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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b2836 b0586 b2744 b3708 b3008 b0910 b2930 b4232 b3697 b3925 b0871 b3236 b2883 b2797 b3117 b1814 b4471 b3946 b0825 b4374 b0675 b4381 b2406 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.758321 (mmol/gDw/h)
  Minimum Production Rate : 0.013805 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.072072
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.225766
  EX_pi_e : 0.745286
  EX_so4_e : 0.190960
  EX_k_e : 0.148019
  EX_fe2_e : 0.012179
  EX_mg2_e : 0.006578
  EX_ca2_e : 0.003947
  EX_cl_e : 0.003947
  EX_cu2_e : 0.000538
  EX_mn2_e : 0.000524
  EX_zn2_e : 0.000259
  EX_ni2_e : 0.000245
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.815041
  EX_co2_e : 26.193068
  EX_h_e : 8.017526
  EX_thym_e : 0.511081
  Auxiliary production reaction : 0.013805
  EX_mththf_e : 0.000340
  DM_5drib_c : 0.000171
  DM_4crsol_c : 0.000169

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