解:$(1)$因为$x=5^{m+2}=5^m ×5^2,$
所以$5^m=\frac {1}{25}x。$
$ $因为$25^m=5^{2m}=(5^m)^2,$
所以$y=(5^m)^2 - 3=(\frac {1}{25}x)^2 - 3=\frac {1}{625}x^2 - 3。$
$(2)$当$x=-3$时,
$ y=\frac {1}{625}×(-3)^2 - 3=\frac {9}{625}-3=-\frac {1866}{625}=-2\frac {616}{625}。$