Labelled, directed edges for graphs. (A, B) Binding transitions. (C–J) Non-binding transitions. Each example shows a source (left) and a target (right) microstate connected by a labelled edge (curved, barbed arrow). Grey ovals signify background components that make up the microstate. A nominal transcription start site is shown. The magenta shape in (C), (D), (G), (H) and (I) depicts a component of the source microstate that is specifically involved in the reaction represented by the edge. A small dashed arrow signifies an enzymatic action by a component in the source microstate (magenta shape), which remains bound after catalysis. The yellow disc depicts RNA polymerase with a nascent mRNA molecule in the elongating state. The edge-label formula in (B) comes from the rapid equilibrium assumption discussed in the text and is derived in the Methods. 3D, three dimensional; TF, transcription factor; Me, methylation; P, phosphorylation; Ub, ubiquitination.