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 : rhcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b2836 b3553 b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b3617 b0160 b2687 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b0112 b0114 b0509 b3125 b2366 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.511049 (mmol/gDw/h)
  Minimum Production Rate : 0.764950 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.190922
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.049531
  EX_so4_e : 0.893642
  EX_pi_e : 0.492961
  EX_k_e : 0.099753
  EX_fe2_e : 0.008208
  EX_mg2_e : 0.004433
  EX_cl_e : 0.002660
  EX_ca2_e : 0.002660
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000353
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 40.984247
  EX_co2_e : 23.663415
  EX_h_e : 8.933404
  EX_ac_e : 3.471702
  DM_oxam_c : 0.765293
  Auxiliary production reaction : 0.764950
  DM_5drib_c : 0.000343
  EX_glyclt_e : 0.000342
  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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