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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b3399 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2925 b2097 b3617 b0030 b1004 b3713 b1109 b0046 b2883 b1982 b3946 b2210 b0825 b1623 b0261 b1602 b4381 b2406 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.366092 (mmol/gDw/h)
  Minimum Production Rate : 1.384054 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.382432
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.105927
  EX_pi_e : 3.121243
  EX_so4_e : 0.092189
  EX_k_e : 0.071459
  EX_fe2_e : 0.005880
  EX_mg2_e : 0.003176
  EX_cl_e : 0.001906
  EX_ca2_e : 0.001906
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 49.903556
  EX_co2_e : 27.779586
  EX_h_e : 8.500263
  EX_ac_e : 2.368108
  Auxiliary production reaction : 1.384054
  DM_5drib_c : 0.000246
  EX_glyclt_e : 0.000245
  DM_4crsol_c : 0.000082

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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