HHsearch alignment for GI: 254780382 and conserved domain: TIGR01169

>TIGR01169 rplA_bact ribosomal protein L1; InterPro: IPR005878 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 L1 is the largest protein from the large ribosomal subunit. In Escherichia coli, L1 is known to bind to the 23S rRNA. This model describe s bacterial and chloroplast ribosomal protein L1. Most mitochondrial L1 sequences are sufficiently divergent to be the contained in a different entry (IPR005879 from INTERPRO).; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=92.33  E-value=0.056  Score=31.67  Aligned_cols=61  Identities=26%  Similarity=0.300  Sum_probs=38.5

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99827985178999999999986065214782799982858999999999874102333221000012222222222210
Q gi|254780382|r   42 CGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLER  121 (465)
Q Consensus        42 i~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~lil~PtreLa~Qi~~~~~~~~~~~~l~~~~~~gg~~~~~~~~~l~~  121 (465)
T Consensus        60 ~vvLP~GtGK~~--------------------RVaVfa~G-----~~~~eA~~AGAD-------~VG~~DLie~Ik~G~~  107 (227)
T TIGR01169        60 TVVLPHGTGKTV--------------------RVAVFAKG-----EKAKEAKAAGAD-------YVGSDDLIEKIKKGWL  107 (227)
T ss_pred             EEECCCCCCCCE--------------------EEEEECCC-----HHHHHHHHCCCE-------EECCHHHHHHHHCCCC
T ss_conf             386576778625--------------------89997164-----348889870980-------4448879999955898


Q ss_pred             HHHHHHCCCCHHH
Q ss_conf             1122102210233
Q gi|254780382|r  122 GADVLICTPGRIL  134 (465)
Q Consensus       122 ~~~IiV~TP~rl~  134 (465)
T Consensus       108 dFDV~IATPDmM~  120 (227)
T TIGR01169       108 DFDVVIATPDMMR  120 (227)
T ss_pred             CEEEEECCHHHHH
T ss_conf             5025882757768