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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b2297 b2458 b0030 b2407 b3124 b1779 b1982 b3616 b3589 b0261 b4388 b4381 b2406 b0112 b0114 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 : 0.424001 (mmol/gDw/h)
  Minimum Production Rate : 0.812587 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.900539
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.204824
  EX_pi_e : 0.408994
  EX_so4_e : 0.106772
  EX_k_e : 0.082762
  EX_fe2_e : 0.006810
  EX_mg2_e : 0.003678
  EX_ca2_e : 0.002207
  EX_cl_e : 0.002207
  EX_cu2_e : 0.000301
  EX_mn2_e : 0.000293
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 42.284138
  EX_co2_e : 25.398384
  EX_h_e : 9.244634
  EX_ac_e : 2.097304
  DM_oxam_c : 0.813061
  DM_5drib_c : 0.812871
  DM_4crsol_c : 0.812681
  Auxiliary production reaction : 0.812587
  EX_glyc__R_e : 0.000142

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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