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 (50 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b4384 b2744 b1479 b0512 b2297 b2458 b0030 b3236 b2883 b2463 b1982 b3616 b3589 b2210 b1623 b0261 b4381 b2406 b0112 b4064 b4464 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.473384 (mmol/gDw/h)
  Minimum Production Rate : 1.789681 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.028899
  EX_nh4_e : 10.533212
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.246310
  EX_so4_e : 0.119207
  EX_k_e : 0.092401
  EX_fe2_e : 0.007603
  EX_mg2_e : 0.004107
  EX_cl_e : 0.002464
  EX_ca2_e : 0.002464
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000327
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 46.329722
  EX_co2_e : 19.421104
  EX_h_e : 14.054438
  EX_ac_e : 2.494410
  Auxiliary production reaction : 1.789681
  EX_alltn_e : 0.012916
  DM_5drib_c : 0.000318
  DM_4crsol_c : 0.000106

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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