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 (39 of 132: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM3646 STM1749 STM2463 STM4108 STM2285 STM3526 STM0322 STM4567 STM4326 STM1884 STM2952 STM2947 STM3709 STM3529 STM1135 STM4183 STM0974 STM1448 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM0977 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.221886 (mmol/gDw/h)
  Minimum Production Rate : 0.017952 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.463168
  EX_pi_e : 0.214725
  EX_k_e : 0.039407
  EX_so4_e : 0.027066
  EX_mg2_e : 0.001752
  EX_fe2_e : 0.001626
  EX_ca2_e : 0.001051
  EX_cl_e : 0.001051
  EX_cobalt2_e : 0.000701
  EX_cu2_e : 0.000701
  EX_mn2_e : 0.000701
  EX_mobd_e : 0.000701
  EX_zn2_e : 0.000701

Product: (mmol/gDw/h)
  EX_h2o_e : 25.318429
  EX_co2_e : 19.093694
  EX_h_e : 1.886614
  EX_acald_e : 0.776044
  Auxiliary production reaction : 0.017952
  EX_glyc__R_e : 0.005547
  EX_glyald_e : 0.000154
  DM_hmfurn_c : 0.000099

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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