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 : 2ombzl_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b0474 b2518 b2744 b3708 b3008 b0871 b2779 b2925 b2097 b1612 b1611 b4122 b2690 b2797 b3117 b1814 b4471 b0675 b2361 b0822 b2913 b4381 b2868 b1727 b0114 b1539 b2492 b0904 b1533 b3927 b3821 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.363973 (mmol/gDw/h)
  Minimum Production Rate : 0.022328 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 41.679747
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.968970
  EX_pi_e : 0.351090
  EX_so4_e : 0.091656
  EX_k_e : 0.071045
  EX_fe2_e : 0.005846
  EX_mg2_e : 0.003157
  EX_ca2_e : 0.001894
  EX_cl_e : 0.001894
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000252
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 53.128232
  EX_co2_e : 42.407249
  EX_h_e : 4.160565
  EX_fum_e : 0.389072
  Auxiliary production reaction : 0.022328
  EX_xan_e : 0.009524
  DM_5drib_c : 0.000082
  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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