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 : din_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (94 of 94: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM2421 STM1749 STM2463 STM4275 STM4567 STM0840 STM0842 STM3068 STM2141 STM0974 STM0152 STM3359 STM0772 STM4585 STM3704 STM0518 STM4484 STM0542 STM0935 STM1480 STM4126 STM2338 STM2466 STM2422 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.241994 (mmol/gDw/h)
  Minimum Production Rate : 0.188451 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 14.326357
  EX_nh4_e : 5.045076
  EX_glc__D_e : 5.000000
  EX_pi_e : 0.214606
  EX_k_e : 0.042978
  EX_so4_e : 0.029519
  EX_mg2_e : 0.001911
  EX_fe2_e : 0.001774
  EX_ca2_e : 0.001146
  EX_cl_e : 0.001146
  EX_cu2_e : 0.000764
  EX_mn2_e : 0.000764
  EX_mobd_e : 0.000764
  EX_zn2_e : 0.000764
  EX_cobalt2_e : 0.000764

Product: (mmol/gDw/h)
  EX_h2o_e : 23.816580
  EX_co2_e : 13.070884
  EX_h_e : 4.929144
  EX_ser__L_e : 1.247560
  EX_ac_e : 0.499343
  Auxiliary production reaction : 0.188451
  EX_thym_e : 0.188451
  DM_hmfurn_c : 0.000108

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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