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 : 12dgr120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (6 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM2285 STM3526 STM0169 STM0861 STM4326 STM1511 STM2952 STM0321 STM1620 STM1448 STM1326 STM4062 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM2051 STM0007 STM2473   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.238641 (mmol/gDw/h)
  Minimum Production Rate : 0.054720 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.629857
  EX_pi_e : 0.211633
  EX_k_e : 0.042383
  EX_so4_e : 0.029110
  EX_mg2_e : 0.001884
  EX_fe2_e : 0.001749
  EX_ca2_e : 0.001130
  EX_cl_e : 0.001130
  EX_cobalt2_e : 0.000754
  EX_cu2_e : 0.000754
  EX_mn2_e : 0.000754
  EX_mobd_e : 0.000754
  EX_zn2_e : 0.000754

Product: (mmol/gDw/h)
  EX_h2o_e : 25.636826
  EX_co2_e : 19.003175
  EX_h_e : 2.167160
  EX_ac_e : 0.132119
  Auxiliary production reaction : 0.054720
  EX_glyclt_e : 0.011932
  DM_hmfurn_c : 0.000106

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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