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 (74 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2836 b3553 b1241 b0351 b3403 b3926 b2930 b4232 b3697 b3925 b0871 b1850 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b2690 b4139 b1033 b1493 b3517 b3945 b1602 b0507 b2913 b4381 b1297 b2492 b0904 b3029 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.456968 (mmol/gDw/h)
  Minimum Production Rate : 0.722325 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.718763
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.935221
  EX_pi_e : 0.440795
  EX_so4_e : 0.115074
  EX_k_e : 0.089197
  EX_fe2_e : 0.007339
  EX_mg2_e : 0.003964
  EX_ca2_e : 0.002379
  EX_cl_e : 0.002379
  EX_cu2_e : 0.000324
  EX_mn2_e : 0.000316
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.396989
  EX_co2_e : 39.058172
  EX_h_e : 4.198809
  EX_glyc_e : 0.728457
  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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