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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b3844 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0452 b0114 b2366 b2492 b0904 b3035 b2578 b1533 b3927 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.543181 (mmol/gDw/h)
  Minimum Production Rate : 0.345004 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.496616
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.246935
  EX_pi_e : 0.868960
  EX_so4_e : 0.136784
  EX_k_e : 0.106025
  EX_fe2_e : 0.008724
  EX_mg2_e : 0.004712
  EX_ca2_e : 0.002827
  EX_cl_e : 0.002827
  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 : 51.415143
  EX_co2_e : 33.964978
  EX_h_e : 6.688430
  Auxiliary production reaction : 0.345004
  EX_ac_e : 0.316233
  DM_oxam_c : 0.000608
  DM_5drib_c : 0.000364
  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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