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 : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3115 b1849 b2296 b3617 b1623 b3665 b0675 b2361 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483242 (mmol/gDw/h)
  Minimum Production Rate : 1.828249 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.240853
  EX_nh4_e : 10.703716
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.294387
  EX_so4_e : 0.121690
  EX_k_e : 0.094325
  EX_fe2_e : 0.007761
  EX_mg2_e : 0.004192
  EX_ca2_e : 0.002515
  EX_cl_e : 0.002515
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 46.002670
  EX_co2_e : 20.443852
  EX_h_e : 12.472076
  EX_ac_e : 2.547112
  Auxiliary production reaction : 1.828249
  DM_mththf_c : 0.000216
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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