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 (9 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b2297 b2458 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b2835 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.547828 (mmol/gDw/h)
  Minimum Production Rate : 1.639309 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.417216
  EX_o2_e : 267.425058
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.555804
  EX_pi_e : 0.528438
  EX_so4_e : 0.137954
  EX_k_e : 0.106932
  EX_mg2_e : 0.004752
  EX_ca2_e : 0.002851
  EX_cl_e : 0.002851
  EX_cu2_e : 0.000388
  EX_mn2_e : 0.000379
  EX_zn2_e : 0.000187
  EX_ni2_e : 0.000177
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991201
  EX_h2o_e : 537.976605
  EX_co2_e : 20.235765
  Auxiliary production reaction : 1.639309
  EX_ac_e : 1.261705
  DM_5drib_c : 0.000368
  DM_4crsol_c : 0.000122

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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