>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes. Length = 581

Score = 86.9 bits (215), Expect = 2e-17 Identities = 80/306 (26%), Positives = 121/306 (39%), Gaps = 60/306 (19%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 IA HVDHGKTTL+ L +G+ R+ E EK+RG+TI Sbjct: 2 IIATAGHVDHGKTTLLKAL---TGI--AADRLPE--------EKKRGMTIDLGFAYFPLP 48 Query: 81 DVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTK--FVVGKALKIGLRPI 138 D R+ +D PGH F +++ +++VDA EG M QT V L I I Sbjct: 49 DYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHT-I 107 Query: 139 VVVNKVDRSD-ARADEVINEVFD-LFSALDATDAQLDFPILYGSGR--------FGWMSD 188 VV+ K DR + + L S + +A++ F +G+ + + Sbjct: 108 VVITKADRVNEEEIKRTEMFMKQILNSYIFLKNAKI-FKTSAKTGQGIGELKKELKNLLE 166 Query: 189 SSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSN 248 S D R Q L + +D FK+ G G +VTG SG +K Sbjct: 167 SLDIKRIQKP---LRMAIDRA---------FKVKGA--------GTVVTGTAFSGEVKVG 206 Query: 249 QNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVS--IAGLVKATVADTFCDP 306 N++ L P V RV I A Q ++ A+AG ++ + + ++ Sbjct: 207 DNLR-LLPINHEV---RVKAIQAQ----NQDVEIAYAGQRIALNLMDVEPESLKRGLL-- 256 Query: 307 SIDEPL 312 I P Sbjct: 257 -ILTPE 261

RPSBLAST alignment for GI: 254780233 and conserved domain: TIGR00475