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