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 : pa181_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (31 of 124: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM2285 STM3526 STM4567 STM4326 STM2952 STM0321 STM3709 STM1620 STM3542 STM4485 STM0368 STM1448 STM1326 STM4062 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM0977 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.232923 (mmol/gDw/h)
  Minimum Production Rate : 0.041806 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.566837
  EX_pi_e : 0.248367
  EX_k_e : 0.041367
  EX_so4_e : 0.028412
  EX_mg2_e : 0.001839
  EX_fe2_e : 0.001707
  EX_ca2_e : 0.001103
  EX_cl_e : 0.001103
  EX_cobalt2_e : 0.000736
  EX_cu2_e : 0.000736
  EX_mn2_e : 0.000736
  EX_mobd_e : 0.000736
  EX_zn2_e : 0.000736

Product: (mmol/gDw/h)
  EX_h2o_e : 25.666813
  EX_co2_e : 19.078313
  EX_h_e : 2.115228
  EX_ac_e : 0.128953
  Auxiliary production reaction : 0.041806
  EX_glyclt_e : 0.011646
  DM_hmfurn_c : 0.000104

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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