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 : uacmamu_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b1478 b1241 b0351 b3831 b3614 b0910 b4152 b0871 b2297 b2458 b2779 b2925 b2097 b2781 b3617 b0030 b1612 b1611 b4122 b0651 b2162 b1779 b2690 b1759 b0675 b4015 b0411 b0822 b0614 b4138 b4123 b0621 b4381 b0452 b0529 b2197 b3918 b0789 b1249 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.429309 (mmol/gDw/h)
  Minimum Production Rate : 0.226668 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.349258
  EX_o2_e : 280.496819
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.472050
  EX_pi_e : 0.867449
  EX_so4_e : 0.108108
  EX_k_e : 0.083798
  EX_mg2_e : 0.003724
  EX_ca2_e : 0.002235
  EX_cl_e : 0.002235
  EX_cu2_e : 0.000304
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993105
  EX_h2o_e : 545.871227
  EX_co2_e : 30.033796
  EX_succ_e : 1.395136
  EX_ac_e : 1.300031
  Auxiliary production reaction : 0.226668
  EX_ura_e : 0.077775
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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