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 : camp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (96 of 100: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM2927 STM1463 STM3747 STM2421 STM1749 STM2463 STM4275 STM3680 STM1750 STM3709 STM1620 STM2167 STM0974 STM0152 STM1211 STM2317 STM4569 STM2338 STM2466 STM0208 STM3802 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 : 0.240708 (mmol/gDw/h)
  Minimum Production Rate : 0.186762 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.191019
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.586445
  EX_pi_e : 0.400228
  EX_k_e : 0.042750
  EX_so4_e : 0.029362
  EX_mg2_e : 0.001900
  EX_fe2_e : 0.001764
  EX_ca2_e : 0.001140
  EX_cl_e : 0.001140
  EX_cobalt2_e : 0.000760
  EX_cu2_e : 0.000760
  EX_mn2_e : 0.000760
  EX_mobd_e : 0.000760
  EX_zn2_e : 0.000760

Product: (mmol/gDw/h)
  EX_h2o_e : 26.116356
  EX_co2_e : 17.052539
  EX_h_e : 2.871123
  EX_acald_e : 0.800864
  Auxiliary production reaction : 0.186762
  EX_ac_e : 0.071409
  EX_glyclt_e : 0.012035
  DM_hmfurn_c : 0.000107

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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