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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (99 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: STM0758 STM4061 STM0620 STM3747 STM3952 STM1749 STM2463 STM0737 STM2654 STM3016 STM3066 STM3614 STM3869 STM1771 STM3709 STM0866 STM0086 STM3457 STM0974 STM4299 STM2403 STM3062 STM0785 STM0832 STM4184 STM1480 STM1806 STM0039 STM2338 STM2466 STM3661 STM4301 STM3599 STM4325 STM0627 STM3959 STM1793 STM0741   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.014952 (mmol/gDw/h)
  Minimum Production Rate : 0.004265 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.164762
  EX_o2_e : 0.020395
  EX_pi_e : 0.013257
  EX_k_e : 0.002655
  EX_so4_e : 0.001823
  EX_mg2_e : 0.000118
  EX_fe2_e : 0.000110
  EX_ca2_e : 0.000071
  EX_cl_e : 0.000071
  EX_cobalt2_e : 0.000047
  EX_cu2_e : 0.000047
  EX_mn2_e : 0.000047
  EX_mobd_e : 0.000047
  EX_zn2_e : 0.000047

Product: (mmol/gDw/h)
  EX_h_e : 9.950121
  EX_lac__D_e : 9.755855
  EX_h2o_e : 0.437699
  EX_ac_e : 0.042578
  EX_pyr_e : 0.012023
  EX_co2_e : 0.007050
  EX_succ_e : 0.006457

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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