<jats:title>ABSTRACT</jats:title> <jats:p> Genome sequencing of <jats:italic>Streptomyces</jats:italic> species has highlighted numerous potential genes of secondary metabolite biosynthesis. The mining of cryptic genes is important for exploring chemical diversity. Here we report the metabolite-guided genome mining and functional characterization of a cryptic gene by biochemical studies. Based on systematic purification of metabolites from <jats:italic>Streptomyces</jats:italic> sp. SN-593, we isolated a novel compound, 6-dimethylallylindole (DMAI)-3-carbaldehyde. Although many 6-DMAI compounds have been isolated from a variety of organisms, an enzyme catalyzing the transfer of a dimethylallyl group to the C-6 indole ring has not been reported so far. A homology search using known prenyltransferase sequences against the draft sequence of the <jats:italic>Streptomyces</jats:italic> sp. SN-593 genome revealed the <jats:italic>iptA</jats:italic> gene. The IptA protein showed 27% amino acid identity to cyanobacterial LtxC, which catalyzes the transfer of a geranyl group to (−)-indolactam V. A BLAST search against IptA revealed much-more-similar homologs at the amino acid level than LtxC, namely, SAML0654 (60%) from <jats:italic>Streptomyces ambofaciens</jats:italic> ATCC 23877 and SCO7467 (58%) from <jats:italic>S. coelicolor</jats:italic> A3(2). Phylogenetic analysis showed that IptA was distinct from bacterial aromatic prenyltransferases and fungal indole prenyltransferases. Detailed kinetic analyses of IptA showed the highest catalytic efficiency (6.13 min <jats:sup>−1</jats:sup> μM <jats:sup>−1</jats:sup> ) for <jats:sc>l</jats:sc> -Trp in the presence of dimethylallyl pyrophosphate (DMAPP), suggesting that the enzyme is a 6-dimethylallyl- <jats:sc>l</jats:sc> -Trp synthase (6-DMATS). Substrate specificity analyses of IptA revealed promiscuity for indole derivatives, and its reaction products were identified as novel 6-DMAI compounds. Moreover, Δ <jats:italic>iptA</jats:italic> mutants abolished the production of 6-DMAI-3-carbaldehyde as well as 6-dimethylallyl- <jats:sc>l</jats:sc> -Trp, suggesting that the <jats:italic>iptA</jats:italic> gene is involved in the production of 6-DMAI-3-carbaldehyde.