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 : btn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b2836 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467032 (mmol/gDw/h)
  Minimum Production Rate : 0.232917 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.267702
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.140681
  EX_so4_e : 0.583441
  EX_pi_e : 0.450502
  EX_k_e : 0.091161
  EX_fe2_e : 0.007501
  EX_mg2_e : 0.004052
  EX_ca2_e : 0.002431
  EX_cl_e : 0.002431
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 44.954759
  EX_co2_e : 27.263600
  EX_h_e : 8.861930
  EX_ac_e : 2.706116
  DM_oxam_c : 0.466356
  DM_5drib_c : 0.233230
  EX_meoh_e : 0.232918
  DM_amob_c : 0.232918
  Auxiliary production reaction : 0.232917
  EX_glyc__R_e : 0.000156
  DM_4crsol_c : 0.000104

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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