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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b3399 b3942 b1732 b4069 b2744 b2297 b2458 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b2690 b2463 b1982 b2210 b0675 b2361 b3551 b0261 b0411 b2799 b3945 b1602 b0153 b4219 b1832 b1778 b4381 b2406 b1727 b0114 b0584 b0529 b2492 b0904 b3927 b1380 b1710 b2480 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.323220 (mmol/gDw/h)
  Minimum Production Rate : 0.710357 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.626506
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.665911
  EX_pi_e : 2.442851
  EX_so4_e : 0.081393
  EX_k_e : 0.063090
  EX_fe2_e : 0.005191
  EX_mg2_e : 0.002804
  EX_ca2_e : 0.001682
  EX_cl_e : 0.001682
  EX_cu2_e : 0.000229
  EX_mn2_e : 0.000223
  EX_zn2_e : 0.000110
  EX_ni2_e : 0.000104

Product: (mmol/gDw/h)
  EX_h2o_e : 46.665717
  EX_co2_e : 30.517480
  EX_h_e : 8.324989
  EX_ac_e : 3.891288
  Auxiliary production reaction : 0.710357
  EX_fum_e : 0.354689
  EX_etoh_e : 0.288239
  EX_ade_e : 0.008819
  DM_5drib_c : 0.000217
  DM_4crsol_c : 0.000072

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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