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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b3617 b1238 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b0507 b4381 b2406 b0112 b2943 b0452 b0114 b1539 b2492 b0904 b1533 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.514531 (mmol/gDw/h)
  Minimum Production Rate : 0.513197 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.039890
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.149846
  EX_pi_e : 1.522713
  EX_so4_e : 0.642766
  EX_k_e : 0.100433
  EX_mg2_e : 0.004464
  EX_fe2_e : 0.004246
  EX_fe3_e : 0.004017
  EX_ca2_e : 0.002678
  EX_cl_e : 0.002678
  EX_cu2_e : 0.000365
  EX_mn2_e : 0.000356
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.475219
  EX_co2_e : 22.651191
  EX_h_e : 8.997596
  EX_ac_e : 2.724775
  Auxiliary production reaction : 0.513197
  DM_oxam_c : 0.000576
  DM_5drib_c : 0.000345
  EX_glyclt_e : 0.000344
  DM_4crsol_c : 0.000115

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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