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 : mmcoa__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b0871 b2925 b2097 b3617 b0030 b2407 b2690 b2388 b1982 b0394 b2797 b3117 b1814 b4471 b0261 b3945 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.597977 (mmol/gDw/h)
  Minimum Production Rate : 0.026613 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.388152
  EX_o2_e : 274.117170
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.645064
  EX_pi_e : 0.656652
  EX_so4_e : 0.177196
  EX_k_e : 0.116721
  EX_mg2_e : 0.005187
  EX_ca2_e : 0.003112
  EX_cl_e : 0.003112
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990396
  EX_h2o_e : 543.630374
  EX_co2_e : 27.284039
  EX_acald_e : 3.751873
  Auxiliary production reaction : 0.026613
  DM_oxam_c : 0.000669
  DM_5drib_c : 0.000401
  DM_4crsol_c : 0.000133

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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