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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 66
  Gene deletion: b3553 b4269 b0493 b3588 b0586 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b1479 b3752 b0871 b2407 b1238 b3236 b0120 b3962 b1982 b1525 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b3449 b4267 b1033 b0675 b1415 b1014 b4014 b0261 b2976 b0822 b2342 b3845 b4388 b1907 b4381 b2406 b0112 b1745 b0114 b0886 b0509 b3125 b2366 b0755 b3612 b2492 b0904 b2578 b1533 b1380 b1912 b0325 b1473 b0494 b4266 b3662 b2842   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.397286 (mmol/gDw/h)
  Minimum Production Rate : 0.088879 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.101799
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.258701
  EX_pi_e : 0.649861
  EX_so4_e : 0.534373
  EX_k_e : 0.077547
  EX_fe2_e : 0.006381
  EX_mg2_e : 0.003446
  EX_ca2_e : 0.002068
  EX_cl_e : 0.002068
  EX_cu2_e : 0.000282
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 50.465451
  EX_co2_e : 37.504859
  EX_h_e : 3.572764
  EX_acald_e : 1.206905
  EX_met__L_e : 0.345450
  Auxiliary production reaction : 0.088879
  DM_oxam_c : 0.000445
  DM_5drib_c : 0.000267
  EX_dxylnt_e : 0.000266
  DM_4crsol_c : 0.000089

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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