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 : ps141_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b2242 b2744 b3614 b0910 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b4374 b0675 b2361 b2291 b4138 b4123 b0621 b3915 b0452 b0306 b3605 b2492 b0904 b2197 b3028 b3918 b4042 b1206 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.470621 (mmol/gDw/h)
  Minimum Production Rate : 0.248092 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.019183
  EX_o2_e : 275.960820
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.998241
  EX_pi_e : 0.702056
  EX_so4_e : 0.118513
  EX_k_e : 0.091862
  EX_mg2_e : 0.004083
  EX_cl_e : 0.002450
  EX_ca2_e : 0.002450
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992439
  EX_h2o_e : 545.022081
  EX_co2_e : 28.950045
  EX_succ_e : 0.490760
  EX_ura_e : 0.333740
  Auxiliary production reaction : 0.248092
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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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