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 : phe__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: STM1749 STM2463 STM4108 STM2285 STM3526 STM4326 STM2952 STM0321 STM2947 STM3529 STM1620 STM2081 STM0491 STM3597 STM0974 STM4408 STM1291 STM0150 STM4184 STM4484 STM0568 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM3248 STM0519 STM1937 STM3241 STM0973 STM4467 STM3802 STM2196 STM3240 STM0007 STM2473 STM0402 STM0608 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.246916 (mmol/gDw/h)
  Minimum Production Rate : 0.169632 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 16.551887
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.980647
  EX_pi_e : 0.218971
  EX_k_e : 0.043852
  EX_so4_e : 0.030119
  EX_mg2_e : 0.001949
  EX_fe2_e : 0.001810
  EX_ca2_e : 0.001170
  EX_cl_e : 0.001170
  EX_cobalt2_e : 0.000780
  EX_cu2_e : 0.000780
  EX_mn2_e : 0.000780
  EX_mobd_e : 0.000780
  EX_zn2_e : 0.000780

Product: (mmol/gDw/h)
  EX_h2o_e : 24.842757
  EX_co2_e : 17.097574
  EX_h_e : 2.365204
  EX_acald_e : 0.629940
  Auxiliary production reaction : 0.169632
  EX_ile__L_e : 0.089966
  EX_glyclt_e : 0.012346
  DM_hmfurn_c : 0.000110

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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