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 : gdpofuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b4384 b2744 b3708 b2297 b2458 b0030 b1238 b1004 b3713 b1109 b0046 b3236 b2883 b1982 b2797 b3117 b1814 b4471 b1033 b1623 b0261 b0411 b1602 b2913 b4381 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3821 b1380 b3437 b4268 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.470825 (mmol/gDw/h)
  Minimum Production Rate : 0.199440 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.527948
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.082072
  EX_pi_e : 0.853041
  EX_so4_e : 0.118563
  EX_k_e : 0.091902
  EX_fe2_e : 0.007562
  EX_mg2_e : 0.004084
  EX_ca2_e : 0.002451
  EX_cl_e : 0.002451
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.359276
  EX_co2_e : 36.934483
  EX_h_e : 5.198558
  EX_ac_e : 0.274108
  Auxiliary production reaction : 0.199440
  DM_5drib_c : 0.000316
  DM_4crsol_c : 0.000105

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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