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 : ade_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b4382 b1241 b0351 b4384 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b3945 b1602 b0153 b3654 b3714 b3664 b1727 b4064 b4464 b0584 b0529 b2492 b0904 b1380 b2660 b1518 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.509335 (mmol/gDw/h)
  Minimum Production Rate : 0.020151 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.955707
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.601527
  EX_pi_e : 0.491307
  EX_so4_e : 0.128261
  EX_k_e : 0.099419
  EX_fe2_e : 0.008180
  EX_mg2_e : 0.004418
  EX_ca2_e : 0.002651
  EX_cl_e : 0.002651
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.643889
  EX_co2_e : 38.992259
  EX_h_e : 4.780726
  Auxiliary production reaction : 0.020151
  DM_mththf_c : 0.000228
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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