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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b2836 b3399 b4069 b2502 b4384 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b1779 b2690 b2797 b3117 b1814 b4471 b3665 b4374 b0675 b2361 b2291 b3945 b3709 b3161 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b2947 b0591 b2578 b1533 b3927 b1473 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.581665 (mmol/gDw/h)
  Minimum Production Rate : 0.741248 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.944924
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.764431
  EX_pi_e : 1.302326
  EX_so4_e : 0.146475
  EX_k_e : 0.113537
  EX_fe2_e : 0.009342
  EX_mg2_e : 0.005046
  EX_cl_e : 0.003028
  EX_ca2_e : 0.003028
  EX_cu2_e : 0.000412
  EX_mn2_e : 0.000402
  EX_zn2_e : 0.000198
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.459976
  EX_co2_e : 25.978852
  EX_h_e : 8.097923
  EX_pyr_e : 0.932218
  Auxiliary production reaction : 0.741248
  EX_ac_e : 0.338637
  DM_mththf_c : 0.000261
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130

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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