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 : pant__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b1241 b0351 b2744 b0871 b2925 b2097 b3617 b0160 b0517 b2690 b3962 b4139 b4267 b4374 b0675 b2361 b2291 b1493 b3517 b0822 b2799 b0726 b1727 b0114 b0755 b3612 b1539 b2492 b0904 b0508 b4266 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.543770 (mmol/gDw/h)
  Minimum Production Rate : 1.364768 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.966942
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.872670
  EX_pi_e : 0.524524
  EX_so4_e : 0.136932
  EX_k_e : 0.106140
  EX_fe2_e : 0.008733
  EX_mg2_e : 0.004717
  EX_ca2_e : 0.002830
  EX_cl_e : 0.002830
  EX_cu2_e : 0.000386
  EX_mn2_e : 0.000376
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 43.851590
  EX_co2_e : 29.492127
  EX_h_e : 6.361145
  Auxiliary production reaction : 1.364768
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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