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 : fum_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (6 of 8: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b3942 b1732 b4069 b0871 b2297 b2458 b2779 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b2690 b2463 b2210 b3551 b2799 b3945 b1602 b4138 b4123 b0621 b4219 b1832 b1778 b4381 b1727 b0114 b2492 b0904 b1380 b1710 b2480 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.362188 (mmol/gDw/h)
  Minimum Production Rate : 0.697402 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.820829
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.911596
  EX_pi_e : 0.349368
  EX_so4_e : 0.091206
  EX_k_e : 0.070697
  EX_fe2_e : 0.005817
  EX_mg2_e : 0.003142
  EX_ca2_e : 0.001885
  EX_cl_e : 0.001885
  EX_cu2_e : 0.000257
  EX_mn2_e : 0.000250
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_h2o_e : 43.260760
  EX_co2_e : 27.491106
  EX_h_e : 9.744064
  EX_pyr_e : 4.810475
  EX_fum_e : 0.697402
  EX_ac_e : 0.210861
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000081

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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