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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM2927 STM4482 STM0413 STM1749 STM2463 STM4275 STM2009 STM1886 STM3512 STM3541 STM4568 STM2458 STM3709 STM0506 STM0974 STM0152 STM2338 STM2466 STM2332 STM4452 STM3802 STM2196 STM3240 STM2970 STM3243 STM0007 STM2473 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.153843 (mmol/gDw/h)
  Minimum Production Rate : 0.049193 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 6.669430
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.052752
  EX_pi_e : 0.185625
  EX_k_e : 0.027322
  EX_so4_e : 0.018766
  EX_mg2_e : 0.001215
  EX_fe2_e : 0.001128
  EX_cl_e : 0.000729
  EX_ca2_e : 0.000729
  EX_cu2_e : 0.000486
  EX_mn2_e : 0.000486
  EX_mobd_e : 0.000486
  EX_zn2_e : 0.000486
  EX_cobalt2_e : 0.000486

Product: (mmol/gDw/h)
  EX_h2o_e : 12.248970
  EX_h_e : 9.477272
  EX_ac_e : 7.815668
  EX_co2_e : 6.371121
  EX_enter_e : 0.051528
  Auxiliary production reaction : 0.049193
  EX_ade_e : 0.001146
  EX_23dhbzs3_e : 0.000100
  DM_hmfurn_c : 0.000069

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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