MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b4382 b4069 b2744 b3708 b3008 b2297 b2458 b0160 b3844 b3236 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b0153 b4381 b2406 b0452 b0114 b0886 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b0516 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.711492 (mmol/gDw/h)
  Minimum Production Rate : 0.423982 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.552774
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.609673
  EX_pi_e : 0.686310
  EX_so4_e : 0.179168
  EX_k_e : 0.138878
  EX_fe2_e : 0.011427
  EX_mg2_e : 0.006172
  EX_ca2_e : 0.003703
  EX_cl_e : 0.003703
  EX_cu2_e : 0.000504
  EX_mn2_e : 0.000492
  EX_zn2_e : 0.000243
  EX_ni2_e : 0.000230
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.541318
  EX_co2_e : 25.225024
  EX_h_e : 7.877313
  EX_trp__L_e : 0.423982
  EX_ac_e : 0.414221
  EX_alltn_e : 0.019413
  DM_5drib_c : 0.000477
  DM_4crsol_c : 0.000159

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.

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Last updated: 21-Sep-2023
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