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 : sheme_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 21: See next) for growth-coupled production (at least stoichioemetrically feasible)
Gene deletion size : 21
Gene deletion: YOL086C YDL168W YGL256W YBR145W YFL053W YML070W YOR374W YER073W YAL060W YKR039W YMR189W YDR300C YMR250W YDL171C YNL268W YLR348C YKL085W YKL141W YMR118C YDL085W YMR145C (List of alternative genes)
Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
Growth Rate : 0.155518 (mmol/gDw/h)
Minimum Production Rate : 0.010857 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
EX_glc__D_e : 10.000000
EX_o2_e : 2.000000
EX_nh4_e : 0.913775
EX_pi_e : 0.030746
EX_so4_e : 0.012022
EX_fe2_e : 0.010857

Product: (mmol/gDw/h)
EX_h_e : 23.059416
EX_h2o_e : 11.364496
EX_succ_e : 9.388948
EX_acald_e : 4.549018
EX_ac_e : 3.347228
EX_ibutoh_e : 0.151528
Auxiliary production reaction : 0.010857

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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