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 : 25drapp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2883 b1779 b1982 b3616 b3589 b1033 b0675 b2361 b2291 b0261 b0411 b0507 b4381 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454644 (mmol/gDw/h)
  Minimum Production Rate : 0.671037 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.296188
  EX_nh4_e : 10.408980
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.109589
  EX_so4_e : 0.114488
  EX_k_e : 0.088743
  EX_fe2_e : 0.007302
  EX_mg2_e : 0.003944
  EX_ca2_e : 0.002366
  EX_cl_e : 0.002366
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.199149
  EX_co2_e : 24.052359
  EX_h_e : 9.941511
  EX_thymd_e : 1.071588
  Auxiliary production reaction : 0.671037
  EX_ac_e : 0.264687
  DM_oxam_c : 0.000509
  DM_5drib_c : 0.000305
  DM_4crsol_c : 0.000101

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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