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 : ade_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (133 of 133: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4467 b2836 b1478 b3399 b1241 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b0160 b1004 b3713 b1109 b0046 b3236 b1779 b0207 b3012 b2797 b3117 b1814 b4471 b3665 b4374 b0675 b2361 b2291 b2799 b1602 b2223 b3915 b2366 b2492 b0904 b1781 b3001 b1380 b0325 b2660 b1771 b1511 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.463533 (mmol/gDw/h)
  Minimum Production Rate : 0.386925 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.620099
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.940701
  EX_pi_e : 0.447126
  EX_so4_e : 0.116728
  EX_k_e : 0.090478
  EX_fe3_e : 0.007447
  EX_mg2_e : 0.004021
  EX_ca2_e : 0.002413
  EX_cl_e : 0.002413
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.464957
  EX_co2_e : 37.358889
  EX_h_e : 7.040956
  EX_glyclt_e : 0.569936
  EX_ade_e : 0.386917
  EX_ac_e : 0.269863
  DM_mththf_c : 0.000208
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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