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 (80 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b2836 b3831 b1278 b3614 b0910 b3752 b3926 b4152 b2297 b2458 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b1602 b4138 b4123 b0621 b4381 b2406 b0755 b3612 b2492 b0904 b1380 b3918 b2660 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.437739 (mmol/gDw/h)
  Minimum Production Rate : 0.231190 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.285100
  EX_o2_e : 285.793707
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.421119
  EX_pi_e : 0.653436
  EX_so4_e : 0.110232
  EX_k_e : 0.085444
  EX_mg2_e : 0.003797
  EX_ca2_e : 0.002278
  EX_cl_e : 0.002278
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000302
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992969
  EX_h2o_e : 550.363339
  EX_co2_e : 36.038994
  EX_succ_e : 0.456471
  Auxiliary production reaction : 0.231190
  EX_3hpp_e : 0.079232
  DM_5drib_c : 0.000098
  DM_4crsol_c : 0.000098

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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