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 : paps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 36: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b4382 b4069 b4384 b2744 b3708 b3008 b2297 b2458 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b0411 b0114 b2366 b2492 b0904 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.741449 (mmol/gDw/h)
  Minimum Production Rate : 0.314016 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.801648
  EX_o2_e : 274.761399
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.577672
  EX_pi_e : 1.343239
  EX_so4_e : 0.500728
  EX_k_e : 0.144726
  EX_mg2_e : 0.006432
  EX_ca2_e : 0.003859
  EX_cl_e : 0.003859
  EX_cu2_e : 0.000526
  EX_mn2_e : 0.000512
  EX_zn2_e : 0.000253
  EX_ni2_e : 0.000239
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988092
  EX_h2o_e : 549.531671
  EX_co2_e : 25.561769
  EX_ac_e : 0.431661
  Auxiliary production reaction : 0.314016
  DM_5drib_c : 0.000498
  DM_4crsol_c : 0.000165

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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