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 (78 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b3399 b4382 b1241 b4069 b2502 b2744 b3708 b3008 b0512 b0871 b2297 b2458 b2779 b2925 b2097 b2690 b1982 b2797 b3117 b1814 b4471 b3449 b1033 b0675 b2361 b0261 b0822 b4381 b2406 b0112 b0452 b0114 b0509 b3125 b0529 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b1912   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.576087 (mmol/gDw/h)
  Minimum Production Rate : 0.227562 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.280049
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.877498
  EX_pi_e : 1.238382
  EX_so4_e : 0.145070
  EX_k_e : 0.112448
  EX_fe2_e : 0.009253
  EX_mg2_e : 0.004998
  EX_ca2_e : 0.002999
  EX_cl_e : 0.002999
  EX_cu2_e : 0.000408
  EX_mn2_e : 0.000398
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.557037
  EX_co2_e : 26.104091
  EX_h_e : 8.408206
  EX_pyr_e : 1.578815
  EX_ac_e : 0.335390
  Auxiliary production reaction : 0.227562
  EX_alltn_e : 0.015719
  DM_5drib_c : 0.000387
  DM_4crsol_c : 0.000128

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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