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 : adn_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4467 b4382 b4069 b4384 b3926 b3115 b1849 b2296 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b0411 b1602 b2913 b3915 b0114 b0529 b2492 b0904 b1380 b1771 b1517 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.448209 (mmol/gDw/h)
  Minimum Production Rate : 0.207112 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.078873
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.877382
  EX_pi_e : 0.432345
  EX_so4_e : 0.112868
  EX_k_e : 0.087487
  EX_fe3_e : 0.007199
  EX_mg2_e : 0.003888
  EX_ca2_e : 0.002333
  EX_cl_e : 0.002333
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.631923
  EX_co2_e : 37.518625
  EX_h_e : 5.919544
  EX_3hpp_e : 0.496318
  EX_ac_e : 0.260941
  Auxiliary production reaction : 0.207112
  EX_hxan_e : 0.000302
  DM_mththf_c : 0.000201
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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.

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Last updated: 21-Sep-2023
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