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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b3617 b2883 b1982 b0261 b0411 b4381 b0112 b2868 b4064 b4464 b0114 b0509 b3125 b0529 b2492 b0904 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.507092 (mmol/gDw/h)
  Minimum Production Rate : 0.498966 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 19.794641
  EX_nh4_e : 10.364639
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.489144
  EX_so4_e : 0.127696
  EX_k_e : 0.098981
  EX_fe2_e : 0.008144
  EX_mg2_e : 0.004399
  EX_cl_e : 0.002639
  EX_ca2_e : 0.002639
  EX_cu2_e : 0.000360
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.209593
  EX_co2_e : 19.654168
  EX_h_e : 10.341640
  EX_thymd_e : 0.945725
  EX_ade_e : 0.499534
  DM_5drib_c : 0.499307
  DM_4crsol_c : 0.499079
  Auxiliary production reaction : 0.498966
  EX_ac_e : 0.295222

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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