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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2502 b2744 b3708 b1479 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2779 b3236 b2690 b2463 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b4374 b0675 b2361 b2291 b3551 b0261 b3945 b4219 b1832 b1778 b0114 b1539 b2492 b0904 b1533 b1710 b2480 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.322944 (mmol/gDw/h)
  Minimum Production Rate : 0.966660 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.415699
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.421960
  EX_pi_e : 2.244834
  EX_so4_e : 0.081324
  EX_k_e : 0.063036
  EX_mg2_e : 0.002802
  EX_fe2_e : 0.002665
  EX_fe3_e : 0.002522
  EX_ca2_e : 0.001681
  EX_cl_e : 0.001681
  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 : 43.256118
  EX_co2_e : 26.319679
  EX_h_e : 8.318039
  EX_glyc__R_e : 2.962620
  Auxiliary production reaction : 0.966660
  EX_ac_e : 0.743631
  EX_fum_e : 0.337198
  EX_xan_e : 0.000217
  DM_5drib_c : 0.000073
  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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