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 : ins_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (108 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3553 b3942 b1732 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b1479 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2926 b3617 b2407 b3236 b2690 b2463 b3962 b1982 b2210 b4267 b1033 b1415 b3551 b2799 b3945 b4219 b1832 b1778 b4381 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b1710 b2480 b4266 b1518 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.298974 (mmol/gDw/h)
  Minimum Production Rate : 0.294427 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.897598
  EX_o2_e : 279.528318
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.522598
  EX_pi_e : 0.288392
  EX_so4_e : 0.075288
  EX_k_e : 0.058358
  EX_mg2_e : 0.002594
  EX_ca2_e : 0.001556
  EX_cl_e : 0.001556
  EX_cu2_e : 0.000212
  EX_mn2_e : 0.000207
  EX_zn2_e : 0.000102
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995198
  EX_h2o_e : 545.277317
  EX_co2_e : 27.210842
  EX_pyr_e : 3.882545
  EX_thymd_e : 0.557496
  EX_ins_e : 0.294427
  EX_ac_e : 0.174058
  EX_ade_e : 0.000201
  EX_dxylnt_e : 0.000200
  EX_mththf_e : 0.000134
  DM_5drib_c : 0.000067
  DM_4crsol_c : 0.000067

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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