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 : damp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4467 b4069 b4384 b3752 b2297 b2458 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b1602 b2913 b4381 b1727 b0114 b0529 b2492 b0904 b1380 b1511 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.466840 (mmol/gDw/h)
  Minimum Production Rate : 0.161791 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.034768
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.850792
  EX_pi_e : 0.612108
  EX_so4_e : 0.117560
  EX_k_e : 0.091124
  EX_fe2_e : 0.007498
  EX_mg2_e : 0.004050
  EX_ca2_e : 0.002430
  EX_cl_e : 0.002430
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.976891
  EX_co2_e : 37.199528
  EX_h_e : 5.370259
  EX_12ppd__R_e : 0.492095
  EX_ac_e : 0.271788
  Auxiliary production reaction : 0.161791
  DM_mththf_c : 0.000209
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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