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 : adpglc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3399 b0474 b2518 b1241 b0351 b2502 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0512 b0871 b2926 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3946 b0825 b0675 b2361 b0261 b4381 b2406 b0653 b4077 b2663 b0114 b2366 b0529 b2492 b0904 b3653 b1533 b3927 b3825 b2413 b0494 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.354648 (mmol/gDw/h)
  Minimum Production Rate : 0.072125 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.108485
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.229497
  EX_pi_e : 0.486345
  EX_so4_e : 0.089307
  EX_k_e : 0.069225
  EX_fe2_e : 0.005696
  EX_mg2_e : 0.003077
  EX_ca2_e : 0.001846
  EX_cl_e : 0.001846
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 43.817558
  EX_co2_e : 27.937290
  EX_h_e : 8.951244
  EX_pyr_e : 5.437517
  Auxiliary production reaction : 0.072125
  EX_alltn_e : 0.009677
  DM_5drib_c : 0.000238
  DM_4crsol_c : 0.000079

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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