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 (35 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b3617 b0160 b2883 b1623 b3665 b4374 b2361 b2291 b0411 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.481303 (mmol/gDw/h)
  Minimum Production Rate : 1.846104 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.194808
  EX_nh4_e : 10.736348
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.310372
  EX_so4_e : 0.121202
  EX_k_e : 0.093947
  EX_fe2_e : 0.007730
  EX_mg2_e : 0.004175
  EX_cl_e : 0.002505
  EX_ca2_e : 0.002505
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000333
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 46.008436
  EX_co2_e : 20.375816
  EX_h_e : 12.510209
  EX_ac_e : 2.549490
  Auxiliary production reaction : 1.846104
  DM_mththf_c : 0.000216
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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