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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b2836 b4069 b2744 b2297 b2458 b2925 b2097 b2926 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b2690 b4139 b0261 b0411 b3945 b1602 b2913 b4381 b3654 b2868 b3714 b3664 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b3029 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.371204 (mmol/gDw/h)
  Minimum Production Rate : 0.171723 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.040968
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.867588
  EX_pi_e : 0.529789
  EX_so4_e : 0.265200
  EX_k_e : 0.072456
  EX_fe3_e : 0.005962
  EX_mg2_e : 0.003220
  EX_ca2_e : 0.001932
  EX_cl_e : 0.001932
  EX_cu2_e : 0.000263
  EX_mn2_e : 0.000257
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 44.437199
  EX_co2_e : 32.543077
  EX_h_e : 8.976984
  EX_ac_e : 5.045082
  Auxiliary production reaction : 0.171723
  EX_12ppd__S_e : 0.137770
  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.

Last updated: 21-Sep-2023
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