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 : udpLa4n_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3916 b3831 b3614 b0910 b3752 b4152 b2781 b1851 b1612 b1611 b4122 b1759 b3946 b0825 b4138 b4123 b0621 b4381 b2406 b1723 b2835 b3918 b1912 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.686167 (mmol/gDw/h)
  Minimum Production Rate : 0.362396 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.004746
  EX_o2_e : 273.024143
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.746131
  EX_pi_e : 1.386673
  EX_so4_e : 0.172791
  EX_k_e : 0.133935
  EX_mg2_e : 0.005953
  EX_cl_e : 0.003572
  EX_ca2_e : 0.003572
  EX_cu2_e : 0.000486
  EX_mn2_e : 0.000474
  EX_zn2_e : 0.000234
  EX_ni2_e : 0.000222
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988979
  EX_h2o_e : 546.478284
  EX_co2_e : 23.403537
  EX_succ_e : 0.715530
  Auxiliary production reaction : 0.362396
  EX_ura_e : 0.124198
  DM_5drib_c : 0.000154
  DM_4crsol_c : 0.000153

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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