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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b1241 b0351 b4069 b4384 b3752 b2297 b2458 b3617 b2407 b3124 b0907 b1779 b1982 b0261 b4381 b2406 b0112 b2789 b3127 b2975 b0114 b3603 b0755 b3612 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.414281 (mmol/gDw/h)
  Minimum Production Rate : 1.587915 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.307572
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.238405
  EX_pi_e : 1.987533
  EX_so4_e : 0.104324
  EX_k_e : 0.080865
  EX_fe2_e : 0.006654
  EX_mg2_e : 0.003594
  EX_ca2_e : 0.002156
  EX_cl_e : 0.002156
  EX_cu2_e : 0.000294
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.659383
  EX_co2_e : 23.015129
  EX_h_e : 13.002621
  EX_ac_e : 2.843272
  Auxiliary production reaction : 1.587915
  DM_oxam_c : 0.000464
  DM_5drib_c : 0.000278
  EX_dxylnt_e : 0.000185
  DM_4crsol_c : 0.000092

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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