HHsearch alignment for GI: 254780321 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=462.25  Aligned_cols=361  Identities=24%  Similarity=0.421  Sum_probs=309.5

Q ss_pred             CCCHHHCEEEEEECCCCCCHHHHHHHHHHHC------CCCCCCCC-CCEEECCCHHHHHHCCEEEEEEEEEEEECCCCCE
Q ss_conf             9985253179998013898778899999982------98054444-3113058677987195052327999974378843
Q gi|254780321|r    5 PTPLSRIRNFSIVAHIDHGKSTLADRFIQHC------RGLTEREM-SSQVLDNMDIERERGITIKAQTVRLNYTSTDAKD   77 (606)
Q Consensus         5 ~~p~~~IRN~~IiaHvDhGKTTL~d~lL~~t------g~i~~~~~-~~~vlD~~~~EreRGITIka~~~~~~~~~~~~~~   77 (606)
T Consensus         5 L~EV~~RR~FAIISHPDAGKTT~TEK~LLyG~AIQ~AG~VK~r~S~~~A~SDWM~ME~QRGISIT~~VlQF~Y-----~~   79 (530)
T TIGR00503         5 LKEVDKRRTFAIISHPDAGKTTLTEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGISITTSVLQFPY-----RD   79 (530)
T ss_pred             HHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCEEEEEEEEECC-----CC
T ss_conf             5788502554366168887424678888742566522441220012212213788750588144412774145-----77


Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCHHHHHHHH
Q ss_conf             89999617873002799999997302689999868788655899999999709967998326788753211338887755
Q gi|254780321|r   78 YQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEET  157 (606)
Q Consensus        78 y~iNlIDTPGH~DF~~EV~r~l~a~dgaiLvVdA~~Gvq~QT~~~~~~A~~~~l~~I~viNKiD~~~A~~e~v~~ei~~~  157 (606)
T Consensus        80 ~l~NLLDTPGH~DFSEDTYRTL~A~D~~~M~IDaAKG~E~~T~KL~EV~RLR~~PI~TF~NKLDR~~~~P~ELlDEvE~~  159 (530)
T TIGR00503        80 CLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLRDLPILTFINKLDRDIRDPLELLDEVENE  159 (530)
T ss_pred             CEEECCCCCCCCCCCCHHHHHHHHHHHHEEEHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf             45620368588876404679999851230011112561234244542010004744335232065435537888888877


Q ss_pred             HHHHH---------------------------------------------------------------------------
Q ss_conf             53223---------------------------------------------------------------------------
Q gi|254780321|r  158 IGIST---------------------------------------------------------------------------  162 (606)
Q Consensus       158 ~g~~~---------------------------------------------------------------------------  162 (606)
T Consensus       160 L~~~~~~~~~PIG~G~~F~GVY~~~~~~~yLy~r~G~~~~~~~~~~~~~L~~P~L~~~~G~D~~~~l~dELELv~~A~~E  239 (530)
T TIGR00503       160 LKINCAPITYPIGCGKLFKGVYHLLKDEIYLYQRSGTGGTIKAVRVVKGLNNPALDSAVGSDLAQQLRDELELVEGASNE  239 (530)
T ss_pred             HCCCEEEEECCCCCCCCCHHHHHHHCCEEEEEECCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             06411343056578843113554301406676305888416677776326880156776578999998899999863024


