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 : nadhx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b3617 b0030 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b0507 b4381 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b3825 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.496598 (mmol/gDw/h)
  Minimum Production Rate : 0.743006 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.036123
  EX_nh4_e : 10.564814
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.965033
  EX_so4_e : 0.125053
  EX_k_e : 0.096933
  EX_fe2_e : 0.007976
  EX_mg2_e : 0.004308
  EX_ca2_e : 0.002585
  EX_cl_e : 0.002585
  EX_cu2_e : 0.000352
  EX_mn2_e : 0.000343
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 47.469478
  EX_co2_e : 20.237472
  EX_h_e : 10.166139
  EX_ac_e : 1.886724
  Auxiliary production reaction : 0.743006
  DM_oxam_c : 0.000556
  DM_5drib_c : 0.000333
  EX_glyclt_e : 0.000332
  DM_4crsol_c : 0.000111

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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