HHsearch alignment for GI: 254780484 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=99.53 E-value=4.5e-13 Score=94.28 Aligned_cols=120 Identities=15% Similarity=0.258 Sum_probs=84.0
Q ss_pred CEEEEECCCCCCHHHHHHHHH---CC-CCEEEE----CCCCCEE------EECCEEEEEEEEEEEECCCEEEEEECCHHH
Q ss_conf 689997489988989999973---89-737987----3888414------521202665556785089649999760010
Q gi|254780484|r 30 PEIAFSGRSNVGKSSLINILV---NR-KNLART----SNAPGRT------QHLNFFVPKDFSNLKNNLPAMALVDMPGYG 95 (212)
Q Consensus 30 p~VaivG~~NvGKSSLiNaL~---g~-~~~a~~----~~~p~tt------~~~~~~~~~~~~~~~~~~~~~~~~DtpG~~ 95 (212)
T Consensus 3 Rniai~gH~gaGKTtL~EalL~~~G~i~r~G~V~~~~~~g~t~~D~~~eE~~R~iSi~~~~~~~~w~~~kinliDTPG~~ 82 (267)
T cd04169 3 RTFAIISHPDAGKTTLTEKLLLFGGAIREAGAVKARKSRKHATSDWMEIEKQRGISVTSSVMQFEYRDCVINLLDTPGHE 82 (267)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCHHHHHHCCCEEECCEEEEEECCEEEEEEECCCCH
T ss_conf 17999847999989999999986686333854630368886046887999865944863637887899899999796977
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf 1112244789888899877776642000001122357887545455432102575322122221111
Q gi|254780484|r 96 YARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKL 162 (212)
Q Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~nK~D~~ 162 (212)
T Consensus 83 DF~~-------------e~~~al~v~D~AviVv~a~~GVe~~T~~~w~~a~~~~iP~iifINKmDr~ 136 (267)
T cd04169 83 DFSE-------------DTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGIPIITFINKLDRE 136 (267)
T ss_pred HHHH-------------HHHHHHHHHHCEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCC
T ss_conf 8999-------------99999988645479952566653558999999997299979998534567