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 : pan4p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b2836 b2242 b0474 b2518 b3831 b1278 b3752 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b4161 b1415 b4014 b2976 b4138 b4123 b0621 b4381 b2406 b2492 b0904 b2197 b3028 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.532600 (mmol/gDw/h)
  Minimum Production Rate : 0.250619 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.480568
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.008656
  EX_pi_e : 0.764368
  EX_so4_e : 0.384738
  EX_k_e : 0.103960
  EX_fe2_e : 0.008554
  EX_mg2_e : 0.004620
  EX_ca2_e : 0.002772
  EX_cl_e : 0.002772
  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 : 49.411517
  EX_co2_e : 31.650080
  EX_h_e : 6.759907
  EX_succ_e : 0.555391
  EX_ura_e : 0.377692
  Auxiliary production reaction : 0.250619
  DM_5drib_c : 0.000120
  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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