A step to more realistic benchmark data was made in 2003 [ 28], generating simulated gene expression data using equations based on enzyme kinetics (for use of these data in method evaluations, see e.g. [ 8, 29]).
Other common types of sensors are based on enzyme reactions.
More importantly for enzyme discovery, EC assignments can facilitate word searches based on enzyme function.
FunnyBase links annotated genes to enzymes in KEGG pathways based on enzyme commission (EC) numbers.
to reverse engineer models directly from those data; the other approach is based on combining enzyme kinetic data to build mechanistic biochemical network models.
Based on data from enzyme assay and gene deletions, it appears that pforA is the gene encoding the primary PFOR enzyme in T. saccharolyticum, which is different from the gene cluster, pforB, as suggested by Shaw et al. [ 9].
It is up to the user to determine what organisms the genes should be sourced from based on limited enzyme kinetic data, which genetic system to use to regulate expression, and which organism to use as an appropriate host.
The 51 subfamilies (numbered GH5_1 to GH5_53 as explained elsewhere) have been categorized based on available enzyme activity data, to aid their individual descriptions, below.
Gene ontology (GO) terms describing the molecular function, biological process and subcellular compartment (11) and Enzyme Commission (EC) numbers (8) are assigned to each enzyme based on experimental data reported in the literature.
Calculations based on manufacturer-provided data on enzyme activity suggest that 0.1 U/ml AChE can hydrolyze a single application of 10 μM ACh within approximately 5.7 seconds, yet this was obviously a coarse estimation, not taking into account our specific experimental conditions.
