HHsearch alignment for GI: 254780264 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=100.00 E-value=6.2e-42 Score=287.99 Aligned_cols=124 Identities=24% Similarity=0.413 Sum_probs=110.6
Q ss_pred EEEEECCCCCCHHHHHHHHHHHCCCCCCCCEECCCCEECCCHHHHHHHCCCEEEEEEEEEECCC---------CCCCEEE
Q ss_conf 7999868788977899999998087321422017956137808898708537640799996077---------7871389
Q gi|254780264|r 12 NFGIMAHIDAGKTTTTERILYYAGKSHKIGEVHDGSATMDWMEQEQERGITITSASTTVFWPGR---------DGGQKKL 82 (701)
Q Consensus 12 Nv~iiaHvd~GKTTL~d~LL~~~g~i~~~g~v~~g~~~~D~~~~E~eRgITi~ss~~sl~~~~~---------~~~~~~i 82 (701)
T Consensus 2 NV~iiGHVDhGKTTL~~~L~~~~~-----------~~~~D~~~eE~eRGITi~~g~~~~~~~~~~~~~~~~~~~~~~~~i 70 (192)
T cd01889 2 NVGVLGHVDSGKTSLAKALSEIAS-----------TAAFDKNPQSQERGITLDLGFSSFYVDKPKHLRELINPGEENLQI 70 (192)
T ss_pred EEEEEEECCCCHHHHHHHHHHHCC-----------CHHHHCCHHHHHCCCCEEEEEEEEEECCCCCCCCCCCCCCCCEEE
T ss_conf 899997617899999999983335-----------012213588997797167100137851442211232346774589
Q ss_pred EEEECCCCCCCHHHHHHHHHHHCEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCC
Q ss_conf 9981798755289999999860456999955888883479999999873997899981767658
Q gi|254780264|r 83 TIIDTPGHVDFTMEVERSIRVTDGAIALLDSNAGVEPQTETVWRQADKYSVPRVIFCNKMDKMG 146 (701)
Q Consensus 83 NlIDTPGH~DF~~Ev~~aL~~~DgailvVDa~eGv~~qT~~vlr~~~~~~lp~ilvINKiDr~~ 146 (701)
T Consensus 71 ~~IDtPGH~df~~~~~~g~~~~D~ailvVda~~G~~~QT~eh~~~~~~~~~~~iv~iNK~D~v~ 134 (192)
T cd01889 71 TLVDCPGHASLIRTIIGGAQIIDLMLLVVDATKGIQTQTAECLVIGEILCKKLIVVLNKIDLIP 134 (192)
T ss_pred EEEECCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCC
T ss_conf 9987798388998888887432652799987888878999999999985899799997412788