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 : ind3eth_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (170 of 187: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: YPL061W YBR208C YML035C YNL270C YEL063C YOR348C YKL192C YNL141W YPL265W YKR039W YOL020W YOR120W YLL043W YDR272W YPL262W YBR263W YLR231C YHL016C YJL121C YLR164W YDR178W YBR176W YDL085W YMR145C YML120C YKL184W   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.154380 (mmol/gDw/h)
  Minimum Production Rate : 0.267085 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_nh4_e : 1.192970
  EX_pi_e : 0.057050
  EX_o2_e : 0.017142
  EX_so4_e : 0.011934

Product: (mmol/gDw/h)
  EX_co2_e : 16.833077
  EX_etoh_e : 16.082181
  EX_h2o_e : 4.465705
  EX_h_e : 1.804017
  EX_2hb_e : 0.573645
  EX_ind3eth_e : 0.267085
  EX_succ_e : 0.075670
  EX_nadp_e : 0.008843

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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