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 : gdpddman_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b0160 b1238 b3616 b3589 b3665 b0675 b2361 b4381 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.529396 (mmol/gDw/h)
  Minimum Production Rate : 0.521702 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.363165
  EX_nh4_e : 10.300279
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.554064
  EX_so4_e : 0.133313
  EX_k_e : 0.103334
  EX_fe2_e : 0.008503
  EX_mg2_e : 0.004593
  EX_cl_e : 0.002756
  EX_ca2_e : 0.002756
  EX_cu2_e : 0.000375
  EX_mn2_e : 0.000366
  EX_zn2_e : 0.000181
  EX_ni2_e : 0.000171
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.162642
  EX_co2_e : 19.434218
  EX_h_e : 8.711950
  EX_thymd_e : 0.987165
  Auxiliary production reaction : 0.521702
  EX_ac_e : 0.308207
  DM_mththf_c : 0.000237
  DM_5drib_c : 0.000119
  DM_4crsol_c : 0.000118

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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