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 : prlp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b4069 b4384 b2744 b3708 b3008 b0910 b3115 b1849 b2296 b2926 b0030 b2883 b1982 b2797 b3117 b1814 b4471 b1623 b0261 b4381 b2406 b0452 b4064 b4464 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b2835 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.463537 (mmol/gDw/h)
  Minimum Production Rate : 0.183103 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.155087
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.921674
  EX_pi_e : 0.813336
  EX_so4_e : 0.116728
  EX_k_e : 0.090479
  EX_fe2_e : 0.007445
  EX_mg2_e : 0.004021
  EX_ca2_e : 0.002413
  EX_cl_e : 0.002413
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.307698
  EX_co2_e : 37.686630
  EX_h_e : 5.444542
  EX_ac_e : 0.269865
  Auxiliary production reaction : 0.183103
  DM_5drib_c : 0.000311
  DM_4crsol_c : 0.000103

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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