>cd01889 SelB_euk SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and euk

Probab=95.49 E-value=0.028 Score=37.58 Aligned_cols=125 Identities=22% Similarity=0.267 Sum_probs=62.0 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 99623443334688999999998614895078205422100477999985103474222332103689999999999741 Q gi|254780711|r 103 IMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAIRATQSARDG 182 (461) Q Consensus 103 IllvGl~GsGKTTT~aKLA~~~~~~~~~kV~lv~~Dt~R~aA~eQL~~~a~~~~v~~~~~~~~~dp~~i~~~a~~~a~~~ 182 (461) T Consensus 3 V~iiGHVDhGKTTL~~~L~~~~----~~----~~~D~~---~eE~eRGITi~~g~~~~~~~~~-~~~----~~~~~~~~~ 66 (192) T cd01889 3 VGVLGHVDSGKTSLAKALSEIA----ST----AAFDKN---PQSQERGITLDLGFSSFYVDKP-KHL----RELINPGEE 66 (192) T ss_pred EEEEEECCCCHHHHHHHHHHHC----CC----HHHHCC---HHHHHCCCCEEEEEEEEEECCC-CCC----CCCCCCCCC T ss_conf 9999761789999999998333----50----122135---8899779716710013785144-221----123234677 Q ss_pred CCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHCC---H--HHHHHHHHHHHHCCCCCEEEEECCC Q ss_conf 58869983344222112468999999851385110003101112---2--5688889887635844077641157 Q gi|254780711|r 183 GYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILLVADALTG---Q--DAVHLARNFDKIVDLTGIILTRMDG 252 (461) Q Consensus 183 ~~D~iiiDTaGR~~~d~~lm~El~~i~~~~~p~e~~lV~da~~G---q--~a~~~a~~F~~~~~i~giIlTKlD~ 252 (461) T Consensus 67 ~~~i~~IDtPGH----~df~~~~~~--g~~~~D~ailvVda~~G~~~QT~eh~~~~~~~~--~~~-iv~iNK~D~ 132 (192) T cd01889 67 NLQITLVDCPGH----ASLIRTIIG--GAQIIDLMLLVVDATKGIQTQTAECLVIGEILC--KKL-IVVLNKIDL 132 (192) T ss_pred CEEEEEEECCCC----HHHHHHHHH--HHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCC--CCE-EEEEECCCC T ss_conf 458999877983----889988888--874326527999878888789999999999858--997-999974127

HHsearch alignment for GI: 254780711 and conserved domain: cd01889