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 : 2ombzl_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2407 b3616 b3589 b2406 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.531084 (mmol/gDw/h)
  Minimum Production Rate : 0.254631 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.581687
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.735666
  EX_pi_e : 0.512287
  EX_so4_e : 0.133738
  EX_k_e : 0.103664
  EX_fe2_e : 0.008530
  EX_mg2_e : 0.004607
  EX_ca2_e : 0.002764
  EX_cl_e : 0.002764
  EX_cu2_e : 0.000377
  EX_mn2_e : 0.000367
  EX_zn2_e : 0.000181
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 40.741841
  EX_co2_e : 23.916436
  EX_h_e : 5.401321
  EX_ac_e : 0.521506
  DM_mththf_c : 0.254869
  Auxiliary production reaction : 0.254631
  DM_5drib_c : 0.000119
  DM_4crsol_c : 0.000118

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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