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 : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (103 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b2836 b4382 b3942 b1732 b1241 b0351 b4069 b4384 b3708 b1479 b3752 b3115 b1849 b2296 b2779 b2407 b3236 b2463 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b4267 b1415 b3551 b1014 b3945 b4219 b1832 b1778 b2406 b0112 b2868 b0114 b2366 b2492 b0904 b1533 b1380 b0325 b1710 b2480 b0508 b4266 b3662 b1518 b1813 b0221 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359109 (mmol/gDw/h)
  Minimum Production Rate : 0.537535 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.582140
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.567226
  EX_pi_e : 1.421469
  EX_so4_e : 0.090431
  EX_k_e : 0.070095
  EX_mg2_e : 0.003115
  EX_fe2_e : 0.002964
  EX_fe3_e : 0.002804
  EX_ca2_e : 0.001869
  EX_cl_e : 0.001869
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 50.745426
  EX_co2_e : 33.735856
  EX_h_e : 6.280930
  EX_ac_e : 1.364440
  Auxiliary production reaction : 0.537535
  EX_glyald_e : 0.063911
  EX_ade_e : 0.000242
  EX_dxylnt_e : 0.000240
  DM_mththf_c : 0.000161
  DM_5drib_c : 0.000081
  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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