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 : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3942 b1732 b1241 b0351 b2744 b3708 b3008 b1479 b0871 b3115 b1849 b2296 b2925 b2097 b3617 b3236 b1779 b2690 b2463 b2797 b3117 b1814 b4471 b2210 b3551 b1701 b1805 b3945 b4219 b1832 b1778 b4381 b2406 b2868 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 : 0.357830 (mmol/gDw/h)
  Minimum Production Rate : 0.061961 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.165644
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.174336
  EX_pi_e : 0.469087
  EX_so4_e : 0.090109
  EX_k_e : 0.069846
  EX_mg2_e : 0.003104
  EX_fe2_e : 0.002953
  EX_fe3_e : 0.002794
  EX_ca2_e : 0.001863
  EX_cl_e : 0.001863
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 43.550998
  EX_co2_e : 27.817402
  EX_h_e : 9.453830
  EX_pyr_e : 5.045103
  EX_mal__L_e : 0.435103
  Auxiliary production reaction : 0.061961
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000080

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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