That animation doesn't resemble a water wave at all. In a water wave, every single point of the surface does a circular movement (elliptic in shallow water). This resembles a transverse wave at best. It doesn't even look like the surface of a water wave. Take a look at this (for instance):
http://www.acs.psu.edu/drussell/demos/waves/wavemotion.html
Sure - I said they look similar "insofar as all smooth wave functions look sort of similar", which is to say, only to the extent that they're both waves. But none of the interesting physical characteristics of a water wave are present.
No relation at all. They just look similar insofar as all smooth wave functions look sort of similar at small enough amplitudes.
But yeah, the sinusoidal equation doesn't show the initial perturbation, since it's not modeling a perturbation at all.