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_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3942 b1732 b3846 b1241 b0351 b3073 b1479 b2779 b2925 b2097 b3236 b2690 b2463 b3962 b0104 b3616 b3589 b2210 b4267 b0675 b1415 b3551 b1014 b0822 b0726 b4388 b4138 b4123 b0621 b4219 b1832 b1778 b1727 b0114 b0509 b3125 b2492 b0904 b1380 b0325 b1710 b2480 b4042 b4266 b1813 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.440396 (mmol/gDw/h)
  Minimum Production Rate : 0.077408 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 40.749540
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.756241
  EX_pi_e : 0.424809
  EX_so4_e : 0.110901
  EX_k_e : 0.085962
  EX_mg2_e : 0.003820
  EX_fe2_e : 0.003635
  EX_fe3_e : 0.003439
  EX_ca2_e : 0.002292
  EX_cl_e : 0.002292
  EX_cu2_e : 0.000312
  EX_mn2_e : 0.000304
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.317991
  EX_co2_e : 41.612659
  EX_h_e : 4.205084
  EX_mal__L_e : 0.077408
  EX_dxylnt_e : 0.000295
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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