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 (22 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b2502 b4384 b2744 b3708 b3008 b0871 b2797 b3117 b1814 b4471 b3665 b4374 b0675 b2361 b2291 b3654 b3714 b3664 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b4141 b1798 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.772097 (mmol/gDw/h)
  Minimum Production Rate : 0.089101 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.432031
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.962291
  EX_pi_e : 1.012074
  EX_so4_e : 0.283531
  EX_k_e : 0.150708
  EX_fe2_e : 0.012401
  EX_mg2_e : 0.006698
  EX_ca2_e : 0.004019
  EX_cl_e : 0.004019
  EX_cu2_e : 0.000547
  EX_mn2_e : 0.000534
  EX_zn2_e : 0.000263
  EX_ni2_e : 0.000249
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.428879
  EX_co2_e : 26.168803
  EX_h_e : 7.361639
  Auxiliary production reaction : 0.089101
  EX_mththf_e : 0.000346
  DM_5drib_c : 0.000174
  DM_4crsol_c : 0.000172

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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