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 (80 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b2242 b3553 b3831 b3614 b0910 b3752 b2297 b2458 b0963 b2781 b3617 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b3616 b3589 b2210 b1033 b1852 b4138 b4123 b0621 b4381 b2406 b2492 b0904 b2197 b3028 b3918 b1912 b1695 b1206 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386509 (mmol/gDw/h)
  Minimum Production Rate : 0.407113 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 987.787362
  EX_o2_e : 269.725347
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.721935
  EX_pi_e : 0.372829
  EX_so4_e : 0.097331
  EX_k_e : 0.075444
  EX_mg2_e : 0.003353
  EX_ca2_e : 0.002012
  EX_cl_e : 0.002012
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993792
  EX_h2o_e : 536.433387
  EX_co2_e : 21.123383
  EX_succ_e : 3.737296
  Auxiliary production reaction : 0.407113
  EX_ura_e : 0.273834
  EX_ac_e : 0.225020
  EX_hxa_e : 0.000635
  DM_5drib_c : 0.000087
  DM_4crsol_c : 0.000086

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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