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

Gene deletion strategy (49 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2502 b2744 b2297 b2458 b2779 b2925 b2097 b2926 b3617 b1982 b3946 b0825 b0675 b2361 b0261 b4381 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.515594 (mmol/gDw/h)
  Minimum Production Rate : 0.005207 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.795729
  EX_o2_e : 277.017295
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.829690
  EX_pi_e : 0.497345
  EX_so4_e : 0.129837
  EX_k_e : 0.100640
  EX_mg2_e : 0.004473
  EX_ca2_e : 0.002684
  EX_cl_e : 0.002684
  EX_cu2_e : 0.000366
  EX_mn2_e : 0.000356
  EX_zn2_e : 0.000176
  EX_ni2_e : 0.000167
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991719
  EX_h2o_e : 545.342873
  EX_co2_e : 27.890362
  EX_ac_e : 2.197188
  EX_thymd_e : 0.630660
  Auxiliary production reaction : 0.005207
  DM_5drib_c : 0.000346
  DM_4crsol_c : 0.000115

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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