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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b3846 b2341 b4384 b2744 b3708 b3008 b0871 b2407 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b3709 b3161 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0886 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.746797 (mmol/gDw/h)
  Minimum Production Rate : 0.103351 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.343166
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.788797
  EX_pi_e : 1.030418
  EX_so4_e : 0.291409
  EX_k_e : 0.145769
  EX_fe2_e : 0.011994
  EX_mg2_e : 0.006478
  EX_ca2_e : 0.003887
  EX_cl_e : 0.003887
  EX_cu2_e : 0.000529
  EX_mn2_e : 0.000516
  EX_zn2_e : 0.000255
  EX_ni2_e : 0.000241
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.551509
  EX_co2_e : 26.040196
  EX_h_e : 7.171918
  Auxiliary production reaction : 0.103351
  DM_5drib_c : 0.000168
  DM_4crsol_c : 0.000167

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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