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 : idp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (102 of 104: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM2927 STM1749 STM2463 STM4275 STM0371 STM4108 STM2009 STM4570 STM1885 STM2952 STM3709 STM1620 STM2167 STM0694 STM3045 STM0974 STM0152 STM4484 STM0542 STM1211 STM2317 STM1480 STM2338 STM2466 STM1627 STM1567 STM2461   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.171576 (mmol/gDw/h)
  Minimum Production Rate : 0.208528 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.731290
  EX_so4_e : 0.907707
  EX_pi_e : 0.569213
  EX_k_e : 0.030472
  EX_mg2_e : 0.001355
  EX_fe2_e : 0.001257
  EX_cl_e : 0.000813
  EX_ca2_e : 0.000813
  EX_cobalt2_e : 0.000542
  EX_cu2_e : 0.000542
  EX_mn2_e : 0.000542
  EX_mobd_e : 0.000542
  EX_zn2_e : 0.000542

Product: (mmol/gDw/h)
  EX_h2o_e : 26.942825
  EX_co2_e : 19.612108
  EX_h_e : 0.971062
  EX_h2s_e : 0.886778
  EX_ac_e : 0.563843
  Auxiliary production reaction : 0.208528
  EX_5dglcn_e : 0.085668
  EX_glyclt_e : 0.008579
  EX_ade_e : 0.001278
  EX_glyc_e : 0.000119
  DM_hmfurn_c : 0.000077

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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