>cd04171 SelB 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 eukaryo

Probab=99.40 E-value=5.3e-12 Score=100.72 Aligned_cols=84 Identities=24% Similarity=0.345 Sum_probs=56.0 Q ss_pred CEEEEEECCCCCHHHHHHHHHCCCC--CCCCCCCCCCCCCCEEEEECCCHHHHHHHHHCCCCEEEEEEEEEEECCCCCCC Q ss_conf 2486752888788899998740489--87366686744883379976855587776421865023357999851223543 Q gi|254780226|r 3 FKCGIIGLPNVGKSTLFNALTRTAS--AQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVPTRMSFVDIAGLVRG 80 (367) Q Consensus 3 ~kiGlvG~pn~GKST~f~alT~~~~--~~~~~ypFtTi~pn~g~~~v~d~~~~~l~~~~~~~~~~p~~i~~iDvaGLv~g 80 (367) T Consensus 1 ~vVaivG~~n~GKSTL~n~L~g~~~d~~~~e~~~giTi~~~~~~~~~~~-----------~-----~~i~~iDtPG---- 60 (164) T cd04171 1 MIIGTAGHIDHGKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLDLPS-----------G-----KRLGFIDVPG---- 60 (164) T ss_pred CEEEEECCCCCCHHHHHHHHHCCCCCCCHHHHCCCEEEEEEEEEEECCC-----------C-----CEEEEEECCC---- T ss_conf 9999992688729999999849646633333348637985468786489-----------9-----8999994878---- Q ss_pred CCCCCCCHHHHHHHHHCCCEEEEEECCCC Q ss_conf 22246632899998730374788501234 Q gi|254780226|r 81 ASKGEGLGNQFLAHIREVDAIIHVLRCFK 109 (367) Q Consensus 81 A~~G~GlGN~FL~~ir~aDalihVVdaf~ 109 (367) T Consensus 61 -h~--~~~~~~~~~~~~aD~~llVvda~~ 86 (164) T cd04171 61 -HE--KFIKNMLAGAGGIDLVLLVVAADE 86 (164) T ss_pred -HH--HHHHHHHHHHHHCCEEEEEEECCC T ss_conf -79--999999998742672589986177

HHsearch alignment for GI: 254780226 and conserved domain: cd04171