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 : alltn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b1478 b0238 b0125 b1241 b4069 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b0937 b0477 b4139 b4015 b0505 b3945 b1602 b2913 b4381 b3654 b3714 b3664 b4064 b4464 b0529 b2492 b0904 b2954 b1380 b1518 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.469254 (mmol/gDw/h)
  Minimum Production Rate : 0.012594 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.380007
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.118276
  EX_pi_e : 0.452645
  EX_so4_e : 0.118167
  EX_k_e : 0.091595
  EX_mg2_e : 0.004071
  EX_fe2_e : 0.003873
  EX_fe3_e : 0.003664
  EX_ca2_e : 0.002442
  EX_cl_e : 0.002442
  EX_cu2_e : 0.000333
  EX_mn2_e : 0.000324
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.822555
  EX_co2_e : 37.293773
  EX_h_e : 4.638923
  EX_12ppd__S_e : 0.949236
  EX_ac_e : 0.273193
  EX_alltn_e : 0.012594
  DM_mththf_c : 0.000210
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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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