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 : 2dr1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 40: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2926 b2407 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b4381 b2406 b0114 b2366 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.416555 (mmol/gDw/h)
  Minimum Production Rate : 0.623431 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.172425
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.745622
  EX_pi_e : 1.025243
  EX_so4_e : 0.104897
  EX_k_e : 0.081309
  EX_fe2_e : 0.006690
  EX_mg2_e : 0.003614
  EX_ca2_e : 0.002168
  EX_cl_e : 0.002168
  EX_cu2_e : 0.000295
  EX_mn2_e : 0.000288
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 49.490302
  EX_co2_e : 34.749647
  EX_h_e : 6.033521
  EX_ac_e : 0.959184
  Auxiliary production reaction : 0.623431
  EX_thym_e : 0.623431
  DM_5drib_c : 0.000094
  DM_4crsol_c : 0.000093

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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