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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b0871 b2797 b3117 b1814 b4471 b2440 b1623 b3665 b0675 b2361 b4381 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3927 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.795131 (mmol/gDw/h)
  Minimum Production Rate : 0.122035 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.681247
  EX_o2_e : 274.990526
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.587348
  EX_pi_e : 0.889024
  EX_so4_e : 0.200230
  EX_k_e : 0.155204
  EX_mg2_e : 0.006898
  EX_cl_e : 0.004139
  EX_ca2_e : 0.004139
  EX_cu2_e : 0.000564
  EX_mn2_e : 0.000549
  EX_zn2_e : 0.000271
  EX_ni2_e : 0.000257
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987229
  EX_h2o_e : 547.864427
  EX_co2_e : 26.751563
  Auxiliary production reaction : 0.122035
  DM_mththf_c : 0.000356
  DM_5drib_c : 0.000179
  DM_4crsol_c : 0.000177

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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