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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (97 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM2927 STM1463 STM3747 STM2421 STM1749 STM2463 STM4275 STM1290 STM4567 STM4568 STM1511 STM2458 STM3709 STM0974 STM0152 STM0150 STM2338 STM2466 STM0208 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 : 0.307898 (mmol/gDw/h)
  Minimum Production Rate : 0.230846 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_fe2_e : 17.221604
  EX_h_e : 12.760580
  EX_glc__D_e : 5.000000
  EX_nh4_e : 4.587542
  EX_pi_e : 0.503897
  EX_so4_e : 0.268404
  EX_k_e : 0.054683
  EX_mg2_e : 0.002431
  EX_ca2_e : 0.001459
  EX_cl_e : 0.001459
  EX_cobalt2_e : 0.000972
  EX_cu2_e : 0.000972
  EX_mn2_e : 0.000972
  EX_mobd_e : 0.000972
  EX_zn2_e : 0.000972

Product: (mmol/gDw/h)
  EX_h2o_e : 33.688860
  EX_fe3_e : 17.219347
  EX_co2_e : 13.509497
  EX_ac_e : 1.115753
  Auxiliary production reaction : 0.230846
  EX_gua_e : 0.008048
  DM_hmfurn_c : 0.000137

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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