MetNetComp

MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iMM904 [2].
Target metabolite : pendp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 52: See next) for growth-coupled production (at least stoichioemetrically feasible)
Gene deletion size : 25
Gene deletion: YHR104W YOL086C YDL168W YMR303C YGL256W YBR145W YBR068C YDR046C YBR069C YGR087C YLR044C YLR134W YDR148C YCL025C YKR039W YIL053W YER062C YBR263W YDR300C YMR250W YNL104C YLR348C YCL064C YKL218C YKL184W (List of alternative genes)
Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
Growth Rate : 0.163270 (mmol/gDw/h)
Minimum Production Rate : 0.001919 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
EX_glc__D_e : 10.000000
EX_nh4_e : 9.692010
EX_o2_e : 2.000000
EX_pi_e : 0.036117
EX_so4_e : 0.012621

Product: (mmol/gDw/h)
EX_h_e : 22.406204
EX_h2o_e : 16.715865
EX_ala__L_e : 8.778274
EX_succ_e : 6.404278
EX_2mbtoh_e : 0.426363
Auxiliary production reaction : 0.001919

Visualization
1. Download JSON file.
2. Go to Escher site [3].
3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
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