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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b4382 b4069 b4384 b3752 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b3665 b1602 b2913 b2406 b3915 b3654 b3714 b3664 b1727 b0114 b0529 b2492 b0904 b1380 b1771 b3662 b1517 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.474262 (mmol/gDw/h)
  Minimum Production Rate : 0.219470 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.258400
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.219344
  EX_pi_e : 0.676946
  EX_so4_e : 0.338899
  EX_k_e : 0.092573
  EX_fe3_e : 0.007617
  EX_mg2_e : 0.004114
  EX_ca2_e : 0.002469
  EX_cl_e : 0.002469
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000328
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.096975
  EX_co2_e : 37.739218
  EX_h_e : 5.299848
  EX_ac_e : 0.276109
  Auxiliary production reaction : 0.219470
  EX_12ppd__S_e : 0.015503
  DM_mththf_c : 0.000212
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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