HHsearch alignment for GI: 254780264 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=99.97 E-value=2.1e-30 Score=214.00 Aligned_cols=115 Identities=28% Similarity=0.424 Sum_probs=104.0
Q ss_pred EEEECCCCCCHHHHHHHHHHHCCCCCCCCEECCCCEECCCHHHHHHHCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCC
Q ss_conf 99986878897789999999808732142201795613780889870853764079999607778713899981798755
Q gi|254780264|r 13 FGIMAHIDAGKTTTTERILYYAGKSHKIGEVHDGSATMDWMEQEQERGITITSASTTVFWPGRDGGQKKLTIIDTPGHVD 92 (701)
Q Consensus 13 v~iiaHvd~GKTTL~d~LL~~~g~i~~~g~v~~g~~~~D~~~~E~eRgITi~ss~~sl~~~~~~~~~~~iNlIDTPGH~D 92 (701)
T Consensus 3 VaivG~~n~GKSTL~n~L~---g~------------~~d~~~~e~~~giTi~~~~~~~~~~~----~~~i~~iDtPGh~~ 63 (164)
T cd04171 3 IGTAGHIDHGKTTLIKALT---GI------------ETDRLPEEKKRGITIDLGFAYLDLPS----GKRLGFIDVPGHEK 63 (164)
T ss_pred EEEECCCCCCHHHHHHHHH---CC------------CCCCCHHHHCCCEEEEEEEEEEECCC----CCEEEEEECCCHHH
T ss_conf 9999268872999999984---96------------46633333348637985468786489----98999994878799
Q ss_pred CHHHHHHHHHHHCEEEEEEECCCCCCHHHHHHHHHHHHCCCC-EEEEECCCCCCC
Q ss_conf 289999999860456999955888883479999999873997-899981767658
Q gi|254780264|r 93 FTMEVERSIRVTDGAIALLDSNAGVEPQTETVWRQADKYSVP-RVIFCNKMDKMG 146 (701)
Q Consensus 93 F~~Ev~~aL~~~DgailvVDa~eGv~~qT~~vlr~~~~~~lp-~ilvINKiDr~~ 146 (701)
T Consensus 64 ~~~~~~~~~~~aD~~llVvda~~g~~~q~~e~~~~~~~~~i~~~ivvlNK~D~v~ 118 (164)
T cd04171 64 FIKNMLAGAGGIDLVLLVVAADEGIMPQTREHLEILELLGIKRGLVVLTKADLVD 118 (164)
T ss_pred HHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCC
T ss_conf 9999999874267258998617788888999999998738872787346342579