HHsearch alignment for GI: 254780725 and conserved domain: cd01889
>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=93.21 E-value=0.26 Score=27.25 Aligned_cols=66 Identities=11% Similarity=0.072 Sum_probs=50.6
Q ss_pred HCCCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCC
Q ss_conf 1288899738888--89899999862012543578776889999999999998198767538999565898
Q gi|254780725|r 273 QIFPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTP 341 (427)
Q Consensus 273 ~~yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~ 341 (427)
T Consensus 66 ~~~~i~~IDtPGH~df~~~~~~g~~~~D~ailvVda~~G~~~QT~eh~~~~~~~~~---~~iv~iNK~D~v 133 (192)
T cd01889 66 ENLQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDATKGIQTQTAECLVIGEILCK---KLIVVLNKIDLI 133 (192)
T ss_pred CCEEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCCC---CEEEEEECCCCC
T ss_conf 74589998779838899888888743265279998788887899999999998589---979999741278