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 : ap4a_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b4069 b2744 b3708 b3115 b1849 b2296 b0160 b1779 b1982 b2797 b3117 b1814 b4471 b2440 b4374 b0675 b2361 b2291 b0261 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.477809 (mmol/gDw/h)
  Minimum Production Rate : 0.101199 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.292989
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.172285
  EX_pi_e : 0.865694
  EX_so4_e : 0.120322
  EX_k_e : 0.093265
  EX_fe2_e : 0.007674
  EX_mg2_e : 0.004145
  EX_ca2_e : 0.002487
  EX_cl_e : 0.002487
  EX_cu2_e : 0.000339
  EX_mn2_e : 0.000330
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.156738
  EX_co2_e : 37.806753
  EX_h_e : 5.275665
  EX_ac_e : 0.278174
  Auxiliary production reaction : 0.101199
  DM_5drib_c : 0.000321
  DM_4crsol_c : 0.000107

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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