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 : pe140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (98 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM4326 STM1511 STM1885 STM2952 STM2947 STM3709 STM1620 STM0370 STM3597 STM1326 STM4062 STM2403 STM4408 STM1291 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM0977 STM3661 STM1933 STM1124 STM3063 STM4467 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.022362 (mmol/gDw/h)
  Minimum Production Rate : 0.029864 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.214081
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.327833
  EX_pi_e : 0.101236
  EX_k_e : 0.003971
  EX_so4_e : 0.002728
  EX_mg2_e : 0.000177
  EX_fe2_e : 0.000164
  EX_ca2_e : 0.000106
  EX_cl_e : 0.000106
  EX_cobalt2_e : 0.000071
  EX_cu2_e : 0.000071
  EX_mn2_e : 0.000071
  EX_mobd_e : 0.000071
  EX_zn2_e : 0.000071

Product: (mmol/gDw/h)
  EX_h2o_e : 11.556361
  EX_co2_e : 10.463740
  EX_dha_e : 4.891638
  EX_h_e : 0.263909
  EX_acald_e : 0.086914
  Auxiliary production reaction : 0.029864
  EX_lipa_e : 0.025770
  EX_glyclt_e : 0.001118

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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