Cutoff determination using custom functional gene (nifH) database

Dear All,
I am trying to determine taxonomic cutoff for custom nifH database. I have downloaded whole genomes containing 16s and nifH genes. I have aligned both 16s & nifH genes separately after extracting from those genomes. I carried out dist.seqs with lower triangular matrices output. I would like to know how to determine the cutoff from hereon after obtaining the distances. I have attached lower triangular matrices of both 16s and nifH 2 files (16s and nifH lower triangle matrices).
I followed the methodology of a paper in determining the cut off for mcrA (Taxonomic database and cut-off value for processing mcrA gene 454 pyrosequencing data by MOTHUR, 10.1016/j.mimet.2014.05.006)

Please give your suggestions.
Thanks in advance