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 : aconm_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (92 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b1478 b3399 b1241 b0351 b2502 b2744 b0871 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b0937 b1982 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b2913 b0529 b1539 b2492 b0904 b3927 b1380 b0606 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442515 (mmol/gDw/h)
  Minimum Production Rate : 0.012858 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.108476
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.844902
  EX_pi_e : 0.426853
  EX_so4_e : 0.111434
  EX_k_e : 0.086376
  EX_fe2_e : 0.007107
  EX_mg2_e : 0.003839
  EX_ca2_e : 0.002303
  EX_cl_e : 0.002303
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.638143
  EX_co2_e : 32.782416
  EX_h_e : 8.606795
  EX_glyclt_e : 4.449297
  EX_ade_e : 0.013156
  Auxiliary production reaction : 0.012858
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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