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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b3399 b4269 b0493 b3588 b3003 b3011 b4384 b2744 b0871 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1982 b4139 b1623 b0411 b1602 b4381 b1727 b0114 b0755 b3612 b0529 b2492 b0904 b3029 b1380 b2660 b0515 b1771 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483649 (mmol/gDw/h)
  Minimum Production Rate : 0.116975 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.204539
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.860162
  EX_pi_e : 0.700481
  EX_so4_e : 0.121792
  EX_k_e : 0.094405
  EX_mg2_e : 0.004196
  EX_fe2_e : 0.003992
  EX_fe3_e : 0.003776
  EX_ca2_e : 0.002517
  EX_cl_e : 0.002517
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.320146
  EX_co2_e : 38.912709
  EX_h_e : 4.967556
  Auxiliary production reaction : 0.116975
  EX_hxan_e : 0.012981
  DM_mththf_c : 0.000217
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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