I am a PhD students and I am currently analysing texts with SFL. I have some difficulty deviding the clauses and deciding when a clause is embedded and when its is a ranked clause. for exmaple, if someone can help me with this particular sentence:

In the acidic environment of the endosome, the PA protein enables the two enzymes to enter the cell cytoplasm.."

is "to enter the cell cytoplasm" is embedded or not?

also in the sentence:
"Both enzymes are not active by themselves, but are made active when attached to the PA protein..."

is "when attached to the PA protein" embedded?

How do I tell?...