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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4467 b3399 b2744 b2930 b4232 b3697 b3925 b0871 b2926 b1004 b3713 b1109 b0046 b2690 b2210 b0675 b0822 b4381 b1727 b0114 b0529 b2492 b0904 b1380 b0789 b1249 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.373491 (mmol/gDw/h)
  Minimum Production Rate : 0.270830 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.028706
  EX_o2_e : 280.009815
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.043696
  EX_pi_e : 0.901932
  EX_so4_e : 0.094053
  EX_k_e : 0.072903
  EX_mg2_e : 0.003240
  EX_ca2_e : 0.001944
  EX_cl_e : 0.001944
  EX_cu2_e : 0.000265
  EX_mn2_e : 0.000258
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994001
  EX_h2o_e : 544.148699
  EX_co2_e : 28.942830
  EX_pyr_e : 4.784292
  Auxiliary production reaction : 0.270830
  DM_oxam_c : 0.010024
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

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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