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 : pa160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM3646 STM1749 STM2463 STM4108 STM2285 STM3526 STM3091 STM0169 STM0861 STM4326 STM3709 STM3529 STM1135 STM3597 STM4408 STM1291 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM1124 STM0402 STM0608   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.217334 (mmol/gDw/h)
  Minimum Production Rate : 0.033069 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.395055
  EX_pi_e : 0.225807
  EX_k_e : 0.038599
  EX_so4_e : 0.026511
  EX_mg2_e : 0.001716
  EX_fe2_e : 0.001593
  EX_ca2_e : 0.001030
  EX_cl_e : 0.001030
  EX_cu2_e : 0.000686
  EX_mn2_e : 0.000686
  EX_mobd_e : 0.000686
  EX_zn2_e : 0.000686
  EX_cobalt2_e : 0.000686

Product: (mmol/gDw/h)
  EX_h2o_e : 25.254839
  EX_co2_e : 19.197159
  EX_h_e : 1.906953
  EX_acald_e : 0.554470
  EX_ac_e : 0.064475
  Auxiliary production reaction : 0.033069
  EX_glyald_e : 0.000151
  DM_hmfurn_c : 0.000097

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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