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 : xtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2744 b2297 b2458 b2926 b0160 b1238 b3236 b1982 b3616 b3589 b2210 b0675 b2361 b4381 b0114 b0529 b2492 b0904 b0516 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.509396 (mmol/gDw/h)
  Minimum Production Rate : 0.974940 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.725759
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.409154
  EX_pi_e : 3.416187
  EX_so4_e : 0.128276
  EX_k_e : 0.099431
  EX_fe2_e : 0.008181
  EX_mg2_e : 0.004419
  EX_ca2_e : 0.002651
  EX_cl_e : 0.002651
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.022043
  EX_co2_e : 25.882149
  EX_h_e : 8.359743
  EX_ac_e : 1.721370
  Auxiliary production reaction : 0.974940
  EX_alltn_e : 0.001989
  DM_mththf_c : 0.001647
  DM_5drib_c : 0.000342
  DM_4crsol_c : 0.000114

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
Contact