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 (82 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: STM0620 STM4482 STM2792 STM1749 STM2463 STM0737 STM2654 STM0441 STM2555 STM0934 STM2285 STM3526 STM3512 STM3541 STM4283 STM3866 STM1620 STM2167 STM0785 STM4184 STM1211 STM2317 STM0935 STM3179 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 : 0.013684 (mmol/gDw/h)
  Minimum Production Rate : 0.009404 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.150793
  EX_o2_e : 0.024168
  EX_pi_e : 0.012133
  EX_k_e : 0.002430
  EX_so4_e : 0.001668
  EX_mg2_e : 0.000108
  EX_fe2_e : 0.000100
  EX_ca2_e : 0.000065
  EX_cl_e : 0.000065
  EX_cobalt2_e : 0.000043
  EX_cu2_e : 0.000043
  EX_mn2_e : 0.000043
  EX_mobd_e : 0.000043
  EX_zn2_e : 0.000043

Product: (mmol/gDw/h)
  EX_h_e : 9.921913
  EX_lac__D_e : 9.746011
  EX_h2o_e : 0.471284
  EX_ac_e : 0.033441
  EX_pyr_e : 0.016373
  EX_co2_e : 0.011888
  Auxiliary production reaction : 0.009400
  EX_glyclt_e : 0.000684

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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