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 : nadphx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b4382 b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2925 b2097 b2407 b0583 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b0261 b0507 b2406 b0112 b0114 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b3825 b1380 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.553054 (mmol/gDw/h)
  Minimum Production Rate : 0.233246 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.437898
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.613466
  EX_pi_e : 1.236297
  EX_so4_e : 0.139270
  EX_k_e : 0.107952
  EX_fe2_e : 0.008883
  EX_mg2_e : 0.004798
  EX_ca2_e : 0.002879
  EX_cl_e : 0.002879
  EX_cu2_e : 0.000392
  EX_mn2_e : 0.000382
  EX_zn2_e : 0.000189
  EX_ni2_e : 0.000179
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.322965
  EX_co2_e : 28.031642
  EX_h_e : 8.427196
  EX_ac_e : 2.172912
  Auxiliary production reaction : 0.234272
  DM_oxam_c : 0.000619
  DM_5drib_c : 0.000371
  DM_4crsol_c : 0.000123

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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