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 : glyc_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b4382 b3942 b1732 b1241 b0351 b4069 b4384 b3926 b3115 b1849 b2296 b2926 b2407 b1004 b3713 b1109 b0046 b2463 b2210 b1033 b3551 b1602 b4219 b1832 b1778 b3915 b0529 b2492 b0904 b1380 b1710 b2480 b1771 b1517 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492722 (mmol/gDw/h)
  Minimum Production Rate : 0.552502 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.177901
  EX_o2_e : 284.913343
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.321359
  EX_pi_e : 0.475283
  EX_so4_e : 0.124077
  EX_k_e : 0.096176
  EX_mg2_e : 0.004274
  EX_ca2_e : 0.002565
  EX_cl_e : 0.002565
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992086
  EX_h2o_e : 548.698026
  EX_co2_e : 36.676599
  EX_glyc_e : 0.552502
  EX_etoh_e : 0.433547
  EX_ac_e : 0.286856
  DM_mththf_c : 0.000221
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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
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