HHsearch alignment for GI: 254780321 and conserved domain: cd04169
>cd04169 RF3 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from the ribosome. RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state. GDP/GTP exchange occurs, followed by the release of the class I RF. Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome. RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts.
Probab=100.00 E-value=0 Score=384.90 Aligned_cols=176 Identities=35% Similarity=0.578 Sum_probs=158.6
Q ss_pred HCEEEEEECCCCCCHHHHHHHHHHHCCCCCCC-------CCCCEEECCCHHHHHHCCEEEEEEEEEEEECCCCCEEEEEE
Q ss_conf 53179998013898778899999982980544-------44311305867798719505232799997437884389999
Q gi|254780321|r 10 RIRNFSIVAHIDHGKSTLADRFIQHCRGLTER-------EMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNL 82 (606)
Q Consensus 10 ~IRN~~IiaHvDhGKTTL~d~lL~~tg~i~~~-------~~~~~vlD~~~~EreRGITIka~~~~~~~~~~~~~~y~iNl 82 (606)
T Consensus 1 ~~Rniai~gH~gaGKTtL~EalL~~~G~i~r~G~V~~~~~~g~t~~D~~~eE~~R~iSi~~~~~~~~w-----~~~kinl 75 (267)
T cd04169 1 RRRTFAIISHPDAGKTTLTEKLLLFGGAIREAGAVKARKSRKHATSDWMEIEKQRGISVTSSVMQFEY-----RDCVINL 75 (267)
T ss_pred CCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCHHHHHHCCCEEECCEEEEEE-----CCEEEEE
T ss_conf 90179998479999899999999866863338546303688860468879998659448636378878-----9989999
Q ss_pred EECCCCCHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 61787300279999999730268999986878865589999999970996799832678875321133888775553223
Q gi|254780321|r 83 IDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGIST 162 (606)
Q Consensus 83 IDTPGH~DF~~EV~r~l~a~dgaiLvVdA~~Gvq~QT~~~~~~A~~~~l~~I~viNKiD~~~A~~e~v~~ei~~~~g~~~ 162 (606)
T Consensus 76 iDTPG~~DF~~e~~~al~v~D~AviVv~a~~GVe~~T~~~w~~a~~~~iP~iifINKmDr~~adf~~~l~~i~~~lg~~~ 155 (267)
T cd04169 76 LDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGIPIITFINKLDREGRDPLELLDEIEEELGIDC 155 (267)
T ss_pred EECCCCHHHHHHHHHHHHHHHCEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHCCCC
T ss_conf 97969778999999999886454799525666535589999999972999799985345678987899999999868775
Q ss_pred ----------------------------------------------------------------------------H---
Q ss_conf ----------------------------------------------------------------------------2---
Q gi|254780321|r 163 ----------------------------------------------------------------------------E--- 163 (606)
Q Consensus 163 ----------------------------------------------------------------------------~--- 163 (606)
T Consensus 156 vpi~lPig~~~~f~GvVDl~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~e~~~e~~el~~e~~~~~~~e~i~ 235 (267)
T cd04169 156 TPLTWPIGMGKDFKGVYDRRTGEVELYDRGAGGATIAPEETKGLDDPKLDELGGDLAEQLREELELLEGAGPEFDQEAFL 235 (267)
T ss_pred CEEEEEECCCCCEEEEEECCCCEEEEECCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 11687751699447999867798998007889954542578867779999975999999973356775365505199998
Q ss_pred -----HHHHHHHHCCCCCCHHHHHHHHHHHCC
Q ss_conf -----100011100223200678776321000
Q gi|254780321|r 164 -----DALLVSAKTGEGIPLLLERIVQQLPSP 190 (606)
Q Consensus 164 -----~ii~vSAktG~GV~~LLd~Iv~~iP~P 190 (606)
T Consensus 236 ~g~i~PV~~GSA~~~~GV~~LLd~I~~~lPsP 267 (267)
T cd04169 236 AGELTPVFFGSALNNFGVQELLDALVDLAPAP 267 (267)
T ss_pred HCCEEEEEEEECCCCCCHHHHHHHHHHHCCCC
T ss_conf 29787899988898809999999999767899