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 : dgmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b2744 b2297 b2458 b2779 b3617 b3236 b0907 b3962 b4267 b1415 b3945 b4381 b2868 b0114 b0529 b2492 b0904 b1380 b0325 b0508 b4266 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.404098 (mmol/gDw/h)
  Minimum Production Rate : 0.509608 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.217887
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.954561
  EX_pi_e : 0.899404
  EX_so4_e : 0.101760
  EX_k_e : 0.078877
  EX_fe2_e : 0.006490
  EX_mg2_e : 0.003506
  EX_ca2_e : 0.002103
  EX_cl_e : 0.002103
  EX_cu2_e : 0.000287
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.655985
  EX_co2_e : 34.774409
  EX_h_e : 8.047762
  EX_ac_e : 1.744231
  Auxiliary production reaction : 0.509608
  EX_xan_e : 0.010574
  EX_mththf_e : 0.000181
  EX_dxylnt_e : 0.000180
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000090

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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