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 (58 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b2502 b2744 b3115 b1849 b2296 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b0675 b2361 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b2975 b3603 b0529 b2492 b0904 b1380 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.328710 (mmol/gDw/h)
  Minimum Production Rate : 0.508384 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.803705
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.153569
  EX_pi_e : 1.842227
  EX_so4_e : 0.082776
  EX_k_e : 0.064162
  EX_fe2_e : 0.005279
  EX_mg2_e : 0.002852
  EX_ca2_e : 0.001711
  EX_cl_e : 0.001711
  EX_cu2_e : 0.000233
  EX_mn2_e : 0.000227
  EX_zn2_e : 0.000112
  EX_ni2_e : 0.000106

Product: (mmol/gDw/h)
  EX_h2o_e : 52.149551
  EX_co2_e : 33.211869
  EX_h_e : 6.894314
  EX_ac_e : 1.287234
  Auxiliary production reaction : 0.508384
  EX_ade_e : 0.008969
  DM_5drib_c : 0.000221
  DM_4crsol_c : 0.000073

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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