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 (45 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3399 b3942 b1732 b4069 b2744 b3708 b3008 b1479 b3115 b1849 b2296 b2925 b2097 b0160 b3236 b2690 b2463 b1982 b2797 b3117 b1814 b4471 b2210 b4374 b0675 b2361 b2291 b0261 b3945 b0114 b2366 b2492 b0904 b2947 b0591 b2578 b1533 b3927 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.707544 (mmol/gDw/h)
  Minimum Production Rate : 0.323858 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.426213
  EX_o2_e : 273.701179
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.415641
  EX_pi_e : 0.682502
  EX_so4_e : 0.303886
  EX_k_e : 0.138108
  EX_mg2_e : 0.006138
  EX_cl_e : 0.003683
  EX_ca2_e : 0.003683
  EX_cu2_e : 0.000502
  EX_mn2_e : 0.000489
  EX_zn2_e : 0.000241
  EX_ni2_e : 0.000229
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988636
  EX_h2o_e : 547.211601
  EX_co2_e : 25.689114
  EX_ac_e : 0.537635
  EX_trp__L_e : 0.323858
  EX_met__L_e : 0.125712
  DM_oxam_c : 0.000792
  DM_5drib_c : 0.000475
  DM_4crsol_c : 0.000158

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.

Last updated: 21-Sep-2023
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