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 : frdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4467 b1241 b0351 b3831 b4069 b4384 b0512 b2297 b2458 b2925 b2097 b3617 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b1982 b2498 b1727 b0114 b0529 b2492 b0904 b1380 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.394037 (mmol/gDw/h)
  Minimum Production Rate : 0.332898 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.737287
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.280944
  EX_pi_e : 1.045887
  EX_so4_e : 0.099226
  EX_k_e : 0.076913
  EX_fe2_e : 0.006329
  EX_mg2_e : 0.003418
  EX_ca2_e : 0.002051
  EX_cl_e : 0.002051
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 49.306993
  EX_co2_e : 35.007325
  EX_h_e : 4.944578
  EX_ac_e : 0.631266
  EX_thym_e : 0.401863
  Auxiliary production reaction : 0.332898
  EX_xtsn_e : 0.055147
  EX_alltn_e : 0.000265
  EX_glyclt_e : 0.000264
  DM_mththf_c : 0.000177
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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