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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3399 b3942 b1732 b4069 b2502 b2744 b3708 b3008 b1479 b2297 b2458 b3236 b2883 b2463 b2797 b3117 b1814 b4471 b2210 b2440 b4374 b2361 b2291 b3551 b4219 b1832 b1778 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b3927 b2240 b1710 b2480 b1511 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.546351 (mmol/gDw/h)
  Minimum Production Rate : 0.173818 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.233273
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.771010
  EX_pi_e : 1.049296
  EX_so4_e : 0.137582
  EX_k_e : 0.106644
  EX_mg2_e : 0.004740
  EX_fe2_e : 0.004509
  EX_fe3_e : 0.004266
  EX_ca2_e : 0.002844
  EX_cl_e : 0.002844
  EX_cu2_e : 0.000387
  EX_mn2_e : 0.000378
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 50.571644
  EX_co2_e : 32.221203
  EX_h_e : 7.352361
  EX_fum_e : 0.743824
  EX_ac_e : 0.318078
  Auxiliary production reaction : 0.174094
  DM_mththf_c : 0.000245
  DM_5drib_c : 0.000123
  DM_4crsol_c : 0.000122

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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