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