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 : 5aprbu_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b4384 b3752 b0871 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b0477 b4139 b1033 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b2913 b4381 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b1695 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.450551 (mmol/gDw/h)
  Minimum Production Rate : 0.245230 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.871779
  EX_o2_e : 287.879802
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.847053
  EX_pi_e : 0.679386
  EX_so4_e : 0.113459
  EX_k_e : 0.087944
  EX_mg2_e : 0.003909
  EX_ca2_e : 0.002345
  EX_cl_e : 0.002345
  EX_cu2_e : 0.000319
  EX_mn2_e : 0.000311
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992762
  EX_h2o_e : 552.209344
  EX_co2_e : 38.668384
  EX_etoh_e : 0.316010
  Auxiliary production reaction : 0.244782
  EX_hxan_e : 0.000504
  DM_5drib_c : 0.000302
  DM_4crsol_c : 0.000100

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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