HHsearch alignment for GI: 254780321 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=0 Score=339.70 Aligned_cols=172 Identities=27% Similarity=0.399 Sum_probs=147.0
Q ss_pred EEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHCCEEEEEEEEEEE---------ECCCCCEEEEEEE
Q ss_conf 7999801389877889999998298054444311305867798719505232799997---------4378843899996
Q gi|254780321|r 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNY---------TSTDAKDYQLNLI 83 (606)
Q Consensus 13 N~~IiaHvDhGKTTL~d~lL~~tg~i~~~~~~~~vlD~~~~EreRGITIka~~~~~~~---------~~~~~~~y~iNlI 83 (606)
T Consensus 2 NV~iiGHVDhGKTTL~~~L~~~~~~--------~~~D~~~eE~eRGITi~~g~~~~~~~~~~~~~~~~~~~~~~~~i~~I 73 (192)
T cd01889 2 NVGVLGHVDSGKTSLAKALSEIAST--------AAFDKNPQSQERGITLDLGFSSFYVDKPKHLRELINPGEENLQITLV 73 (192)
T ss_pred EEEEEEECCCCHHHHHHHHHHHCCC--------HHHHCCHHHHHCCCCEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEE
T ss_conf 8999976178999999999833350--------12213588997797167100137851442211232346774589998
Q ss_pred ECCCCCHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCC-----CCCHHHHHHHHH
Q ss_conf 178730027999999973026899998687886558999999997099679983267887532-----113388877555
Q gi|254780321|r 84 DTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHEIITVLNKADLPSAD-----PDRVKKQIEETI 158 (606)
Q Consensus 84 DTPGH~DF~~EV~r~l~a~dgaiLvVdA~~Gvq~QT~~~~~~A~~~~l~~I~viNKiD~~~A~-----~e~v~~ei~~~~ 158 (606)
T Consensus 74 DtPGH~df~~~~~~g~~~~D~ailvVda~~G~~~QT~eh~~~~~~~~~~~iv~iNK~D~v~~~~~~~~~~~i~~~l~~~l 153 (192)
T cd01889 74 DCPGHASLIRTIIGGAQIIDLMLLVVDATKGIQTQTAECLVIGEILCKKLIVVLNKIDLIPEEERERKIEKMKKKLQKTL 153 (192)
T ss_pred ECCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 77983889988888874326527999878888789999999999858997999974127881577999999999999998
Q ss_pred ---HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCC
Q ss_conf ---3223210001110022320067877632100011
Q gi|254780321|r 159 ---GISTEDALLVSAKTGEGIPLLLERIVQQLPSPTS 192 (606)
Q Consensus 159 ---g~~~~~ii~vSAktG~GV~~LLd~Iv~~iP~P~~ 192 (606)
T Consensus 154 ~~~~~~~~~iipiSA~~G~gi~eL~~~i~~lip~p~~ 190 (192)
T cd01889 154 EKTRFKNSPIIPVSAKPGGGEAELGKDLNNLIVLPLI 190 (192)
T ss_pred HHCCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCC
T ss_conf 6538999849995789884989999888761899963