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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b2297 b2458 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b2440 b0261 b2406 b0452 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.722354 (mmol/gDw/h)
  Minimum Production Rate : 0.337137 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.678685
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.608893
  EX_pi_e : 0.696787
  EX_so4_e : 0.181903
  EX_k_e : 0.140999
  EX_fe2_e : 0.011602
  EX_mg2_e : 0.006266
  EX_ca2_e : 0.003760
  EX_cl_e : 0.003760
  EX_cu2_e : 0.000512
  EX_mn2_e : 0.000499
  EX_zn2_e : 0.000246
  EX_ni2_e : 0.000233
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.555016
  EX_co2_e : 25.255766
  EX_h_e : 8.865293
  EX_ac_e : 0.420545
  Auxiliary production reaction : 0.337137
  EX_enter_e : 0.040595
  DM_5drib_c : 0.000485
  DM_4crsol_c : 0.000161
  EX_etha_e : 0.000058

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