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 : lald__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b1478 b1241 b4069 b2930 b4232 b3697 b3925 b2297 b2458 b2926 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b1525 b4139 b1033 b2661 b1602 b0509 b3125 b2492 b0904 b3029 b1380 b2660 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.481072 (mmol/gDw/h)
  Minimum Production Rate : 0.133755 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.197351
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.195540
  EX_pi_e : 0.464045
  EX_so4_e : 0.121144
  EX_k_e : 0.093902
  EX_fe3_e : 0.007727
  EX_mg2_e : 0.004173
  EX_cl_e : 0.002504
  EX_ca2_e : 0.002504
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.992705
  EX_co2_e : 39.292779
  EX_h_e : 4.708084
  EX_ac_e : 0.280074
  Auxiliary production reaction : 0.133755
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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