HHsearch alignment for GI: 254780648 and conserved domain: cd04171

>cd04171 SelB 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 eukaryo
Probab=99.92  E-value=3.3e-25  Score=172.61  Aligned_cols=150  Identities=23%  Similarity=0.273  Sum_probs=106.7

Q ss_pred             EEEEECCCCCCCEEEEEECCCCC---HHHHHHHCCCEECCEEEEE-CCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             12442167775303541014540---1212110000001026632-9868998226421247311677512344333335
Q gi|254780648|r  162 IGIIGLPNAGKSTFLASVTRAKP---KIADYPFTTLYPNLGIVKE-GYKEFILADIPGIIKNAHQGAGIGDRFLKHTERT  237 (335)
Q Consensus       162 VglVG~PNaGKSTLln~ls~ak~---kIa~ypFTT~~P~lGvv~~-~~~~~~i~D~PGlIegA~~~~glG~~FLrhIer~  237 (335)
T Consensus         3 VaivG~~n~GKSTL~n~L~g~~~d~~~~e~~~giTi~~~~~~~~~~~~~~i~~iDtPGh-----~~--~~~~~~~~~~~a   75 (164)
T cd04171           3 IGTAGHIDHGKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLDLPSGKRLGFIDVPGH-----EK--FIKNMLAGAGGI   75 (164)
T ss_pred             EEEECCCCCCHHHHHHHHHCCCCCCCHHHHCCCEEEEEEEEEEECCCCCEEEEEECCCH-----HH--HHHHHHHHHHHC
T ss_conf             99992688729999999849646633333348637985468786489989999948787-----99--999999987426


Q ss_pred             HHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCC-EEEEEECCCCCCHHHHHHHHHHHHHHC------CCCEEEEECC
Q ss_conf             788752022221101346667899877766750598-899997465899889999999999862------9948999888
Q gi|254780648|r  238 HVLLHIVSALEENVQAAYQCILDELSAYNSELRKKI-EIVGLSQIDTVDSDTLARKKNELATQC------GQVPFEFSSI  310 (335)
Q Consensus       238 ~vLl~VVD~s~~d~~~~~~~I~~EL~~y~~~L~~Kp-~IIVlNKiDl~~~e~~~~~~~~l~~~~------~~~vi~ISA~  310 (335)
T Consensus        76 D~~llVvda~~g-~~~q~~e~~~~~~~-----~~i~~~ivvlNK~D~v~~~~~~~~~~~i~~~l~~~~~~~~pii~iSA~  149 (164)
T cd04171          76 DLVLLVVAADEG-IMPQTREHLEILEL-----LGIKRGLVVLTKADLVDEDWLELVEEEIRELLAGTFLADAPIFPVSAV  149 (164)
T ss_pred             CEEEEEEECCCC-CCHHHHHHHHHHHH-----CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECC
T ss_conf             725899861778-88889999999987-----388727873463425797899999999999997439999829994698


Q ss_pred             CCCCHHHHHHHHHH
Q ss_conf             78899999999999
Q gi|254780648|r  311 TGHGIPQILECLHD  324 (335)
Q Consensus       311 tg~GI~eL~~~I~e  324 (335)
T Consensus       150 tG~Gi~eL~~~I~e  163 (164)
T cd04171         150 TGEGIEELKEYLDE  163 (164)
T ss_pred             CCCCHHHHHHHHHH
T ss_conf             98299999999984