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 (41 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3399 b4382 b4069 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b0160 b2690 b1982 b2688 b2797 b3117 b1814 b4471 b0596 b0675 b2361 b0261 b3945 b4381 b2406 b2868 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b2413   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.722572 (mmol/gDw/h)
  Minimum Production Rate : 0.146714 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.531191
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.460853
  EX_pi_e : 0.696997
  EX_so4_e : 0.466003
  EX_k_e : 0.141041
  EX_fe2_e : 0.011605
  EX_mg2_e : 0.006268
  EX_ca2_e : 0.003761
  EX_cl_e : 0.003761
  EX_cu2_e : 0.000512
  EX_mn2_e : 0.000499
  EX_zn2_e : 0.000246
  EX_ni2_e : 0.000233
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 46.799224
  EX_co2_e : 25.798063
  EX_h_e : 7.433043
  EX_ac_e : 0.704716
  EX_met__L_e : 0.284045
  EX_trp__L_e : 0.146714
  EX_xan_e : 0.018907
  EX_ade_e : 0.000809
  DM_5drib_c : 0.000485
  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.

Last updated: 21-Sep-2023
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