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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b1241 b0351 b4069 b3708 b2930 b4232 b3697 b3925 b2297 b2458 b2779 b3617 b2797 b3117 b1814 b4471 b3946 b0825 b4381 b2406 b0511 b0114 b1539 b2492 b0904 b0515 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.361155 (mmol/gDw/h)
  Minimum Production Rate : 0.851399 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.666161
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.157439
  EX_pi_e : 0.348372
  EX_so4_e : 0.090946
  EX_k_e : 0.070495
  EX_fe2_e : 0.005801
  EX_mg2_e : 0.003133
  EX_ca2_e : 0.001880
  EX_cl_e : 0.001880
  EX_cu2_e : 0.000256
  EX_mn2_e : 0.000250
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_h2o_e : 49.210812
  EX_co2_e : 30.308315
  EX_h_e : 10.751936
  EX_ac_e : 3.176383
  Auxiliary production reaction : 0.851399
  DM_mththf_c : 0.000162
  EX_glyc__R_e : 0.000121
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000081

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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