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 : gsn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b3617 b2407 b3124 b1982 b0411 b0114 b0755 b3612 b0529 b2492 b0904 b0516 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.405437 (mmol/gDw/h)
  Minimum Production Rate : 0.775970 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.011925
  EX_o2_e : 284.310791
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.264865
  EX_pi_e : 0.391087
  EX_so4_e : 0.102097
  EX_k_e : 0.079138
  EX_mg2_e : 0.003517
  EX_ca2_e : 0.002110
  EX_cl_e : 0.002110
  EX_cu2_e : 0.000287
  EX_mn2_e : 0.000280
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993488
  EX_h2o_e : 552.095021
  EX_co2_e : 32.845060
  EX_ac_e : 1.370066
  EX_gsn_e : 0.775970
  EX_alltn_e : 0.001583
  DM_mththf_c : 0.001311
  DM_5drib_c : 0.000272
  DM_4crsol_c : 0.000090

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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