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 (69 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b2836 b1478 b3399 b1241 b4069 b2744 b3708 b2297 b2458 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b0121 b1982 b4139 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b2913 b3915 b2975 b3603 b1539 b2492 b0904 b2954 b1298 b1533 b3029 b1380 b4141 b1798 b0221 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.475081 (mmol/gDw/h)
  Minimum Production Rate : 0.073697 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.015173
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.648672
  EX_pi_e : 0.679057
  EX_so4_e : 0.193233
  EX_k_e : 0.092733
  EX_fe3_e : 0.007632
  EX_mg2_e : 0.004121
  EX_ca2_e : 0.002473
  EX_cl_e : 0.002473
  EX_cu2_e : 0.000337
  EX_mn2_e : 0.000328
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.122306
  EX_co2_e : 38.103290
  EX_h_e : 4.946499
  EX_ac_e : 0.350183
  Auxiliary production reaction : 0.073597
  EX_ade_e : 0.000532
  DM_5drib_c : 0.000319
  DM_4crsol_c : 0.000106

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.

Last updated: 09-Jul-2025
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