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 (39 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b2779 b0030 b2883 b1779 b1982 b3616 b3589 b0261 b0411 b2913 b4381 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 : 0.414278 (mmol/gDw/h)
  Minimum Production Rate : 1.587908 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.307487
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.240213
  EX_pi_e : 1.987523
  EX_so4_e : 0.104324
  EX_k_e : 0.080864
  EX_fe2_e : 0.006654
  EX_mg2_e : 0.003594
  EX_ca2_e : 0.002156
  EX_cl_e : 0.002156
  EX_cu2_e : 0.000294
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.662460
  EX_co2_e : 23.014615
  EX_h_e : 13.003808
  EX_ac_e : 2.843166
  Auxiliary production reaction : 1.587908
  EX_ade_e : 0.000464
  DM_5drib_c : 0.000278
  EX_glyc__R_e : 0.000139
  DM_4crsol_c : 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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