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

Gene deletion strategy (39 of 101: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM0758 STM4061 STM3747 STM3952 STM3680 STM1522 STM3091 STM3066 STM3614 STM3866 STM1884 STM3986 STM3880 STM1620 STM2081 STM0974 STM2472 STM0832 STM1211 STM2317 STM1480 STM1806 STM0039 STM2041 STM4301 STM3599 STM4325 STM0627 STM3959 STM4456 STM3763   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.012768 (mmol/gDw/h)
  Minimum Production Rate : 0.078048 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.140701
  EX_o2_e : 0.066018
  EX_pi_e : 0.011321
  EX_k_e : 0.002268
  EX_so4_e : 0.001557
  EX_mg2_e : 0.000101
  EX_fe3_e : 0.000094
  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_h_e : 9.749171
  EX_lac__D_e : 9.412587
  EX_h2o_e : 0.372161
  EX_idon__L_e : 0.131858
  EX_12ppd__R_e : 0.078019
  EX_co2_e : 0.050371
  EX_succ_e : 0.047877
  EX_glyclt_e : 0.000638

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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