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 (20 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b4069 b2744 b3708 b3008 b3115 b1849 b2296 b0160 b1982 b2797 b3117 b1814 b4471 b2440 b4374 b0675 b2361 b2291 b0261 b0507 b3709 b3161 b0112 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b0494 b0594 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.713537 (mmol/gDw/h)
  Minimum Production Rate : 0.450398 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.145523
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.609724
  EX_pi_e : 0.688282
  EX_so4_e : 0.179683
  EX_k_e : 0.139277
  EX_fe2_e : 0.011460
  EX_mg2_e : 0.006190
  EX_ca2_e : 0.003714
  EX_cl_e : 0.003714
  EX_cu2_e : 0.000506
  EX_mn2_e : 0.000493
  EX_zn2_e : 0.000243
  EX_ni2_e : 0.000230
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.349651
  EX_co2_e : 24.892387
  EX_h_e : 7.880032
  Auxiliary production reaction : 0.450398
  EX_ac_e : 0.415411
  DM_oxam_c : 0.002786
  DM_5drib_c : 0.002466
  DM_4crsol_c : 0.002146
  EX_glyclt_e : 0.001987

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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