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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (118 of 118: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: STM3646 STM2421 STM1749 STM2463 STM4275 STM2122 STM2285 STM2009 STM3526 STM0169 STM0861 STM1750 STM3709 STM2283 STM1135 STM2167 STM3553 STM0974 STM0152 STM0785 STM1211 STM2317 STM0935 STM3179 STM4569 STM2338 STM2466 STM3885 STM3793 STM3802 STM2196 STM3240 STM2970 STM3243 STM0007 STM2473 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.012904 (mmol/gDw/h)
  Minimum Production Rate : 0.003633 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.173374
  EX_co2_e : 0.068029
  EX_pi_e : 0.015096
  EX_o2_e : 0.002877
  EX_k_e : 0.002292
  EX_so4_e : 0.001573
  EX_mg2_e : 0.000102
  EX_fe2_e : 0.000095
  EX_ca2_e : 0.000061
  EX_cl_e : 0.000061
  EX_cobalt2_e : 0.000041
  EX_cu2_e : 0.000041
  EX_mn2_e : 0.000041
  EX_mobd_e : 0.000041
  EX_zn2_e : 0.000041

Product: (mmol/gDw/h)
  EX_h_e : 9.962906
  EX_lac__D_e : 9.678386
  EX_h2o_e : 0.510558
  EX_pyr_e : 0.083302
  EX_ac_e : 0.053016
  EX_enter_e : 0.004073
  Auxiliary production reaction : 0.003655
  EX_glyc__R_e : 0.000323
  EX_23dhbzs3_e : 0.000100
  EX_hxan_e : 0.000096

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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