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 (20 of 124: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3646 STM2285 STM3526 STM4326 STM1511 STM1135 STM3542 STM4485 STM4183 STM0370 STM1448 STM1326 STM4062 STM3069 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM1124   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.233468 (mmol/gDw/h)
  Minimum Production Rate : 0.043611 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.572850
  EX_pi_e : 0.250656
  EX_k_e : 0.041464
  EX_so4_e : 0.028479
  EX_mg2_e : 0.001843
  EX_fe2_e : 0.001711
  EX_ca2_e : 0.001106
  EX_cl_e : 0.001106
  EX_cobalt2_e : 0.000737
  EX_cu2_e : 0.000737
  EX_mn2_e : 0.000737
  EX_mobd_e : 0.000737
  EX_zn2_e : 0.000737

Product: (mmol/gDw/h)
  EX_h2o_e : 25.716895
  EX_co2_e : 19.106131
  EX_h_e : 2.060188
  EX_ac_e : 0.069261
  Auxiliary production reaction : 0.043611
  EX_glyclt_e : 0.011673
  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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