This is the protein sequence dataset used for determining reads derived from denitrification genes in Illumina read samples. The protein types in the dataset are the active site containing subunits from the following proteins: Nap – periplasmic nitrate reductase; Nar – membrane associated nitrate reductase; NirK – copper containing nitrite reductase; NirS- heme-containing nitrite reductase; cNor – cytochrome c oxidizing nitrite reductase; qNor – quinol oxidizing nitric oxide reductase and Nos – nitrous oxide reductase. Sequences were initially obtained from the data available from the Integrated Microbial Genomes (IMG) system (https://img.jgi.doe.gov/cgi-bin/m/main.cgi). Related proteins were then aligned and proteins predicted to not be related or that were significantly shorter in length than group average were removed.