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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (103 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4382 b3942 b1732 b4069 b4384 b3708 b3008 b3752 b3115 b1849 b2296 b2925 b2097 b2926 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b2440 b0411 b3945 b2406 b0114 b2366 b2492 b0904 b1533 b3927 b0515 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.398536 (mmol/gDw/h)
  Minimum Production Rate : 0.503305 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.801847
  EX_o2_e : 281.203871
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.310381
  EX_pi_e : 1.391041
  EX_so4_e : 0.100359
  EX_k_e : 0.077791
  EX_mg2_e : 0.003457
  EX_cl_e : 0.002074
  EX_ca2_e : 0.002074
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993599
  EX_h2o_e : 544.596530
  EX_co2_e : 33.057988
  EX_ac_e : 4.026924
  Auxiliary production reaction : 0.503305
  EX_alltn_e : 0.001556
  EX_mththf_e : 0.001288
  DM_5drib_c : 0.000267
  DM_4crsol_c : 0.000089

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.

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Last updated: 21-Sep-2023
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