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 : eig3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b0512 b2297 b2458 b3617 b1004 b3713 b1109 b0046 b1779 b1982 b2797 b3117 b1814 b4471 b2210 b1033 b4374 b0675 b2361 b2291 b1602 b0114 b2366 b2492 b0904 b1533 b1380 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393340 (mmol/gDw/h)
  Minimum Production Rate : 1.177550 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.726673
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.604199
  EX_pi_e : 1.556968
  EX_so4_e : 0.099051
  EX_k_e : 0.076777
  EX_fe2_e : 0.006317
  EX_mg2_e : 0.003412
  EX_ca2_e : 0.002047
  EX_cl_e : 0.002047
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 51.253127
  EX_co2_e : 34.976499
  EX_h_e : 6.876053
  Auxiliary production reaction : 1.177550
  EX_ac_e : 0.905728
  EX_alltn_e : 0.000265
  DM_mththf_c : 0.000176
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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