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