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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b4069 b3708 b3115 b1849 b2296 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b2797 b3117 b1814 b4471 b2210 b1602 b4381 b2406 b1727 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b3825 b1380 b2660 b1771 b1517 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393320 (mmol/gDw/h)
  Minimum Production Rate : 0.117414 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.628274
  EX_o2_e : 281.631624
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.770265
  EX_pi_e : 0.496813
  EX_so4_e : 0.099046
  EX_k_e : 0.076773
  EX_mg2_e : 0.003412
  EX_cl_e : 0.002047
  EX_ca2_e : 0.002047
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993683
  EX_h2o_e : 543.991803
  EX_co2_e : 34.701061
  EX_12ppd__S_e : 2.489723
  EX_ac_e : 0.228986
  Auxiliary production reaction : 0.117414
  EX_ade_e : 0.010556
  DM_mththf_c : 0.000176
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000088

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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