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 : ps181_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (26 of 132: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM0158 STM4482 STM2285 STM3526 STM3512 STM3541 STM4326 STM1511 STM1620 STM1448 STM1326 STM4062 STM3069 STM4184 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 : 0.232323 (mmol/gDw/h)
  Minimum Production Rate : 0.042483 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.602712
  EX_pi_e : 0.248513
  EX_k_e : 0.041261
  EX_so4_e : 0.028339
  EX_mg2_e : 0.001834
  EX_fe2_e : 0.001703
  EX_ca2_e : 0.001101
  EX_cl_e : 0.001101
  EX_cobalt2_e : 0.000734
  EX_cu2_e : 0.000734
  EX_mn2_e : 0.000734
  EX_mobd_e : 0.000734
  EX_zn2_e : 0.000734

Product: (mmol/gDw/h)
  EX_h2o_e : 25.727400
  EX_co2_e : 19.067755
  EX_h_e : 2.050081
  EX_ac_e : 0.068921
  Auxiliary production reaction : 0.042483
  EX_glyclt_e : 0.011616
  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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