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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b3115 b1849 b2296 b2925 b2097 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b3665 b0261 b1701 b1805 b2406 b0114 b2366 b2492 b0904 b2947 b3035 b2578 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.721206 (mmol/gDw/h)
  Minimum Production Rate : 0.054812 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.374058
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.278654
  EX_pi_e : 0.750492
  EX_so4_e : 0.612459
  EX_k_e : 0.140774
  EX_fe2_e : 0.011583
  EX_mg2_e : 0.006256
  EX_cl_e : 0.003754
  EX_ca2_e : 0.003754
  EX_cu2_e : 0.000511
  EX_mn2_e : 0.000498
  EX_zn2_e : 0.000246
  EX_ni2_e : 0.000233
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 46.122442
  EX_co2_e : 26.043195
  EX_h_e : 7.160262
  EX_ac_e : 0.850721
  EX_met__L_e : 0.430845
  Auxiliary production reaction : 0.054812
  EX_ade_e : 0.000807
  DM_5drib_c : 0.000484
  DM_4crsol_c : 0.000161

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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