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 : acald_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 20: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b2297 b2458 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b2690 b1033 b1493 b3517 b4015 b0726 b3945 b1602 b2913 b1297 b1380 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.542898 (mmol/gDw/h)
  Minimum Production Rate : 2.889482 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.702134
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.863253
  EX_pi_e : 0.523683
  EX_so4_e : 0.136713
  EX_k_e : 0.105970
  EX_fe2_e : 0.008719
  EX_mg2_e : 0.004710
  EX_ca2_e : 0.002826
  EX_cl_e : 0.002826
  EX_cu2_e : 0.000385
  EX_mn2_e : 0.000375
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 45.641867
  EX_co2_e : 31.305430
  EX_h_e : 5.304432
  EX_acald_e : 2.889482
  EX_ac_e : 0.316068
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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