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 : cpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 38: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2779 b3617 b0030 b3236 b2883 b1982 b2210 b1623 b4381 b4064 b4464 b0114 b0529 b2492 b0904 b2954 b0515 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.533203 (mmol/gDw/h)
  Minimum Production Rate : 1.020503 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.217454
  EX_nh4_e : 10.869384
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.534833
  EX_so4_e : 0.134271
  EX_k_e : 0.104077
  EX_fe2_e : 0.008564
  EX_mg2_e : 0.004626
  EX_ca2_e : 0.002775
  EX_cl_e : 0.002775
  EX_cu2_e : 0.000378
  EX_mn2_e : 0.000368
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 50.628698
  EX_co2_e : 24.287684
  EX_h_e : 10.791434
  EX_ac_e : 1.801817
  Auxiliary production reaction : 1.020503
  EX_alltn_e : 0.002082
  DM_mththf_c : 0.001724
  DM_5drib_c : 0.000358
  DM_4crsol_c : 0.000119

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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