MetNetComp Database / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iHN637 [2].
Target metabolite : pe120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (1 of 6: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 7
  Gene deletion: CLJU_RS11880 CLJU_RS00610 CLJU_RS01155 CLJU_RS08715 CLJU_RS06110 CLJU_RS18530 CLJU_RS05590   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.093378 (mmol/gDw/h)
  Minimum Production Rate : 0.348589 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fru_e : 5.000000
  EX_nh4_e : 1.139695
  EX_pi_e : 0.456781
  EX_so4_e : 0.100175
  EX_k_e : 0.017852
  EX_fe2_e : 0.001291
  EX_mg2_e : 0.000793
  EX_ca2_e : 0.000476
  EX_cl_e : 0.000476
  EX_fol_e : 0.000083
  EX_cu2_e : 0.000065
  EX_mn2_e : 0.000063
  EX_ribflv_e : 0.000042
  EX_zn2_e : 0.000031
  EX_ni2_e : 0.000030
  EX_cobalt2_e : 0.000023
  EX_thm_e : 0.000021

Product: (mmol/gDw/h)
  EX_co2_e : 8.691412
  EX_h2o_e : 5.491487
  EX_h2_e : 4.469845
  EX_etoh_e : 1.730989
  EX_h_e : 1.717045
  EX_ac_e : 1.631758
  Auxiliary production reaction : 0.348589
  EX_met__L_e : 0.082542
  DM_succ_c : 0.011808
  DM_mththf_c : 0.000208

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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] Orth, J. D., Fleming, R. M., Palsson, B. Ø. (2010). Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide. EcoSal plus, 4(1).
[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: 27-Sep-2023
Contact