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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3708 b3008 b0512 b0871 b2779 b3617 b0160 b1238 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b4381 b2406 b0114 b2366 b2492 b0904 b1533 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.565963 (mmol/gDw/h)
  Minimum Production Rate : 0.680590 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.644829
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.843546
  EX_pi_e : 1.226521
  EX_so4_e : 0.142521
  EX_k_e : 0.110472
  EX_fe2_e : 0.009090
  EX_mg2_e : 0.004910
  EX_ca2_e : 0.002946
  EX_cl_e : 0.002946
  EX_cu2_e : 0.000401
  EX_mn2_e : 0.000391
  EX_zn2_e : 0.000193
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.079868
  EX_co2_e : 26.632402
  EX_h_e : 7.931489
  EX_acald_e : 1.656142
  Auxiliary production reaction : 0.680590
  EX_alltn_e : 0.002210
  DM_mththf_c : 0.001830
  DM_5drib_c : 0.000380
  DM_4crsol_c : 0.000126

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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