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 : bwco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4384 b2744 b3708 b3008 b0910 b3752 b0512 b0871 b2926 b2883 b1982 b2797 b3117 b1814 b4471 b2440 b1623 b0411 b4381 b0114 b2366 b2492 b0904 b1533 b3927 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.703667 (mmol/gDw/h)
  Minimum Production Rate : 0.025328 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.861095
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.055002
  EX_pi_e : 0.754744
  EX_so4_e : 0.278508
  EX_k_e : 0.137351
  EX_tungs_e : 0.025328
  EX_fe2_e : 0.011302
  EX_mg2_e : 0.006104
  EX_ca2_e : 0.003663
  EX_cl_e : 0.003663
  EX_cu2_e : 0.000499
  EX_mn2_e : 0.000486
  EX_zn2_e : 0.000240
  EX_ni2_e : 0.000227
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 50.109268
  EX_co2_e : 30.280750
  EX_h_e : 6.617100
  Auxiliary production reaction : 0.025328
  EX_alltn_e : 0.018886
  DM_mththf_c : 0.000315
  DM_5drib_c : 0.000158
  DM_4crsol_c : 0.000157

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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