Many approaches, each will highlight only aspects: Sequence the whole transcriptome, do differential proteomics and analyze changes in signalling, e.g., phosphorylation, histone acetylation, etc.

Which methods are available to you?

CoIP followed by a proteomic investigation of the eluent may help to clarify the interactome of the target effector protein...

I want to predict these interactions computationally.

Sequence of effector

and Target proteome are available.

One commonly used strategy for predicting protein-protein interactions (PPIs) is through computational methods that use protein sequence, structure, and other features to identify potential interacting partners. Here are a few tools and databases that may be useful for your project:

It's worth noting that computational methods for predicting PPIs are not always accurate, and experimental validation is typically required to confirm the interactions identified by these methods. However, these tools and databases can be a useful starting point for identifying potential interacting partners and building a hypothesis about the interaction network between your pathogenic effector protein and the host proteome.