HHsearch alignment for GI: 254780711 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=97.02 E-value=0.00075 Score=49.58 Aligned_cols=152 Identities=15% Similarity=0.168 Sum_probs=81.1
Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECC---CCC---CCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 1899623443334688999999998614895078205---422---1004779999851034742223321036899999
Q gi|254780711|r 101 LVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASL---DVH---RPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAIR 174 (461)
Q Consensus 101 ~vIllvGl~GsGKTTT~aKLA~~~~~~~~~kV~lv~~---Dt~---R~aA~eQL~~~a~~~~v~~~~~~~~~dp~~i~~~ 174 (461)
T Consensus 3 Rniai~gH~gaGKTtL~EalL~~~G~--i~r~G~V~~~~~~g~t~~D~~~eE~~R------~iSi~~~------------ 62 (267)
T cd04169 3 RTFAIISHPDAGKTTLTEKLLLFGGA--IREAGAVKARKSRKHATSDWMEIEKQR------GISVTSS------------ 62 (267)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHCCC--CCCCCEEEECCCCCCCCCCCHHHHHHC------CCEEECC------------
T ss_conf 17999847999989999999986686--333854630368886046887999865------9448636------------
Q ss_pred HHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHCCHHHH-HHHHHHHHHCCCC-CEEEEECCC
Q ss_conf 99999741588699833442221124689999998513851100031011122568-8889887635844-077641157
Q gi|254780711|r 175 ATQSARDGGYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILLVADALTGQDAV-HLARNFDKIVDLT-GIILTRMDG 252 (461)
Q Consensus 175 a~~~a~~~~~D~iiiDTaGR~~~d~~lm~El~~i~~~~~p~e~~lV~da~~Gq~a~-~~a~~F~~~~~i~-giIlTKlD~ 252 (461)
T Consensus 63 -~~~~~w~~~kinliDTPG~----~DF~~e~~~al~v~--D~AviVv~a~~GVe~~T~~~w~~a~~~~iP~iifINKmDr 135 (267)
T cd04169 63 -VMQFEYRDCVINLLDTPGH----EDFSEDTYRTLTAV--DSAVMVIDAAKGVEPQTRKLFEVCRLRGIPIITFINKLDR 135 (267)
T ss_pred -EEEEEECCEEEEEEECCCC----HHHHHHHHHHHHHH--HCEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCC
T ss_conf -3788789989999979697----78999999999886--4547995256665355899999999729997999853456
Q ss_pred -CCCCCHHH-HHHHHHCCCHHH----EECCCCC
Q ss_conf -66330367-778884787302----6158672
Q gi|254780711|r 253 -DGRGGAAL-SMRTVTGKPIKA----IGTGEKI 279 (461)
Q Consensus 253 -~akgG~al-s~~~~~~~PI~f----ig~GE~~ 279 (461)
T Consensus 136 ~~adf~~~l~~i~~~lg~~~vpi~lPig~~~~f 168 (267)
T cd04169 136 EGRDPLELLDEIEEELGIDCTPLTWPIGMGKDF 168 (267)
T ss_pred CCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCE
T ss_conf 789878999999998687751168775169944