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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b2836 b3399 b2744 b3708 b3008 b0871 b2925 b2097 b0160 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b4374 b0675 b2361 b2291 b0261 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b3447   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.629472 (mmol/gDw/h)
  Minimum Production Rate : 0.072218 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.118823
  EX_o2_e : 276.553636
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.304471
  EX_pi_e : 0.751628
  EX_so4_e : 0.230731
  EX_k_e : 0.122869
  EX_mg2_e : 0.005461
  EX_ca2_e : 0.003276
  EX_cl_e : 0.003276
  EX_cu2_e : 0.000446
  EX_mn2_e : 0.000435
  EX_zn2_e : 0.000215
  EX_ni2_e : 0.000203
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989890
  EX_h2o_e : 546.824239
  EX_co2_e : 27.036188
  EX_pyr_e : 1.869166
  Auxiliary production reaction : 0.072218
  DM_oxam_c : 0.000704
  DM_5drib_c : 0.000422
  DM_4crsol_c : 0.000140

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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