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 : ps160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM3646 STM0158 STM1749 STM2463 STM2285 STM3526 STM4567 STM4326 STM1511 STM1884 STM0321 STM0840 STM0842 STM2947 STM0525 STM3247 STM2959 STM2492 STM1135 STM4183 STM1448 STM3069 STM4484 STM2317 STM3179 STM1480 STM4126 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.239557 (mmol/gDw/h)
  Minimum Production Rate : 0.010071 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.650026
  EX_pi_e : 0.222516
  EX_k_e : 0.042545
  EX_so4_e : 0.029222
  EX_mg2_e : 0.001891
  EX_fe2_e : 0.001756
  EX_ca2_e : 0.001135
  EX_cl_e : 0.001135
  EX_cobalt2_e : 0.000757
  EX_cu2_e : 0.000757
  EX_mn2_e : 0.000757
  EX_mobd_e : 0.000757
  EX_zn2_e : 0.000757

Product: (mmol/gDw/h)
  EX_h2o_e : 25.568859
  EX_co2_e : 18.924386
  EX_h_e : 2.036865
  EX_acald_e : 0.704115
  Auxiliary production reaction : 0.010071
  EX_glyc__R_e : 0.005989
  DM_hmfurn_c : 0.000107

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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