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 (109 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b0586 b3831 b4069 b4384 b3708 b3008 b0910 b3752 b2297 b2458 b2779 b2926 b2407 b0517 b1982 b2797 b3117 b1814 b4471 b0261 b0505 b4381 b2406 b0112 b0511 b0114 b0529 b1539 b2492 b0904 b2947 b2578 b1533 b3927 b3825 b0494 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.628724 (mmol/gDw/h)
  Minimum Production Rate : 0.342588 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.893367
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.705758
  EX_pi_e : 1.291647
  EX_so4_e : 0.158325
  EX_k_e : 0.122723
  EX_fe2_e : 0.010098
  EX_mg2_e : 0.005454
  EX_ca2_e : 0.003273
  EX_cl_e : 0.003273
  EX_cu2_e : 0.000446
  EX_mn2_e : 0.000434
  EX_zn2_e : 0.000214
  EX_ni2_e : 0.000203
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.038210
  EX_co2_e : 29.461894
  EX_h_e : 6.716005
  EX_thym_e : 0.456389
  EX_ac_e : 0.366034
  Auxiliary production reaction : 0.342588
  EX_xan_e : 0.000704
  DM_5drib_c : 0.000422
  DM_4crsol_c : 0.000140

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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