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 : adphep_DD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b0160 b1238 b1982 b3616 b3589 b0675 b2361 b0261 b4381 b0112 b0114 b0529 b2492 b0904 b0515   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.555611 (mmol/gDw/h)
  Minimum Production Rate : 0.439008 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.824109
  EX_nh4_e : 10.054357
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.413962
  EX_so4_e : 0.139914
  EX_k_e : 0.108451
  EX_fe2_e : 0.008924
  EX_mg2_e : 0.004820
  EX_cl_e : 0.002892
  EX_ca2_e : 0.002892
  EX_cu2_e : 0.000394
  EX_mn2_e : 0.000384
  EX_zn2_e : 0.000189
  EX_ni2_e : 0.000179
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.837914
  EX_co2_e : 20.446461
  EX_h_e : 8.280966
  EX_thymd_e : 0.928141
  Auxiliary production reaction : 0.439008
  EX_alltn_e : 0.000622
  DM_5drib_c : 0.000373
  DM_4crsol_c : 0.000124

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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