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 : ins_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b4382 b4069 b4384 b3752 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b0477 b4139 b1602 b0507 b2913 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b3029 b1380 b1771 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.488321 (mmol/gDw/h)
  Minimum Production Rate : 0.053609 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.940363
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.488265
  EX_pi_e : 0.471038
  EX_so4_e : 0.122969
  EX_k_e : 0.095317
  EX_fe3_e : 0.007843
  EX_mg2_e : 0.004236
  EX_ca2_e : 0.002542
  EX_cl_e : 0.002542
  EX_cu2_e : 0.000346
  EX_mn2_e : 0.000337
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.277609
  EX_co2_e : 38.850224
  EX_h_e : 4.993793
  EX_ac_e : 0.284294
  EX_ins_e : 0.053609
  EX_glyclt_e : 0.000329
  DM_mththf_c : 0.000219
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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