MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : dhna_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM3646 STM0620 STM1597 STM1749 STM2463 STM0737 STM2654 STM0441 STM3680 STM0169 STM0861 STM4283 STM1511 STM3866 STM1135 STM2167 STM2472 STM0785 STM4184 STM0542 STM1211 STM2317 STM0935 STM2338 STM2466 STM0007 STM2473 STM0054 STM3353   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.012724 (mmol/gDw/h)
  Minimum Production Rate : 0.008741 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_o2_e : 4.887844
  EX_nh4_e : 0.140214
  EX_pi_e : 0.011281
  EX_k_e : 0.002260
  EX_so4_e : 0.001551
  EX_mg2_e : 0.000100
  EX_fe2_e : 0.000093
  EX_ca2_e : 0.000060
  EX_cl_e : 0.000060
  EX_cobalt2_e : 0.000040
  EX_cu2_e : 0.000040
  EX_mn2_e : 0.000040
  EX_mobd_e : 0.000040
  EX_zn2_e : 0.000040

Product: (mmol/gDw/h)
  EX_h2o_e : 10.185456
  EX_h_e : 9.901969
  EX_pyr_e : 9.778319
  EX_etoh_e : 0.022480
  EX_co2_e : 0.017676
  Auxiliary production reaction : 0.008740
  EX_ac_e : 0.007044

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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: 27-Sep-2023
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