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 : dadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b2297 b2458 b2925 b2097 b0030 b2407 b3236 b2690 b3616 b3589 b2210 b3665 b0675 b0822 b1727 b0114 b0529 b2492 b0904 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.456468 (mmol/gDw/h)
  Minimum Production Rate : 0.583410 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.117460
  EX_o2_e : 278.927429
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.848398
  EX_pi_e : 1.607131
  EX_so4_e : 0.114948
  EX_k_e : 0.089099
  EX_mg2_e : 0.003960
  EX_ca2_e : 0.002376
  EX_cl_e : 0.002376
  EX_cu2_e : 0.000324
  EX_mn2_e : 0.000315
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992669
  EX_h2o_e : 548.373571
  EX_co2_e : 28.735786
  EX_ac_e : 3.345826
  Auxiliary production reaction : 0.583410
  EX_ade_e : 0.000307
  EX_mththf_e : 0.000204
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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