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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b0160 b1238 b3616 b3589 b3665 b0675 b2361 b0261 b4381 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.519633 (mmol/gDw/h)
  Minimum Production Rate : 0.768005 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.945059
  EX_nh4_e : 10.365777
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.269247
  EX_so4_e : 0.130854
  EX_k_e : 0.101429
  EX_fe2_e : 0.008346
  EX_mg2_e : 0.004508
  EX_ca2_e : 0.002705
  EX_cl_e : 0.002705
  EX_cu2_e : 0.000368
  EX_mn2_e : 0.000359
  EX_zn2_e : 0.000177
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.352929
  EX_co2_e : 19.673520
  EX_h_e : 9.062898
  EX_thymd_e : 1.224884
  Auxiliary production reaction : 0.768005
  EX_ac_e : 0.302523
  DM_5drib_c : 0.000117
  DM_4crsol_c : 0.000116

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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