Prophage genomics reveals patterns in phage genome organization and replication

Han Suh Kang; Katelyn McNair; Daniel A. Cuevas; Barbara A. Bailey; Anca M. Segall; Robert A. Edwards

Five-mer profiles of the amino acid sequences were used to identify an eight-residue motif in one of the catalytic region of tyrosine recombinases with a consensus sequence of HDLRHTFA (Fig. 5A) . The very strong conservation of five of the amino acids (bolded) suggests that they participate in the catalytic activity of these recombinases. Several of these amino acids were identified earlier as invariant among tyrosine integrases or nearly so (44) (45) (46) , and both of the histidines, the leucine, and the arginine have been experimentally demonstrated to participate in DNA recognition, binding, and/or catalysis (41) . Alignment of one hundred randomly selected tyrosine integrases from the condensed integrase set shows that the proteins that contained the motif were grouped together (Fig. 5B) , offering a potential route to identify tyrosine recombinases.