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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3752 b3115 b1849 b2296 b2779 b3617 b2407 b3236 b0907 b1779 b1982 b2210 b0261 b2406 b0112 b0114 b0529 b2492 b0904 b0515 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.412644 (mmol/gDw/h)
  Minimum Production Rate : 1.581644 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.444947
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.203305
  EX_pi_e : 1.979684
  EX_so4_e : 0.103912
  EX_k_e : 0.080545
  EX_fe2_e : 0.006627
  EX_mg2_e : 0.003580
  EX_ca2_e : 0.002148
  EX_cl_e : 0.002148
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.714098
  EX_co2_e : 23.160911
  EX_h_e : 12.952102
  EX_ac_e : 2.832043
  Auxiliary production reaction : 1.581644
  EX_alltn_e : 0.000462
  DM_5drib_c : 0.000277
  DM_4crsol_c : 0.000092
  EX_glyc__R_e : 0.000092

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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