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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (26 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b2883 b2797 b3117 b1814 b4471 b1623 b3665 b0411 b4381 b2406 b3654 b3714 b3664 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b4141 b1798 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.778720 (mmol/gDw/h)
  Minimum Production Rate : 0.079678 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.620681
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.967849
  EX_pi_e : 0.990191
  EX_so4_e : 0.275775
  EX_k_e : 0.152001
  EX_fe2_e : 0.012507
  EX_mg2_e : 0.006755
  EX_ca2_e : 0.004053
  EX_cl_e : 0.004053
  EX_cu2_e : 0.000552
  EX_mn2_e : 0.000538
  EX_zn2_e : 0.000266
  EX_ni2_e : 0.000252
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.439869
  EX_co2_e : 26.362162
  EX_h_e : 7.394220
  Auxiliary production reaction : 0.079678
  DM_mththf_c : 0.000349
  DM_5drib_c : 0.000175
  DM_4crsol_c : 0.000174

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