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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b4069 b4384 b3708 b3115 b1849 b2296 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b2406 b2868 b0837 b0124 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b3821 b3662 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.548039 (mmol/gDw/h)
  Minimum Production Rate : 0.232474 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.952172
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.850513
  EX_pi_e : 0.761116
  EX_so4_e : 0.138007
  EX_k_e : 0.106973
  EX_fe2_e : 0.008802
  EX_mg2_e : 0.004754
  EX_cl_e : 0.002853
  EX_ca2_e : 0.002853
  EX_cu2_e : 0.000389
  EX_mn2_e : 0.000379
  EX_zn2_e : 0.000187
  EX_ni2_e : 0.000177
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.572684
  EX_co2_e : 34.539591
  EX_h_e : 6.286400
  EX_ac_e : 0.319061
  Auxiliary production reaction : 0.232474
  EX_ade_e : 0.000369
  EX_mththf_e : 0.000246
  DM_5drib_c : 0.000123
  DM_4crsol_c : 0.000122

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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