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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b2836 b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0261 b4381 b2406 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.774294 (mmol/gDw/h)
  Minimum Production Rate : 0.076142 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.727714
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.896170
  EX_pi_e : 0.975315
  EX_so4_e : 0.271125
  EX_k_e : 0.151137
  EX_fe2_e : 0.012436
  EX_mg2_e : 0.006717
  EX_ca2_e : 0.004030
  EX_cl_e : 0.004030
  EX_cu2_e : 0.000549
  EX_mn2_e : 0.000535
  EX_zn2_e : 0.000264
  EX_ni2_e : 0.000250
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.413192
  EX_co2_e : 26.392378
  EX_h_e : 7.393956
  Auxiliary production reaction : 0.076142
  EX_pyr_e : 0.049276
  DM_oxam_c : 0.000866
  DM_5drib_c : 0.000520
  DM_4crsol_c : 0.000173

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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