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 (49 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2407 b3124 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b2440 b0261 b2406 b0112 b2789 b3127 b0452 b2975 b0114 b3603 b2366 b2492 b0904 b3035 b1533 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492339 (mmol/gDw/h)
  Minimum Production Rate : 0.736613 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.370387
  EX_nh4_e : 10.474099
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.684751
  EX_so4_e : 0.123981
  EX_k_e : 0.096101
  EX_fe2_e : 0.007907
  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 : 49.050101
  EX_co2_e : 20.578820
  EX_h_e : 10.078863
  EX_ac_e : 1.870890
  Auxiliary production reaction : 0.736613
  DM_oxam_c : 0.000551
  DM_5drib_c : 0.000330
  DM_4crsol_c : 0.000110
  EX_etha_e : 0.000040

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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