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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b2925 b2097 b2926 b3617 b3236 b2883 b3946 b2210 b0825 b0411 b4381 b2868 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.537415 (mmol/gDw/h)
  Minimum Production Rate : 0.677494 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.987129
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.586134
  EX_pi_e : 2.550875
  EX_so4_e : 0.135332
  EX_k_e : 0.104900
  EX_fe2_e : 0.008631
  EX_mg2_e : 0.004662
  EX_ca2_e : 0.002797
  EX_cl_e : 0.002797
  EX_cu2_e : 0.000381
  EX_mn2_e : 0.000371
  EX_zn2_e : 0.000183
  EX_ni2_e : 0.000174
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 49.886247
  EX_co2_e : 26.742938
  EX_h_e : 8.540278
  EX_ac_e : 2.175185
  Auxiliary production reaction : 0.677494
  EX_ade_e : 0.014424
  DM_mththf_c : 0.000241
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000120

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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