HHsearch alignment for GI: 254780941 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=99.96  E-value=1.3e-29  Score=211.44  Aligned_cols=153  Identities=22%  Similarity=0.303  Sum_probs=121.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHCCCEEEE--CCCCCCEEEEEEEEEEE-CCEEEEEEECCCCHHHCCCCCCCCCCHHHHHHH
Q ss_conf             899833899868899999868920210--58888602127899973-994899998798401012357532100234555
Q gi|254780941|r   24 CVALVGATNAGKSTLVNRFVGAKVSIV--THKVQTTRSIVRGIVSE-KESQIVFLDTPGIFNAKDSYHKLMIRLSWSTIK  100 (311)
Q Consensus        24 ~VaivG~pN~GKSTL~N~l~g~~vsiv--S~k~~TTr~~i~gi~~~-~~~qiifvDTPG~~~~~~~l~~~~~~~~~~~l~  100 (311)
T Consensus         2 vVaivG~~n~GKSTL~n~L~g~~~d~~~~e~~~giTi~~~~~~~~~~~~~~i~~iDtPGh--------~~~~~~~~~~~~   73 (164)
T cd04171           2 IIGTAGHIDHGKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLDLPSGKRLGFIDVPGH--------EKFIKNMLAGAG   73 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHCCCCCCCHHHHCCCEEEEEEEEEEECCCCCEEEEEECCCH--------HHHHHHHHHHHH
T ss_conf             999992688729999999849646633333348637985468786489989999948787--------999999999874


Q ss_pred             HHHHHCCCCHHHHHHHCCHHHHHHHHHHCCCC-CEEEEEECCCHHHHHHHHHHHHHHHCC-----CCCCCCCCCCCCCCC
Q ss_conf             53210011000010000000122345442872-025787211010434578888641001-----233431100013874
Q gi|254780941|r  101 HADIVCLVVDSHRELKVNIHDLLKEIAKRSSR-LILILNKIDCVKPERLLEQAEIANKLV-----FIEKTFMVSATKGHG  174 (311)
Q Consensus       101 ~aDiil~VvDa~~~~~~~~~~il~~l~~~~~p-~IiVlNKiDlv~~~~l~~~~~~~~~~~-----~~~~i~~ISAk~g~G  174 (311)
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             2678999998
Q gi|254780941|r  175 CDDVLNYLCS  184 (311)
Q Consensus       175 id~L~~~L~~  184 (311)
T Consensus       154 i~eL~~~I~e  163 (164)
T cd04171         154 IEELKEYLDE  163 (164)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999984