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 : dtdp4addg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 107: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b3831 b1278 b3614 b0910 b3752 b4152 b2779 b2925 b2097 b2781 b1851 b1612 b1611 b4122 b1759 b1200 b2342 b3845 b4138 b4123 b0621 b2913 b4381 b2406 b3918 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.610298 (mmol/gDw/h)
  Minimum Production Rate : 0.044772 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.056116
  EX_o2_e : 276.931350
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.316485
  EX_pi_e : 0.678241
  EX_so4_e : 0.153685
  EX_k_e : 0.119126
  EX_mg2_e : 0.005294
  EX_ca2_e : 0.003177
  EX_cl_e : 0.003177
  EX_cu2_e : 0.000433
  EX_mn2_e : 0.000422
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.897680
  EX_h2o_e : 547.928722
  EX_co2_e : 28.099226
  EX_succ_e : 0.636414
  EX_ura_e : 0.110466
  EX_pheme_e : 0.092518
  Auxiliary production reaction : 0.044772
  DM_mththf_c : 0.000273
  DM_5drib_c : 0.000137
  DM_4crsol_c : 0.000136

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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