HHsearch alignment for GI: 254780255 and conserved domain: TIGR01008
>TIGR01008 rpsC_E_A ribosomal protein S3; InterPro: IPR005703 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 ribosomal protein S3 of the eukaryotic cytosol and of the archaea.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=0 Score=298.27 Aligned_cols=179 Identities=36% Similarity=0.556 Sum_probs=168.6
Q ss_pred HHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHC--CCC-CEEEEEEEEECCCCCCH
Q ss_conf 999999998774226422155325885189999737410013565348998987640--358-70578799813755337
Q gi|254780255|r 37 LKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSN--MTN-SEIHLSVNEVPKPEINA 113 (227)
Q Consensus 37 ~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~--~~~-~~v~i~v~ei~~p~~~A 113 (227)
T Consensus 13 ~~idE~l~~El~~AGYsgvdv~~TPlGT~vii~AerPg~VIGr~G~rIr~LT~~l~~Rf~Fg~enPqi~V~~v~~P~L~A 92 (204)
T TIGR01008 13 LLIDEFLKKELREAGYSGVDVRKTPLGTKVIIYAERPGLVIGRGGRRIRELTEKLQKRFKFGLENPQIDVEEVENPELNA 92 (204)
T ss_pred HHHHHHHHHHHHHCCCCCCEEEECCCCCEEEEEEECCCCEECCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCH
T ss_conf 77888999988651777551687778967999983686377279721889999998752058999658764178989888
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEEEEECCCCC--CCEEEECEEEEEEEEE
Q ss_conf 78799999998759636899999999853238855999970367864222157875255324--5200003056899995
Q gi|254780255|r 114 TLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPL--QTLRAHIDYGTAVAET 191 (227)
Q Consensus 114 ~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~e~Ar~e~~~~G~vpl--~t~~a~idy~~~~a~T 191 (227)
T Consensus 93 ~v~A~~iA~~LeRG~hFRRaAY~~~rriM~aGAkGvEv~iSGKL~~-eRAr~~KF~~G~~~k~G~Pa~~lV~~g~a~a~~ 171 (204)
T TIGR01008 93 KVQAEKIARSLERGLHFRRAAYTAVRRIMEAGAKGVEVTISGKLTG-ERARTEKFAAGYLKKSGEPAEELVDKGFAIALL 171 (204)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHH-HHHHHHHCCCCEEEECCCCHHHHHHHHHHEEEC
T ss_conf 8999999999845347789999999999825695279998274178-778752101784898138768887766440114
Q ss_pred CCCEEEEEEEEEECCCC-------CCCCCCCC
Q ss_conf 38266799997328853-------77211343
Q gi|254780255|r 192 AYGSCGIKVYVSLRDEV-------SDSDSTIP 216 (227)
Q Consensus 192 ~~G~~GvKVwi~~~~~~-------~~~~~~~~ 216 (227)
T Consensus 172 k~GVlGV~V~Im~Pd~~sRtGPkaLPD~v~I~ 203 (204)
T TIGR01008 172 KLGVLGVKVKIMPPDVKSRTGPKALPDEVEIK 203 (204)
T ss_pred CCCEEEEEEEEECCCCCCCCCCCCCCCEEEEE
T ss_conf 89702268888669797478888779437863