HHsearch alignment for GI: 254780784 and conserved domain: TIGR00717

>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 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 S1 contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities . Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=99.63  E-value=2.2e-15  Score=143.73  Aligned_cols=250  Identities=26%  Similarity=0.346  Sum_probs=142.3

Q ss_pred             EEEEEEEECCCCCCCHH-----HHHHHHHHHHHHCCCCCCCCCCEEEEEEEEECCEEEEEEECC-CCCCCCC--CCCEEE
Q ss_conf             89998531102785223-----566777798762595022541213320044088289986314-4220136--551001
Q gi|254780784|r  422 TLRIVSEITESDGSSSM-----ATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDIS-GDEDHLG--HMDFKV  493 (699)
Q Consensus       422 tirv~~evl~sngsssm-----a~vc~~slal~dagvp~~~~VaGiamGLi~~~~~~~iLtDI~-G~ED~~G--dMDFKv  493 (699)
T Consensus        68 ~v~V~l~~~~~~~g~~~LS~~ka~r~~~~~~l~~~~~-~~~~V~G~I~~kvekKGGf~V--dl~aGv~AFLP~Sq~d~k~  144 (534)
T TIGR00717        68 EVEVYLDRVEDRIGETVLSREKAQRKEAWIKLEKAYE-EGSIVEGKIVGKVEKKGGFIV--DLEAGVEAFLPGSQVDVKK  144 (534)
T ss_pred             EEEEEEEEECCCCCCCEEECCHHHHHHHHHHHHHHHH-CCCEEEEEEEEEEECCCCEEE--ECCCCEEEECCCCCCCCCC
T ss_conf             7999998442899970230452578889999999861-698456798776605657799--9236817861646046626


Q ss_pred             -------EECCCCCEEEECCCCC-----CCC--CH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             -------0055651244324536-----556--88-99999999999999999999984356674332244875799997
Q gi|254780784|r  494 -------AGTDSGITAMQMDMKI-----GGI--SE-NIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAI  558 (699)
Q Consensus       494 -------aGT~~GiTa~QmDiK~-----~gi--~~-~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i  558 (699)
T Consensus       145 ~~~~~~~~g~~~~f~i~k~d~~rqhrGn~nivvSRr~~lE~---~~~~~r~e~le~l~~g~~v-~GvVk~---------i  211 (534)
T TIGR00717       145 IKDLDSLIGKTLKFKIIKLDKKRQHRGNNNIVVSRRAYLEE---ERSQAREELLEKLKEGEVV-KGVVKN---------I  211 (534)
T ss_pred             CCCCCCCCCCEEEEEEEEECCHHCCCCCCCEEEEEEEEECH---HHHHHHHHHHHHCCCCCEE-EEEEEE---------E
T ss_conf             66403034307789999863100125799769941001042---5688898887615558576-108888---------8


Q ss_pred             CCCCEEEEECCCCHHHHHHHHHHCC----------EEEEECCEEEEEEECCHHHHHHHHHHH------------HHHCCC
Q ss_conf             7115000037860779989998688----------899808808999968989999999999------------985247
Q gi|254780784|r  559 PPDQIRNVIGMGGKVIRGIVEQTGA----------KVNIDDDGTVKIASSSLAEIEAAREMI------------RSITDV  616 (699)
Q Consensus       559 ~~~ki~~~iG~gG~~ik~i~~~~~~----------~i~i~d~g~v~i~~~~~~~~~~a~~~i------------~~~~~~  616 (699)
T Consensus       212 T~fGGv~Fvdlgg--~dGLLH~~d~sWkr~~~P~e~~~~G~~~~Vkv~~~D~~~-----~Ri~LsLK~~~~dPW~~i~~~  284 (534)
T TIGR00717       212 TDFGGVAFVDLGG--VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEK-----KRISLSLKQLKEDPWEEIEKK  284 (534)
T ss_pred             CCCCCEEEEECCC--EEECCCHHHCCCCCCCCCHHHCCCCCEEEEEEEEECCCC-----CEEEEEEECCCCCCCHHHHHH
T ss_conf             8987499998164--332035012147887883464007988999999652657-----607787120588830899983


Q ss_pred             CCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCC-CCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECCCCC
Q ss_conf             54686789999999415369982879710488663144-4547855603259889999997868-998666873047787
Q gi|254780784|r  617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLST-ERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVDQNT  694 (699)
Q Consensus       617 ~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~-~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~~  694 (699)
T Consensus       285 ~~~G~~~~G~Vt~~~dyGvFvEi~eGiEGlvH~SE~sW~kk~~~P~~~v~~Gd~Ve~~vl~iD~~~rR~sLsLKQ~~~nP  364 (534)
T TIGR00717       285 FPVGDKIKGRVTNLTDYGVFVEIEEGIEGLVHVSEISWVKKNSHPSKVVKIGDEVEVMVLDIDPERRRISLSLKQCKANP  364 (534)
T ss_pred             CCCCCEEEEEEEEECCCEEEEEECCCCEEEECCEEEECCCCCCCHHHCEECCCEEEEEEEEEECCCCEEEEEEECCCCCC
T ss_conf             88997889999988377079992389423423144405788558158054387999999855456784989751067781