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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3846 b2341 b4069 b4384 b3708 b3008 b2297 b2458 b0030 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b0596 b3665 b0261 b4381 b2406 b0452 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.710614 (mmol/gDw/h)
  Minimum Production Rate : 0.180608 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.608535
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.942801
  EX_pi_e : 1.227287
  EX_so4_e : 0.359555
  EX_k_e : 0.138707
  EX_fe2_e : 0.011413
  EX_mg2_e : 0.006165
  EX_ca2_e : 0.003699
  EX_cl_e : 0.003699
  EX_cu2_e : 0.000504
  EX_mn2_e : 0.000491
  EX_zn2_e : 0.000242
  EX_ni2_e : 0.000230
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.869847
  EX_co2_e : 25.303778
  EX_h_e : 7.669520
  EX_ac_e : 0.594318
  Auxiliary production reaction : 0.180608
  EX_ade_e : 0.000795
  DM_5drib_c : 0.000477
  DM_4crsol_c : 0.000158

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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