>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=5.4e-39 Score=284.69 Aligned_cols=157 Identities=27% Similarity=0.336 Sum_probs=124.9 Q ss_pred EEEEEECCCCCHHHHHHHHHHHHH-------HHCCCCCCEECCCEEEEE--------------CCCCEEEEEECCCHHHH Q ss_conf 389862368504467778864222-------100123100012149995--------------17843888851661578 Q gi|254780787|r 385 VVTIMGHVDHGKTSLLDAIRKADV-------AKGEIGGITQHIGAYQVA--------------YQGKNITFLDTPGHAAF 443 (884) Q Consensus 385 vv~v~ghvd~GKt~lld~~r~~~~-------~~~e~ggitq~iga~~~~--------------~~~~~~~~iDtPGh~~f 443 (884) T Consensus 2 NV~iiGHVDhGKTTL~~~L~~~~~~~~~D~~~eE~eRGITi~~g~~~~~~~~~~~~~~~~~~~~~~~~i~~IDtPGH~df 81 (192) T cd01889 2 NVGVLGHVDSGKTSLAKALSEIASTAAFDKNPQSQERGITLDLGFSSFYVDKPKHLRELINPGEENLQITLVDCPGHASL 81 (192) T ss_pred EEEEEEECCCCHHHHHHHHHHHCCCHHHHCCHHHHHCCCCEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEECCCCHHH T ss_conf 89999761789999999998333501221358899779716710013785144221123234677458999877983889 Q ss_pred HHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEECCCCCCCCCCC-CHHHHHHHCCC--CCCCCCCCCC Q ss_conf 99986664206805999983667402357778989970994156123312443320-00221000013--2000123474 Q gi|254780787|r 444 YEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDKLGADP-QKVRMSLLKHD--VFVESMGGDI 520 (884) Q Consensus 444 ~~~r~rg~~~~d~~ilvv~~~~g~~~qt~e~~~~~~~~~~p~iva~nk~d~~~~~~-~~~~~~~~~~~--~~~~~~~~~~ 520 (884) T Consensus 82 ~~~~~~g~~~~D~ailvVda~~G~~~QT~eh~~~~~~~~~~~iv~iNK~D~v~~~~~~~~~~~i~~~l~~~l~~~~~~~~ 161 (192) T cd01889 82 IRTIIGGAQIIDLMLLVVDATKGIQTQTAECLVIGEILCKKLIVVLNKIDLIPEEERERKIEKMKKKLQKTLEKTRFKNS 161 (192) T ss_pred HHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 98888887432652799987888878999999999985899799997412788157799999999999999865389998 Q ss_pred EEEEEEECCCCCCCCCCCCHH Q ss_conf 036311002477411221000 Q gi|254780787|r 521 LDVEISAKNNLNLDKLLDAIL 541 (884) Q Consensus 521 ~~~~~~~~~~~~~~~~~~~~~ 541 (884) T Consensus 162 ~iipiSA~~G~gi~eL~~~i~ 182 (192) T cd01889 162 PIIPVSAKPGGGEAELGKDLN 182 (192) T ss_pred EEEEEECCCCCCHHHHHHHHH T ss_conf 499957898849899998887

HHsearch alignment for GI: 254780787 and conserved domain: cd01889