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 : hxan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4384 b2744 b3708 b3008 b0871 b2407 b2797 b3117 b1814 b4471 b0261 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b3825 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.797182 (mmol/gDw/h)
  Minimum Production Rate : 0.183873 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.926880
  EX_o2_e : 275.115272
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.344987
  EX_pi_e : 0.768966
  EX_so4_e : 0.200746
  EX_k_e : 0.155604
  EX_mg2_e : 0.006916
  EX_cl_e : 0.004149
  EX_ca2_e : 0.004149
  EX_cu2_e : 0.000565
  EX_mn2_e : 0.000551
  EX_zn2_e : 0.000272
  EX_ni2_e : 0.000257
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987196
  EX_h2o_e : 549.059811
  EX_co2_e : 26.359991
  Auxiliary production reaction : 0.183873
  DM_5drib_c : 0.000179
  DM_4crsol_c : 0.000178

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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