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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b1241 b0351 b4069 b3708 b2297 b2458 b3617 b0030 b2407 b1238 b2883 b2797 b3117 b1814 b4471 b4381 b2406 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b3821 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.522449 (mmol/gDw/h)
  Minimum Production Rate : 0.521589 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.429962
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.293525
  EX_pi_e : 1.547136
  EX_so4_e : 0.653152
  EX_k_e : 0.101978
  EX_fe2_e : 0.008391
  EX_mg2_e : 0.004532
  EX_cl_e : 0.002719
  EX_ca2_e : 0.002719
  EX_cu2_e : 0.000370
  EX_mn2_e : 0.000361
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.251496
  EX_co2_e : 22.066467
  EX_h_e : 9.132671
  EX_ac_e : 2.767437
  Auxiliary production reaction : 0.521589
  EX_mththf_e : 0.000234
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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.

Last updated: 21-Sep-2023
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