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 : xdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b3927 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.751629 (mmol/gDw/h)
  Minimum Production Rate : 0.298721 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.577016
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.312415
  EX_pi_e : 1.322468
  EX_so4_e : 0.189275
  EX_k_e : 0.146713
  EX_fe2_e : 0.012072
  EX_mg2_e : 0.006520
  EX_ca2_e : 0.003912
  EX_cl_e : 0.003912
  EX_cu2_e : 0.000533
  EX_mn2_e : 0.000519
  EX_zn2_e : 0.000256
  EX_ni2_e : 0.000243
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.718113
  EX_co2_e : 25.285013
  EX_h_e : 8.240020
  EX_ac_e : 0.437588
  Auxiliary production reaction : 0.298721
  DM_5drib_c : 0.000504
  DM_4crsol_c : 0.000168

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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