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 : ddca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM4108 STM2285 STM3526 STM4326 STM1511 STM2952 STM0840 STM0842 STM1620 STM3542 STM4485 STM1448 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM0977 STM1124 STM0007 STM2473   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.252704 (mmol/gDw/h)
  Minimum Production Rate : 0.095596 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.784832
  EX_pi_e : 0.224104
  EX_k_e : 0.044880
  EX_so4_e : 0.030825
  EX_mg2_e : 0.001995
  EX_fe2_e : 0.001852
  EX_ca2_e : 0.001197
  EX_cl_e : 0.001197
  EX_cobalt2_e : 0.000798
  EX_cu2_e : 0.000798
  EX_mn2_e : 0.000798
  EX_mobd_e : 0.000798
  EX_zn2_e : 0.000798

Product: (mmol/gDw/h)
  EX_h2o_e : 25.869002
  EX_co2_e : 18.902384
  EX_h_e : 2.325526
  Auxiliary production reaction : 0.095596
  EX_ac_e : 0.074967
  EX_glyclt_e : 0.012635
  DM_hmfurn_c : 0.000113

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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