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 (38 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b3617 b2797 b3117 b1814 b4471 b1623 b3665 b4374 b0675 b2361 b2291 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b3821 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504102 (mmol/gDw/h)
  Minimum Production Rate : 0.503273 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.058077
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.967167
  EX_pi_e : 1.996078
  EX_so4_e : 0.630216
  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 : 45.266143
  EX_co2_e : 21.385477
  EX_h_e : 9.315234
  EX_ac_e : 2.670254
  Auxiliary production reaction : 0.503273
  EX_mththf_e : 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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