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 : hdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b2242 b2744 b3614 b0910 b0963 b2781 b3617 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b3616 b3589 b4374 b0675 b4014 b2976 b1701 b1805 b4138 b4123 b0621 b4381 b2406 b2197 b3028 b3918 b4042 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.526379 (mmol/gDw/h)
  Minimum Production Rate : 0.278004 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.032595
  EX_o2_e : 278.020687
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.431407
  EX_pi_e : 0.507748
  EX_so4_e : 0.132553
  EX_k_e : 0.102745
  EX_mg2_e : 0.004566
  EX_cl_e : 0.002740
  EX_ca2_e : 0.002740
  EX_cu2_e : 0.000373
  EX_mn2_e : 0.000364
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991546
  EX_h2o_e : 546.569050
  EX_co2_e : 30.257762
  EX_succ_e : 0.548904
  EX_ura_e : 0.373280
  Auxiliary production reaction : 0.278004
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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