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 (58 of 127: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM3010 STM3646 STM2927 STM1463 STM3747 STM0413 STM4275 STM2555 STM4568 STM1718 STM1135 STM2167 STM0694 STM3045 STM0974 STM0152 STM1211 STM2317 STM2502 STM2501 STM1480 STM2338 STM2466 STM2332 STM3968 STM2498 STM2050   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.280398 (mmol/gDw/h)
  Minimum Production Rate : 0.026485 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.293785
  EX_pi_e : 0.301634
  EX_k_e : 0.049799
  EX_so4_e : 0.034204
  EX_mg2_e : 0.002214
  EX_fe2_e : 0.002055
  EX_ca2_e : 0.001328
  EX_cl_e : 0.001328
  EX_cobalt2_e : 0.000885
  EX_cu2_e : 0.000885
  EX_mn2_e : 0.000885
  EX_mobd_e : 0.000885
  EX_zn2_e : 0.000885

Product: (mmol/gDw/h)
  EX_h2o_e : 26.680463
  EX_co2_e : 18.339086
  EX_h_e : 2.584595
  EX_ac_e : 0.083183
  Auxiliary production reaction : 0.026485
  EX_thymd_e : 0.009180
  DM_hmfurn_c : 0.000125

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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