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 : 4abut_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 112: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM0620 STM2792 STM1749 STM2463 STM2285 STM3526 STM4326 STM1511 STM2952 STM0840 STM0842 STM1620 STM4183 STM1448 STM3359 STM4484 STM0399 STM0935 STM3179 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM0977 STM1124 STM0733 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.077377 (mmol/gDw/h)
  Minimum Production Rate : 1.042000 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 10.264749
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.291292
  EX_pi_e : 0.068618
  EX_k_e : 0.013742
  EX_so4_e : 0.009439
  EX_mg2_e : 0.000611
  EX_fe2_e : 0.000567
  EX_ca2_e : 0.000367
  EX_cl_e : 0.000367
  EX_cobalt2_e : 0.000244
  EX_cu2_e : 0.000244
  EX_mn2_e : 0.000244
  EX_mobd_e : 0.000244
  EX_zn2_e : 0.000244

Product: (mmol/gDw/h)
  EX_h2o_e : 16.196827
  EX_co2_e : 11.625100
  EX_h_e : 5.579861
  EX_ac_e : 2.481431
  Auxiliary production reaction : 2.438593
  EX_acald_e : 0.328400
  EX_glyclt_e : 0.003869
  DM_hmfurn_c : 0.000035

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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