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 : phe__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM1886 STM1290 STM4326 STM1135 STM3542 STM4485 STM4183 STM0150 STM4484 STM0568 STM2317 STM3179 STM1480 STM4126 STM3248 STM0519 STM1937 STM2041 STM0007 STM2473   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.246891 (mmol/gDw/h)
  Minimum Production Rate : 0.169614 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.890386
  EX_pi_e : 0.218949
  EX_k_e : 0.043848
  EX_so4_e : 0.030116
  EX_mg2_e : 0.001949
  EX_fe2_e : 0.001809
  EX_ca2_e : 0.001170
  EX_cl_e : 0.001170
  EX_cu2_e : 0.000780
  EX_mn2_e : 0.000780
  EX_mobd_e : 0.000780
  EX_zn2_e : 0.000780
  EX_cobalt2_e : 0.000780

Product: (mmol/gDw/h)
  EX_h2o_e : 26.250194
  EX_co2_e : 18.595759
  EX_h_e : 2.426318
  Auxiliary production reaction : 0.169614
  EX_ac_e : 0.151312
  EX_glyclt_e : 0.012345
  DM_hmfurn_c : 0.000110

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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