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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b3399 b4069 b2744 b3708 b3008 b3115 b1849 b2296 b0160 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.545456 (mmol/gDw/h)
  Minimum Production Rate : 0.053310 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.838321
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.691132
  EX_pi_e : 0.686079
  EX_so4_e : 0.350596
  EX_k_e : 0.106469
  EX_mobd_e : 0.053314
  EX_fe2_e : 0.008761
  EX_mg2_e : 0.004732
  EX_ca2_e : 0.002839
  EX_cl_e : 0.002839
  EX_cu2_e : 0.000387
  EX_mn2_e : 0.000377
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.699059
  EX_co2_e : 34.948230
  EX_h_e : 5.703810
  EX_ac_e : 0.530796
  Auxiliary production reaction : 0.053310
  DM_oxam_c : 0.000610
  DM_5drib_c : 0.000366
  DM_4crsol_c : 0.000122

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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