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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (88 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b1478 b3399 b1241 b4069 b2502 b2744 b3708 b3008 b0910 b3115 b1849 b2296 b2925 b2097 b2926 b1238 b2690 b1982 b2797 b3117 b1814 b4471 b3449 b0675 b2361 b0261 b0822 b0507 b3709 b4381 b2406 b3161 b0112 b0452 b2975 b0114 b3603 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b0594   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.597981 (mmol/gDw/h)
  Minimum Production Rate : 0.379882 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.112804
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.218577
  EX_pi_e : 0.576816
  EX_so4_e : 0.150584
  EX_k_e : 0.116722
  EX_fe2_e : 0.009604
  EX_mg2_e : 0.005187
  EX_ca2_e : 0.003112
  EX_cl_e : 0.003112
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 49.409400
  EX_co2_e : 30.577978
  EX_h_e : 6.603727
  Auxiliary production reaction : 0.379882
  EX_ac_e : 0.348136
  DM_oxam_c : 0.000669
  DM_5drib_c : 0.000401
  DM_4crsol_c : 0.000133

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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