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 : cdg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b3617 b0160 b1982 b0675 b2361 b2291 b0261 b0507 b4381 b0112 b0114 b0529 b2492 b0904 b0516   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.509957 (mmol/gDw/h)
  Minimum Production Rate : 0.750547 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.446148
  EX_nh4_e : 10.920147
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.491908
  EX_so4_e : 0.128417
  EX_k_e : 0.099540
  EX_fe2_e : 0.008190
  EX_mg2_e : 0.004424
  EX_ca2_e : 0.002654
  EX_cl_e : 0.002654
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.876140
  EX_co2_e : 19.678411
  EX_h_e : 11.897748
  EX_thymd_e : 1.201250
  EX_ac_e : 1.047437
  Auxiliary production reaction : 0.750547
  EX_alltn_e : 0.001991
  DM_5drib_c : 0.001762
  DM_4crsol_c : 0.001534
  EX_glyclt_e : 0.001420

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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