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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4467 b3399 b2744 b3708 b3008 b0512 b0871 b2779 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b3946 b0825 b2440 b1602 b4381 b0114 b1539 b2492 b0904 b1533 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.384957 (mmol/gDw/h)
  Minimum Production Rate : 0.058845 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.062357
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.493057
  EX_pi_e : 0.371332
  EX_so4_e : 0.096940
  EX_k_e : 0.075141
  EX_fe2_e : 0.006183
  EX_mg2_e : 0.003340
  EX_ca2_e : 0.002004
  EX_cl_e : 0.002004
  EX_cu2_e : 0.000273
  EX_mn2_e : 0.000266
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 43.566972
  EX_co2_e : 28.133005
  EX_h_e : 9.018191
  EX_pyr_e : 4.548696
  EX_glyc__R_e : 0.596803
  Auxiliary production reaction : 0.058845
  EX_alltn_e : 0.010332
  DM_5drib_c : 0.000087
  DM_4crsol_c : 0.000086

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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