>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=97.01 E-value=0.0021 Score=44.27 Aligned_cols=143 Identities=22% Similarity=0.317 Sum_probs=74.1 Q ss_pred EEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 23113544444247899999998522674267743451245688999997530353212235866124542289999651 Q gi|254780709|r 113 VILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDAAALAYEAFKQAQAK 192 (321) Q Consensus 113 vil~vG~nG~GKTTT~aKLA~~~~~~g~kV~lva~DtfR~aA~eQL~~~a~~~~v~~~~~~~~~dp~~v~~~a~~~a~~~ 192 (321) T Consensus 2 vVaivG~~n~GKSTL~n~L~g------~~-----~d--~~------~~-e~~~giTi-------~~~---~~~~~~--~~ 49 (164) T cd04171 2 IIGTAGHIDHGKTTLIKALTG------IE-----TD--RL------PE-EKKRGITI-------DLG---FAYLDL--PS 49 (164) T ss_pred EEEEECCCCCCHHHHHHHHHC------CC-----CC--CC------HH-HHCCCEEE-------EEE---EEEEEC--CC T ss_conf 999992688729999999849------64-----66--33------33-33486379-------854---687864--89 Q ss_pred CCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHH--HHHHHHHHHHHCCCCE--EEEECCCC Q ss_conf 4875998654333211577899998998763022234301123102335225--7789998764358976--99965457 Q gi|254780709|r 193 KVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQVLDATTGQN--ALRQVEMFHAVAGTTG--LIMTKMDG 268 (321) Q Consensus 193 ~~DvvliDTAGR~~~~~~lm~EL~ki~~v~~~~~~~~p~~~~lVlda~~gq~--~~~~a~~F~~~~~~~g--~I~TKlD~ 268 (321) T Consensus 50 ~~~i~~iDtPG--h--~~~~~~~---~~~~~-----~aD~~llVvda~~g~~~q~~e~~~~~-~~~~i~~~ivvlNK~D~ 116 (164) T cd04171 50 GKRLGFIDVPG--H--EKFIKNM---LAGAG-----GIDLVLLVVAADEGIMPQTREHLEIL-ELLGIKRGLVVLTKADL 116 (164) T ss_pred CCEEEEEECCC--H--HHHHHHH---HHHHH-----HCCEEEEEEECCCCCCHHHHHHHHHH-HHCCCCCEEEEEECCCC T ss_conf 98999994878--7--9999999---99874-----26725899861778888899999999-87388727873463425 Q ss_pred CCCHHH--HHH-HHHH------HCCCEEEEEC--CCCCCCCCC Q ss_conf 870699--999-9999------7698899975--898132555 Q gi|254780709|r 269 TARGGG--LIP-IVVT------HKIPVYFLGV--GEGINDLEP 300 (321) Q Consensus 269 ta~~G~--~ls-~~~~------~~~Pi~fig~--Ge~i~Dl~~ 300 (321) T Consensus 117 v~~~~~~~~~~~i~~~l~~~~~~~~pii~iSA~tG~Gi~eL~~ 159 (164) T cd04171 117 VDEDWLELVEEEIRELLAGTFLADAPIFPVSAVTGEGIEELKE 159 (164) T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHH T ss_conf 7978999999999999974399998299946989829999999

HHsearch alignment for GI: 254780709 and conserved domain: cd04171