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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (5 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b2297 b2458 b0030 b2407 b0583 b1982 b2797 b3117 b1814 b4471 b0261 b3709 b2406 b3161 b0112 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b1473 b0515 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.541903 (mmol/gDw/h)
  Minimum Production Rate : 0.344323 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.008288
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.543584
  EX_pi_e : 0.522723
  EX_so4_e : 0.136462
  EX_k_e : 0.105776
  EX_fe2_e : 0.008704
  EX_mg2_e : 0.004701
  EX_ca2_e : 0.002821
  EX_cl_e : 0.002821
  EX_cu2_e : 0.000384
  EX_mn2_e : 0.000374
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 50.404188
  EX_co2_e : 33.335184
  EX_h_e : 5.985786
  Auxiliary production reaction : 0.344323
  EX_ac_e : 0.315489
  EX_alltn_e : 0.000606
  DM_5drib_c : 0.000364
  DM_4crsol_c : 0.000121

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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