HHsearch alignment for GI: 254780941 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=99.70 E-value=4.1e-16 Score=124.11 Aligned_cols=151 Identities=19% Similarity=0.246 Sum_probs=100.7
Q ss_pred EEEEECCCCCCHHHHHHHHHCC-----CEEEECCC--CCCE--------------EEEEEEEEEECCEEEEEEECCCCHH
Q ss_conf 8998338998688999998689-----20210588--8860--------------2127899973994899998798401
Q gi|254780941|r 24 CVALVGATNAGKSTLVNRFVGA-----KVSIVTHK--VQTT--------------RSIVRGIVSEKESQIVFLDTPGIFN 82 (311)
Q Consensus 24 ~VaivG~pN~GKSTL~N~l~g~-----~vsivS~k--~~TT--------------r~~i~gi~~~~~~qiifvDTPG~~~ 82 (311)
T Consensus 4 niai~gH~gaGKTtL~EalL~~~G~i~r~G~V~~~~~~g~t~~D~~~eE~~R~iSi~~~~~~~~w~~~kinliDTPG~~D 83 (267)
T cd04169 4 TFAIISHPDAGKTTLTEKLLLFGGAIREAGAVKARKSRKHATSDWMEIEKQRGISVTSSVMQFEYRDCVINLLDTPGHED 83 (267)
T ss_pred EEEEECCCCCCHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCHHHHHHCCCEEECCEEEEEECCEEEEEEECCCCHH
T ss_conf 79998479999899999999866863338546303688860468879998659448636378878998999997969778
Q ss_pred HCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHCCCCC
Q ss_conf 01235753210023455553210011000010000000122345442872025787211010434578888641001233
Q gi|254780941|r 83 AKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKIDCVKPERLLEQAEIANKLVFIE 162 (311)
Q Consensus 83 ~~~~l~~~~~~~~~~~l~~aDiil~VvDa~~~~~~~~~~il~~l~~~~~p~IiVlNKiDlv~~~~l~~~~~~~~~~~~~~ 162 (311)
T Consensus 84 --------F~~e~~~al~v~D~AviVv~a~~GVe~~T~~~w~~a~~~~iP~iifINKmDr~~ad-f~~~l~~i~~~lg~- 153 (267)
T cd04169 84 --------FSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGIPIITFINKLDREGRD-PLELLDEIEEELGI- 153 (267)
T ss_pred --------HHHHHHHHHHHHHCEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCC-HHHHHHHHHHHHCC-
T ss_conf --------99999999988645479952566653558999999997299979998534567898-78999999998687-
Q ss_pred CCCCCC--CCCCCCHHHHHHHHHH
Q ss_conf 431100--0138742678999998
Q gi|254780941|r 163 KTFMVS--ATKGHGCDDVLNYLCS 184 (311)
Q Consensus 163 ~i~~IS--Ak~g~Gid~L~~~L~~ 184 (311)
T Consensus 154 ~~vpi~lPig~~~~f~GvVDl~~~ 177 (267)
T cd04169 154 DCTPLTWPIGMGKDFKGVYDRRTG 177 (267)
T ss_pred CCCEEEEEECCCCCEEEEEECCCC
T ss_conf 751168775169944799986779