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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (10 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b2406 b0112 b2868 b0114 b1539 b2492 b0904 b1533 b3821 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.522553 (mmol/gDw/h)
  Minimum Production Rate : 0.521226 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.432385
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.295037
  EX_pi_e : 1.546510
  EX_so4_e : 0.652815
  EX_k_e : 0.101999
  EX_fe2_e : 0.008393
  EX_mg2_e : 0.004533
  EX_ca2_e : 0.002720
  EX_cl_e : 0.002720
  EX_cu2_e : 0.000370
  EX_mn2_e : 0.000361
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.254509
  EX_co2_e : 22.067405
  EX_h_e : 9.135203
  EX_ac_e : 2.767173
  Auxiliary production reaction : 0.521226
  EX_ade_e : 0.000585
  DM_5drib_c : 0.000351
  DM_4crsol_c : 0.000117

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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