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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b2836 b3399 b4382 b4384 b2744 b3708 b3008 b0512 b0871 b2925 b2097 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b3945 b0511 b0114 b1539 b2492 b0904 b1533 b3927 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.775202 (mmol/gDw/h)
  Minimum Production Rate : 0.096411 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.695388
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.005619
  EX_pi_e : 0.844176
  EX_so4_e : 0.195211
  EX_k_e : 0.151314
  EX_fe2_e : 0.012451
  EX_mg2_e : 0.006725
  EX_ca2_e : 0.004035
  EX_cl_e : 0.004035
  EX_cu2_e : 0.000550
  EX_mn2_e : 0.000536
  EX_zn2_e : 0.000264
  EX_ni2_e : 0.000250
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.011909
  EX_co2_e : 25.984205
  EX_h_e : 7.756369
  EX_acser_e : 0.245771
  Auxiliary production reaction : 0.096411
  EX_xan_e : 0.000522
  DM_mththf_c : 0.000347
  DM_5drib_c : 0.000174
  DM_4crsol_c : 0.000173

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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