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 : pa120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM3646 STM4482 STM1749 STM2463 STM2285 STM3526 STM0322 STM3512 STM3541 STM4570 STM4326 STM2952 STM0840 STM0842 STM3709 STM1135 STM4183 STM0974 STM1448 STM3062 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM2051 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.228712 (mmol/gDw/h)
  Minimum Production Rate : 0.026379 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.520439
  EX_pi_e : 0.229207
  EX_k_e : 0.040619
  EX_so4_e : 0.027899
  EX_mg2_e : 0.001806
  EX_fe2_e : 0.001676
  EX_ca2_e : 0.001083
  EX_cl_e : 0.001083
  EX_cobalt2_e : 0.000722
  EX_cu2_e : 0.000722
  EX_mn2_e : 0.000722
  EX_mobd_e : 0.000722
  EX_zn2_e : 0.000722

Product: (mmol/gDw/h)
  EX_h2o_e : 25.361136
  EX_co2_e : 19.003172
  EX_h_e : 2.071275
  EX_acald_e : 0.583498
  EX_ac_e : 0.126622
  Auxiliary production reaction : 0.026379
  EX_glyc__R_e : 0.005718
  DM_hmfurn_c : 0.000102

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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