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 : preq0_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b3617 b2407 b1982 b0675 b2361 b0261 b0112 b2975 b0114 b3603 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 : 0.508051 (mmol/gDw/h)
  Minimum Production Rate : 0.749864 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.594425
  EX_nh4_e : 11.631735
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.490069
  EX_so4_e : 0.127937
  EX_k_e : 0.099168
  EX_fe2_e : 0.008160
  EX_mg2_e : 0.004407
  EX_ca2_e : 0.002644
  EX_cl_e : 0.002644
  EX_cu2_e : 0.000360
  EX_mn2_e : 0.000351
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 49.430090
  EX_co2_e : 19.829549
  EX_h_e : 11.859215
  EX_thymd_e : 1.197468
  EX_ac_e : 1.045645
  Auxiliary production reaction : 0.749864
  DM_oxam_c : 0.000569
  DM_5drib_c : 0.000341
  DM_4crsol_c : 0.000113

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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