HHsearch alignment for GI: 254780806 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=93.56 E-value=0.069 Score=30.51 Aligned_cols=81 Identities=14% Similarity=0.237 Sum_probs=45.6
Q ss_pred CCCCCCEEEECCCCC--CCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCC-HHH
Q ss_conf 027820331013332--22210112331001111123113788875335777655432026774310020231253-100
Q gi|254780806|r 122 SDFSYIFLDCPPSFN--LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRN-SLS 198 (265)
Q Consensus 122 ~~yD~IiiD~pp~~~--~~~~~al~aad~viip~~p~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~-~~~ 198 (265)
T Consensus 66 ~~~~i~~IDtPGH~df~~~~~~g~~~~D~ailvVda~~G-~~--~QT~eh~~~~-~~~~~--~~i-v~iNK~D~v~~~~~ 138 (192)
T cd01889 66 ENLQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDATKG-IQ--TQTAECLVIG-EILCK--KLI-VVLNKIDLIPEEER 138 (192)
T ss_pred CCEEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEECCCC-CC--HHHHHHHHHH-HHCCC--CEE-EEEECCCCCCHHHH
T ss_conf 745899987798388998888887432652799987888-87--8999999999-98589--979-99974127881577
Q ss_pred HHHHHHHHHHH
Q ss_conf 11268999880
Q gi|254780806|r 199 QQVVSDVRKNL 209 (265)
Q Consensus 199 ~~~~~~l~~~~ 209 (265)
T Consensus 139 ~~~~~~i~~~l 149 (192)
T cd01889 139 ERKIEKMKKKL 149 (192)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999999