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 : glyc_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (10 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4467 b1241 b0351 b3926 b0871 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1602 b0153 b4381 b0529 b2492 b0904 b0591 b1380 b2660 b1771 b1511 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.509557 (mmol/gDw/h)
  Minimum Production Rate : 0.060480 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.309804
  EX_o2_e : 287.782758
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.503171
  EX_pi_e : 0.491522
  EX_so4_e : 0.128317
  EX_k_e : 0.099462
  EX_mg2_e : 0.004420
  EX_ca2_e : 0.002652
  EX_cl_e : 0.002652
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991816
  EX_h2o_e : 552.293865
  EX_co2_e : 38.902449
  EX_glyc_e : 0.060480
  DM_mththf_c : 0.000228
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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