HHsearch alignment for GI: 254780150 and conserved domain: cd04171
>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=100.00 E-value=4.6e-42 Score=279.87 Aligned_cols=161 Identities=42% Similarity=0.605 Sum_probs=141.1
Q ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHCCCEEEEEEEEEEC-CCEEEEEEECCCCHHHHHHHHHHH
Q ss_conf 9999904689887899999987644420013126868698629206378999821-990899984787302467798774
Q gi|254780150|r 14 GLSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYET-DKRFYSHIDCPGHADYVKNMITGA 92 (392)
Q Consensus 14 ni~~iGhvd~GKSTL~~~L~~~~~~~~~~~~~~D~~~~E~~rGiTi~~~~~~~~~-~~~~i~iiD~PGH~~f~~~mi~g~ 92 (392)
T Consensus 2 vVaivG~~n~GKSTL~n~L~g~---------~~d~~~~e~~~giTi~~~~~~~~~~~~~~i~~iDtPGh~~~~~~~~~~~ 72 (164)
T cd04171 2 IIGTAGHIDHGKTTLIKALTGI---------ETDRLPEEKKRGITIDLGFAYLDLPSGKRLGFIDVPGHEKFIKNMLAGA 72 (164)
T ss_pred EEEEECCCCCCHHHHHHHHHCC---------CCCCCHHHHCCCEEEEEEEEEEECCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 9999926887299999998496---------4663333334863798546878648998999994878799999999987
Q ss_pred HCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCEEEEEEEEEEEEECCCCEEEE
Q ss_conf 00233145201234433210677888863187602331002333561222110123210011101453221023311467
Q gi|254780150|r 93 TQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALC 172 (392)
Q Consensus 93 ~~~D~ailvVda~~G~~~QT~eh~~l~~~lgi~~iIv~iNKmD~v~~~~~~~~i~~~i~~~l~~~~~~~~~pii~~sa~~ 172 (392)
T Consensus 73 ~~aD~~llVvda~~g~~~q~~e~~~~~~~~~i~~~ivvlNK~D~v~~~~-~~~~~~~i~~~l~~~~~-~~~pii~iSA~t 150 (164)
T cd04171 73 GGIDLVLLVVAADEGIMPQTREHLEILELLGIKRGLVVLTKADLVDEDW-LELVEEEIRELLAGTFL-ADAPIFPVSAVT 150 (164)
T ss_pred HHCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHH-HHHHHHHHHHHHHHCCC-CCCEEEEEECCC
T ss_conf 4267258998617788888999999998738872787346342579789-99999999999974399-998299946989
Q ss_pred EEECCCCCCCCCCCCCHHHHHHC
Q ss_conf 64114445652123320344310
Q gi|254780150|r 173 ALQGTNKELGEDSIHALMKAVDT 195 (392)
Q Consensus 173 g~~~~n~~~~~~~~~~Ll~~i~~ 195 (392)
T Consensus 151 G~----------Gi~eL~~~I~e 163 (164)
T cd04171 151 GE----------GIEELKEYLDE 163 (164)
T ss_pred CC----------CHHHHHHHHHH
T ss_conf 82----------99999999984