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 : ametam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4069 b2744 b3708 b3008 b2297 b2458 b0160 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b2291 b0261 b4381 b3915 b0452 b0114 b1539 b2492 b0904 b1533 b3927 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.734632 (mmol/gDw/h)
  Minimum Production Rate : 0.186278 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.252142
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.051633
  EX_pi_e : 0.708631
  EX_so4_e : 0.371273
  EX_k_e : 0.143395
  EX_fe3_e : 0.011799
  EX_mg2_e : 0.006373
  EX_cl_e : 0.003824
  EX_ca2_e : 0.003824
  EX_cu2_e : 0.000521
  EX_mn2_e : 0.000508
  EX_zn2_e : 0.000251
  EX_ni2_e : 0.000237
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.824572
  EX_co2_e : 26.009254
  EX_h_e : 7.748419
  EX_ac_e : 0.613971
  Auxiliary production reaction : 0.186278
  DM_5drib_c : 0.000493
  DM_4crsol_c : 0.000164

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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