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1. #THERMODYNAMICS CALCULATOR GENERATOR#
2. #THERMODYNAMICS CALCULATOR CODE#
3. #THERMODYNAMICS CALCULATOR FREE#

necator H16 (denoted i CN1361), which is directly constructed from the BioCyc database to improve the readability and reusability of the model. We present a genome-scale metabolic model (GSM) of C. Understanding the complex metabolic behaviour of this bacterium is a prerequisite for the design of successful engineering strategies for optimising product yields. In this regard Cupriavidus necator H16 represents a particularly promising microbial chassis due to its ability to grow on a wide range of low-cost feedstocks, including the waste gas carbon dioxide, whilst also naturally producing large quantities of polyhydroxybutyrate (PHB) during nutrient-limited conditions. Therefore, iJL1426 will lead to a better understanding of the metabolic capabilities and, thus, is helpful in a systematic metabolic engineering approach.Įxploiting biological processes to recycle renewable carbon into high value platform chemicals provides a sustainable and greener alternative to current reliance on petrochemicals. The experimental results showed that the highest erythromycin titer was 1442.8 μg/mL at an n-propanol supplementation rate of 0.05 g/L/h, which was 45.0% higher than that without n-propanol supplementation, and the erythromycin-specific synthesis rate was also increased by 30.3%. Finally, iJL1426 was used to guide the optimal addition strategy of n-propanol during industrial erythromycin fermentation to demonstrate its ability. Furthermore, by comparing the single knockout targets with earlier published results, four genes coincided within the range of successful knockouts. Moreover, the simulation results were consistent with the physiological observation and 13 C metabolic flux analysis obtained from the experimental data. The accurate rates of the growth predictions for the 27 carbon and 31 nitrogen sources available were 92.6% and 100%, respectively. The final model included 1426 genes, 1858 reactions, and 1687 metabolites. To develop an accurate model-driven strategy for the efficient production of erythromycin, a genome-scale metabolic model (iJL1426) was reconstructed for the industrial strain. However, little is known about the regulation in terms of its metabolism. Saccharopolyspora erythraea is considered to be an effective host for erythromycin. These proof-of-principle demonstrations may ultimately find their way to the manufacture of diverse chemicals from ethanol and other simple carbon compounds. We illustrated how the ATP generating module can power cell-free biochemical pathways by converting mevalonate into isoprenol at a titer of 12.5 ± 0.8 mM and a maximum productivity of 1.0 ± 0.05 mM/h.

#THERMODYNAMICS CALCULATOR GENERATOR#

Our ATP generator reached titers of 27 ± 6 mM ATP and 59 ± 15 mM acetone with maximum ATP synthesis rate of 2.8 ± 0.6 mM/h and acetone of 7.8 ± 0.8 mM/h. The ATP generator produces acetone as a value-added side product.

#THERMODYNAMICS CALCULATOR FREE#

Here we show how ethanol can be converted with a cell free system into acetyl-CoA, a central precursor for myriad biochemicals, and how we can use the energy stored in ethanol to generate ATP, another key molecule important for powering biochemical pathways. Carbon-negative ethanol might therefore provide a feedstock for building a wider range of sustainable chemicals. Here we describe the database characteristics and implementation and demonstrate its use.Įthanol is a widely available carbon compound that can be increasingly produced with a net negative carbon balance.

#THERMODYNAMICS CALCULATOR CODE#

The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standardįormats.

() enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metaboliteĬoncentrations. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemicalĬompounds and reactions with a simple and powerful online search and calculation interface. ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. However, thermodynamic data on biochemical compoundsĬan be difficult to find and is cumbersome to perform calculations with manually. The laws of thermodynamics constrain the action of biochemical systems.