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 (25 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM1749 STM2463 STM4108 STM2285 STM3526 STM4326 STM1511 STM1885 STM2952 STM0321 STM2947 STM3529 STM1620 STM0491 STM0974 STM1448 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.227933 (mmol/gDw/h)
  Minimum Production Rate : 0.052267 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.511854
  EX_pi_e : 0.202137
  EX_k_e : 0.040481
  EX_so4_e : 0.027804
  EX_mg2_e : 0.001800
  EX_fe2_e : 0.001671
  EX_ca2_e : 0.001080
  EX_cl_e : 0.001080
  EX_cobalt2_e : 0.000720
  EX_cu2_e : 0.000720
  EX_mn2_e : 0.000720
  EX_mobd_e : 0.000720
  EX_zn2_e : 0.000720

Product: (mmol/gDw/h)
  EX_h2o_e : 25.267636
  EX_co2_e : 18.983906
  EX_h_e : 2.188764
  EX_acald_e : 0.581510
  EX_ac_e : 0.192770
  Auxiliary production reaction : 0.052267
  EX_glyclt_e : 0.011397
  EX_glyald_e : 0.000158
  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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