HHsearch alignment for GI: 254780809 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=99.84 E-value=6.3e-21 Score=165.02 Aligned_cols=132 Identities=27% Similarity=0.292 Sum_probs=99.8
Q ss_pred CEEEECCCCCCHHHHHHHHHCCHHCCCC--CCCCCCEEECCCCCCC-CCEEEEEEECCHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf 0243114663188899998552000234--5468721100012456-835899950810002410356666788899850
Q gi|254780809|r 221 KIVILGHSNAGKSSLFNALAKKDVAIVT--DIPGTTRDVLTIDLDL-EGYLVKISDTAGIRETDDIVEKEGIKRTFLEVE 297 (440)
Q Consensus 221 ~v~i~G~pN~GKSSL~N~L~~~~~aIVs--~~~GTTRD~i~~~~~i-~g~~~~l~DTaGir~t~d~IE~~GI~ra~~~i~ 297 (440)
T Consensus 2 vVaivG~~n~GKSTL~n~L~g~~~d~~~~e~~~giTi~~~~~~~~~~~~~~i~~iDtPGh~~-------~-~~~~~~~~~ 73 (164)
T cd04171 2 IIGTAGHIDHGKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLDLPSGKRLGFIDVPGHEK-------F-IKNMLAGAG 73 (164)
T ss_pred EEEEECCCCCCHHHHHHHHHCCCCCCCHHHHCCCEEEEEEEEEEECCCCCEEEEEECCCHHH-------H-HHHHHHHHH
T ss_conf 99999268872999999984964663333334863798546878648998999994878799-------9-999999874
Q ss_pred HHCCEEECCCCCCH---HHH---HH--HCCCC-CCCCCCCCCCCCCCCH------------------HHHHHHHHHHHHH
Q ss_conf 30110201358985---663---43--12898-5322223334465420------------------0000133332323
Q gi|254780809|r 298 NADLILLLKEINSK---KEI---SF--PKNID-FIFIGTKSDLYSTYTE------------------EYDHLISSFTGEG 350 (440)
Q Consensus 298 ~aDlil~v~D~~~~---~~~---~~--~~~~~-~i~V~NK~Dl~~~~~~------------------~~~~~ISaktg~G 350 (440)
T Consensus 74 ~aD~~llVvda~~g~~~q~~e~~~~~~~~~i~~~ivvlNK~D~v~~~~~~~~~~~i~~~l~~~~~~~~pii~iSA~tG~G 153 (164)
T cd04171 74 GIDLVLLVVAADEGIMPQTREHLEILELLGIKRGLVVLTKADLVDEDWLELVEEEIRELLAGTFLADAPIFPVSAVTGEG 153 (164)
T ss_pred HCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCC
T ss_conf 26725899861778888899999999873887278734634257978999999999999974399998299946989829
Q ss_pred HHHHHHHHHH
Q ss_conf 5899999999
Q gi|254780809|r 351 LEELINKIKS 360 (440)
Q Consensus 351 i~~L~~~I~~ 360 (440)
T Consensus 154 i~eL~~~I~e 163 (164)
T cd04171 154 IEELKEYLDE 163 (164)
T ss_pred HHHHHHHHHH
T ss_conf 9999999984