HHsearch alignment for GI: 254780226 and conserved domain: cd01889

>cd01889 SelB_euk 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 euk
Probab=97.50  E-value=0.00094  Score=45.09  Aligned_cols=96  Identities=22%  Similarity=0.313  Sum_probs=50.3

Q ss_pred             CEEEEEECCCCCHHHHHHHHHCCCCCCC-CCCC-----CCCCCCCEEEEECCCHHHHHHHHHCCCCEEEEEEEEEEECCC
Q ss_conf             2486752888788899998740489873-6668-----674488337997685558777642186502335799985122
Q gi|254780226|r    3 FKCGIIGLPNVGKSTLFNALTRTASAQA-ANYP-----FCTIEPNSGEVAVPDPRMHKLAEIAESKDLVPTRMSFVDIAG   76 (367)
Q Consensus         3 ~kiGlvG~pn~GKST~f~alT~~~~~~~-~~yp-----FtTi~pn~g~~~v~d~~~~~l~~~~~~~~~~p~~i~~iDvaG   76 (367)
T Consensus         1 ~NV~iiGHVDhGKTTL~~~L~~~~~~~~~D~~~eE~eRGITi~~g~~~~~~~~~~~--~~~~~~-~~~~~~~i~~IDtPG   77 (192)
T cd01889           1 VNVGVLGHVDSGKTSLAKALSEIASTAAFDKNPQSQERGITLDLGFSSFYVDKPKH--LRELIN-PGEENLQITLVDCPG   77 (192)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHHCCCHHHHCCHHHHHCCCCEEEEEEEEEECCCCC--CCCCCC-CCCCCEEEEEEECCC
T ss_conf             98999976178999999999833350122135889977971671001378514422--112323-467745899987798


Q ss_pred             CCCCCCCCCCCHHHHHHHHHCCCEEEEEECCC
Q ss_conf             35432224663289999873037478850123
Q gi|254780226|r   77 LVRGASKGEGLGNQFLAHIREVDAIIHVLRCF  108 (367)
Q Consensus        77 Lv~gA~~G~GlGN~FL~~ir~aDalihVVdaf  108 (367)
T Consensus        78 H~df-------~~~~~~g~~~~D~ailvVda~  102 (192)
T cd01889          78 HASL-------IRTIIGGAQIIDLMLLVVDAT  102 (192)
T ss_pred             CHHH-------HHHHHHHHHHCCCCEEEEECC
T ss_conf             3889-------988888874326527999878