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 (32 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b3617 b2407 b1779 b1982 b0675 b2361 b0112 b2868 b0114 b0529 b2492 b0904 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.396971 (mmol/gDw/h)
  Minimum Production Rate : 1.290990 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.883780
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.870567
  EX_pi_e : 1.673910
  EX_so4_e : 0.099965
  EX_k_e : 0.077486
  EX_fe2_e : 0.006376
  EX_mg2_e : 0.003444
  EX_ca2_e : 0.002066
  EX_cl_e : 0.002066
  EX_cu2_e : 0.000281
  EX_mn2_e : 0.000274
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 52.199934
  EX_co2_e : 35.259410
  EX_h_e : 6.230842
  Auxiliary production reaction : 1.290990
  EX_acald_e : 0.349297
  EX_ade_e : 0.000267
  DM_mththf_c : 0.000178
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000089

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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