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 : rhcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b3399 b4069 b2744 b3708 b3008 b2297 b2458 b0160 b2687 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b4381 b2406 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.733332 (mmol/gDw/h)
  Minimum Production Rate : 0.218871 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.632715
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.138795
  EX_pi_e : 0.707377
  EX_so4_e : 0.403539
  EX_k_e : 0.143141
  EX_mg2_e : 0.006362
  EX_fe2_e : 0.006052
  EX_fe3_e : 0.005726
  EX_cl_e : 0.003817
  EX_ca2_e : 0.003817
  EX_cu2_e : 0.000520
  EX_mn2_e : 0.000507
  EX_zn2_e : 0.000250
  EX_ni2_e : 0.000237
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 46.656021
  EX_co2_e : 26.636998
  EX_h_e : 7.170809
  EX_ac_e : 0.645807
  Auxiliary production reaction : 0.218871
  DM_5drib_c : 0.000492
  DM_4crsol_c : 0.000164

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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