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