HHsearch alignment for GI: 254780787 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=5.1e-33  Score=243.85  Aligned_cols=155  Identities=28%  Similarity=0.419  Sum_probs=127.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH---HHHHCCCCCCEECCCEEEEEC-CCCEEEEEECCCHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             3898623685044677788642---221001231000121499951-784388885166157899986664206805999
Q gi|254780787|r  385 VVTIMGHVDHGKTSLLDAIRKA---DVAKGEIGGITQHIGAYQVAY-QGKNITFLDTPGHAAFYEMRARGARVTDIAVLV  460 (884)
Q Consensus       385 vv~v~ghvd~GKt~lld~~r~~---~~~~~e~ggitq~iga~~~~~-~~~~~~~iDtPGh~~f~~~r~rg~~~~d~~ilv  460 (884)
T Consensus         2 vVaivG~~n~GKSTL~n~L~g~~~d~~~~e~~~giTi~~~~~~~~~~~~~~i~~iDtPGh~~~~~~~~~~~~~aD~~llV   81 (164)
T cd04171           2 IIGTAGHIDHGKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLDLPSGKRLGFIDVPGHEKFIKNMLAGAGGIDLVLLV   81 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHCCCCCCCHHHHCCCEEEEEEEEEEECCCCCEEEEEECCCHHHHHHHHHHHHHHCCEEEEE
T ss_conf             99999268872999999984964663333334863798546878648998999994878799999999987426725899


Q ss_pred             EECCCCCCHHHHHHHHHHHHCCCC-EEEECCCCCCCCCCC-CHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCCCCCC
Q ss_conf             983667402357778989970994-156123312443320-002210000132000123474036311002477411221
Q gi|254780787|r  461 LAADEEIMPQAIESINHAKAADVS-IIVAINKIDKLGADP-QKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLD  538 (884)
Q Consensus       461 v~~~~g~~~qt~e~~~~~~~~~~p-~iva~nk~d~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  538 (884)
T Consensus        82 vda~~g~~~q~~e~~~~~~~~~i~~~ivvlNK~D~v~~~~~~~~~~~i~~~l~--~~~~~~~pii~iSA~tG~Gi~eL~~  159 (164)
T cd04171          82 VAADEGIMPQTREHLEILELLGIKRGLVVLTKADLVDEDWLELVEEEIRELLA--GTFLADAPIFPVSAVTGEGIEELKE  159 (164)
T ss_pred             EECCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHH--HCCCCCCEEEEEECCCCCCHHHHHH
T ss_conf             86177888889999999987388727873463425797899999999999997--4399998299946989829999999


Q ss_pred             CHH
Q ss_conf             000
Q gi|254780787|r  539 AIL  541 (884)
Q Consensus       539 ~~~  541 (884)
T Consensus       160 ~I~  162 (164)
T cd04171         160 YLD  162 (164)
T ss_pred             HHH
T ss_conf             998