How to quantify gaps in multiple sequence alignments

Question

[dec986]

Consider a trivially small multiple sequence alignment (MSA) of four peptides:

AAAA
-AAA
--AA
---A

I quantify gaps along the "x" axis, by simply stating what fraction of proteins are present/defined at that position. The small MSA above, would have values of 1,2,3,4. I call this "mean # of proteins" or "mean protein presence".

My explanation of this metric is confusing other people.

Is there a more commonly accepted metric that would explain this concept more simply? and be less confusing to others?

[Dunois]

Isn't this usually looked at the "other way around" in terms of the column occupancy (http://prody.csb.pitt.edu/tutorials/evol_tutorial/msaanalysis.html)?