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 : malcoame_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b2297 b2458 b3617 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3449 b0261 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.586572 (mmol/gDw/h)
  Minimum Production Rate : 0.292541 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.202198
  EX_o2_e : 272.166366
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.382715
  EX_pi_e : 1.443434
  EX_so4_e : 0.440252
  EX_k_e : 0.114495
  EX_mg2_e : 0.005089
  EX_ca2_e : 0.003053
  EX_cl_e : 0.003053
  EX_cu2_e : 0.000416
  EX_mn2_e : 0.000405
  EX_zn2_e : 0.000200
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990579
  EX_h2o_e : 545.195274
  EX_co2_e : 23.566879
  EX_ac_e : 2.521101
  Auxiliary production reaction : 0.292541
  DM_5drib_c : 0.000394
  DM_4crsol_c : 0.000131

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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