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 : nadh_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b4381 b3915 b0529 b2492 b0904 b1380 b2660 b0606 b0221 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390095 (mmol/gDw/h)
  Minimum Production Rate : 0.401573 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.075857
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.077222
  EX_pi_e : 1.179435
  EX_so4_e : 0.098234
  EX_k_e : 0.076144
  EX_fe3_e : 0.006265
  EX_mg2_e : 0.003384
  EX_ca2_e : 0.002030
  EX_cl_e : 0.002030
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 53.315532
  EX_co2_e : 34.879437
  EX_h_e : 5.962616
  Auxiliary production reaction : 0.401573
  EX_ac_e : 0.310919
  EX_ade_e : 0.010644
  DM_5drib_c : 0.000262
  DM_4crsol_c : 0.000087

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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