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 : pgp160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3831 b1278 b3614 b0910 b3752 b4152 b2925 b2097 b2781 b1612 b1611 b4122 b1779 b2690 b1759 b3945 b4138 b4123 b0621 b4381 b2406 b2197 b3825 b3918 b0494 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.384573 (mmol/gDw/h)
  Minimum Production Rate : 0.203110 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.544114
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.698793
  EX_pi_e : 0.777182
  EX_so4_e : 0.096843
  EX_k_e : 0.075066
  EX_fe2_e : 0.006177
  EX_mg2_e : 0.003336
  EX_ca2_e : 0.002002
  EX_cl_e : 0.002002
  EX_cu2_e : 0.000273
  EX_mn2_e : 0.000266
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 46.331326
  EX_co2_e : 33.801862
  EX_h_e : 4.677997
  EX_succ_e : 0.401030
  EX_ura_e : 0.272719
  Auxiliary production reaction : 0.203110
  DM_5drib_c : 0.000087
  DM_4crsol_c : 0.000086

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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