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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (107 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b4069 b2930 b4232 b3697 b3925 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b3908 b1656 b4139 b0675 b0261 b0822 b1602 b2913 b4381 b3654 b3714 b3664 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b0516 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.401067 (mmol/gDw/h)
  Minimum Production Rate : 0.131081 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.022323
  EX_o2_e : 281.921581
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.029955
  EX_pi_e : 0.780114
  EX_so4_e : 0.100997
  EX_k_e : 0.078286
  EX_mg2_e : 0.003479
  EX_ca2_e : 0.002088
  EX_cl_e : 0.002088
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993558
  EX_h2o_e : 544.982964
  EX_co2_e : 32.484623
  EX_ac_e : 4.849769
  Auxiliary production reaction : 0.131081
  EX_alltn_e : 0.010764
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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