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 (61 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b1278 b0871 b3115 b1849 b2296 b2925 b2097 b3617 b3236 b1779 b2690 b2210 b4374 b0675 b2361 b0822 b4381 b2868 b1727 b0114 b0529 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.533840 (mmol/gDw/h)
  Minimum Production Rate : 0.672986 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.700810
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.514677
  EX_pi_e : 2.533903
  EX_so4_e : 0.134432
  EX_k_e : 0.104202
  EX_fe2_e : 0.008574
  EX_mg2_e : 0.004631
  EX_ca2_e : 0.002779
  EX_cl_e : 0.002779
  EX_cu2_e : 0.000378
  EX_mn2_e : 0.000369
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 49.806140
  EX_co2_e : 26.071374
  EX_h_e : 8.535662
  EX_ac_e : 1.467477
  EX_pyr_e : 0.759771
  Auxiliary production reaction : 0.672986
  EX_xan_e : 0.013968
  EX_hxan_e : 0.000359
  DM_mththf_c : 0.000239
  DM_5drib_c : 0.000120
  DM_4crsol_c : 0.000119

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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