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 : nac_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b2242 b0474 b2518 b3831 b2744 b3752 b2930 b4232 b3697 b3925 b0871 b2779 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0907 b2690 b2210 b4374 b4161 b2361 b2291 b1415 b3945 b4138 b4123 b0621 b0114 b2492 b0904 b3028 b1813 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.352899 (mmol/gDw/h)
  Minimum Production Rate : 0.186382 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.594149
  EX_o2_e : 279.984783
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.125407
  EX_pi_e : 0.340408
  EX_so4_e : 0.088867
  EX_k_e : 0.068883
  EX_mg2_e : 0.003061
  EX_ca2_e : 0.001837
  EX_cl_e : 0.001837
  EX_cu2_e : 0.000250
  EX_mn2_e : 0.000244
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994332
  EX_h2o_e : 543.762206
  EX_co2_e : 27.905740
  EX_pyr_e : 4.920939
  EX_succ_e : 0.368000
  Auxiliary production reaction : 0.186382
  EX_ura_e : 0.063876
  EX_dxylnt_e : 0.000157
  DM_5drib_c : 0.000079
  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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