Table 3.

Simple Regulatory Rules

Regulator presence	Regulator function	DNA binding conformation	Effector presence (i)		Discrete expression level
		P	Absent	→	Off
	Positive		Present	→	Off
		P-i	Absent	→	Off
Absence			Present	→	Off
		P	Absent	→	On
	Negative		Present	→	On
		P-i	Absent	→	On
			Present	→	On
		P	Absent	→	On
	Positive		Present	→	Off
Presence		P-i	Absent	→	Off
			Present	→	On
		P	Absent	→	Off
	Negative		Present	→	On
		P-i	Absent	→	On
			Present	→	Off

This table describes the rules determining gene expression when a single protein regulates genes. The rules show the regulatory protein complexes (protein and effector-metabolite), when present. We distinguish two types of conformation of regulators notated as P when they bind to their DNA-binding site with no effector, and as P-i regulators when they bind to DNA with the effector present. In the case of an absent protein, we assume that the expression state depends on the promoter strength.