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__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3553 b1478 b4382 b3942 b1732 b0238 b0125 b1241 b0351 b4069 b4384 b3752 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b0937 b1982 b0477 b1033 b3551 b0261 b2799 b3945 b1602 b0507 b4219 b1832 b1778 b2406 b2868 b4064 b4464 b0755 b3612 b0529 b2492 b0904 b1380 b1710 b2480 b3662 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.332055 (mmol/gDw/h)
  Minimum Production Rate : 0.406896 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.388332
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.354213
  EX_pi_e : 1.540991
  EX_so4_e : 0.083618
  EX_k_e : 0.064815
  EX_fe2_e : 0.005333
  EX_mg2_e : 0.002881
  EX_cl_e : 0.001728
  EX_ca2_e : 0.001728
  EX_cu2_e : 0.000235
  EX_mn2_e : 0.000229
  EX_zn2_e : 0.000113
  EX_ni2_e : 0.000107

Product: (mmol/gDw/h)
  EX_h2o_e : 52.366018
  EX_co2_e : 33.390413
  EX_h_e : 7.648028
  EX_ac_e : 1.642719
  Auxiliary production reaction : 0.406896
  EX_xan_e : 0.229479
  EX_ade_e : 0.000372
  DM_5drib_c : 0.000223
  DM_4crsol_c : 0.000074

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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