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 : xdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4382 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2407 b3236 b1982 b2797 b3117 b1814 b4471 b2210 b3665 b2406 b0452 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1511 b3662 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.471034 (mmol/gDw/h)
  Minimum Production Rate : 0.199809 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.712062
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.887946
  EX_pi_e : 0.853980
  EX_so4_e : 0.118616
  EX_k_e : 0.091942
  EX_fe2_e : 0.007565
  EX_mg2_e : 0.004086
  EX_ca2_e : 0.002452
  EX_cl_e : 0.002452
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.956616
  EX_co2_e : 38.117038
  EX_h_e : 5.203288
  EX_ac_e : 0.274229
  Auxiliary production reaction : 0.199809
  EX_ade_e : 0.000317
  DM_mththf_c : 0.000211
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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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