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

Gene deletion strategy (40 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b2926 b3617 b0030 b2407 b1982 b4374 b2361 b2291 b0261 b0507 b2406 b0112 b0511 b0114 b0529 b2492 b0904 b0516 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.428889 (mmol/gDw/h)
  Minimum Production Rate : 1.643909 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 987.203288
  EX_o2_e : 275.426934
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.565613
  EX_pi_e : 2.057618
  EX_so4_e : 0.108003
  EX_k_e : 0.083716
  EX_mg2_e : 0.003721
  EX_cl_e : 0.002232
  EX_ca2_e : 0.002232
  EX_cu2_e : 0.000304
  EX_mn2_e : 0.000296
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993112
  EX_h2o_e : 547.532532
  EX_co2_e : 23.054608
  EX_ac_e : 2.271176
  Auxiliary production reaction : 1.643909
  EX_xan_e : 0.000480
  DM_5drib_c : 0.000288
  EX_glyclt_e : 0.000287
  DM_4crsol_c : 0.000096

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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