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 : eig3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b4384 b2744 b3115 b1849 b2296 b3617 b0030 b2883 b1982 b1623 b4374 b2361 b2291 b0261 b0411 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.561440 (mmol/gDw/h)
  Minimum Production Rate : 2.151971 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.277850
  EX_nh4_e : 10.367451
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.693540
  EX_so4_e : 0.141382
  EX_k_e : 0.109589
  EX_fe2_e : 0.009017
  EX_mg2_e : 0.004870
  EX_ca2_e : 0.002922
  EX_cl_e : 0.002922
  EX_cu2_e : 0.000398
  EX_mn2_e : 0.000388
  EX_zn2_e : 0.000191
  EX_ni2_e : 0.000181
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.986060
  EX_co2_e : 22.400115
  EX_h_e : 10.283809
  Auxiliary production reaction : 2.151971
  EX_ac_e : 0.821128
  DM_5drib_c : 0.000377
  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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