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 : glyc_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b2066 b1241 b0351 b4069 b4384 b3926 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b2498 b3945 b1602 b2913 b3915 b0529 b1539 b2492 b0904 b1380 b1518 b0606 b0221 b2285 b1008 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.463289 (mmol/gDw/h)
  Minimum Production Rate : 0.322424 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.465952
  EX_o2_e : 284.923120
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.003485
  EX_pi_e : 0.446892
  EX_so4_e : 0.116665
  EX_k_e : 0.090431
  EX_mg2_e : 0.004019
  EX_cl_e : 0.002411
  EX_ca2_e : 0.002411
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992559
  EX_h2o_e : 547.982904
  EX_co2_e : 37.208692
  EX_etoh_e : 1.133831
  EX_glyc_e : 0.322424
  EX_ac_e : 0.269721
  DM_mththf_c : 0.000208
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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