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 : uri_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b0474 b2518 b1241 b0351 b3831 b0910 b3752 b4152 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b2690 b1033 b0675 b0411 b0822 b1602 b4138 b4123 b0621 b1727 b2492 b0904 b1380 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.405304 (mmol/gDw/h)
  Minimum Production Rate : 0.214059 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.422979
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.952086
  EX_pi_e : 0.390958
  EX_so4_e : 0.102064
  EX_k_e : 0.079112
  EX_fe2_e : 0.006510
  EX_mg2_e : 0.003516
  EX_ca2_e : 0.002110
  EX_cl_e : 0.002110
  EX_cu2_e : 0.000287
  EX_mn2_e : 0.000280
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 47.184524
  EX_co2_e : 32.883137
  EX_h_e : 8.429449
  EX_succ_e : 1.947277
  EX_ac_e : 0.235962
  Auxiliary production reaction : 0.214059
  EX_ura_e : 0.073361
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000090

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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