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 : frdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2779 b3617 b0160 b1612 b1611 b4122 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0114 b2366 b2492 b0904 b1533 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.388155 (mmol/gDw/h)
  Minimum Production Rate : 0.387517 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.111701
  EX_o2_e : 282.098058
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.192042
  EX_pi_e : 1.149450
  EX_so4_e : 0.097745
  EX_k_e : 0.075765
  EX_mg2_e : 0.003367
  EX_ca2_e : 0.002020
  EX_cl_e : 0.002020
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993766
  EX_h2o_e : 547.454864
  EX_co2_e : 34.848282
  EX_ac_e : 0.893528
  EX_fum_e : 0.404765
  Auxiliary production reaction : 0.387517
  DM_mththf_c : 0.000174
  DM_5drib_c : 0.000087
  DM_4crsol_c : 0.000087

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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