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 : pgp120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 67: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b3831 b2744 b3614 b0910 b3752 b4152 b2779 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b2361 b2291 b0411 b4138 b4123 b0621 b3915 b2197 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462104 (mmol/gDw/h)
  Minimum Production Rate : 0.243650 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.371071
  EX_o2_e : 277.549281
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.646088
  EX_pi_e : 0.933048
  EX_so4_e : 0.116367
  EX_k_e : 0.090200
  EX_mg2_e : 0.004009
  EX_ca2_e : 0.002405
  EX_cl_e : 0.002405
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992578
  EX_h2o_e : 545.535449
  EX_co2_e : 30.484933
  EX_succ_e : 0.481879
  EX_ura_e : 0.327700
  Auxiliary production reaction : 0.243650
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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