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 : 4fe4s_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 16: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4382 b3942 b1732 b4384 b2744 b3708 b3008 b0512 b0871 b2407 b3236 b2797 b3117 b1814 b4471 b2440 b2913 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.709646 (mmol/gDw/h)
  Minimum Production Rate : 0.060382 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.900653
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.675202
  EX_pi_e : 0.684529
  EX_so4_e : 0.420231
  EX_fe2_e : 0.252925
  EX_k_e : 0.138518
  EX_mg2_e : 0.006156
  EX_ca2_e : 0.003694
  EX_cl_e : 0.003694
  EX_cu2_e : 0.000503
  EX_mn2_e : 0.000490
  EX_zn2_e : 0.000242
  EX_ni2_e : 0.000229
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 49.679179
  EX_co2_e : 30.859606
  EX_h_e : 6.410832
  Auxiliary production reaction : 0.060382
  EX_alltn_e : 0.002770
  DM_mththf_c : 0.000318
  DM_5drib_c : 0.000160
  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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