HHsearch alignment for GI: 254780456 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=100.00  E-value=0  Score=936.18  Aligned_cols=518  Identities=50%  Similarity=0.864  Sum_probs=507.5

Q ss_pred             HHHHHHHHHHHCCCCCCC-CCEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCC
Q ss_conf             889999885402146389-8779999999819--9899994796036789975056643556378987999999974799
Q gi|254780456|r    9 EDFATLLEESFTKKDLAE-NCVTKGIVVGLEK--DTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSF   85 (576)
Q Consensus         9 ~~f~~ll~~~~~~~~~~~-G~iv~G~V~~i~~--~~v~vdig~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~~~   85 (576)
T Consensus         1 ~~f~~ll~E~~~~~e~~~~G~i~~G~VV~i~~ndd~v~VDvG~KsEg~ip~~Ef~~~~G~l~~~~Gd~v~V~l~~~~~~~   80 (534)
T TIGR00717         1 EEFAKLLEESLKTEETRPKGSIVKGTVVKINKNDDTVFVDVGLKSEGRIPVEEFLDAQGELEIQVGDEVEVYLDRVEDRI   80 (534)
T ss_pred             CCHHHHHHHHCCCCCCCCCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCHHHCCCCCCCCEEECCCEEEEEEEEECCCC
T ss_conf             97177554100211335688555327899816888999983156312341768268888400005887999998442899


Q ss_pred             CEEEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEE--CCCEEEEEC-CCHHHHHCCCCCCCCCCCCCCCCCCEEEECC
Q ss_conf             8599968787555758999998528976999999996--795599974-4020000011234543334555553023111
Q gi|254780456|r   86 GEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQV--KGGMTVDLN-GEVAFLPRSQIDIRPVRDVTPLMHEPQLFEI  162 (576)
Q Consensus        86 g~i~lS~~k~~~~~~~~~i~~a~~~g~~v~g~V~~~~--k~G~~V~i~-gi~~FlP~s~~~~~~~~d~~~~vG~~i~~~I  162 (576)
T Consensus        81 g~~~LS~~ka~r~~~~~~l~~~~~~~~~V~G~I~~kvekKGGf~Vdl~aGv~AFLP~Sq~d~k~~~~~~~~~g~~~~f~i  160 (534)
T TIGR00717        81 GETVLSREKAQRKEAWIKLEKAYEEGSIVEGKIVGKVEKKGGFIVDLEAGVEAFLPGSQVDVKKIKDLDSLIGKTLKFKI  160 (534)
T ss_pred             CCCEEECCHHHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCEEEECCCCEEEECCCCCCCCCCCCCCCCCCCCEEEEEE
T ss_conf             97023045257888999999986169845679877660565779992368178616460466266640303430778999


Q ss_pred             CCCCCCC-----CCEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCC--CEEEECCCEEEEEEEECCCCCCC
Q ss_conf             3354323-----3112212111222221211100011222330246788753147--17774483157886420244444
Q gi|254780456|r  163 LKMDKRR-----GNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYG--VFVDLSGVDGLLHVTDIAWHRIL  235 (576)
Q Consensus       163 i~~d~~~-----~~ivvS~k~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~g--~~V~~~g~~g~i~~~~ls~~~~~  235 (576)
T Consensus       161 ~k~d~~rqhrGn~nivvSRr~~lE~~~~~~r~e~le~l~~g~~v~GvVk~iT~fGGv~Fvdlgg~dGLLH~~d~sWkr~~  240 (534)
T TIGR00717       161 IKLDKKRQHRGNNNIVVSRRAYLEEERSQAREELLEKLKEGEVVKGVVKNITDFGGVAFVDLGGVDGLLHITDMSWKRVK  240 (534)
T ss_pred             EEECCHHCCCCCCCEEEEEEEEECHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCEEEEECCCEEECCCHHHCCCCCCC
T ss_conf             98631001257997699410010425688898887615558576108888889874999981643320350121478878


