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 : dhna_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM4483 STM1749 STM2463 STM0441 STM3680 STM1886 STM3866 STM1570 STM1620 STM4036 STM2167 STM3542 STM4485 STM2472 STM0150 STM0568 STM1211 STM2317 STM0935 STM2338 STM2466 STM1937 STM0733 STM0007 STM2473 STM0054 STM3353   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.012952 (mmol/gDw/h)
  Minimum Production Rate : 0.008884 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_o2_e : 4.946290
  EX_nh4_e : 0.142723
  EX_pi_e : 0.011483
  EX_k_e : 0.002300
  EX_so4_e : 0.001579
  EX_mg2_e : 0.000102
  EX_fe2_e : 0.000095
  EX_ca2_e : 0.000061
  EX_cl_e : 0.000061
  EX_cobalt2_e : 0.000041
  EX_cu2_e : 0.000041
  EX_mn2_e : 0.000041
  EX_mobd_e : 0.000041
  EX_zn2_e : 0.000041

Product: (mmol/gDw/h)
  EX_h2o_e : 10.245009
  EX_h_e : 9.911980
  EX_pyr_e : 9.777680
  EX_co2_e : 0.048016
  EX_for_e : 0.011118
  Auxiliary production reaction : 0.008897
  EX_ac_e : 0.003841
  EX_glyclt_e : 0.000648

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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