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 (77 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 60
  Gene deletion: b3553 b4382 b3942 b1732 b0586 b1241 b0351 b4069 b4384 b1278 b3708 b1479 b2297 b2458 b2926 b3617 b0030 b2407 b3844 b3236 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b4267 b1033 b0675 b1415 b3551 b1014 b4014 b0261 b2976 b0822 b0507 b3709 b4219 b1832 b1778 b2406 b3161 b0112 b3915 b0452 b4265 b0114 b1539 b2492 b0904 b1533 b1380 b0325 b1710 b2480 b1473 b4266 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.300401 (mmol/gDw/h)
  Minimum Production Rate : 0.316577 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.092598
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.725901
  EX_pi_e : 1.239497
  EX_so4_e : 0.657453
  EX_k_e : 0.058636
  EX_fe3_e : 0.004826
  EX_mg2_e : 0.002606
  EX_cl_e : 0.001564
  EX_ca2_e : 0.001564
  EX_cu2_e : 0.000213
  EX_mn2_e : 0.000208
  EX_zn2_e : 0.000102
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 49.506972
  EX_co2_e : 34.713978
  EX_h_e : 5.623504
  EX_ac_e : 2.173105
  Auxiliary production reaction : 0.316576
  EX_met__L_e : 0.265229
  DM_oxam_c : 0.000336
  DM_5drib_c : 0.000202
  EX_dxylnt_e : 0.000201
  DM_4crsol_c : 0.000067

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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