HHsearch alignment for GI: 254780233 and conserved domain: TIGR00503

>TIGR00503 prfC peptide chain release factor 3; InterPro: IPR004548 Peptide chain release factor 3 increases the formation of ribosomal termination complexes and stimulates activity of RF-1 and RF-2. It binds to guanine nucleotides and has a strong preference for UGA stop codons. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis sp. (strain PCC 6803), and in Staphylococcus aureus.; GO: 0005525 GTP binding, 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=401.91  Aligned_cols=353  Identities=25%  Similarity=0.391  Sum_probs=282.7

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCC------EECCCCHHHHHCCCEEEEEEEEEEECCEEEEEECCC
Q ss_conf             24314999854689877889999998396142322000------003885779870960646799999899799997289
Q gi|254780233|r   17 MQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSE------RVMDCNDLEKERGITILAKVTSIVWNDVRINIVDTP   90 (624)
Q Consensus        17 ~~IRNiaIiaHvDhGKTTL~d~LL~~sG~~~~~~~v~~------~vmD~~~~EreRGITI~a~~~~~~~~~~~iNiiDTP   90 (624)
T Consensus         9 ~~RR~FAIISHPDAGKTT~TEK~LLyG~AIQ~AG~VK~r~S~~~A~SDWM~ME~QRGISIT~~VlQF~Y~~~l~NLLDTP   88 (530)
T TIGR00503         9 DKRRTFAIISHPDAGKTTLTEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGISITTSVLQFPYRDCLVNLLDTP   88 (530)
T ss_pred             HHCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCEEEEEEEEECCCCCEEECCCCC
T ss_conf             50255436616888742467888874256652244122001221221378875058814441277414577456203685


Q ss_pred             CCCCCHHHHHHHHHHHCEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHH--------
Q ss_conf             875407999999874217899997687886478999999997299789999754366740256899999888--------
Q gi|254780233|r   91 GHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIVVVNKVDRSDARADEVINEVFDLF--------  162 (624)
Q Consensus        91 GH~DF~gEVer~l~~~DgaiLvVdA~eGv~~QT~~vl~~A~~~~l~~IvvINKiDr~~a~~~~v~~ei~dlf--------  162 (624)
T Consensus        89 GH~DFSEDTYRTL~A~D~~~M~IDaAKG~E~~T~KL~EV~RLR~~PI~TF~NKLDR~~~~P~ELlDEvE~~L~~~~~~~~  168 (530)
T TIGR00503        89 GHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLRDLPILTFINKLDRDIRDPLELLDEVENELKINCAPIT  168 (530)
T ss_pred             CCCCCCCHHHHHHHHHHHHEEEHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHCCCEEEEE
T ss_conf             88876404679999851230011112561234244542010004744335232065435537888888877064113430


Q ss_pred             -----------------------HHCC-------------CCHHH----------------C--------C---------
Q ss_conf             -----------------------6226-------------73011----------------0--------4---------
Q gi|254780233|r  163 -----------------------SALD-------------ATDAQ----------------L--------D---------  173 (624)
Q Consensus       163 -----------------------~~l~-------------a~de~----------------l--------d---------  173 (624)
T Consensus       169 ~PIG~G~~F~GVY~~~~~~~yLy~r~G~~~~~~~~~~~~~L~~P~L~~~~G~D~~~~l~dELELv~~A~~EFd~~~~~~G  248 (530)
T TIGR00503       169 YPIGCGKLFKGVYHLLKDEIYLYQRSGTGGTIKAVRVVKGLNNPALDSAVGSDLAQQLRDELELVEGASNEFDLAAFLGG  248 (530)
T ss_pred             CCCCCCCCCHHHHHHHCCEEEEEECCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             56578843113554301406676305888416677776326880156776578999998899999863024568998538


Q ss_pred             --HHHHHHHHHCCEECCCCCCCCCCCCHHHHHHHHCCCCCCCCC----------CCHHHCCCCCCCCC---CCCCEEEEE
Q ss_conf             --266887886591646742233486413555321024542233----------20000011110136---777349999
Q gi|254780233|r  174 --FPILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPVIS----------EGEFKMIGTILEKD---PFLGRIVTG  238 (624)
Q Consensus       174 --~Pv~~~Sa~~G~~~~~~~~~~~~gl~~Lld~Ii~~iP~P~~~----------e~pl~~~V~~i~~d---~y~Gria~g  238 (624)
T Consensus       249 E~TPVFFG~Al~N-----------FGV~~~L~~l~~~A~~P~~~~~~~~TvE~~~e~FsGFVFK~QANMDPKHRDRvAFl  317 (530)
T TIGR00503       249 ELTPVFFGTALGN-----------FGVDHFLDGLLQYAPKPEARQSDTRTVEPTEEKFSGFVFKLQANMDPKHRDRVAFL  317 (530)
T ss_pred             CCCCEECCCCHHH-----------HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEE
T ss_conf             6463111000101-----------00899999999860788876567754023433544228886337988633505777


Q ss_pred             EECCCCCCCCCEEEEECCCCCCEEECCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCC
Q ss_conf             96078051598899960578501211455301103665344411254554322223321012211055652112336666
Q gi|254780233|r  239 RIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQPID  318 (624)
Q Consensus       239 RV~sGtlk~Gd~V~vl~~~g~~~~~~kV~~L~~~~G~~r~~v~ea~AGDIvaIaGl~~~~iGDTL~~~~~p~~Lp~i~i~  318 (624)
T Consensus       318 RV~SGKyEK~M~~k~~R----~gK~V~~S~~~~~~A~~R~~v~~AYaGD~iGL~N~G~~~IGDT~~~GE~-~~f~gIP~F  392 (530)
T TIGR00503       318 RVVSGKYEKGMKLKHVR----TGKDVVLSDALTLMAGDREHVEEAYAGDIIGLHNHGTIQIGDTFTQGEK-LKFTGIPNF  392 (530)
T ss_pred             EEECCEEECCCEECCCC----CCCEEEECCHHHHHHCCHHHHHHCCCCCEEEECCCCCEEECCCCCCCCE-EEECCCCCC
T ss_conf             76413463475661421----3553686323565440212231127776531068842674772024865-663877886


Q ss_pred             CCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEE-CCC-CCEEEEEECCHHHHHHHHHHHHHCCEEEE
Q ss_conf             5421578612686554444321017889999999730283799998-599-97599996364568888741233480330
Q gi|254780233|r  319 PPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEGNIALKIEE-SSS-KDAFFVSGRGELQLAVLIETMRREGFELA  396 (624)
Q Consensus       319 ~Ptis~~f~vn~sP~ag~eg~~~ts~~l~~rL~ke~~~dvsL~ve~-~~~-~~~~~v~GrGeLHL~IliE~mRREG~E~~  396 (624)
T Consensus       393 ~PELF~~~R~~D-P~--------~~K~l~KG~~~L~EEG-AVQv~~~l~~~krD~I~~AVG~LQF~VV~~RL~~E-Y~VE  461 (530)
T TIGR00503       393 APELFRRLRLKD-PL--------KQKQLLKGLVQLSEEG-AVQVLRPLDNNKRDLIVGAVGVLQFDVVVYRLKEE-YNVE  461 (530)
T ss_pred             CHHHHHHHHCCC-CH--------HHHHHHCCCHHCCCCC-HHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCC-CCEE
T ss_conf             678999862138-34--------5566550410002264-32323113214776055420114688998873001-3403