What is a functional screen?
From the abstract of the linked article (Guttman, 2002):


  We used an in vivo genetic screen to identify 13 effectors [...]. Although sharing little overall homology, the amino-terminal regions of these effectors had strikingly similar amino acid compositions.


And from the body:


  The screen relied on the type III secretion signal and the endogenous promoter of the hop gene and was thus highly specific. 


Hence, the authors search and identify proteins with a secretory signal under the regulation of a hop promoter. A functional screen in this paper refers to the analysis of protein samples to detect the presence of proteins with a particular function.