An alpha subtype methylase that recognizes the double-stranded sequence 5'-GGTGA-3', probably methylates A-5 on the top strand, and protects the DNA from cleavage by the HphI endonuclease. a 2'-deoxyadenosine in DNA + S-adenosyl-L-methionine = an N(6)-methyl-2'-deoxyadenosine in DNA + H(+) + S-adenosyl-L-homocysteine Both this methylase and M1.HphI protect DNA from cleavage by HphI. Belongs to the N(4)/N(6)-methyltransferase family.