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 (81 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 69
  Gene deletion: b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b3073 b2744 b3708 b3008 b1479 b0871 b2297 b2458 b2925 b2097 b2926 b1238 b3124 b3236 b2690 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b0596 b1623 b3665 b0675 b2361 b1748 b1014 b0261 b2799 b3945 b1907 b4381 b2406 b0112 b2789 b3127 b4265 b2975 b0114 b3603 b0306 b1539 b3605 b2492 b0904 b2578 b1533 b2835 b1380 b0508 b1473 b0514 b4266 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.301437 (mmol/gDw/h)
  Minimum Production Rate : 0.016502 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.681084
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.726684
  EX_so4_e : 0.415435
  EX_pi_e : 0.340273
  EX_k_e : 0.058838
  EX_fe2_e : 0.004841
  EX_mg2_e : 0.002615
  EX_ca2_e : 0.001569
  EX_cl_e : 0.001569
  EX_cu2_e : 0.000214
  EX_mn2_e : 0.000208
  EX_zn2_e : 0.000103
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 42.183486
  EX_co2_e : 27.987892
  EX_h_e : 7.754109
  EX_pyr_e : 5.256017
  EX_acald_e : 0.905743
  EX_met__L_e : 0.323026
  EX_etha_e : 0.030965
  Auxiliary production reaction : 0.016502
  EX_ade_e : 0.000337
  DM_5drib_c : 0.000202
  EX_dxylnt_e : 0.000202
  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.

---

Last updated: 09-Jul-2025
Contact