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 : dgmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2066 b1241 b0351 b4069 b4384 b3752 b3115 b1849 b2296 b2925 b2097 b2926 b3617 b2407 b2690 b2498 b0675 b0822 b2868 b1727 b0114 b0529 b2492 b0904 b4042 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.562741 (mmol/gDw/h)
  Minimum Production Rate : 0.719237 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.711435
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.675630
  EX_pi_e : 1.262060
  EX_so4_e : 0.141709
  EX_k_e : 0.109843
  EX_fe2_e : 0.009038
  EX_mg2_e : 0.004882
  EX_ca2_e : 0.002929
  EX_cl_e : 0.002929
  EX_cu2_e : 0.000399
  EX_mn2_e : 0.000389
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.608354
  EX_co2_e : 26.113297
  EX_h_e : 10.565392
  EX_ac_e : 1.796628
  Auxiliary production reaction : 0.719237
  EX_ade_e : 0.000379
  DM_mththf_c : 0.000252
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000125

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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