[1][2] RegulonDB also models the organization of the genes in transcription units, operons and regulons.

In bacteria, such as E. coli, genes, are regulated by sequence elements in promoters and related binding sites).

This set of predicted binding sites corresponds to 12,574 TF → gene regulatory interactions; this represents a recovery of 52% of the 1592 annotated regulatory interactions in the database for the 93 TFs for which RegulonDB has a position-weight matrix (PWM).

A TU may also include regulatory protein binding sites affecting this promoter and a terminator.

A promoter is defined in RegulonDB as the nucleotide sequence 60 bases upstream and 20 downstream from the precise initiation of transcription or +1.

The graphic display of a TU will always contain only one promoter -when known- with the binding sites that regulate its activity, followed by the transcribed genes.