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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4382 b4069 b4384 b3708 b3752 b2297 b2458 b2407 b1982 b2797 b3117 b1814 b4471 b0411 b2406 b2943 b0452 b0511 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b0516 b1518 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.729598 (mmol/gDw/h)
  Minimum Production Rate : 0.309490 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.323052
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.119523
  EX_pi_e : 1.013265
  EX_so4_e : 0.183727
  EX_k_e : 0.142412
  EX_fe2_e : 0.011718
  EX_mg2_e : 0.006329
  EX_cl_e : 0.003798
  EX_ca2_e : 0.003798
  EX_cu2_e : 0.000517
  EX_mn2_e : 0.000504
  EX_zn2_e : 0.000249
  EX_ni2_e : 0.000236
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.780313
  EX_co2_e : 26.104831
  EX_h_e : 8.368526
  EX_ac_e : 0.424762
  Auxiliary production reaction : 0.309490
  EX_xan_e : 0.000491
  DM_mththf_c : 0.000327
  DM_5drib_c : 0.000164
  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
Contact