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 : his__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2926 b3617 b2883 b1982 b1623 b3665 b0675 b2361 b4388 b4381 b0112 b4064 b4464 b0114 b0529 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.500436 (mmol/gDw/h)
  Minimum Production Rate : 1.892625 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.868029
  EX_nh4_e : 11.084219
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.482723
  EX_so4_e : 0.126020
  EX_k_e : 0.097682
  EX_fe2_e : 0.008037
  EX_mg2_e : 0.004341
  EX_cl_e : 0.002605
  EX_ca2_e : 0.002605
  EX_cu2_e : 0.000355
  EX_mn2_e : 0.000346
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 49.616735
  EX_co2_e : 25.042502
  EX_h_e : 11.806942
  Auxiliary production reaction : 1.892625
  EX_ac_e : 1.529184
  EX_ade_e : 0.000337
  DM_mththf_c : 0.000224
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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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