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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b3708 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b3617 b0160 b1238 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b0675 b2361 b0261 b4381 b2406 b0112 b0452 b0114 b0509 b3125 b1539 b2492 b0904 b3035 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.495242 (mmol/gDw/h)
  Minimum Production Rate : 0.603680 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.669803
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.556483
  EX_pi_e : 0.477713
  EX_so4_e : 0.124712
  EX_k_e : 0.096668
  EX_fe2_e : 0.007954
  EX_mg2_e : 0.004296
  EX_ca2_e : 0.002578
  EX_cl_e : 0.002578
  EX_cu2_e : 0.000351
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 43.936125
  EX_co2_e : 26.027612
  EX_h_e : 9.260095
  EX_ac_e : 3.500817
  EX_trp__L_e : 0.603680
  DM_oxam_c : 0.000554
  DM_5drib_c : 0.000332
  EX_glyclt_e : 0.000331
  DM_4crsol_c : 0.000110

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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