>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=2.1e-34 Score=250.42 Aligned_cols=156 Identities=33% Similarity=0.395 Sum_probs=131.2 Q ss_pred EEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHCCEEEEEEEEEEEECCCCCEEEEEEEECCCCCHHHH Q ss_conf 99980138987788999999829805444431130586779871950523279999743788438999961787300279 Q gi|254780321|r 14 FSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTY 93 (606) Q Consensus 14 ~~IiaHvDhGKTTL~d~lL~~tg~i~~~~~~~~vlD~~~~EreRGITIka~~~~~~~~~~~~~~y~iNlIDTPGH~DF~~ 93 (606) T Consensus 3 VaivG~~n~GKSTL~n~L---~g~---------~~d~~~~e~~~giTi~~~~~~~~~~----~~~~i~~iDtPGh~~~~~ 66 (164) T cd04171 3 IGTAGHIDHGKTTLIKAL---TGI---------ETDRLPEEKKRGITIDLGFAYLDLP----SGKRLGFIDVPGHEKFIK 66 (164) T ss_pred EEEECCCCCCHHHHHHHH---HCC---------CCCCCHHHHCCCEEEEEEEEEEECC----CCCEEEEEECCCHHHHHH T ss_conf 999926887299999998---496---------4663333334863798546878648----998999994878799999 Q ss_pred HHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCCC-EEEEECCCCCCCCC-CCCHHHHHHHHH---HHHHHHHHHH Q ss_conf 999999730268999986878865589999999970996-79983267887532-113388877555---3223210001 Q gi|254780321|r 94 EVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHE-IITVLNKADLPSAD-PDRVKKQIEETI---GISTEDALLV 168 (606) Q Consensus 94 EV~r~l~a~dgaiLvVdA~~Gvq~QT~~~~~~A~~~~l~-~I~viNKiD~~~A~-~e~v~~ei~~~~---g~~~~~ii~v 168 (606) T Consensus 67 ~~~~~~~~aD~~llVvda~~g~~~q~~e~~~~~~~~~i~~~ivvlNK~D~v~~~~~~~~~~~i~~~l~~~~~~~~pii~i 146 (164) T cd04171 67 NMLAGAGGIDLVLLVVAADEGIMPQTREHLEILELLGIKRGLVVLTKADLVDEDWLELVEEEIRELLAGTFLADAPIFPV 146 (164) T ss_pred HHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEE T ss_conf 99998742672589986177888889999999987388727873463425797899999999999997439999829994 Q ss_pred HHHCCCCCCHHHHHHHH Q ss_conf 11002232006787763 Q gi|254780321|r 169 SAKTGEGIPLLLERIVQ 185 (606) Q Consensus 169 SAktG~GV~~LLd~Iv~ 185 (606) T Consensus 147 SA~tG~Gi~eL~~~I~e 163 (164) T cd04171 147 SAVTGEGIEELKEYLDE 163 (164) T ss_pred ECCCCCCHHHHHHHHHH T ss_conf 69898299999999984

HHsearch alignment for GI: 254780321 and conserved domain: cd04171