HHsearch alignment for GI: 254780263 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=341.96 Aligned_cols=172 Identities=28% Similarity=0.489 Sum_probs=150.7
Q ss_pred EEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHCCCEEEEEEEEEE--------------CCCEEEEEEEC
Q ss_conf 7999990468988789999998764442001312686869862920637899982--------------19908999847
Q gi|254780263|r 13 LGLSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYE--------------TDKRFYSHIDC 78 (392)
Q Consensus 13 ~ni~~iGhvd~GKSTL~~~L~~~~~~~~~~~~~~D~~~~E~~rGiTi~~~~~~~~--------------~~~~~i~iiD~ 78 (392)
T Consensus 1 ~NV~iiGHVDhGKTTL~~~L~~~~~~-----~~~D~~~eE~eRGITi~~g~~~~~~~~~~~~~~~~~~~~~~~~i~~IDt 75 (192)
T cd01889 1 VNVGVLGHVDSGKTSLAKALSEIAST-----AAFDKNPQSQERGITLDLGFSSFYVDKPKHLRELINPGEENLQITLVDC 75 (192)
T ss_pred CEEEEEEECCCCHHHHHHHHHHHCCC-----HHHHCCHHHHHCCCCEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEC
T ss_conf 98999976178999999999833350-----1221358899779716710013785144221123234677458999877
Q ss_pred CCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCCCHH---HHHHCCCCCCEEEE
Q ss_conf 873024677987740023314520123443321067788886318760233100233356122---21101232100111
Q gi|254780263|r 79 PGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDE---LLDISEYEIRDLLK 155 (392)
Q Consensus 79 PGH~~f~~~mi~g~~~~D~ailvVda~~G~~~QT~eh~~l~~~lgi~~iIv~iNKmD~v~~~~---~~~~i~~~i~~~l~ 155 (392)
T Consensus 76 PGH~df~~~~~~g~~~~D~ailvVda~~G~~~QT~eh~~~~~~~~~~-~iv~iNK~D~v~~~~~~~~~~~i~~~l~~~l~ 154 (192)
T cd01889 76 PGHASLIRTIIGGAQIIDLMLLVVDATKGIQTQTAECLVIGEILCKK-LIVVLNKIDLIPEEERERKIEKMKKKLQKTLE 154 (192)
T ss_pred CCCHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCCCC-EEEEEECCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 98388998888887432652799987888878999999999985899-79999741278815779999999999999986
Q ss_pred EEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCHHHHHHCCCCCCC
Q ss_conf 0145322102331146764114445652123320344310252222
Q gi|254780263|r 156 EHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQ 201 (392)
Q Consensus 156 ~~~~~~~~pii~~sa~~g~~~~n~~~~~~~~~~Ll~~i~~~~~~p~ 201 (392)
T Consensus 155 ~~~~~-~~~iipiSA~~G~----------gi~eL~~~i~~lip~p~ 189 (192)
T cd01889 155 KTRFK-NSPIIPVSAKPGG----------GEAELGKDLNNLIVLPL 189 (192)
T ss_pred HCCCC-CCEEEEEECCCCC----------CHHHHHHHHHHHCCCCC
T ss_conf 53899-9849995789884----------98999988876189996