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 : preq1_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4384 b2744 b3708 b3008 b0512 b0871 b0030 b1238 b2883 b1982 b2797 b3117 b1814 b4471 b3449 b1623 b0411 b4381 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b0494 b1511 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.785818 (mmol/gDw/h)
  Minimum Production Rate : 0.178302 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.159604
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.390553
  EX_pi_e : 0.758005
  EX_so4_e : 0.197885
  EX_k_e : 0.153386
  EX_fe2_e : 0.012621
  EX_mg2_e : 0.006817
  EX_cl_e : 0.004090
  EX_ca2_e : 0.004090
  EX_cu2_e : 0.000557
  EX_mn2_e : 0.000543
  EX_zn2_e : 0.000268
  EX_ni2_e : 0.000254
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_h2o_e : 49.026710
  EX_co2_e : 26.470924
  EX_h_e : 7.945892
  Auxiliary production reaction : 0.178302
  EX_alltn_e : 0.003068
  DM_mththf_c : 0.002541
  DM_5drib_c : 0.000527
  DM_4crsol_c : 0.000175

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
Contact