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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3399 b3942 b1732 b4069 b2502 b2744 b3708 b3008 b1479 b2930 b4232 b3697 b3925 b2297 b2458 b1238 b3236 b2463 b1982 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b1623 b3665 b0675 b2361 b4381 b2239 b2406 b3453 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b2835 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.725893 (mmol/gDw/h)
  Minimum Production Rate : 0.225919 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.821009
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.381613
  EX_pi_e : 0.926119
  EX_so4_e : 0.182794
  EX_k_e : 0.141689
  EX_fe2_e : 0.011659
  EX_mg2_e : 0.006297
  EX_ca2_e : 0.003778
  EX_cl_e : 0.003778
  EX_cu2_e : 0.000515
  EX_mn2_e : 0.000502
  EX_zn2_e : 0.000248
  EX_ni2_e : 0.000234
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.529867
  EX_co2_e : 25.373305
  EX_h_e : 9.086268
  EX_ac_e : 0.422605
  Auxiliary production reaction : 0.225919
  EX_ade_e : 0.082488
  DM_mththf_c : 0.082001
  DM_5drib_c : 0.000487
  DM_4crsol_c : 0.000162

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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