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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 127: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM3646 STM1193 STM0051 STM2421 STM4275 STM0441 STM2555 STM0661 STM2122 STM2009 STM0180 STM1750 STM2458 STM1135 STM2167 STM2081 STM0974 STM0152 STM1211 STM2317 STM0935 STM4569 STM0039 STM2338 STM2466 STM4349 STM0208 STM1306   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.015463 (mmol/gDw/h)
  Minimum Production Rate : 0.001097 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.177501
  EX_co2_e : 0.045953
  EX_pi_e : 0.015607
  EX_o2_e : 0.003922
  EX_k_e : 0.002746
  EX_so4_e : 0.001885
  EX_mg2_e : 0.000122
  EX_fe2_e : 0.000113
  EX_ca2_e : 0.000073
  EX_cl_e : 0.000073
  EX_cobalt2_e : 0.000049
  EX_cu2_e : 0.000049
  EX_mn2_e : 0.000049
  EX_mobd_e : 0.000049
  EX_zn2_e : 0.000049

Product: (mmol/gDw/h)
  EX_h_e : 9.945984
  EX_lac__D_e : 9.721064
  EX_h2o_e : 0.485881
  EX_pyr_e : 0.084603
  EX_ac_e : 0.004586
  Auxiliary production reaction : 0.000949
  EX_glyc__R_e : 0.000387
  EX_hxan_e : 0.000115

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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