From a pure biology perspective, when a pathogen affects a host, what comes first, the effect of the toxin (effector protein) on the pathways or identification of the structure of the toxin by the immune system?
I doubt it's a before and after. And what "toxin" do you mean? Because LPS is an endotoxin, but it's effect is mediated by the binding of LPS on TLR expressed on immune cells...
So I would say the most likely answer is at the same time.
I will add some points in Shen-An Hwang 's answer. I also don't think it its a "which comes first" question. I think its a conditional question, and depends on lots of variables: which toxin, what pathway, was there been any previous incidence, concentration of toxin etc.
Shen-An Hwang Abhijeet Singh Chandra Somasundaram I am talking about effector proteins secreted by gram negative bacteria (being a comp sci student, my question is very naive, I apologize for that, but my research is in bioinfo)
So again... i think it happens at the same time, just not all to the same proteins. The effector proteins bypass the host cell membrane, but the bacteria have other components that will trigger host cell recognition.