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 : mmcoa__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b3617 b2407 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0411 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3821 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504101 (mmol/gDw/h)
  Minimum Production Rate : 0.503272 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.058145
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.967152
  EX_pi_e : 1.996075
  EX_so4_e : 0.630215
  EX_k_e : 0.098397
  EX_fe2_e : 0.008096
  EX_mg2_e : 0.004373
  EX_ca2_e : 0.002624
  EX_cl_e : 0.002624
  EX_cu2_e : 0.000357
  EX_mn2_e : 0.000348
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.266168
  EX_co2_e : 21.385543
  EX_h_e : 9.315218
  EX_ac_e : 2.670249
  Auxiliary production reaction : 0.503272
  DM_mththf_c : 0.000226
  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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