>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=93.08  E-value=0.23  Score=27.52  Aligned_cols=66  Identities=18%  Similarity=0.164  Sum_probs=44.2

Q ss_pred             CCEEEECCCCC--CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             88899738888--898999998620125435787768899999999999981987675389995658987
Q gi|254780725|r  275 FPLVILDVPHV--WNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPK  342 (427)
Q Consensus       275 yd~VIiD~p~~--~~~~~~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~  342 (427)
T Consensus        51 ~~i~~iDtPGh~~~~~~~~~~~~~aD~~llVvda~~g~~~q~~e~~~~~~~~~i--~~~ivvlNK~D~v~  118 (164)
T cd04171          51 KRLGFIDVPGHEKFIKNMLAGAGGIDLVLLVVAADEGIMPQTREHLEILELLGI--KRGLVVLTKADLVD  118 (164)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCC--CCEEEEEECCCCCC
T ss_conf             899999487879999999998742672589986177888889999999987388--72787346342579