HHsearch alignment for GI: 254780292 and conserved domain: TIGR01077

>TIGR01077 L13_A_E ribosomal protein L13; InterPro: IPR005755 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 L13 is one of the proteins from the large ribosomal subunit . In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=99.96  E-value=2.2e-29  Score=193.31  Aligned_cols=122  Identities=28%  Similarity=0.436  Sum_probs=97.7

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECC-CCCC
Q ss_conf             999789874576799999998465652103455668889997510100156012113333115755763363020-0001
Q gi|254780292|r   17 ILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAK-EILA   95 (155)
Q Consensus        17 ~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~-~~~~   95 (155)
T Consensus         1 ~ViDa~G~ilGRLAS~VAK~lL------------~G~~vVvVnAE~~vItG~~~~~~~~Y~~~-~~~~~~~n~~r~GP~~   67 (144)
T TIGR01077         1 TVIDASGHILGRLASVVAKRLL------------NGERVVVVNAEKIVITGNKYMVFEKYKEF-LRKRTKTNPRRFGPYF   67 (144)
T ss_pred             CEECCCCCHHHHHHHHHHHHHH------------CCCEEEEEECCEEEECCCCHHHHHHHHHH-HHHHHHCCCCCCCCCC
T ss_conf             9567874313768999999875------------79867897226025227830456877887-6313213773679989


Q ss_pred             CCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHH-CCCCC
Q ss_conf             24879999999973089-9854789996270107899971320854761665-28131
Q gi|254780292|r   96 GASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAK-MNPKN  151 (155)
Q Consensus        96 ~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~-~~~kn  151 (155)
T Consensus        68 PR~P~rIf~rtvRGMLP~K~~RGr~Al~RLkVy~G~P~el~~k~~~~v~~A~~~~rL~  125 (144)
T TIGR01077        68 PRRPDRIFKRTVRGMLPWKTARGRAALRRLKVYVGIPKELQGKEFVTVPEALKVSRLS  125 (144)
T ss_pred             CCCCHHHHHHHHCCCCCCCCHHHHHHHHHCEECCCCCCCCCCCEEEEHHHHHHHHCCC
T ss_conf             9870789998640358877743588885150015875851576056610122111268