Consensus         1 ~kiRIkLksyD~~~LD~s~~~Iv~t~~~~ga~~~GPiPLPTk~~~~TVLRSPHv~K~SREqFE~RtHkRLidI~~~~~~t   80 (99)
T ss_conf             95267752058357889999999988861880247898997513788723775166670012110224577885079789

Q ss_pred             HHHHHCCCCCCCCEEEEEC
Q ss_conf             9998647899984589989
Q gi|254780262|r   86 VDALMKLDIAAGVNVVIKL  104 (104)
Q Consensus        86 ~~~l~~~~lp~gV~i~i~~  104 (104)
T Consensus        81 ~daL~~ldLPaGVDv~Ik~   99 (99)
T TIGR01049        81 IDALMKLDLPAGVDVEIKL   99 (99)
T ss_pred             HHHHHCCCCCCCEEEEEEC
T ss_conf             8987504788861688748