>TIGR00082 rbfA ribosome-binding factor A; InterPro: IPR000238 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 , . Ribosome-binding factor A (gene rbfA) is a bacterial protein that associates with free 30S ribosomal subunits. It does not associate with 30S subunits that are part of 70S ribosomes or polysomes. It is essential for efficient processing of 16S rRNA. Ribosome-binding factor A is a protein of from 13 to 15 Kd which is found in most prokaryotic organisms. A putative chloroplastic form seems to exist in plants.; GO: 0006364 rRNA processing.

Probab=99.96  E-value=2.4e-28  Score=180.37  Aligned_cols=114  Identities=29%  Similarity=0.454  Sum_probs=103.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC-EEEEEEEEECCCCCEEEEEEEECCC--CC-HHHHHHHHHHHHHH
Q ss_conf             77773899999999999999995141342012651-6898888985875655999982798--64-77899999985689
Q gi|254780786|r    6 PKNSRRALRVGEEVRSALMWVILNNEFQDRLISRD-VISISEVCMSVDLRVATVYISLPLD--VS-PDRVISALNCNIKF   81 (128)
Q Consensus         6 ~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~-~vtIt~V~vS~Dl~~AkVyvs~~~~--~~-~~~~~~~L~~~~~~   81 (128)
T Consensus         2 A~~~~r~~Rv~~~i~~ei~~~l~~-e~~d~~~~~~~~~~Vt~Ve~S~DL~~A~Vfv~~~~d~D~~~~~~~~~~L~~A~Gf   80 (121)
T TIGR00082         2 ASEFRRKERVESEIKREIGRILIR-EIKDPRVIHGMMLTVTKVEVSKDLQHAKVFVSVLGDKDEEAIEKAVKALKKAKGF   80 (121)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHH-CCCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECCCCHHHHHHHHHHHHHCCCH
T ss_conf             644410445899999999999871-2667631056047766788738805788888741377767899999989827845


Q ss_pred             HHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHH
Q ss_conf             9999999875214578589997386888999999855767
Q gi|254780786|r   82 IRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPK  121 (128)
Q Consensus        82 ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~  121 (128)
T Consensus        81 ir~~l~~~~~-lr~~P~l~Fv~D~Sl~~~~ri~~li~~l~  119 (121)
T TIGR00082        81 IRSLLGQRMR-LRKTPELSFVKDDSLDKGLRIENLINSLK  119 (121)
T ss_pred             HHHHHHHHHC-CCCCCEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             8899987610-01166577754356777788999986420