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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2407 b1982 b2797 b3117 b1814 b4471 b3665 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b2835 b0494 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.749079 (mmol/gDw/h)
  Minimum Production Rate : 0.231468 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.642054
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.018385
  EX_pi_e : 0.954034
  EX_so4_e : 0.188633
  EX_k_e : 0.146215
  EX_fe2_e : 0.012031
  EX_mg2_e : 0.006498
  EX_ca2_e : 0.003899
  EX_cl_e : 0.003899
  EX_cu2_e : 0.000531
  EX_mn2_e : 0.000518
  EX_zn2_e : 0.000255
  EX_ni2_e : 0.000242
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 47.877240
  EX_co2_e : 25.544940
  EX_h_e : 8.506192
  EX_ac_e : 0.694961
  Auxiliary production reaction : 0.231468
  EX_ade_e : 0.000504
  DM_mththf_c : 0.000336
  DM_5drib_c : 0.000169
  DM_4crsol_c : 0.000167

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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