Q ss_pred             CCCEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEECCCC
Q ss_conf             33113326972589999874765279985215554321000000048966589999815966999851420000001111
Q gi|254780456|r  236 HPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQI  315 (576)
Q Consensus       236 ~~~~~~~~G~~v~~~Vl~~d~~~~~i~lslK~l~~dp~~~~~~~~~~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sel  315 (576)
T Consensus       241 ~P~e~~~~G~~~~Vkv~~~D~~~~Ri~LsLK~~~~dPW~~i~~~~~~G~~~~G~Vt~~~dyGvFvEi~eGiEGlvH~SE~  320 (534)
T TIGR00717       241 HPSEYVKVGQEVKVKVIKFDKEKKRISLSLKQLKEDPWEEIEKKFPVGDKIKGRVTNLTDYGVFVEIEEGIEGLVHVSEI  320 (534)
T ss_pred             CCHHHCCCCCEEEEEEEEECCCCCEEEEEEECCCCCCCHHHHHHCCCCCEEEEEEEEECCCEEEEEECCCCEEEECCEEE
T ss_conf             83464007988999999652657607787120588830899983889978899999883770799923894234231444


Q ss_pred             CCCCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCEE
Q ss_conf             01113557421003784579999986215504787520345432100000122222136999998501699970688413
Q gi|254780456|r  316 SWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDG  395 (576)
Q Consensus       316 s~~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~g~~V~l~~~i~g  395 (576)
T Consensus       321 sW~kk~~~P~~~v~~Gd~Ve~~vl~iD~~~rR~sLsLKQ~~~nPw~~f~~~hpvG~~v~gki~~iTd~GaFv~Le~GidG  400 (534)
T TIGR00717       321 SWVKKNSHPSKVVKIGDEVEVMVLDIDPERRRISLSLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEDGIDG  400 (534)
T ss_pred             ECCCCCCCHHHCEECCCEEEEEEEEEECCCCEEEEEEECCCCCCHHHHHHHCCCCCEEEEEEEEEECCEEEEECCCCCCE
T ss_conf             05788558158054387999999855456784989751067781589998489885898888888256899973899223


Q ss_pred             EEEHHHHHCCCCCHHHHHHHCCCCCCEEEEEECCCCCCCCCCCHHHHHCCCCCCHHHHCCCCCCCEEEEEEEEEECCEEE
Q ss_conf             54005530012200123421112342268852156545532011322101110000110047898799999997089089
Q gi|254780456|r  396 MIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIE  475 (576)
Q Consensus       396 ~i~~~dls~~~~~~~~~~~~k~G~~i~~~Vl~id~~~~~i~LS~K~l~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~  475 (576)
T Consensus       401 liH~~D~SW~~~~~~~~~~~~~Gd~ie~~vl~~d~~~k~i~LG~KQL~~nP~~~~~--~~yk~g~~v~g~V~~i~dfG~f  478 (534)
T TIGR00717       401 LIHLSDLSWEKKKREADHLYKKGDEIEAKVLAVDKEKKRISLGVKQLTENPWEEFA--EKYKVGSVVKGKVTEIKDFGAF  478 (534)
T ss_pred             EEECCCCCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEEECCCCHHHHHH--HHCCCCCEEEEEEEEECCCEEE
T ss_conf             89564015311785224410278799999999768566688766426988279999--8658996788888898057069


Q ss_pred             EEECCCCCEEEEEEHHHCCHHHH---CCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf             99617798499999747182121---04201106898799999997057686998703
Q gi|254780456|r  476 VSLIDHKGINSFIRRSDLSRDRV---DQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK  530 (576)
Q Consensus       476 V~l~~~~gv~G~i~~s~is~~~~---~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k  530 (576)
T Consensus       479 v~~--~~GveGli~~~el~~~~~GdP~~~~~~~~vGd~v~ak~v~i~~~~~kV~lSv~  534 (534)
T TIGR00717       479 VEL--PGGVEGLIRKSELSEERDGDPEEKKDEIKVGDEVEAKVVDIDKKNRKVSLSVK  534 (534)
T ss_pred             EEC--CCCEEEEEECCCCCCCCCCCHHHHHHHEECCCEEEEEEEEEECCCCEEEEEEC
T ss_conf             980--79737886230177888888112033410686899999997078985888559