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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (99 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3553 b1241 b0351 b2221 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2690 b1302 b2662 b1033 b4014 b2976 b0614 b0726 b3945 b0507 b2913 b2587 b0755 b3612 b1539 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483339 (mmol/gDw/h)
  Minimum Production Rate : 2.865346 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.794450
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.220017
  EX_pi_e : 0.466231
  EX_so4_e : 0.121714
  EX_k_e : 0.094344
  EX_fe2_e : 0.007763
  EX_mg2_e : 0.004193
  EX_ca2_e : 0.002516
  EX_cl_e : 0.002516
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 45.022055
  EX_co2_e : 29.393070
  EX_h_e : 8.391943
  EX_pyr_e : 2.865346
  EX_ac_e : 1.085165
  EX_glyclt_e : 0.000323
  DM_mththf_c : 0.000217
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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