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 : nac_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b0474 b2518 b1241 b0351 b2744 b0910 b4152 b0871 b2297 b2458 b2779 b2925 b2097 b2926 b1612 b1611 b4122 b2690 b1525 b4374 b0675 b4015 b2661 b0614 b0726 b3945 b4138 b4123 b0621 b0452 b1539 b1380 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.589000 (mmol/gDw/h)
  Minimum Production Rate : 0.274303 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.905721
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.922217
  EX_pi_e : 0.568152
  EX_so4_e : 0.148322
  EX_k_e : 0.114969
  EX_fe2_e : 0.009460
  EX_mg2_e : 0.005110
  EX_ca2_e : 0.003066
  EX_cl_e : 0.003066
  EX_cu2_e : 0.000418
  EX_mn2_e : 0.000407
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.759818
  EX_co2_e : 28.503327
  EX_h_e : 8.798134
  EX_ac_e : 1.322388
  EX_succ_e : 0.614204
  Auxiliary production reaction : 0.274303
  EX_ura_e : 0.143385
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000131

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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