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 : nac_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4382 b0474 b2518 b3831 b0910 b4152 b0871 b2297 b2458 b2925 b2097 b2926 b0030 b3236 b1612 b1611 b4122 b0651 b2162 b3946 b0825 b1493 b3517 b0726 b4138 b4123 b0621 b0114 b0529 b1206 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.636791 (mmol/gDw/h)
  Minimum Production Rate : 0.045045 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.653962
  EX_o2_e : 277.230108
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.735402
  EX_pi_e : 0.614252
  EX_so4_e : 0.160357
  EX_k_e : 0.124297
  EX_mg2_e : 0.005524
  EX_ca2_e : 0.003314
  EX_cl_e : 0.003314
  EX_cu2_e : 0.000451
  EX_mn2_e : 0.000440
  EX_zn2_e : 0.000217
  EX_ni2_e : 0.000206
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989772
  EX_h2o_e : 546.418585
  EX_co2_e : 26.685871
  EX_for_e : 1.882750
  EX_succ_e : 0.664041
  EX_ura_e : 0.406534
  EX_ac_e : 0.370731
  Auxiliary production reaction : 0.045045
  DM_5drib_c : 0.000143
  DM_4crsol_c : 0.000142

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, in press.
[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: 21-Sep-2023
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