Q ss_pred             -----------HHHHHHHHHCCCCCCHHHHHHHHHHHCCCCHH-------HHHCCCCCCCCCEE--ECC-CCCEEEEEEE
Q ss_conf             -----------21000111002232006787763210001111-------22012331012101--147-5725999981
Q gi|254780321|r  163 -----------EDALLVSAKTGEGIPLLLERIVQQLPSPTSPE-------GANAPLKALLIDSW--YNS-YLGVMVLVRI  221 (606)
Q Consensus       163 -----------~~ii~vSAktG~GV~~LLd~Iv~~iP~P~~~~-------~~~~Pl~alVfds~--~D~-~~G~I~~~RV  221 (606)
T Consensus       240 Fd~~~~~~GE~TPVFFG~Al~NFGV~~~L~~l~~~A~~P~~~~~~~~TvE~~~e~FsGFVFK~QANMDPKHRDRvAFlRV  319 (530)
T TIGR00503       240 FDLAAFLGGELTPVFFGTALGNFGVDHFLDGLLQYAPKPEARQSDTRTVEPTEEKFSGFVFKLQANMDPKHRDRVAFLRV  319 (530)
T ss_pred             HHHHHHHCCCCCCEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEE
T ss_conf             56899853864631110001010089999999986078887656775402343354422888633798863350577776


Q ss_pred             CCCCCCCCCEEEEECCCCCCCCCCC-CCCCCCEEEEHHCCCCCHHHHHHCCCCCCCCCCCCEECCCCCCCCCCCCCCCCC
Q ss_conf             6987355845887335564210122-233554124010124712332201100244445420004667853236455222
Q gi|254780321|r  222 INGQLTKGQSIRLMGTNAKYQVERI-GILTPKMIDIEALYPGEIGVMIASIKEVSHTRVGDTITDDSSPTTSALPGFKPI  300 (606)
Q Consensus       222 ~sG~lk~Gd~I~~~~~g~~~~v~~i-g~~~~~~~~v~~l~aGdVG~ii~gik~l~~~~vGDTl~~~~~p~~~~Lp~~~~~  300 (606)
T Consensus       320 ~SGKyEK~M~~k~~R~gK~V~~S~~~~~~A~~R~~v~~AYaGD----~iGL~N~G~~~IGDT~~~GE~~~f~gIP~F~--  393 (530)
T TIGR00503       320 VSGKYEKGMKLKHVRTGKDVVLSDALTLMAGDREHVEEAYAGD----IIGLHNHGTIQIGDTFTQGEKLKFTGIPNFA--  393 (530)
T ss_pred             ECCEEECCCEECCCCCCCEEEECCHHHHHHCCHHHHHHCCCCC----EEEECCCCCEEECCCCCCCCEEEECCCCCCC--
T ss_conf             4134634756614213553686323565440212231127776----5310688426747720248656638778866--


Q ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCCC-CCC-CCCCCEEEEEECCHHHHHHHHHHHHHHCCCEEEEECCC
Q ss_conf             2126642126770245788999988864112211125-676-00042028996376789888988866449506973782
Q gi|254780321|r  301 QPVVFCGLFPVDATQFENLRTAINKLRLNDASFSFEL-ENS-TALGFGFRCGFLGLLHLEIIQERLEREFSLNLIGTSPS  378 (606)
Q Consensus       301 ~P~v~~~i~p~~~~d~~~L~~aL~kL~~~D~sl~~e~-Ets-~aLg~Gfr~gglG~LHLeVi~eRL~rEfg~ev~~t~P~  378 (606)
T Consensus       394 -PELF~~~R~~DP~~~K~l~KG~~~L~EEGAVQv~~~l~~~krD~----I~~AVG~LQF~VV~~RL~~EY~VE~~~E~~~  468 (530)
T TIGR00503       394 -PELFRRLRLKDPLKQKQLLKGLVQLSEEGAVQVLRPLDNNKRDL----IVGAVGVLQFDVVVYRLKEEYNVEAVYEPVN  468 (530)
T ss_pred             -HHHHHHHHCCCCHHHHHHHCCCHHCCCCCHHHHHHHHHHCCCCE----EEEECCHHHHHHHHHHHHCCCCEEEEEECCC
T ss_conf             -78999862138345566550410002264323231132147760----5542011468899887300134035651346


Q ss_pred             CCE
Q ss_conf             330
Q gi|254780321|r  379 VVY  381 (606)
Q Consensus       379 V~Y  381 (606)
T Consensus       469 ~~~  471 (530)
T TIGR00503       469 VAL  471 (530)
T ss_pred             CCH
T ss_conf             301