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 (32 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3008 b3752 b3115 b1849 b2296 b2779 b2926 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b3709 b2406 b3161 b0112 b0114 b1539 b2492 b0904 b2947 b0591 b2578 b1533 b3927 b1473 b0494 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461177 (mmol/gDw/h)
  Minimum Production Rate : 0.291103 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.180368
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.564676
  EX_pi_e : 0.444854
  EX_so4_e : 0.116134
  EX_k_e : 0.090018
  EX_fe2_e : 0.007407
  EX_mg2_e : 0.004001
  EX_ca2_e : 0.002400
  EX_cl_e : 0.002400
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.824411
  EX_co2_e : 37.309730
  EX_h_e : 5.092416
  Auxiliary production reaction : 0.291103
  EX_ac_e : 0.268491
  DM_oxam_c : 0.001800
  DM_5drib_c : 0.001594
  DM_4crsol_c : 0.001387
  EX_glyc__R_e : 0.000642

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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