HHsearch alignment for GI: 254780943 and conserved domain: TIGR01012

>TIGR01012 Sa_S2_E_A ribosomal protein S2; InterPro: IPR005707 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 , . This family describes the ribosomal protein of the eukaryotic cytosol and of Archaea, homologous to S2 of bacteria. It is designated typically as Sa in eukaryotes and Sa or S2 in the archaea. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=94.00  E-value=0.087  Score=31.46  Aligned_cols=123  Identities=16%  Similarity=0.228  Sum_probs=69.5

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEE--EECCHHHCCCC-CCCCCCEEEEECCCCCCHHHHHHHHHHHHCCC
Q ss_conf             6551035203654307999999998625667314--30420100123-34455505775267881899999999863024
Q gi|254780943|r  289 NISGLLVSSCGTSYLAGLVGKFWFERLARLKVEI--DVSSEFRYRDF-VYSSKWASLFISQSGETADTLASLRYMRTQGL  365 (608)
Q Consensus       289 ~~~~I~~vGcGTSy~Aal~~~~~~e~~~~i~v~v--~~asEf~y~~~-~~~~~tlvI~iSQSGeT~dti~Al~~ak~~g~  365 (608)
T Consensus        61 NP~~I~vvS~R---~Yg~~pV~~f~~~tG~~~I~GRf~PGT~TNp~~~~f~EP~-vv~vtDPR~D---~Qa~~EA~~vgi  133 (197)
T TIGR01012        61 NPEDILVVSAR---IYGQKPVLKFAEVTGARAIAGRFIPGTFTNPALKEFREPE-VVVVTDPRAD---HQALKEASEVGI  133 (197)
T ss_pred             CCCCEEEEECC---HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHCCCCCE-EEEECCCCCC---CCHHHHHHCCCC
T ss_conf             82111344015---2224689999876088745665437776402331367873-7997588766---212120001589


Q ss_pred             CEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf             4246511787631000241013674200110007888999999999999977621200157763
Q gi|254780943|r  366 TIGSLVNVLESTIARESDFIFPIKAGPEIGVASTKAFTCQLLVLVIMAIYAGKVRGYINEEQER  429 (608)
Q Consensus       366 ~tiaItN~~~S~la~~aD~~i~~~aG~Ei~VasTKsftaql~~l~llal~l~~~~g~i~~~~~~  429 (608)
T Consensus       134 P~vALcDTd~--~~~~vDl~IP~NN---------KG~~s~al~yWlLaRe~L~~RG~i~~~~~~  186 (197)
T TIGR01012       134 PIVALCDTDN--SLRYVDLVIPTNN---------KGRRSLALIYWLLAREILRMRGVISADEDL  186 (197)
T ss_pred             CEEEEECCCC--CCCCCCEEECCCC---------CHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             6689875887--5000240107986---------136899999999999999753740479874