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 : q8_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2779 b0160 b3616 b3589 b3665 b0675 b2361 b4381 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.377806 (mmol/gDw/h)
  Minimum Production Rate : 0.181141 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.663991
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.080271
  EX_pi_e : 0.364434
  EX_so4_e : 0.095139
  EX_k_e : 0.073745
  EX_fe2_e : 0.006068
  EX_mg2_e : 0.003277
  EX_ca2_e : 0.001966
  EX_cl_e : 0.001966
  EX_cu2_e : 0.000268
  EX_mn2_e : 0.000261
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 44.609551
  EX_co2_e : 32.459056
  EX_h_e : 3.691384
  DM_mththf_c : 0.543591
  EX_ac_e : 0.219953
  Auxiliary production reaction : 0.181141
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000084

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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