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 (20 of 127: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: STM0066 STM3576 STM3646 STM2927 STM0051 STM4482 STM2421 STM4004 STM4290 STM4275 STM0441 STM2555 STM4398 STM3554 STM4164 STM2009 STM0316 STM1886 STM2355 STM4567 STM3512 STM3541 STM3514 STM1304 STM2947 STM2283 STM1135 STM4086 STM0261 STM2167 STM3961 STM0974 STM0152 STM1448 STM1566 STM4299 STM0182 STM0542 STM1211 STM2317 STM0935 STM2502 STM2338 STM2466 STM0208 STM3305 STM3661 STM2022 STM2058 STM2776 STM1746_S STM4559_S STM2864   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.015461 (mmol/gDw/h)
  Minimum Production Rate : 0.001158 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.176259
  EX_co2_e : 0.045946
  EX_pi_e : 0.014796
  EX_o2_e : 0.003611
  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 : 9.948149
  EX_lac__D_e : 9.723483
  EX_h2o_e : 0.481120
  EX_pyr_e : 0.084759
  EX_ac_e : 0.004586
  Auxiliary production reaction : 0.000544
  EX_hxan_e : 0.000519

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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