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 : mal__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b3942 b1732 b1241 b0351 b1479 b0871 b2925 b2097 b3844 b3236 b1779 b2463 b3962 b0104 b3616 b3589 b3946 b2210 b0825 b4267 b1033 b0675 b1415 b3551 b1014 b0822 b2913 b4219 b1832 b1778 b0114 b2492 b0904 b1380 b0325 b1710 b2480 b4266 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.407535 (mmol/gDw/h)
  Minimum Production Rate : 0.070014 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 42.191604
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.401343
  EX_pi_e : 0.393111
  EX_so4_e : 0.102625
  EX_k_e : 0.079548
  EX_fe2_e : 0.006545
  EX_mg2_e : 0.003535
  EX_ca2_e : 0.002121
  EX_cl_e : 0.002121
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 53.823027
  EX_co2_e : 42.991142
  EX_h_e : 3.884895
  Auxiliary production reaction : 0.070014
  EX_dxylnt_e : 0.000273
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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