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 : gua_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (106 of 123: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4467 b0238 b0125 b3831 b2744 b0871 b2779 b1004 b3713 b1109 b0046 b3236 b2883 b0477 b2498 b2361 b2291 b0411 b1602 b0114 b0529 b2492 b0904 b1380 b0515 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.508645 (mmol/gDw/h)
  Minimum Production Rate : 0.082003 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.871865
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.903337
  EX_pi_e : 0.490642
  EX_so4_e : 0.128087
  EX_k_e : 0.099284
  EX_fe2_e : 0.008169
  EX_mg2_e : 0.004412
  EX_ca2_e : 0.002647
  EX_cl_e : 0.002647
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000351
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.963249
  EX_co2_e : 38.711313
  EX_h_e : 5.083648
  Auxiliary production reaction : 0.082003
  DM_mththf_c : 0.000228
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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