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