word usage - X being Y versus X is Y

I was recently chastised by my supervisor for describing something as being something else.

The problem:

"Species A has genes X1, X2 and X3, Species B has genes Y1 and Y2. Protein X3 being the homolog of Y1"

I was told that "being" is plain incorrect but I do not understand why, it reads perfectly fine to me.

The proposed revision was:

"Protein X3 is the homolog of Protein Y1"

Why is this more correct?