HHsearch alignment for GI: 254780255 and conserved domain: TIGR01009

>TIGR01009 rpsC_bact ribosomal protein S3; InterPro: IPR005704 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 S3 is one of the proteins from the small ribosomal subunit. This family describes the bacterial type of ribosomal protein S3 and also and many chloroplast forms. Chloroplast and mitochondrial forms have large, variable inserts between conserved N-terminal and C-terminal domains. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00  E-value=0  Score=655.36  Aligned_cols=210  Identities=55%  Similarity=0.933  Sum_probs=206.6

Q ss_pred             CCCCCCCCEEEEE-EECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHH--HCCCCCEEEEECCCC-CEEEEEECCCCCC
Q ss_conf             9864578526650-32062156702731257999989999999998774--226422155325885-1899997374100
Q gi|254780255|r    1 MGQKINPILFRLG-VNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLK--QAGVAKILIERTHKN-CRIIVYSARPGLI   76 (227)
Q Consensus         1 MGQKvnP~g~RLg-~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~--~agis~i~I~Rt~~~-i~I~I~~~kP~~i   76 (227)
T Consensus         1 MGQKv~P~GfRlGPi~K~W~S~WyA~~k~y~~~L~ED~KIR~~i~k~l~~~~a~iS~veIeR~~~~~v~V~IhtArPg~v   80 (217)
T TIGR01009         1 MGQKVNPIGFRLGPITKDWKSRWYADPKEYAELLHEDLKIRNLIKKELKKKNAGISDVEIERTADKKVRVTIHTARPGIV   80 (217)
T ss_pred             CCCEECCCCEECCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCEEEEEEEECCCCEE
T ss_conf             99505786401375214510376588753035666438999987321133543313279981699788999982788658


Q ss_pred             CCCCCHHHHHHHHHHHCCCC--CEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEE
Q ss_conf             13565348998987640358--7057879981375533778799999998759636899999999853238855999970
Q gi|254780255|r   77 IGKKGTDIEKIRKKLSNMTN--SEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIAS  154 (227)
Q Consensus        77 iGkkg~~i~~l~~~L~~~~~--~~v~i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~is  154 (227)
T Consensus        81 IGkkG~~iE~l~~~l~k~~~~~k~v~i~I~EVk~p~ldA~LvA~~IA~QlE~RVSFRrAmK~A~~~~~k~GakGiKv~VS  160 (217)
T TIGR01009        81 IGKKGSEIEKLKKALQKLTGSVKEVQINIKEVKRPELDAQLVAQNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVS  160 (217)
T ss_pred             ECCCCCHHHHHHHHHHHHHCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             85788458999999998847835899989874885738788998999998620204689999999986268988899986


Q ss_pred             CCCCCCCCCEEEEEEECCCCCCCEEEECEEEEEEEEECCCEEEEEEEEEECCCCCC
Q ss_conf             36786422215787525532452000030568999953826679999732885377
Q gi|254780255|r  155 GRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSD  210 (227)
Q Consensus       155 GRl~G~e~Ar~e~~~~G~vpl~t~~a~idy~~~~a~T~~G~~GvKVwi~~~~~~~~  210 (227)
T Consensus       161 GRLgGAEIAR~E~y~EGRvPLHTLRADIDY~~~~A~TTYG~IGVKVWI~kGe~~~~  216 (217)
T TIGR01009       161 GRLGGAEIARTEWYKEGRVPLHTLRADIDYGFAEAKTTYGIIGVKVWIFKGEVLGG  216 (217)
T ss_pred             ECCCCHHHCCCCEEEECCCCCHHHHHHHHHCCCCCEEEEEEEEEEEEEEECCCCCC
T ss_conf             10574211222104327997312220031254412157326779998751502389