Nucleic Acids Research, 2007, Vol. 35, No. 22 7583 Table 4. Small-molecule ligands that regulate the activity of E. coli transcription factors 2-Methylcitrate 3-(3-Hydroxyphenyl)propionate 3-Phenylpropionate Adenosine 50-phosphosulfate Allantoin Allolactose Alpha-L-arabinose An acyl-CoA ATP Beta-D-galactose Bio-50-AMP Choline Cyanate Cyclic-AMP Cytidine D-ribose D-sorbitol D-xylose Formate Fructose-1,6-bisphosphate Fructose-1-phosphate Fructuronate Gluconate Glycolate Glyoxylate Hypoxanthine L-arginine L-ascorbate L-homocysteine L-leucine L-phenylalanine L-rhamnose L-tryptophan L-tyrosine Maltotriose Mannitol Melibiose MoO24 N-acetyl-D-glucosamine N-acetylneuraminate Na+ Ni2+ O-acetyl-L-serine Phosphoenolpyruvate Pyruvate S-adenosyl-L-methionine Salicylate Sn-glycerol-3-phosphate Figure 4. Number of promoters at which each sigma factor initiates transcription. through the desktop (locally installed) version of EcoCyc plus Pathway Tools; we plan to incorporate them in the Web version in fall 2007. Additional regulatory visualizations are available through both the Web and the desktop versions of EcoCyc. At the bottom of most EcoCyc gene pages is a diagram of the TU containing that gene. Clicking on the promoter displays a page of detailed information about the regulation of the TU. Clicking on a TF-binding site in the TU displays the EcoCyc protein page for the TF. This page shows every TU that the TF controls. Protein pages for sigma factors show all TUs that the sigma factor controls. The EcoCyc project is beginning a new eﬀort to encode many additional types of regulation, including attenua- tion, translational regulation and regulation by small RNAs. Our goal is for EcoCyc to capture and compute with all known types of regulation in E. coli. The metabolic network of E. coli A recent collaboration between the Karp and Palsson groups compared the metabolic model within EcoCyc with the model developed by the Palsson group. The comparison resulted in updates to both models (16,17). The resulting metabolic network within EcoCyc consists of 1008 reactions of small-molecule metabolism. A total of 722 of those reactions are assigned to one of the 194 metabolic pathways deﬁned within EcoCyc; the remain- ing 286 reactions are not assigned to a pathway. Approximately 2 3 new metabolic pathways have been Figure 5. EcoCyc Regulatory Overview. Each dot represents one gene. Genes are arranged in three rings. Genes in the innermost ring have no known regulators, but they regulate at least one other gene. Genes in the middle ring are known to be regulated by other genes, and also regulate other genes. Genes in the outermost ring have known regulators, but are not known to regulate any other genes. An arrow from gene A to gene B means that A regulates the transcription of B. The diagram shows all regulatory arrows for genes involved in the MultiFun categories of iron acquisition (green) and drug resistance/ sensitivity (red). reported in the experimental literature per year for the past 5 years, indicating that our knowledge of the E. coli metabolic network is probably still incomplete. The 1008 reactions of E. coli’s small-molecule metabo- lism are catalyzed by 918 enzymes, of which 482 are monomers and 436 are multimers. A total of 354 of the multimers are homomultimers. The enzymes are formed from the products of 991 distinct genes (22% of the genome). One hundred and eighty ﬁve of the enzymes are multifunctional. Other properties of older versions of the metabolic network were discussed in (18). Our ability to connect metabolism to genes in E. coli is incomplete. EcoCyc lists 41 E. coli metabolic enzymes whose activities have been demonstrated biochemically and appear in the literature, but whose genes have yet to be deﬁnitively identiﬁed—although computational hypotheses regarding the identities of some have been published (19,20). These enzymes are listed at