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 : pgp181_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 69: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1054 b2836 b2242 b0474 b2518 b3831 b3752 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b4161 b1415 b4138 b4123 b0621 b4381 b2406 b2197 b3028 b3918 b0789 b1249 b0494 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.443249 (mmol/gDw/h)
  Minimum Production Rate : 0.234100 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.879361
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.415715
  EX_pi_e : 0.895761
  EX_so4_e : 0.111619
  EX_k_e : 0.086519
  EX_fe2_e : 0.007119
  EX_mg2_e : 0.003845
  EX_ca2_e : 0.002307
  EX_cl_e : 0.002307
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 43.777618
  EX_co2_e : 28.868262
  EX_h_e : 5.391746
  EX_succ_e : 0.462217
  EX_ura_e : 0.314329
  Auxiliary production reaction : 0.234100
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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