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 : fgam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (114 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: STM3009 STM3747 STM0051 STM2421 STM1749 STM2463 STM4275 STM4108 STM1750 STM4570 STM1885 STM3709 STM2283 STM1620 STM2167 STM0974 STM0152 STM3069 STM4484 STM1211 STM2317 STM4569 STM1480 STM2338 STM2466 STM2422 STM3802 STM2196 STM3240 STM2970 STM3243 STM2051 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.187096 (mmol/gDw/h)
  Minimum Production Rate : 0.031745 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.125308
  EX_so4_e : 0.466804
  EX_pi_e : 0.197666
  EX_k_e : 0.033228
  EX_mg2_e : 0.001477
  EX_fe2_e : 0.001371
  EX_ca2_e : 0.000886
  EX_cl_e : 0.000886
  EX_cobalt2_e : 0.000591
  EX_cu2_e : 0.000591
  EX_mn2_e : 0.000591
  EX_mobd_e : 0.000591
  EX_zn2_e : 0.000591

Product: (mmol/gDw/h)
  EX_h2o_e : 24.616882
  EX_co2_e : 20.326489
  EX_etoh_e : 1.026239
  EX_h_e : 0.826511
  EX_h2s_e : 0.443982
  EX_ac_e : 0.055504
  Auxiliary production reaction : 0.031745
  EX_glyclt_e : 0.009355
  DM_hmfurn_c : 0.000083

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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