HHsearch alignment for GI: 254780264 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=581.44  Aligned_cols=447  Identities=27%  Similarity=0.431  Sum_probs=375.6

Q ss_pred             CHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCEECCCC----EECCCHHHHHHHCCCEEEEEEEEEECCCCCCCEE
Q ss_conf             710252799986878897789999999808732142201795----6137808898708537640799996077787138
Q gi|254780264|r    6 KIEDSRNFGIMAHIDAGKTTTTERILYYAGKSHKIGEVHDGS----ATMDWMEQEQERGITITSASTTVFWPGRDGGQKK   81 (701)
Q Consensus         6 ~~e~iRNv~iiaHvd~GKTTL~d~LL~~~g~i~~~g~v~~g~----~~~D~~~~E~eRgITi~ss~~sl~~~~~~~~~~~   81 (701)
T Consensus         7 EV~~RR~FAIISHPDAGKTT~TEK~LLyG~AIQ~AG~VK~r~S~~~A~SDWM~ME~QRGISIT~~VlQF~Y~-----~~l   81 (530)
T TIGR00503         7 EVDKRRTFAIISHPDAGKTTLTEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGISITTSVLQFPYR-----DCL   81 (530)
T ss_pred             HHHHCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCEEEEEEEEECCC-----CCE
T ss_conf             885025543661688874246788887425665224412200122122137887505881444127741457-----745


Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHCEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHHHCCCCC
Q ss_conf             99981798755289999999860456999955888883479999999873997899981767658755556664111102
Q gi|254780264|r   82 LTIIDTPGHVDFTMEVERSIRVTDGAIALLDSNAGVEPQTETVWRQADKYSVPRVIFCNKMDKMGADFYRSVEMISSRLG  161 (701)
Q Consensus        82 iNlIDTPGH~DF~~Ev~~aL~~~DgailvVDa~eGv~~qT~~vlr~~~~~~lp~ilvINKiDr~~~d~~~~l~~i~~~l~  161 (701)
T Consensus        82 ~NLLDTPGH~DFSEDTYRTL~A~D~~~M~IDaAKG~E~~T~KL~EV~RLR~~PI~TF~NKLDR~~~~P~ELlDEvE~~L~  161 (530)
T TIGR00503        82 VNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLRDLPILTFINKLDRDIRDPLELLDEVENELK  161 (530)
T ss_pred             EECCCCCCCCCCCCHHHHHHHHHHHHEEEHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHC
T ss_conf             62036858887640467999985123001111256123424454201000474433523206543553788888887706


Q ss_pred             CCCCEECCCCCCCCCCCEEEEEHHHHHHCCC-CCCCCCCCEE-----EEECHH----HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6833000234555665302442234431145-2226985138-----740043----17889999998863002345789
Q gi|254780264|r  162 ANPLVIQLPVGSESNFQGVIDLVEMKALLWK-NEDLGSSWDV-----VEIPED----MKDSANSYRDKMIESIVELDDSA  231 (701)
Q Consensus       162 ~~~~~~~~p~~~~~~~~g~id~~~~~~~~~~-~~~~~~~~~~-----~~~~~~----~~~~~~~~~~~lle~i~~~dd~~  231 (701)
T Consensus       162 ~~~~~~~~PIG~G~~F~GVY~~~~~~~yLy~r~G~~~~~~~~~~~~~L~~P~L~~~~G~D~~~~l~dEL-ELv-------  233 (530)
T TIGR00503       162 INCAPITYPIGCGKLFKGVYHLLKDEIYLYQRSGTGGTIKAVRVVKGLNNPALDSAVGSDLAQQLRDEL-ELV-------  233 (530)
T ss_pred             CCEEEEECCCCCCCCCHHHHHHHCCEEEEEECCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH-HHH-------
T ss_conf             411343056578843113554301406676305888416677776326880156776578999998899-999-------


