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 (15 of 51: 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 b3236 b1982 b0675 b2361 b0261 b4381 b2406 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 : 0.487795 (mmol/gDw/h)
  Minimum Production Rate : 1.844164 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.872965
  EX_nh4_e : 10.853869
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.314693
  EX_so4_e : 0.122836
  EX_k_e : 0.095214
  EX_fe2_e : 0.007834
  EX_mg2_e : 0.004232
  EX_ca2_e : 0.002539
  EX_cl_e : 0.002539
  EX_cu2_e : 0.000346
  EX_mn2_e : 0.000337
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 44.069401
  EX_co2_e : 20.029945
  EX_h_e : 10.793962
  EX_ac_e : 2.570345
  Auxiliary production reaction : 1.844164
  EX_alltn_e : 0.013309
  DM_5drib_c : 0.000327
  DM_4crsol_c : 0.000109

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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