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 (49 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b4069 b4384 b3752 b3115 b1849 b2296 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.446504 (mmol/gDw/h)
  Minimum Production Rate : 0.208964 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.304183
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.287454
  EX_pi_e : 1.057593
  EX_so4_e : 0.112439
  EX_k_e : 0.087154
  EX_fe3_e : 0.007171
  EX_mg2_e : 0.003873
  EX_ca2_e : 0.002324
  EX_cl_e : 0.002324
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.706899
  EX_co2_e : 36.743982
  EX_h_e : 5.417097
  EX_ac_e : 0.259948
  Auxiliary production reaction : 0.208964
  EX_etoh_e : 0.008718
  EX_ade_e : 0.000500
  DM_5drib_c : 0.000300
  DM_4crsol_c : 0.000100

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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