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 : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2407 b2797 b3117 b1814 b4471 b3665 b4381 b2406 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b3927 b3662 b1518 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.731481 (mmol/gDw/h)
  Minimum Production Rate : 0.466084 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.297685
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.298188
  EX_pi_e : 1.171675
  EX_so4_e : 0.184202
  EX_k_e : 0.142780
  EX_mg2_e : 0.006346
  EX_fe2_e : 0.006037
  EX_fe3_e : 0.005711
  EX_ca2_e : 0.003807
  EX_cl_e : 0.003807
  EX_cu2_e : 0.000519
  EX_mn2_e : 0.000505
  EX_zn2_e : 0.000249
  EX_ni2_e : 0.000236
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.970156
  EX_co2_e : 25.394026
  EX_h_e : 8.550963
  Auxiliary production reaction : 0.466084
  EX_ac_e : 0.425858
  DM_mththf_c : 0.000328
  DM_5drib_c : 0.000165
  DM_4crsol_c : 0.000163

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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