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 : eig3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4069 b4384 b3708 b3008 b3115 b1849 b2296 b0030 b2407 b1238 b3124 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2406 b0112 b0114 b0886 b0755 b3612 b0529 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b3821 b0514 b0515 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.458027 (mmol/gDw/h)
  Minimum Production Rate : 0.578230 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.486395
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.112816
  EX_pi_e : 1.023873
  EX_so4_e : 0.115340
  EX_k_e : 0.089404
  EX_fe2_e : 0.007356
  EX_mg2_e : 0.003973
  EX_ca2_e : 0.002384
  EX_cl_e : 0.002384
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000316
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.180469
  EX_co2_e : 37.171370
  EX_h_e : 5.641355
  Auxiliary production reaction : 0.582057
  EX_ac_e : 0.266657
  EX_alltn_e : 0.000513
  DM_5drib_c : 0.000307
  DM_4crsol_c : 0.000102

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 (2023).
[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: 09-Jul-2025
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