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 : nadhx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b2836 b3399 b4069 b2502 b2744 b3708 b3926 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0411 b1602 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b2660 b1517 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.437295 (mmol/gDw/h)
  Minimum Production Rate : 0.185756 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.171197
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.023046
  EX_pi_e : 0.793330
  EX_so4_e : 0.110120
  EX_k_e : 0.085357
  EX_fe2_e : 0.007023
  EX_mg2_e : 0.003794
  EX_cl_e : 0.002276
  EX_ca2_e : 0.002276
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000302
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.717132
  EX_co2_e : 37.640003
  EX_h_e : 5.201412
  EX_ac_e : 0.254587
  Auxiliary production reaction : 0.185756
  EX_mththf_e : 0.000196
  DM_5drib_c : 0.000098
  DM_4crsol_c : 0.000098

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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