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 : glyc__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3708 b3752 b3115 b1849 b2296 b3617 b1238 b3124 b2883 b1982 b2797 b3117 b1814 b4471 b2440 b1623 b0261 b4381 b2406 b0112 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b0494 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.525552 (mmol/gDw/h)
  Minimum Production Rate : 0.393339 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.926860
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.462831
  EX_pi_e : 0.506951
  EX_so4_e : 0.132345
  EX_k_e : 0.102584
  EX_fe2_e : 0.008441
  EX_mg2_e : 0.004559
  EX_ca2_e : 0.002735
  EX_cl_e : 0.002735
  EX_cu2_e : 0.000373
  EX_mn2_e : 0.000363
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 40.055307
  EX_co2_e : 22.244127
  EX_h_e : 8.792875
  EX_ac_e : 1.996727
  DM_oxam_c : 0.786914
  DM_5drib_c : 0.786678
  DM_4crsol_c : 0.786443
  EX_glyc__R_e : 0.393339

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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