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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2502 b2744 b3115 b1849 b2296 b3617 b1982 b0675 b2361 b2291 b0261 b4381 b0112 b0114 b0509 b3125 b0529 b2492 b0904 b0508   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.512850 (mmol/gDw/h)
  Minimum Production Rate : 0.754805 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.473631
  EX_nh4_e : 10.976089
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.249503
  EX_so4_e : 0.129146
  EX_k_e : 0.100105
  EX_fe2_e : 0.008237
  EX_mg2_e : 0.004449
  EX_cl_e : 0.002669
  EX_ca2_e : 0.002669
  EX_cu2_e : 0.000364
  EX_mn2_e : 0.000354
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.046551
  EX_co2_e : 19.453674
  EX_h_e : 10.451628
  EX_thymd_e : 1.208065
  Auxiliary production reaction : 0.754805
  EX_ac_e : 0.298574
  DM_oxam_c : 0.002002
  DM_5drib_c : 0.001772
  DM_4crsol_c : 0.001543
  EX_glyclt_e : 0.001428

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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