An overview of the predicted selenoproteome. (a) A Venn diagram representation of the overlap between the known selenoproteins in the RECODE database (bold line) and the results of our prediction method (plain line) over the same set of organisms as included in RECODE. (b) A pie chart illustrating the types of selenoproteins in our predicted dataset. The dataset was divided into the following groups: formate dehydrogenase (FDH) family enzymes; archaeal methanogenesis selenoproteins (excluding the FDH family); selenophosphate synthetase (SelD); other known selenoproteins (for example, thioredoxin, hesB); glycine reductase genes (GRD); and new candidate selenoproteins. (c) A section of the multiple sequence alignments (MSA) of the newly predicted candidate selenoprotein from P. profundum with its four homologs found in our database. Note the alignment of putative selenocysteine (U denotes selenocysteine) with cysteine residues in the MSA. (d) The MSA of a selenoprotein formylmethanofuran dehydrogenase from M. maripaludis in which the recoded selenocysteine aligns with a set of conserved aspartate residues rather than the cysteine residues. The MSA illustrations were prepared using ALSCRIPT .