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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b4069 b4384 b2297 b2458 b2779 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b0261 b3945 b1602 b2913 b4381 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b0515 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459039 (mmol/gDw/h)
  Minimum Production Rate : 0.159036 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.887816
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.595265
  EX_fe3_e : 1.934455
  EX_pi_e : 0.760863
  EX_so4_e : 0.115595
  EX_k_e : 0.089601
  EX_mg2_e : 0.003982
  EX_ca2_e : 0.002389
  EX_cl_e : 0.002389
  EX_cu2_e : 0.000325
  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 : 52.098413
  EX_co2_e : 39.032183
  EX_h_e : 6.898181
  EX_fe2_e : 1.927082
  EX_ac_e : 0.267246
  Auxiliary production reaction : 0.159036
  EX_ade_e : 0.000309
  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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