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 : prbatp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3500 b3399 b4382 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2781 b0099 b3617 b0160 b2235 b1982 b1623 b0675 b2361 b0261 b0112 b0114 b0529 b2492 b0904 b2954   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.526983 (mmol/gDw/h)
  Minimum Production Rate : 0.518655 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.812544
  EX_nh4_e : 10.249815
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.582952
  EX_so4_e : 0.132705
  EX_k_e : 0.102863
  EX_fe2_e : 0.008464
  EX_mg2_e : 0.004572
  EX_cl_e : 0.002743
  EX_ca2_e : 0.002743
  EX_cu2_e : 0.000374
  EX_mn2_e : 0.000364
  EX_zn2_e : 0.000180
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 48.259473
  EX_co2_e : 20.149322
  EX_h_e : 8.670065
  EX_thymd_e : 0.982586
  Auxiliary production reaction : 0.518655
  EX_ac_e : 0.306802
  DM_5drib_c : 0.000354
  DM_4crsol_c : 0.000118

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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