HHsearch alignment for GI: 254780233 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=5.3e-34  Score=242.47  Aligned_cols=158  Identities=32%  Similarity=0.422  Sum_probs=134.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCEECCCCHHHHHCCCEEEEEEEEEEE-CCEEEEEECCCCCCCCHHHHH
Q ss_conf             9998546898778899999983961423220000038857798709606467999998-997999972898754079999
Q gi|254780233|r   22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVW-NDVRINIVDTPGHADFGGEVE  100 (624)
Q Consensus        22 iaIiaHvDhGKTTL~d~LL~~sG~~~~~~~v~~~vmD~~~~EreRGITI~a~~~~~~~-~~~~iNiiDTPGH~DF~gEVe  100 (624)
T Consensus         3 VaivG~~n~GKSTL~n~L---~g~~----------~d~~~~e~~~giTi~~~~~~~~~~~~~~i~~iDtPGh~~~~~~~~   69 (164)
T cd04171           3 IGTAGHIDHGKTTLIKAL---TGIE----------TDRLPEEKKRGITIDLGFAYLDLPSGKRLGFIDVPGHEKFIKNML   69 (164)
T ss_pred             EEEECCCCCCHHHHHHHH---HCCC----------CCCCHHHHCCCEEEEEEEEEEECCCCCEEEEEECCCHHHHHHHHH
T ss_conf             999926887299999998---4964----------663333334863798546878648998999994878799999999


Q ss_pred             HHHHHHCEEEEEEECCCCCCHHHHHHHHHHHHCCCC-EEEEEECCCCCCC-CHHHHHHHHHHHHHHCCCCHHHCCHHHHH
Q ss_conf             998742178999976878864789999999972997-8999975436674-02568999998886226730110426688
Q gi|254780233|r  101 RILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLR-PIVVVNKVDRSDA-RADEVINEVFDLFSALDATDAQLDFPILY  178 (624)
Q Consensus       101 r~l~~~DgaiLvVdA~eGv~~QT~~vl~~A~~~~l~-~IvvINKiDr~~a-~~~~v~~ei~dlf~~l~a~de~ld~Pv~~  178 (624)
T Consensus        70 ~~~~~aD~~llVvda~~g~~~q~~e~~~~~~~~~i~~~ivvlNK~D~v~~~~~~~~~~~i~~~l~~~~~----~~~pii~  145 (164)
T cd04171          70 AGAGGIDLVLLVVAADEGIMPQTREHLEILELLGIKRGLVVLTKADLVDEDWLELVEEEIRELLAGTFL----ADAPIFP  145 (164)
T ss_pred             HHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCC----CCCEEEE
T ss_conf             987426725899861778888899999999873887278734634257978999999999999974399----9982999


Q ss_pred             HHHHCCEECCCCCCCCCCCCHHHHHHHHC
Q ss_conf             78865916467422334864135553210
Q gi|254780233|r  179 GSGRFGWMSDSSDGSRDQGMVPLLNLIVD  207 (624)
Q Consensus       179 ~Sa~~G~~~~~~~~~~~~gl~~Lld~Ii~  207 (624)
T Consensus       146 iSA~tG-----------~Gi~eL~~~I~e  163 (164)
T cd04171         146 VSAVTG-----------EGIEELKEYLDE  163 (164)
T ss_pred             EECCCC-----------CCHHHHHHHHHH
T ss_conf             469898-----------299999999984