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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b0871 b2297 b2458 b2925 b2097 b2926 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b3945 b4381 b2406 b0452 b0114 b2366 b2492 b0904 b1533 b3927 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.574593 (mmol/gDw/h)
  Minimum Production Rate : 0.225582 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.108375
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.349144
  EX_pi_e : 1.005420
  EX_so4_e : 0.144694
  EX_k_e : 0.112157
  EX_fe2_e : 0.009229
  EX_mg2_e : 0.004985
  EX_cl_e : 0.002991
  EX_ca2_e : 0.002991
  EX_cu2_e : 0.000407
  EX_mn2_e : 0.000397
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.026735
  EX_co2_e : 26.605052
  EX_h_e : 8.832142
  EX_pyr_e : 2.284348
  EX_ac_e : 0.334520
  Auxiliary production reaction : 0.225582
  DM_oxam_c : 0.015678
  DM_5drib_c : 0.000386
  DM_4crsol_c : 0.000128

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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