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 (66 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3831 b3614 b0910 b4152 b2781 b0030 b3844 b1612 b1611 b4122 b0651 b2162 b1759 b2440 b4138 b4123 b0621 b2913 b4381 b2406 b0452 b2197 b3918 b1912 b1206 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.623712 (mmol/gDw/h)
  Minimum Production Rate : 0.006262 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 993.548044
  EX_h_e : 985.621697
  EX_o2_e : 276.981162
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.950058
  EX_pi_e : 0.607898
  EX_so4_e : 0.157063
  EX_k_e : 0.121744
  EX_mg2_e : 0.005411
  EX_cl_e : 0.003246
  EX_ca2_e : 0.003246
  EX_cu2_e : 0.000442
  EX_mn2_e : 0.000431
  EX_zn2_e : 0.000213
  EX_ni2_e : 0.000201
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 993.538026
  EX_h2o_e : 545.308484
  EX_co2_e : 29.169464
  EX_succ_e : 0.650402
  EX_ura_e : 0.442304
  EX_etha_e : 0.323149
  Auxiliary production reaction : 0.006262
  DM_5drib_c : 0.000140
  DM_4crsol_c : 0.000139

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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