The amino acid sequence for the two subunits of the glutamate synthase of Escherichia coli K-12 was compared to the protein sequences compiled in the National Biomedical Research Foundation databank. Similarities were detected between the small glutamate synthase subunit and three members of the flavin-containing pyridine nucleotide-disulphide oxidoreductase superfamily, and also with three members of a lactate dehydrogenase family. Two segments in this glutamate synthase subunit showed similarity to regions previously proposed as part of dinucleotide-binding sites in some members of these two families. Similarity can be extended if the predicted secondary structure is considered. Based on these data, residues 148-260 and 289-409 in the small GOGAT subunit are proposed as dinucleotide-binding regions. Comparison of the amino acid sequence of the large glutamate synthase subunit with the glutamine phosphoribosylamine:pyrophosphate phosphoribosyltransferases of B. subtilis and E. coli revealed a significant similarity between the amino termini of these three enzymes. In these last two amidotransferases, the glutamine-binding site has been located in their amino-terminal region. The comparison with a second group of glutamine amidotransferases did not show any significant global similarity with the large glutamate synthase subunit. However, this polypeptide contains a small segment that shares similarity with a 13-amino acid segment proposed as part of the glutamine-binding site in this second group of amidotransferases.