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 : ipdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b3399 b4069 b2744 b3708 b3926 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1779 b2797 b3117 b1814 b4471 b2440 b1602 b4381 b0114 b1539 b2492 b0904 b1533 b1380 b2660 b1771 b1511 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459347 (mmol/gDw/h)
  Minimum Production Rate : 0.347741 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.402638
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.193583
  EX_pi_e : 1.138572
  EX_so4_e : 0.115673
  EX_k_e : 0.089661
  EX_fe3_e : 0.007378
  EX_mg2_e : 0.003985
  EX_cl_e : 0.002391
  EX_ca2_e : 0.002391
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.499142
  EX_co2_e : 36.483192
  EX_h_e : 5.341789
  EX_fum_e : 0.480695
  Auxiliary production reaction : 0.347741
  EX_ac_e : 0.267426
  EX_gly_e : 0.232669
  DM_mththf_c : 0.000206
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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