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 : nadph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b3553 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b1033 b0596 b0261 b4381 b2406 b0112 b0114 b0509 b3125 b1539 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492342 (mmol/gDw/h)
  Minimum Production Rate : 0.736618 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.370323
  EX_nh4_e : 10.474127
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.684769
  EX_so4_e : 0.123982
  EX_k_e : 0.096102
  EX_fe2_e : 0.007908
  EX_mg2_e : 0.004271
  EX_ca2_e : 0.002563
  EX_cl_e : 0.002563
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.050030
  EX_co2_e : 20.578566
  EX_h_e : 10.078967
  EX_ac_e : 1.870613
  Auxiliary production reaction : 0.736618
  DM_oxam_c : 0.000551
  DM_5drib_c : 0.000330
  EX_glyclt_e : 0.000329
  DM_4crsol_c : 0.000110

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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