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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b1241 b0351 b2930 b4232 b3697 b3925 b0871 b2926 b3617 b1004 b3713 b1109 b0046 b3236 b2690 b1493 b3517 b4015 b3945 b1602 b2913 b1727 b1380 b0606 b0221 b2285 b3893 b1474 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.437742 (mmol/gDw/h)
  Minimum Production Rate : 1.209639 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.305907
  EX_o2_e : 282.241073
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.727574
  EX_pi_e : 0.422248
  EX_so4_e : 0.110232
  EX_k_e : 0.085444
  EX_mg2_e : 0.003797
  EX_ca2_e : 0.002278
  EX_cl_e : 0.002278
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000302
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992969
  EX_h2o_e : 542.900559
  EX_co2_e : 33.282400
  EX_for_e : 3.664916
  EX_12ppd__S_e : 1.209639
  EX_etoh_e : 0.728239
  DM_5drib_c : 0.000098
  DM_4crsol_c : 0.000098

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.

Last updated: 21-Sep-2023
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