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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (106 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM2421 STM1749 STM2463 STM4275 STM3680 STM2009 STM1750 STM4570 STM2952 STM3709 STM0974 STM0152 STM0150 STM2338 STM2466 STM2422 STM3885 STM3793 STM4452 STM3802 STM2196 STM3240 STM2970 STM3243 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.298424 (mmol/gDw/h)
  Minimum Production Rate : 0.245647 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 13.867129
  EX_glc__D_e : 5.000000
  EX_nh4_e : 4.282373
  EX_pi_e : 1.001590
  EX_k_e : 0.053000
  EX_so4_e : 0.036402
  EX_mg2_e : 0.002356
  EX_fe2_e : 0.002187
  EX_ca2_e : 0.001414
  EX_cl_e : 0.001414
  EX_cu2_e : 0.000942
  EX_mn2_e : 0.000942
  EX_mobd_e : 0.000942
  EX_zn2_e : 0.000942
  EX_cobalt2_e : 0.000942

Product: (mmol/gDw/h)
  EX_h2o_e : 25.235756
  EX_co2_e : 13.793079
  EX_h_e : 3.120862
  EX_acald_e : 1.009218
  Auxiliary production reaction : 0.245647
  EX_ac_e : 0.088531
  EX_ade_e : 0.002222
  DM_hmfurn_c : 0.000133

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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