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 (46 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b2926 b0030 b2407 b3124 b1982 b3616 b3589 b0261 b0411 b0112 b0114 b0529 b2492 b0904 b0514 b0515 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.457864 (mmol/gDw/h)
  Minimum Production Rate : 0.673877 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.384850
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.804623
  EX_pi_e : 0.441658
  EX_so4_e : 0.115299
  EX_k_e : 0.089372
  EX_fe2_e : 0.007354
  EX_mg2_e : 0.003972
  EX_cl_e : 0.002383
  EX_ca2_e : 0.002383
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000316
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.115264
  EX_co2_e : 23.798011
  EX_h_e : 10.681722
  EX_thymd_e : 1.078539
  EX_ac_e : 0.940439
  Auxiliary production reaction : 0.673877
  EX_alltn_e : 0.001787
  DM_5drib_c : 0.001582
  DM_4crsol_c : 0.001377
  EX_glyc__R_e : 0.000638

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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