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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3916 b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b3617 b0160 b1851 b1982 b1200 b0675 b2361 b0261 b4381 b2406 b0112 b2868 b0114 b1723 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447449 (mmol/gDw/h)
  Minimum Production Rate : 1.691632 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.915313
  EX_nh4_e : 13.351614
  EX_glc__D_e : 10.000000
  EX_so4_e : 0.626288
  EX_pi_e : 0.431612
  EX_k_e : 0.087339
  EX_fe2_e : 0.007186
  EX_mg2_e : 0.003882
  EX_ca2_e : 0.002329
  EX_cl_e : 0.002329
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.486341
  EX_co2_e : 21.632045
  EX_h_e : 13.961072
  EX_ac_e : 2.357751
  Auxiliary production reaction : 1.691632
  EX_h2s_e : 0.513611
  EX_gua_e : 0.011708
  EX_ade_e : 0.000501
  DM_5drib_c : 0.000300
  DM_4crsol_c : 0.000100

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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