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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3708 b0512 b0871 b2925 b2097 b3617 b2797 b3117 b1814 b4471 b3946 b0825 b4381 b2406 b0511 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 : 0.471077 (mmol/gDw/h)
  Minimum Production Rate : 1.098372 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.390683
  EX_o2_e : 276.538225
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.262528
  EX_pi_e : 0.454404
  EX_so4_e : 0.118627
  EX_k_e : 0.091951
  EX_mg2_e : 0.004087
  EX_ca2_e : 0.002452
  EX_cl_e : 0.002452
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000326
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992434
  EX_h2o_e : 543.815822
  EX_co2_e : 29.004253
  Auxiliary production reaction : 1.098372
  EX_acald_e : 0.822802
  EX_thym_e : 0.012995
  EX_xan_e : 0.012643
  DM_mththf_c : 0.000211
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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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