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 : 4fe4s_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (12 of 16: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b2744 b3708 b3008 b0512 b0871 b2926 b0160 b3236 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b1701 b1805 b0511 b0114 b1539 b2492 b0904 b1533 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.709619 (mmol/gDw/h)
  Minimum Production Rate : 0.061239 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.343947
  EX_o2_e : 278.833112
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.665740
  EX_pi_e : 0.684503
  EX_so4_e : 0.423654
  EX_k_e : 0.138513
  EX_mg2_e : 0.006156
  EX_ca2_e : 0.003694
  EX_cl_e : 0.003694
  EX_cu2_e : 0.000503
  EX_mn2_e : 0.000490
  EX_zn2_e : 0.000242
  EX_ni2_e : 0.000229
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.743645
  EX_h2o_e : 549.545852
  EX_co2_e : 30.869406
  Auxiliary production reaction : 0.061239
  EX_xan_e : 0.000478
  DM_mththf_c : 0.000318
  DM_5drib_c : 0.000160
  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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