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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4382 b0474 b2518 b1241 b0351 b4069 b2502 b4384 b2744 b3752 b2297 b2458 b2781 b0099 b2883 b1982 b3616 b3589 b1623 b0411 b0114 b0529 b2492 b0904 b2954 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.629427 (mmol/gDw/h)
  Minimum Production Rate : 0.804468 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.935053
  EX_nh4_e : 10.015630
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.020553
  EX_so4_e : 0.158502
  EX_k_e : 0.122860
  EX_fe2_e : 0.010109
  EX_mg2_e : 0.005460
  EX_ca2_e : 0.003276
  EX_cl_e : 0.003276
  EX_cu2_e : 0.000446
  EX_mn2_e : 0.000435
  EX_zn2_e : 0.000215
  EX_ni2_e : 0.000203
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.748837
  EX_co2_e : 22.669328
  EX_h_e : 9.117110
  EX_ac_e : 1.724748
  Auxiliary production reaction : 0.804468
  DM_mththf_c : 0.000282
  DM_5drib_c : 0.000142
  DM_4crsol_c : 0.000140

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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