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 (29 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM0620 STM1749 STM2463 STM2654 STM2555 STM0934 STM2285 STM3526 STM0169 STM0861 STM3866 STM1620 STM2167 STM4183 STM0785 STM0150 STM0568 STM1211 STM2317 STM0935 STM3179 STM2338 STM2466 STM1937 STM0733 STM0007 STM2473   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.014345 (mmol/gDw/h)
  Minimum Production Rate : 0.015530 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.163755
  EX_o2_e : 0.089804
  EX_pi_e : 0.018395
  EX_k_e : 0.002548
  EX_so4_e : 0.001749
  EX_mg2_e : 0.000113
  EX_fe2_e : 0.000105
  EX_ca2_e : 0.000068
  EX_cl_e : 0.000068
  EX_cobalt2_e : 0.000045
  EX_cu2_e : 0.000045
  EX_mn2_e : 0.000045
  EX_mobd_e : 0.000045
  EX_zn2_e : 0.000045

Product: (mmol/gDw/h)
  EX_h_e : 9.762057
  EX_lac__D_e : 9.554288
  EX_h2o_e : 0.741384
  EX_co2_e : 0.169345
  EX_succ_e : 0.022471
  Auxiliary production reaction : 0.015530
  EX_ac_e : 0.013617
  EX_lipa_cold_e : 0.002838
  EX_glyclt_e : 0.000717

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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