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 : hcys__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 16
  Gene deletion: CLJU_RS05830 CLJU_RS08100 CLJU_RS08095 CLJU_RS09865 CLJU_RS09915 CLJU_RS20875 CLJU_RS02035 CLJU_RS07210 CLJU_RS03475 CLJU_RS08715 CLJU_RS11985 CLJU_RS10610 CLJU_RS10705 CLJU_RS18495 CLJU_RS18530 CLJU_RS05590   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.099817 (mmol/gDw/h)
  Minimum Production Rate : 0.283279 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fru_e : 5.000000
  EX_nh4_e : 1.043538
  EX_so4_e : 0.302128
  EX_pi_e : 0.115653
  EX_k_e : 0.019083
  EX_fe2_e : 0.001380
  EX_mg2_e : 0.000848
  EX_ca2_e : 0.000509
  EX_cl_e : 0.000509
  EX_fol_e : 0.000089
  EX_cu2_e : 0.000069
  EX_mn2_e : 0.000068
  EX_ribflv_e : 0.000045
  EX_zn2_e : 0.000033
  EX_ni2_e : 0.000032
  EX_cobalt2_e : 0.000025
  EX_thm_e : 0.000022

Product: (mmol/gDw/h)
  EX_co2_e : 8.339716
  EX_h2o_e : 4.828694
  EX_etoh_e : 3.899156
  EX_btd_RR_e : 2.094751
  Auxiliary production reaction : 0.283279
  EX_h_e : 0.271585
  DM_succ_c : 0.012622
  EX_ala__D_e : 0.002836
  DM_mththf_c : 0.000223

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
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