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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (108 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM2927 STM1463 STM3747 STM2421 STM0413 STM1749 STM2463 STM4275 STM4568 STM1511 STM0694 STM3045 STM0974 STM0152 STM0150 STM3957 STM2338 STM2466 STM3103 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.305750 (mmol/gDw/h)
  Minimum Production Rate : 0.253953 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 11.436064
  EX_glc__D_e : 5.000000
  EX_nh4_e : 4.893120
  EX_pi_e : 0.779052
  EX_k_e : 0.054301
  EX_so4_e : 0.037296
  EX_mg2_e : 0.002414
  EX_fe2_e : 0.002241
  EX_ca2_e : 0.001448
  EX_cl_e : 0.001448
  EX_cu2_e : 0.000966
  EX_mn2_e : 0.000966
  EX_mobd_e : 0.000966
  EX_zn2_e : 0.000966
  EX_cobalt2_e : 0.000966

Product: (mmol/gDw/h)
  EX_h2o_e : 24.098445
  EX_co2_e : 10.590386
  EX_h_e : 4.732536
  EX_ac_e : 1.124695
  Auxiliary production reaction : 0.253953
  DM_hmfurn_c : 0.000136

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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