HHsearch alignment for GI: 254780806 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=98.43 E-value=8e-07 Score=59.33 Aligned_cols=92 Identities=17% Similarity=0.233 Sum_probs=61.3
Q ss_pred HCCCCCCEEEECCCCCC--CCCCHHHHHHHCCCCCCCCCHHHH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHH
Q ss_conf 10278203310133322--221011233100111112311378-887533577765543202677431002023125310
Q gi|254780806|r 121 TSDFSYIFLDCPPSFNL--LTMNAMAAADSILVPLQCEFFALE-GLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSL 197 (265)
Q Consensus 121 ~~~yD~IiiD~pp~~~~--~~~~al~aad~viip~~p~~~s~~-~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~ 197 (265)
T Consensus 68 w~~~kinliDTPG~~DF~~e~~~al~v~D~AviVv~a~~-GVe~~T~~---~w~~a~~~---~iP~i-ifINKmDr~~ad 139 (267)
T cd04169 68 YRDCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAK-GVEPQTRK---LFEVCRLR---GIPII-TFINKLDREGRD 139 (267)
T ss_pred ECCEEEEEEECCCCHHHHHHHHHHHHHHHCEEEEEECCC-CCCHHHHH---HHHHHHHC---CCCEE-EEEECCCCCCCC
T ss_conf 899899999796977899999999988645479952566-65355899---99999972---99979-998534567898
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 01126899988085201562678
Q gi|254780806|r 198 SQQVVSDVRKNLGGKVYNTVIPR 220 (265)
Q Consensus 198 ~~~~~~~l~~~~~~~v~~~~Ip~ 220 (265)
T Consensus 140 f~~~l~~i~~~lg~~~vpi~lPi 162 (267)
T cd04169 140 PLELLDEIEEELGIDCTPLTWPI 162 (267)
T ss_pred HHHHHHHHHHHHCCCCCEEEEEE
T ss_conf 78999999998687751168775