Completing the annotation of a genome sequence requires identifying the regulatory sequences that control gene expression. To identify these sequences, we developed an algorithm that searches for short, conserved sequence motifs in the genomes of related species. The method is effective in finding motifs de novo and for refining known regulatory motifs in Saccharomyces cerevisiae. We tested one novel motif prediction of the algorithm and found it to be the binding site of Stp2; it is significantly different from the previously predicted Stp2 binding site. We show that Stp2 physically interacts with this sequence motif, and that stp2 mutations affect the expression of genes associated with the motif. We demonstrate that the Stp2 binding site also interacts genetically with Stp1, a regulator of amino acid permease genes and, with Sfp1, a key regulator of cell growth. These results illuminate an important transcriptional circuit that regulates cell growth through external nutrient uptake.