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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (107 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM0051 STM2421 STM1749 STM2463 STM4275 STM0371 STM0661 STM4570 STM1620 STM2167 STM0974 STM0152 STM1211 STM2317 STM4569 STM1480 STM2338 STM2466 STM3802 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 : 0.240231 (mmol/gDw/h)
  Minimum Production Rate : 0.123069 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.410263
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.148602
  EX_pi_e : 0.582250
  EX_k_e : 0.042665
  EX_so4_e : 0.029304
  EX_mg2_e : 0.001897
  EX_fe2_e : 0.001761
  EX_cl_e : 0.001138
  EX_ca2_e : 0.001138
  EX_cu2_e : 0.000759
  EX_mn2_e : 0.000759
  EX_mobd_e : 0.000759
  EX_zn2_e : 0.000759
  EX_cobalt2_e : 0.000759

Product: (mmol/gDw/h)
  EX_h2o_e : 25.328345
  EX_co2_e : 17.825533
  EX_h_e : 2.374951
  EX_etoh_e : 0.737743
  Auxiliary production reaction : 0.123069
  EX_ac_e : 0.071267
  EX_glyclt_e : 0.012012
  EX_ade_e : 0.001789
  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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