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 (36 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b0474 b2518 b4069 b4384 b3708 b3008 b2297 b2458 b2779 b2925 b2097 b0030 b2407 b1238 b2690 b1982 b2797 b3117 b1814 b4471 b3449 b0261 b3945 b4381 b2406 b0452 b2868 b0114 b2366 b2492 b0904 b0591 b2578 b1533 b3927 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.376567 (mmol/gDw/h)
  Minimum Production Rate : 0.239223 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.020925
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.547021
  EX_pi_e : 0.363239
  EX_so4_e : 0.094827
  EX_k_e : 0.073503
  EX_fe2_e : 0.006048
  EX_mg2_e : 0.003267
  EX_ca2_e : 0.001960
  EX_cl_e : 0.001960
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 39.499308
  EX_co2_e : 27.637643
  EX_h_e : 8.770461
  EX_glyc__R_e : 4.611052
  EX_trp__L_e : 0.239223
  EX_ac_e : 0.219232
  EX_hxan_e : 0.000421
  DM_5drib_c : 0.000253
  DM_4crsol_c : 0.000084

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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