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 (61 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3708 b3008 b0871 b2925 b2097 b3617 b2883 b2690 b2797 b3117 b1814 b4471 b3945 b4381 b2406 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.626371 (mmol/gDw/h)
  Minimum Production Rate : 0.090804 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.066759
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.974450
  EX_so4_e : 0.822608
  EX_pi_e : 0.785808
  EX_k_e : 0.122263
  EX_fe2_e : 0.010060
  EX_mg2_e : 0.005434
  EX_ca2_e : 0.003260
  EX_cl_e : 0.003260
  EX_cu2_e : 0.000444
  EX_mn2_e : 0.000433
  EX_zn2_e : 0.000214
  EX_ni2_e : 0.000202
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 45.169221
  EX_co2_e : 25.845887
  EX_h_e : 5.453685
  EX_acald_e : 1.832912
  EX_met__L_e : 0.574072
  Auxiliary production reaction : 0.090804
  DM_mththf_c : 0.000281
  DM_5drib_c : 0.000141
  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.

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Last updated: 21-Sep-2023
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