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 : dadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b0871 b2925 b2097 b2926 b2690 b3616 b3589 b0675 b0822 b4381 b2406 b0511 b0114 b2492 b0904 b1912 b0515 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.335300 (mmol/gDw/h)
  Minimum Production Rate : 0.276032 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.494311
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.001368
  EX_pi_e : 0.875497
  EX_so4_e : 0.084435
  EX_k_e : 0.065448
  EX_fe2_e : 0.005385
  EX_mg2_e : 0.002909
  EX_cl_e : 0.001745
  EX_ca2_e : 0.001745
  EX_cu2_e : 0.000238
  EX_mn2_e : 0.000232
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 44.864263
  EX_co2_e : 27.727675
  EX_h_e : 8.878830
  EX_pyr_e : 4.693835
  EX_acald_e : 0.833621
  Auxiliary production reaction : 0.276032
  DM_mththf_c : 0.000150
  DM_5drib_c : 0.000075
  DM_4crsol_c : 0.000075

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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