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 (69 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b3399 b3942 b1732 b4069 b2502 b2744 b3708 b1479 b0871 b3115 b1849 b2296 b2925 b2097 b2926 b3236 b2690 b2463 b1982 b2797 b3117 b1814 b4471 b2210 b4374 b0675 b2361 b2291 b3945 b2868 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1511 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.581336 (mmol/gDw/h)
  Minimum Production Rate : 0.246598 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.815382
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.513328
  EX_pi_e : 0.807359
  EX_so4_e : 0.146392
  EX_k_e : 0.113473
  EX_fe2_e : 0.009337
  EX_mg2_e : 0.005043
  EX_ca2_e : 0.003026
  EX_cl_e : 0.003026
  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 : 46.962540
  EX_co2_e : 26.229011
  EX_h_e : 9.333901
  EX_pyr_e : 1.925763
  EX_ac_e : 0.338446
  Auxiliary production reaction : 0.246598
  EX_ade_e : 0.000391
  EX_mththf_e : 0.000260
  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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