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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b3617 b2883 b1982 b0675 b2361 b0261 b4381 b0112 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 : 0.524724 (mmol/gDw/h)
  Minimum Production Rate : 1.549299 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.947596
  EX_nh4_e : 11.238760
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.506152
  EX_so4_e : 0.132136
  EX_k_e : 0.102423
  EX_fe2_e : 0.008428
  EX_mg2_e : 0.004552
  EX_ca2_e : 0.002731
  EX_cl_e : 0.002731
  EX_cu2_e : 0.000372
  EX_mn2_e : 0.000363
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.760483
  EX_co2_e : 19.287216
  EX_h_e : 10.698646
  Auxiliary production reaction : 1.549299
  EX_thymd_e : 0.461942
  EX_ac_e : 0.305487
  DM_5drib_c : 0.000352
  DM_4crsol_c : 0.000117

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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