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__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b2836 b3553 b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b2925 b2097 b2926 b1004 b3713 b1109 b0046 b2690 b0593 b1982 b2797 b3117 b1814 b4471 b2210 b2265 b1033 b2440 b4374 b0675 b2361 b2291 b0261 b0822 b1602 b0112 b1727 b0114 b0509 b3125 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359677 (mmol/gDw/h)
  Minimum Production Rate : 0.152358 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.017090
  EX_o2_e : 281.828845
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.951386
  EX_pi_e : 0.804020
  EX_so4_e : 0.090574
  EX_k_e : 0.070206
  EX_mg2_e : 0.003120
  EX_ca2_e : 0.001872
  EX_cl_e : 0.001872
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000249
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994223
  EX_h2o_e : 544.759572
  EX_co2_e : 32.216428
  EX_ac_e : 4.909686
  Auxiliary production reaction : 0.152358
  DM_oxam_c : 0.000402
  DM_5drib_c : 0.000241
  DM_4crsol_c : 0.000080

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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