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 : xtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b3617 b2407 b3236 b2388 b1982 b0394 b2210 b4381 b2406 b0114 b0529 b2492 b0904 b0515 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.561188 (mmol/gDw/h)
  Minimum Production Rate : 1.074065 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.444355
  EX_nh4_e : 10.365806
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.763520
  EX_so4_e : 0.141318
  EX_k_e : 0.109540
  EX_fe2_e : 0.009013
  EX_mg2_e : 0.004868
  EX_ca2_e : 0.002921
  EX_cl_e : 0.002921
  EX_cu2_e : 0.000398
  EX_mn2_e : 0.000388
  EX_zn2_e : 0.000191
  EX_ni2_e : 0.000181
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.210904
  EX_co2_e : 22.413300
  EX_h_e : 9.209700
  EX_ac_e : 1.896387
  Auxiliary production reaction : 1.074065
  EX_alltn_e : 0.002191
  DM_mththf_c : 0.001814
  DM_5drib_c : 0.000377
  DM_4crsol_c : 0.000125

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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