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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b3399 b4069 b2744 b2297 b2458 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b0937 b1982 b4139 b0675 b2361 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b2954 b3029 b1380 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445830 (mmol/gDw/h)
  Minimum Production Rate : 0.177779 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.936607
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.108288
  EX_pi_e : 0.785608
  EX_so4_e : 0.112269
  EX_k_e : 0.087023
  EX_mg2_e : 0.003868
  EX_fe2_e : 0.003679
  EX_fe3_e : 0.003481
  EX_ca2_e : 0.002321
  EX_cl_e : 0.002321
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.878776
  EX_co2_e : 37.325114
  EX_h_e : 5.131691
  EX_ac_e : 0.259556
  Auxiliary production reaction : 0.177779
  EX_gly_e : 0.048909
  EX_glyclt_e : 0.012164
  DM_5drib_c : 0.000299
  DM_4crsol_c : 0.000099

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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