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 (55 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b4069 b4384 b2744 b3708 b0910 b2297 b2458 b2926 b0160 b1982 b2797 b3117 b1814 b4471 b2440 b3665 b0675 b2361 b4381 b2406 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.666625 (mmol/gDw/h)
  Minimum Production Rate : 0.265335 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.446678
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.263078
  EX_pi_e : 0.908365
  EX_so4_e : 0.167870
  EX_k_e : 0.130121
  EX_fe2_e : 0.010707
  EX_mg2_e : 0.005783
  EX_cl_e : 0.003470
  EX_ca2_e : 0.003470
  EX_cu2_e : 0.000473
  EX_mn2_e : 0.000461
  EX_zn2_e : 0.000227
  EX_ni2_e : 0.000215
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.731710
  EX_co2_e : 29.204812
  EX_h_e : 7.576901
  EX_ac_e : 0.388100
  Auxiliary production reaction : 0.265335
  EX_ade_e : 0.000449
  DM_mththf_c : 0.000299
  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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