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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b3553 b1478 b3399 b1241 b0351 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b2779 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b1623 b0261 b0411 b2799 b3945 b1602 b0507 b2913 b2223 b4381 b3915 b0529 b2492 b0904 b1380 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.325214 (mmol/gDw/h)
  Minimum Production Rate : 0.438518 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.469582
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.322358
  EX_pi_e : 1.629259
  EX_so4_e : 0.081895
  EX_k_e : 0.063480
  EX_fe3_e : 0.005223
  EX_mg2_e : 0.002821
  EX_cl_e : 0.001693
  EX_ca2_e : 0.001693
  EX_cu2_e : 0.000231
  EX_mn2_e : 0.000225
  EX_zn2_e : 0.000111
  EX_ni2_e : 0.000105

Product: (mmol/gDw/h)
  EX_h2o_e : 53.197324
  EX_co2_e : 33.298525
  EX_h_e : 7.096815
  EX_ac_e : 1.608877
  Auxiliary production reaction : 0.438518
  EX_xan_e : 0.176237
  EX_hxan_e : 0.008873
  DM_5drib_c : 0.000218
  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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