Q ss_pred             HHHHHCCCCCCHHHHHHHHCCEEECCEEEECCCCCEECCCCHHHHHHHHHHHCCCHHHEECCCCCCCCCCCCCCCCCCCC
Q ss_conf             99863277899889873000003101003234310001221024889898717862130001222245675210112345
Q gi|254780264|r  232 MDSYLQGESFSSDRIRSLIRLGTISVKFFPVLCGSSFKNKGVQPLLDAVVDYLPSPLDVRAIKGVDVKSNSEIDVSAVDS  311 (701)
Q Consensus       232 ~~~~l~~~~~~~~~l~~~l~~~~~~~~~~pv~~gsa~~~~Gv~~LLd~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~  311 (701)
T Consensus       234 -----------~~A~~EFd~~~~~~GE~TPVFFG~Al~NFGV~~~L~~l~~~A~~P~~~~~~~~TvE~----------~~  292 (530)
T TIGR00503       234 -----------EGASNEFDLAAFLGGELTPVFFGTALGNFGVDHFLDGLLQYAPKPEARQSDTRTVEP----------TE  292 (530)
T ss_pred             -----------HHHHHHHHHHHHHCCCCCCEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC----------CC
T ss_conf             -----------863024568998538646311100010100899999999860788876567754023----------43


Q ss_pred             CCCCEECCCCCCC--C-CCCCEEHHHHHCCCCCCCCEEEEECCCCCCEEHHHHHHHCCCEEEEEECCCCCEEEECCCCCC
Q ss_conf             6542010332116--5-467100001101334568368983265541110453210474454200356732641387444
Q gi|254780264|r  312 SPLSMLAFKVMAD--S-FVGSLTFCRIYSGKISKGDSLLNTVKGKKERVGRMLQMHSNSREDIDEAYCGDIIALAGLKET  388 (701)
Q Consensus       312 ~pl~~~v~K~~~d--~-~~G~~a~~RV~SGtL~~gd~i~~~~~~~~~kV~~l~~~~g~~~~~v~~a~aGdIv~I~Gl~~~  388 (701)
T Consensus       293 e~FsGFVFK~QANMDPKHRDRvAFlRV~SGKyEK~M~~k~~R~gK~V~~S~~~~~~A~~R~~v~~AYaGD~iGL~N~G~~  372 (530)
T TIGR00503       293 EKFSGFVFKLQANMDPKHRDRVAFLRVVSGKYEKGMKLKHVRTGKDVVLSDALTLMAGDREHVEEAYAGDIIGLHNHGTI  372 (530)
T ss_pred             CCCCCEEEEEECCCCCCCCCEEEEEEEECCEEECCCEECCCCCCCEEEECCHHHHHHCCHHHHHHCCCCCEEEECCCCCE
T ss_conf             35442288863379886335057777641346347566142135536863235654402122311277765310688426


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHCCCCCEEEEEECCC--CEEEEEECCHHHHHHH
Q ss_conf             32110127788410156636652135777615643220257888854102742014450457--5468760664789999
Q gi|254780264|r  389 TTGDTLCDPSRPIVLERMDFPEPVIQIAIEPKSKGDQERMSLALSRLVAEDPSLRVSMDPNS--GQTNLSGMGELHLEII  466 (701)
Q Consensus       389 ~~gdTl~~~~~~~~~~~~~~~~Pvv~vaIep~~~~d~~kL~~~L~~L~~~Dp~l~v~~~~et--GE~il~g~GElhLev~  466 (701)
T Consensus       373 ~IGDT~~~GE~-~~f~gIP~F~PELF~~~R~~DP~~~K~l~KG~~~L~EEGA-VQv~~~l~~~krD~I~~AVG~LQF~VV  450 (530)
T TIGR00503       373 QIGDTFTQGEK-LKFTGIPNFAPELFRRLRLKDPLKQKQLLKGLVQLSEEGA-VQVLRPLDNNKRDLIVGAVGVLQFDVV  450 (530)
T ss_pred             EECCCCCCCCE-EEECCCCCCCHHHHHHHHCCCCHHHHHHHCCCHHCCCCCH-HHHHHHHHHCCCCEEEEECCHHHHHHH
T ss_conf             74772024865-6638778866789998621383455665504100022643-232311321477605542011468899


Q ss_pred             HHHHHHHCCCCCEECCCCCCCC
Q ss_conf             9998741113320105410110
Q gi|254780264|r  467 VDRMLREFKVDANVGAPYVSYR  488 (701)
Q Consensus       467 l~~L~~~f~iei~vs~P~V~yr  488 (701)
T Consensus       451 ~~RL~~EY~VE~~~E~~~~~~A  472 (530)
T TIGR00503       451 VYRLKEEYNVEAVYEPVNVALA  472 (530)
T ss_pred             HHHHHCCCCEEEEEECCCCCHH
T ss_conf             8873001340356513463010