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 : ckdo_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b0474 b2518 b4069 b2744 b4152 b2297 b2458 b2926 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b2406 b0114 b0529 b2492 b0904 b3821 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.582027 (mmol/gDw/h)
  Minimum Production Rate : 0.307394 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.192172
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.418719
  EX_pi_e : 0.868821
  EX_so4_e : 0.146566
  EX_k_e : 0.113608
  EX_fe2_e : 0.009348
  EX_mg2_e : 0.005049
  EX_ca2_e : 0.003029
  EX_cl_e : 0.003029
  EX_cu2_e : 0.000413
  EX_mn2_e : 0.000402
  EX_zn2_e : 0.000198
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.935287
  EX_co2_e : 27.357951
  EX_h_e : 8.033488
  EX_succ_e : 0.606933
  EX_ac_e : 0.338848
  Auxiliary production reaction : 0.307394
  EX_ura_e : 0.105349
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130

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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