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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b2779 b3617 b0030 b2407 b1851 b1982 b2797 b3117 b1814 b4471 b3665 b0261 b2406 b0112 b0114 b0509 b3125 b2366 b2492 b0904 b1533 b3821 b1380 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442484 (mmol/gDw/h)
  Minimum Production Rate : 0.662040 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.595116
  EX_o2_e : 275.610283
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.753504
  EX_pi_e : 1.750903
  EX_so4_e : 0.111426
  EX_k_e : 0.086370
  EX_mg2_e : 0.003839
  EX_ca2_e : 0.002303
  EX_cl_e : 0.002303
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992893
  EX_h2o_e : 549.495895
  EX_co2_e : 24.568922
  EX_ac_e : 1.681127
  Auxiliary production reaction : 0.662040
  EX_ade_e : 0.000495
  DM_5drib_c : 0.000297
  EX_glyclt_e : 0.000296
  DM_4crsol_c : 0.000099

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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