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 (71 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4382 b1241 b0351 b3831 b4384 b3614 b0910 b3752 b4152 b3115 b1849 b2296 b2779 b2925 b2097 b2781 b3617 b1612 b1611 b4122 b1759 b3962 b3946 b0825 b4267 b4015 b0411 b2799 b4388 b4138 b4123 b0621 b0529 b1539 b2197 b3918 b1912 b0508 b4266 b1206 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.434162 (mmol/gDw/h)
  Minimum Production Rate : 0.229301 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.010055
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.533985
  EX_pi_e : 0.877397
  EX_so4_e : 0.109331
  EX_k_e : 0.084745
  EX_fe2_e : 0.006973
  EX_mg2_e : 0.003766
  EX_ca2_e : 0.002260
  EX_cl_e : 0.002260
  EX_cu2_e : 0.000308
  EX_mn2_e : 0.000300
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 43.179935
  EX_co2_e : 28.117643
  EX_h_e : 8.628375
  EX_glyc__R_e : 1.802849
  EX_ac_e : 1.315019
  EX_succ_e : 0.452741
  Auxiliary production reaction : 0.229301
  EX_ura_e : 0.078585
  DM_5drib_c : 0.000098
  DM_4crsol_c : 0.000097

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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