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 : 6hmhptpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2925 b2097 b3617 b0030 b1851 b2883 b1982 b3946 b0825 b0261 b4381 b2406 b0112 b2868 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 : 0.475023 (mmol/gDw/h)
  Minimum Production Rate : 1.478284 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.320299
  EX_nh4_e : 13.380411
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.414777
  EX_so4_e : 0.119620
  EX_k_e : 0.092721
  EX_fe2_e : 0.007629
  EX_mg2_e : 0.004121
  EX_ca2_e : 0.002472
  EX_cl_e : 0.002472
  EX_cu2_e : 0.000337
  EX_mn2_e : 0.000328
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 55.066155
  EX_co2_e : 22.551461
  EX_h_e : 13.480869
  EX_ac_e : 2.344249
  Auxiliary production reaction : 1.478284
  EX_ade_e : 0.171758
  DM_5drib_c : 0.171545
  DM_4crsol_c : 0.171332

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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