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