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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3553 b1241 b0351 b3831 b4069 b4384 b3708 b0910 b3752 b2297 b2458 b2926 b3617 b2407 b1238 b3962 b1982 b2143 b0477 b4139 b0104 b2797 b3117 b1814 b4471 b4267 b1033 b2440 b0596 b3665 b1415 b1014 b0261 b2799 b3945 b0507 b4381 b2406 b0112 b0452 b0114 b1539 b2492 b0904 b2954 b1533 b1380 b4266 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.319534 (mmol/gDw/h)
  Minimum Production Rate : 0.343426 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.045289
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.752318
  EX_so4_e : 0.693048
  EX_pi_e : 0.308224
  EX_k_e : 0.062371
  EX_fe3_e : 0.005132
  EX_mg2_e : 0.002772
  EX_ca2_e : 0.001663
  EX_cl_e : 0.001663
  EX_cu2_e : 0.000227
  EX_mn2_e : 0.000221
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_h2o_e : 47.842369
  EX_co2_e : 35.430784
  EX_h_e : 5.322075
  EX_ac_e : 2.304670
  EX_met__L_e : 0.612583
  EX_trp__L_e : 0.343426
  EX_ade_e : 0.000358
  DM_5drib_c : 0.000214
  EX_dxylnt_e : 0.000214
  EX_etha_e : 0.000158
  DM_4crsol_c : 0.000071

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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