In bacteria, such as E. coli, genes, are regulated by sequence elements in promoters and related binding sites). RegulonDB provides a database of such regulatory elements, their binding sites and the transcription factors that bind to these sites in E. coli. RegulonDB 9.0 includes 184 experimentally determined transcription factors (TFs) as well as 120 computationally predicted TFs, that is, a total of 304.
The complete repertoire of 189 genetic sensory-response units (GENSOR units) are reported, integrating their signal, regulatory interactions, and metabolic pathways. A total of 78 GENSOR units have their four components highlighted; 119 include the genetic switch and the response, and 2 contain only the genetic switch.
A total of 103 TFs have a known effector in RegulonDB, including 25 two-component systems. There were enough sites to build a motif for 93 TFs to infer 16,207 predicted TF 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). If only TFs with a good-quality PWM are taken into account, the total number of predicted TF → gene interactions is 8,714, recovering 672 (57%) of annotated interactions for this TF subset. Semi-automatic curation produced a total of 3,195 regulatory interactions for 199 TFs.