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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b2297 b2458 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b2799 b3945 b1602 b2975 b3603 b2492 b0904 b1380 b2660 b1517 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.491327 (mmol/gDw/h)
  Minimum Production Rate : 0.290420 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.481973
  EX_o2_e : 286.176669
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.306293
  EX_pi_e : 1.054777
  EX_so4_e : 0.123726
  EX_k_e : 0.095904
  EX_mg2_e : 0.004262
  EX_ca2_e : 0.002557
  EX_cl_e : 0.002557
  EX_cu2_e : 0.000348
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992109
  EX_h2o_e : 551.359473
  EX_co2_e : 37.807984
  Auxiliary production reaction : 0.290420
  EX_ac_e : 0.286044
  DM_mththf_c : 0.000220
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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