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 : 12dgr161_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: STM3646 STM2285 STM3526 STM0322 STM0169 STM0861 STM4326 STM1511 STM3068 STM2141 STM1135 STM4183 STM0368 STM3597 STM4408 STM1291 STM3069 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM0007 STM2473 STM0402 STM0608   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.229165 (mmol/gDw/h)
  Minimum Production Rate : 0.050045 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.525425
  EX_pi_e : 0.203229
  EX_k_e : 0.040700
  EX_so4_e : 0.027954
  EX_mg2_e : 0.001809
  EX_fe2_e : 0.001680
  EX_ca2_e : 0.001086
  EX_cl_e : 0.001086
  EX_cu2_e : 0.000724
  EX_mn2_e : 0.000724
  EX_mobd_e : 0.000724
  EX_zn2_e : 0.000724
  EX_cobalt2_e : 0.000724

Product: (mmol/gDw/h)
  EX_h2o_e : 25.574872
  EX_co2_e : 19.107058
  EX_h_e : 2.081101
  EX_ac_e : 0.126873
  Auxiliary production reaction : 0.050045
  EX_glyclt_e : 0.011458
  DM_hmfurn_c : 0.000102

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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