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 : acetol_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3553 b1478 b1241 b0351 b2930 b4232 b3697 b3925 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1302 b2662 b1033 b4015 b3945 b1602 b2913 b1380 b0606 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.532620 (mmol/gDw/h)
  Minimum Production Rate : 0.677407 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.238504
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.752254
  EX_pi_e : 0.513769
  EX_so4_e : 0.134124
  EX_k_e : 0.103964
  EX_fe2_e : 0.008554
  EX_mg2_e : 0.004620
  EX_ca2_e : 0.002772
  EX_cl_e : 0.002772
  EX_cu2_e : 0.000378
  EX_mn2_e : 0.000368
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.778860
  EX_co2_e : 33.713830
  EX_h_e : 6.090093
  EX_ac_e : 1.196165
  Auxiliary production reaction : 0.677407
  DM_5drib_c : 0.000120
  DM_4crsol_c : 0.000119

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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