Abstract Systems analysis of metabolic and growth functions in microbial organisms is
rapidly developing and maturing. Such studies are enabled by reconstruction, at the …

Geochemical cycling and industrial pollution have made toxic metal ions a pervasive
environmental pressure throughout the world. Biofilm formation is a strategy that …

Network reconstructions are a common denominator in systems biology. Bottom–up
metabolic network reconstructions have been developed over the last 10 years. These …

Absolute metabolite concentrations are critical to a quantitative understanding of cellular
metabolism, as concentrations impact both the free energies and rates of metabolic …

Abstract EcoCyc (http://EcoCyc. org) is a model organism database built on the genome
sequence of Escherichia coli K-12 MG1655. Expert manual curation of the functions of …

Due to the rapid release of new data from genome sequencing projects, the majority of
protein sequences in public databases have not been experimentally characterized; rather …

Pathway Tools is a production-quality software environment for creating a type of model-
organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc …

Aminoglycoside antibiotics, such as gentamicin and kanamycin, directly target the ribosome,
yet the mechanisms by which these bactericidal drugs induce cell death are not fully …

With advances in sequencing technology, uncharacterized proteins and domains of
unknown function (DUFs) are rapidly accumulating in sequence databases and offer an …

Central carbon metabolism uses a complex series of enzymatic steps to convert sugars into
metabolic precursors. These precursors are then used to generate the entire biomass of the …