As far as I have understood, your task is the following:
you have two fasta-files. One of them contains all the proteins of your favorite organism,
the second file contains only transcription factors from the same organism.
You need to select proteins from the whole proteome-file
that are not in your second fasta-file with transcription factors, is it correct?
Look at the following post
A: Print Different Id From Sequence Comparison Of Two Fasta Files
There are different scripts on different languages, you will definitely find something suitable to you.
For example, bash comand-line function diff, it's OK for your problem in my opinion.
Or perl solution with a hash of "unseen" proteins.
Chapter 5.11 in the Cookbook. "Finding Common or Different Keys in Two Hashes".
So you can use whatever you prefer.