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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4382 b3942 b1732 b4069 b4384 b3708 b3752 b2297 b2458 b2925 b2097 b2926 b2407 b3236 b2690 b2797 b3117 b1814 b4471 b2210 b2440 b3945 b0114 b1539 b2492 b0904 b1533 b3927 b0515 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.397904 (mmol/gDw/h)
  Minimum Production Rate : 0.126546 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.036350
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.931132
  EX_pi_e : 0.383821
  EX_so4_e : 0.100200
  EX_k_e : 0.077668
  EX_fe2_e : 0.006391
  EX_mg2_e : 0.003452
  EX_cl_e : 0.002071
  EX_ca2_e : 0.002071
  EX_cu2_e : 0.000282
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 44.469743
  EX_co2_e : 32.568316
  EX_h_e : 9.206414
  EX_ac_e : 4.916511
  Auxiliary production reaction : 0.126546
  EX_alltn_e : 0.000268
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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