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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b2297 b2458 b2779 b1238 b1982 b2797 b3117 b1814 b4471 b3449 b1623 b3665 b0675 b2361 b4381 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b0494 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.666220 (mmol/gDw/h)
  Minimum Production Rate : 0.282606 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.335114
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.327785
  EX_pi_e : 0.925246
  EX_so4_e : 0.167768
  EX_k_e : 0.130042
  EX_fe2_e : 0.010700
  EX_mg2_e : 0.005779
  EX_ca2_e : 0.003468
  EX_cl_e : 0.003468
  EX_cu2_e : 0.000472
  EX_mn2_e : 0.000460
  EX_zn2_e : 0.000227
  EX_ni2_e : 0.000215
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.755383
  EX_co2_e : 29.049206
  EX_h_e : 7.642025
  EX_ac_e : 0.387864
  Auxiliary production reaction : 0.282606
  EX_ade_e : 0.000448
  DM_mththf_c : 0.000298
  DM_5drib_c : 0.000150
  DM_4crsol_c : 0.000149

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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